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, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
36 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
38 ;;; This file is part of GNU Guix.
40 ;;; GNU Guix is free software; you can redistribute it and/or modify it
41 ;;; under the terms of the GNU General Public License as published by
42 ;;; the Free Software Foundation; either version 3 of the License, or (at
43 ;;; your option) any later version.
45 ;;; GNU Guix is distributed in the hope that it will be useful, but
46 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
47 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
48 ;;; GNU General Public License for more details.
50 ;;; You should have received a copy of the GNU General Public License
51 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
53 (define-module (gnu packages cran)
54 #:use-module ((guix licenses) #:prefix license:)
55 #:use-module (guix packages)
56 #:use-module (guix download)
57 #:use-module (guix git-download)
58 #:use-module (guix utils)
59 #:use-module (guix build-system gnu)
60 #:use-module (guix build-system r)
61 #:use-module (gnu packages)
62 #:use-module (gnu packages algebra)
63 #:use-module (gnu packages autotools)
64 #:use-module (gnu packages base)
65 #:use-module (gnu packages bioinformatics)
66 #:use-module (gnu packages c)
67 #:use-module (gnu packages compression)
68 #:use-module (gnu packages crypto)
69 #:use-module (gnu packages curl)
70 #:use-module (gnu packages databases)
71 #:use-module (gnu packages fontutils)
72 #:use-module (gnu packages fribidi)
73 #:use-module (gnu packages gcc)
74 #:use-module (gnu packages geo)
75 #:use-module (gnu packages ghostscript)
76 #:use-module (gnu packages gl)
77 #:use-module (gnu packages gnome)
78 #:use-module (gnu packages graph)
79 #:use-module (gnu packages gtk)
80 #:use-module (gnu packages haskell-xyz)
81 #:use-module (gnu packages icu4c)
82 #:use-module (gnu packages image)
83 #:use-module (gnu packages imagemagick)
84 #:use-module (gnu packages java)
85 #:use-module (gnu packages javascript)
86 #:use-module (gnu packages libevent)
87 #:use-module (gnu packages lisp-xyz)
88 #:use-module (gnu packages machine-learning)
89 #:use-module (gnu packages maths)
90 #:use-module (gnu packages mpi)
91 #:use-module (gnu packages multiprecision)
92 #:use-module (gnu packages networking)
93 #:use-module (gnu packages node)
94 #:use-module (gnu packages pcre)
95 #:use-module (gnu packages pdf)
96 #:use-module (gnu packages perl)
97 #:use-module (gnu packages pkg-config)
98 #:use-module (gnu packages pulseaudio) ;libsndfile
99 #:use-module (gnu packages python)
100 #:use-module (gnu packages python-xyz)
101 #:use-module (gnu packages sqlite)
102 #:use-module (gnu packages statistics)
103 #:use-module (gnu packages tcl)
104 #:use-module (gnu packages textutils)
105 #:use-module (gnu packages tls)
106 #:use-module (gnu packages version-control)
107 #:use-module (gnu packages web)
108 #:use-module (gnu packages xml)
109 #:use-module (gnu packages xorg))
111 (define-public r-brio
118 (uri (cran-uri "brio" version))
121 "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
122 (properties `((upstream-name . "brio")))
123 (build-system r-build-system)
124 (home-page "https://github.com/r-lib/brio")
125 (synopsis "Basic R input output")
127 "This package provides functions to handle basic input output. These
128 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
129 files and provide more explicit control over line endings.")
130 (license license:expat)))
132 (define-public r-cachem
139 (uri (cran-uri "cachem" version))
142 "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh"))))
143 (properties `((upstream-name . "cachem")))
144 (build-system r-build-system)
146 `(("r-fastmap" ,r-fastmap)
147 ("r-rlang" ,r-rlang)))
148 (home-page "https://cachem.r-lib.org/")
149 (synopsis "Cache R objects with automatic pruning")
151 "This package provides key-value stores with automatic pruning. Caches
152 can limit either their total size or the age of the oldest object (or both),
153 automatically pruning objects to maintain the constraints.")
154 (license license:expat)))
156 (define-public r-diffobj
163 (uri (cran-uri "diffobj" version))
166 "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q"))))
167 (properties `((upstream-name . "diffobj")))
168 (build-system r-build-system)
169 (propagated-inputs `(("r-crayon" ,r-crayon)))
170 (native-inputs `(("r-knitr" ,r-knitr)))
171 (home-page "https://github.com/brodieG/diffobj")
172 (synopsis "Diffs for R objects")
174 "Generate a colorized diff of two R objects for an intuitive
175 visualization of their differences.")
176 (license license:gpl2+)))
178 (define-public r-waldo
185 (uri (cran-uri "waldo" version))
188 "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr"))))
189 (properties `((upstream-name . "waldo")))
190 (build-system r-build-system)
193 ("r-diffobj" ,r-diffobj)
196 ("r-rematch2" ,r-rematch2)
198 ("r-tibble" ,r-tibble)))
199 (home-page "https://github.com/r-lib/waldo")
200 (synopsis "Find differences between R objects")
202 "Compare complex R objects and reveal the key differences. This package
203 was designed particularly for use in testing packages where being able to
204 quickly isolate key differences makes understanding test failures much
206 (license license:expat)))
208 (define-public r-rticles
215 (uri (cran-uri "rticles" version))
218 "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818"))))
219 (properties `((upstream-name . "rticles")))
220 (build-system r-build-system)
222 `(("r-knitr" ,r-knitr)
223 ("r-rmarkdown" ,r-rmarkdown)
224 ("r-tinytex" ,r-tinytex)
227 (home-page "https://github.com/rstudio/rticles")
228 (synopsis "Article formats for R Markdown")
230 "This package provides a suite of custom R Markdown formats and templates
231 for authoring journal articles and conference submissions.")
232 (license license:gpl3)))
234 (define-public r-bezier
240 (uri (cran-uri "bezier" version))
243 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
244 (build-system r-build-system)
245 (home-page "https://cran.r-project.org/web/packages/bezier/")
246 (synopsis "Bezier curve and spline toolkit")
248 "This package is a toolkit for working with Bezier curves and splines.
249 The package provides functions for point generation, arc length estimation,
250 degree elevation and curve fitting.")
251 (license license:gpl2+)))
260 (uri (cran-uri "V8" version))
263 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
264 (properties `((upstream-name . "V8")))
265 (build-system r-build-system)
268 (modify-phases %standard-phases
269 (add-after 'unpack 'find-v8
270 (lambda* (#:key inputs #:allow-other-keys)
271 (substitute* "configure"
273 (string-append "PKG_LIBS="
274 (assoc-ref inputs "node")
275 "/lib/libnode.so.64\n")))
276 (setenv "INCLUDE_DIR"
278 (assoc-ref inputs "node")
282 (assoc-ref inputs "node") "/lib"))
285 `(("node" ,libnode)))
288 ("r-jsonlite" ,r-jsonlite)
291 `(("r-knitr" ,r-knitr)))
292 (home-page "https://jeroen.cran.dev/V8")
293 (synopsis "Embedded JavaScript and WebAssembly engine for R")
295 "This package provides an R interface to V8: Google's JavaScript and
296 WebAssembly engine.")
297 (license license:expat)))
306 (uri (cran-uri "DOT" version))
309 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
310 (properties `((upstream-name . "DOT")))
311 (build-system r-build-system)
314 (home-page "http://haghish.com/dot")
315 (synopsis "Render and Export DOT Graphs in R")
317 "This package provides tools to render DOT diagram markup language in R
318 and also provides the possibility to export the graphs in PostScript and
319 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
320 programming packages such as @code{knitr} and @code{rmarkdown}.")
321 (license license:expat)))
323 (define-public r-clipr
330 (uri (cran-uri "clipr" version))
333 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
334 (build-system r-build-system)
336 `(("r-knitr" ,r-knitr)))
337 (home-page "https://github.com/mdlincoln/clipr")
338 (synopsis "Read and write from the system clipboard")
340 "This package provides simple utility functions to read from and write to
341 the system clipboards.")
342 (license license:gpl3)))
350 (uri (cran-uri "zoo" version))
353 "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
354 (build-system r-build-system)
356 `(("r-lattice" ,r-lattice)))
357 (home-page "http://zoo.R-Forge.R-project.org/")
358 (synopsis "S3 infrastructure for regular and irregular time series")
359 (description "This package contains an S3 class with methods for totally
360 ordered indexed observations. It is particularly aimed at irregular time
361 series of numeric vectors/matrices and factors.")
362 (license license:gpl2+)))
364 (define-public r-ggalluvial
366 (name "r-ggalluvial")
370 (uri (cran-uri "ggalluvial" version))
373 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
374 (properties `((upstream-name . "ggalluvial")))
375 (build-system r-build-system)
377 `(("r-dplyr" ,r-dplyr)
378 ("r-ggplot2" ,r-ggplot2)
379 ("r-lazyeval" ,r-lazyeval)
382 ("r-tidyselect" ,r-tidyselect)))
384 `(("r-knitr" ,r-knitr)))
385 (home-page "http://corybrunson.github.io/ggalluvial/")
386 (synopsis "Alluvial plots for ggplot2")
387 (description "This package provides alluvial plots for @code{ggplot2}.
388 Alluvial plots use variable-width ribbons and stacked bar plots to represent
389 multi-dimensional or repeated-measures data with categorical or ordinal
391 (license license:gpl3)))
393 (define-public r-ggpmisc
399 (uri (cran-uri "ggpmisc" version))
402 "0nb0lpwqph9334s9sq77mk3nd22icy9d9hywz4awhf6nvp5rcc2v"))))
403 (build-system r-build-system)
405 `(("r-dplyr" ,r-dplyr)
406 ("r-generics" ,r-generics)
408 ("r-ggplot2" ,r-ggplot2)
409 ("r-gridextra" ,r-gridextra)
410 ("r-lubridate" ,r-lubridate)
411 ("r-magrittr" ,r-magrittr)
414 ("r-polynom" ,r-polynom)
416 ("r-scales" ,r-scales)
417 ("r-splus2r" ,r-splus2r)
418 ("r-stringr" ,r-stringr)
419 ("r-tibble" ,r-tibble)
423 `(("r-knitr" ,r-knitr)))
424 (home-page "https://www.r4photobiology.info/")
425 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
426 (description "This package provides extensions to @code{ggplot2},
427 respecting the grammar of its graphics paradigm.")
428 (license license:gpl2+)))
430 (define-public r-gprofiler
437 (uri (cran-uri "gProfileR" version))
440 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
441 (properties `((upstream-name . "gProfileR")))
442 (build-system r-build-system)
445 ("r-rcurl" ,r-rcurl)))
446 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
447 (synopsis "Interface to the g:Profiler toolkit")
449 "This package provides tools for functional enrichment analysis,
450 gene identifier conversion and mapping homologous genes across related
451 organisms via the @code{g:Profiler} toolkit.")
452 (license license:gpl2+)))
454 (define-public r-gprofiler2
456 (name "r-gprofiler2")
461 (uri (cran-uri "gprofiler2" version))
464 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
465 (properties `((upstream-name . "gprofiler2")))
466 (build-system r-build-system)
468 `(("r-crosstalk" ,r-crosstalk)
470 ("r-ggplot2" ,r-ggplot2)
471 ("r-gridextra" ,r-gridextra)
472 ("r-jsonlite" ,r-jsonlite)
473 ("r-plotly" ,r-plotly)
476 ("r-viridislite" ,r-viridislite)))
477 (native-inputs `(("r-knitr" ,r-knitr)))
478 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
479 (synopsis "Interface to the g:Profiler toolset")
481 "This package provides a toolset for functional enrichment analysis and
482 visualization, gene/protein/SNP identifier conversion and mapping orthologous
483 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
487 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
489 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
491 @item @code{g:Orth}, orthology search across species;
492 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
493 genes and variant effects.
496 This package is an R interface corresponding to the 2019 update of
497 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
499 (license license:gpl2+)))
501 (define-public r-oenb
508 (uri (cran-uri "oenb" version))
511 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
512 (properties `((upstream-name . "oenb")))
513 (build-system r-build-system)
515 `(("r-dplyr" ,r-dplyr)
517 (native-inputs `(("r-knitr" ,r-knitr)))
518 (home-page "https://github.com/franzmohr/oenb")
519 (synopsis "Tools for the OeNB Data Web Service")
521 "Tools to access data from the data web service of the
522 @acronym{OeNB, Oesterreichische Nationalbank},
523 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
524 (license license:gpl2+)))
526 (define-public r-scales
533 (uri (cran-uri "scales" version))
535 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
536 (build-system r-build-system)
538 `(("r-farver" ,r-farver)
539 ("r-labeling" ,r-labeling)
540 ("r-lifecycle" ,r-lifecycle)
541 ("r-munsell" ,r-munsell)
542 ("r-rcolorbrewer" ,r-rcolorbrewer)
544 ("r-viridislite" ,r-viridislite)))
545 (home-page "https://github.com/hadley/scales")
546 (synopsis "Scale functions for visualization")
548 "This package provides graphical scales that map data to aesthetics, and
549 provides methods for automatically determining breaks and labels for axes and
551 (license license:expat)))
553 (define-public r-pheatmap
560 (uri (cran-uri "pheatmap" version))
563 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
564 (build-system r-build-system)
566 `(("r-gtable" ,r-gtable)
567 ("r-rcolorbrewer" ,r-rcolorbrewer)
568 ("r-scales" ,r-scales)))
569 (home-page "https://cran.r-project.org/web/packages/pheatmap")
570 (synopsis "Pretty heatmaps")
572 "This package provides an implementation of heatmaps that offers more
573 control over dimensions and appearance.")
574 (license license:gpl2+)))
582 (uri (cran-uri "ecp" version))
585 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
586 (build-system r-build-system)
588 `(("r-rcpp" ,r-rcpp)))
589 (home-page "https://cran.r-project.org/web/packages/ecp/")
590 (synopsis "Multiple change-point analysis of multivariate data")
592 "This package implements various procedures for finding multiple
593 change-points. Two methods make use of dynamic programming and pruning, with
594 no distributional assumptions other than the existence of certain absolute
595 moments in one method. Hierarchical and exact search methods are included.
596 All methods return the set of estimated change-points as well as other summary
598 (license license:gpl2+)))
600 (define-public r-ellipsis
607 (uri (cran-uri "ellipsis" version))
610 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
611 (build-system r-build-system)
613 `(("r-rlang" ,r-rlang)))
614 (home-page "https://github.com/hadley/ellipsis")
615 (synopsis "Tools for working with additional arguments")
617 "In S3 generics, it's useful to take @code{...} so that methods can have
618 additional arguments. But this flexibility comes at a cost: misspelled
619 arguments will be silently ignored. The @code{ellipsis} package is an
620 experiment that allows a generic to warn if any arguments passed in @code{...}
622 (license license:gpl3)))
631 (uri (cran-uri "grr" version))
634 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
635 (build-system r-build-system)
636 (home-page "https://cran.r-project.org/web/packages/grr")
637 (synopsis "Alternative implementations of base R functions")
639 "This package provides alternative implementations of some base R
640 functions, including @code{sort}, @code{order}, and @code{match}. The
641 functions are simplified but can be faster or have other advantages.")
642 (license license:gpl3)))
644 (define-public r-matrix-utils
646 (name "r-matrix-utils")
651 (uri (cran-uri "Matrix.utils" version))
654 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
655 (properties `((upstream-name . "Matrix.utils")))
656 (build-system r-build-system)
659 ("r-matrix" ,r-matrix)))
660 (home-page "https://github.com/cvarrichio/Matrix.utils")
662 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
664 "This package implements data manipulation methods such as @code{cast},
665 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
667 (license license:gpl3)))
669 (define-public r-mboost
675 (uri (cran-uri "mboost" version))
678 "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0"))))
679 (build-system r-build-system)
681 `(("r-lattice" ,r-lattice)
682 ("r-matrix" ,r-matrix)
684 ("r-partykit" ,r-partykit)
685 ("r-quadprog" ,r-quadprog)
687 ("r-survival" ,r-survival)))
688 (home-page "https://github.com/boost-R/mboost")
689 (synopsis "Model-based boosting")
691 "This package provides a functional gradient descent algorithm (boosting)
692 for optimizing general risk functions utilizing component-wise (penalised)
693 least squares estimates or regression trees as base-learners for fitting
694 generalized linear, additive and interaction models to potentially
695 high-dimensional data.")
696 (license license:gpl2)))
698 (define-public r-shadowtext
700 (name "r-shadowtext")
704 (uri (cran-uri "shadowtext" version))
707 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
708 (properties `((upstream-name . "shadowtext")))
709 (build-system r-build-system)
711 `(("r-ggplot2" ,r-ggplot2)
712 ("r-scales" ,r-scales)))
714 `(("r-knitr" ,r-knitr)))
715 (home-page "https://github.com/GuangchuangYu/shadowtext/")
716 (synopsis "Shadow text grob and layer")
717 (description "This package implements @code{shadowtextGrob()} for
718 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
719 These functions draw text grob with background shadow.")
720 (license license:artistic2.0)))
729 (uri (cran-uri "sys" version))
732 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
733 (build-system r-build-system)
734 (home-page "https://github.com/jeroen/sys")
735 (synopsis "Powerful and reliable tools for running system commands in R")
737 "This package provides drop-in replacements for the base @code{system2()}
738 function with fine control and consistent behavior across platforms. It
739 supports clean interruption, timeout, background tasks, and streaming STDIN /
740 STDOUT / STDERR over binary or text connections. The package also provides
741 functions for evaluating expressions inside a temporary fork. Such
742 evaluations have no side effects on the main R process, and support reliable
743 interrupts and timeouts. This provides the basis for a sandboxing
745 (license license:expat)))
747 (define-public r-ashr
753 (uri (cran-uri "ashr" version))
756 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
757 (properties `((upstream-name . "ashr")))
758 (build-system r-build-system)
760 `(("r-etrunct" ,r-etrunct)
761 ("r-invgamma" ,r-invgamma)
762 ("r-matrix" ,r-matrix)
763 ("r-mixsqp" ,r-mixsqp)
765 ("r-squarem" ,r-squarem)
766 ("r-truncnorm" ,r-truncnorm)))
768 `(("r-knitr" ,r-knitr)))
769 (home-page "https://github.com/stephens999/ashr")
770 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
771 (description "This package implements an empirical Bayes approach for
772 large-scale hypothesis testing and false discovery rate estimation.")
773 (license license:gpl3+)))
775 (define-public r-askpass
782 (uri (cran-uri "askpass" version))
785 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
786 (build-system r-build-system)
787 (propagated-inputs `(("r-sys" ,r-sys)))
788 (home-page "https://github.com/jeroen/askpass")
789 (synopsis "Safe password entry for R")
791 "This package provides cross-platform utilities for prompting the user
792 for credentials or a passphrase, for example to authenticate with a server or
793 read a protected key.")
794 (license license:expat)))
796 (define-public r-vegan
803 (uri (cran-uri "vegan" version))
806 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
807 (build-system r-build-system)
809 `(("r-knitr" ,r-knitr) ; needed for vignettes
810 ("gfortran" ,gfortran)))
812 `(("r-cluster" ,r-cluster)
813 ("r-lattice" ,r-lattice)
816 ("r-permute" ,r-permute)))
817 (home-page "https://cran.r-project.org/web/packages/vegan")
818 (synopsis "Functions for community ecology")
820 "The vegan package provides tools for descriptive community ecology. It
821 has most basic functions of diversity analysis, community ordination and
822 dissimilarity analysis. Most of its multivariate tools can be used for other
823 data types as well.")
824 (license license:gpl2+)))
826 (define-public r-tidyverse
833 (uri (cran-uri "tidyverse" version))
836 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
837 (build-system r-build-system)
839 `(("r-broom" ,r-broom)
841 ("r-crayon" ,r-crayon)
842 ("r-dbplyr" ,r-dbplyr)
844 ("r-forcats" ,r-forcats)
845 ("r-ggplot2" ,r-ggplot2)
849 ("r-jsonlite" ,r-jsonlite)
850 ("r-lubridate" ,r-lubridate)
851 ("r-magrittr" ,r-magrittr)
852 ("r-modelr" ,r-modelr)
853 ("r-pillar" ,r-pillar)
856 ("r-readxl" ,r-readxl)
857 ("r-reprex" ,r-reprex)
859 ("r-rstudioapi" ,r-rstudioapi)
861 ("r-stringr" ,r-stringr)
862 ("r-tibble" ,r-tibble)
865 (home-page "https://tidyverse.tidyverse.org")
866 (synopsis "Install and load packages from the \"Tidyverse\"")
868 "The @code{tidyverse} is a set of packages that work in harmony because
869 they share common data representations and API design. This package is
870 designed to make it easy to install and load multiple tidyverse packages in a
872 (license license:gpl3)))
874 (define-public r-rvest
881 (uri (cran-uri "rvest" version))
883 (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53"))))
884 (build-system r-build-system)
887 ("r-lifecycle" ,r-lifecycle)
888 ("r-magrittr" ,r-magrittr)
890 ("r-selectr" ,r-selectr)
891 ("r-tibble" ,r-tibble)
894 `(("r-knitr" ,r-knitr)))
895 (home-page "https://github.com/hadley/rvest")
896 (synopsis "Simple web scraping for R")
898 "@code{r-rvest} helps you scrape information from web pages. It is
899 designed to work with @code{magrittr} to make it easy to express common web
900 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
901 (license license:gpl3)))
903 (define-public r-selectr
910 (uri (cran-uri "selectr" version))
912 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
913 (build-system r-build-system)
915 `(("r-stringr" ,r-stringr)
917 (home-page "https://sjp.co.nz/projects/selectr/")
918 (synopsis "Translate CSS selectors to XPath expressions")
920 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
921 expression. This allows you to use CSS selectors when working with the XML
922 package as it can only evaluate XPath expressions. Also provided are
923 convenience functions useful for using CSS selectors on XML nodes. This
924 package is a port of the Python package @code{cssselect}.")
925 (license license:bsd-3)))
927 (define-public r-reprex
934 (uri (cran-uri "reprex" version))
937 "1lcnxczy28n4g3rvph09va7svcznfyqa7zdggklqb924qvy7flwh"))))
938 (build-system r-build-system)
940 `(("r-callr" ,r-callr)
947 ("r-rmarkdown" ,r-rmarkdown)
948 ("r-rstudioapi" ,r-rstudioapi)
949 ("r-withr" ,r-withr)))
951 `(("r-knitr" ,r-knitr)))
952 (home-page "https://github.com/tidyverse/reprex")
953 (synopsis "Prepare reproducible R code examples for sharing")
955 "This package provides a convenience wrapper that uses the
956 @code{rmarkdown} package to render small snippets of code to target formats
957 that include both code and output. The goal is to encourage the sharing of
958 small, reproducible, and runnable examples on code-oriented websites or email.
959 @code{reprex} also extracts clean, runnable R code from various common formats,
960 such as copy/paste from an R session.")
961 (license license:expat)))
963 (define-public r-reordercluster
965 (name "r-reordercluster")
969 (uri (cran-uri "ReorderCluster" version))
972 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
973 (build-system r-build-system)
975 `(("r-gplots" ,r-gplots)
977 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
978 (synopsis "Reordering the dendrogram according to the class labels")
979 (description "This package provides tools for performing the leaf reordering
980 for the dendrogram that preserves the hierarchical clustering result and at the
981 same time tries to group instances from the same class together.")
982 (license license:gpl3+)))
984 (define-public r-callr
991 (uri (cran-uri "callr" version))
994 "050s7l1ipi6snbj6xnk052l6acycnxjyzv84026adw5x8kki0yz6"))))
995 (build-system r-build-system)
998 ("r-processx" ,r-processx)))
999 (home-page "https://github.com/r-lib/callr#readme")
1000 (synopsis "Call R from R")
1002 "It is sometimes useful to perform a computation in a separate R process,
1003 without affecting the current R process at all. This package does exactly
1005 (license license:expat)))
1007 (define-public r-readxl
1014 (uri (cran-uri "readxl" version))
1017 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1018 (build-system r-build-system)
1020 `(("r-cellranger" ,r-cellranger)
1021 ("r-progress" ,r-progress)
1023 ("r-tibble" ,r-tibble)))
1024 (home-page "https://readxl.tidyverse.org")
1025 (synopsis "Read Excel files")
1027 "This package lets you import Excel files into R. It supports
1028 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1029 the embedded @code{RapidXML} C++ library.")
1030 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1031 ;; 'rapidxml' which is Boost.
1032 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1034 (define-public r-modelr
1041 (uri (cran-uri "modelr" version))
1044 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1045 (build-system r-build-system)
1047 `(("r-broom" ,r-broom)
1048 ("r-magrittr" ,r-magrittr)
1049 ("r-purrr" ,r-purrr)
1050 ("r-rlang" ,r-rlang)
1051 ("r-tibble" ,r-tibble)
1052 ("r-tidyr" ,r-tidyr)
1053 ("r-tidyselect" ,r-tidyselect)
1054 ("r-vctrs" ,r-vctrs)))
1055 (home-page "https://github.com/tidyverse/modelr")
1056 (synopsis "Helper functions for modelling in pipelines")
1058 "Functions for modelling that help you seamlessly integrate modelling
1059 into a pipeline of data manipulation and visualisation.")
1060 (license license:gpl3)))
1062 (define-public r-httpuv
1068 (uri (cran-uri "httpuv" version))
1071 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1072 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1073 ;; only contains fixes for building on Solaris.
1074 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1075 (modules '((guix build utils)))
1078 (delete-file-recursively "src/libuv")
1079 ;; Cannot unbundle http-parser, because it contains local
1082 (build-system r-build-system)
1085 (modify-phases %standard-phases
1086 (add-after 'unpack 'unbundle-libuv
1087 (lambda* (#:key outputs #:allow-other-keys)
1088 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1089 (("\"libuv/include/uv\\.h\"")
1091 ;; Fix https://github.com/rstudio/httpuv/issues/282
1092 (substitute* "src/http.cpp"
1093 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1094 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1097 `(("libuv" ,libuv)))
1100 ("r-later" ,r-later)
1101 ("r-promises" ,r-promises)
1103 ("r-rcpp" ,r-rcpp)))
1104 (home-page "https://github.com/rstudio/httpuv")
1105 (synopsis "HTTP and WebSocket server library for R")
1107 "The httpuv package provides low-level socket and protocol support for
1108 handling HTTP and WebSocket requests directly from within R. It is primarily
1109 intended as a building block for other packages, rather than making it
1110 particularly easy to create complete web applications using httpuv alone.")
1111 ;; This package includes third-party code that was originally released
1112 ;; under various non-copyleft licenses. Full licensing information can be
1113 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1114 (license license:gpl3+)))
1116 (define-public r-jsonlite
1122 (uri (cran-uri "jsonlite" version))
1125 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1126 (build-system r-build-system)
1128 `(("r-knitr" ,r-knitr)))
1129 (home-page "https://arxiv.org/abs/1403.2805")
1130 (synopsis "Robust, high performance JSON parser and generator for R")
1132 "The jsonlite package provides a fast JSON parser and generator optimized
1133 for statistical data and the web. It offers flexible, robust, high
1134 performance tools for working with JSON in R and is particularly powerful for
1135 building pipelines and interacting with a web API. In addition to converting
1136 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1137 and prettify JSON data. The unit tests included with the package verify that
1138 all edge cases are encoded and decoded consistently for use with dynamic data
1139 in systems and applications.")
1140 (license license:expat)))
1142 (define-public r-servr
1148 (uri (cran-uri "servr" version))
1151 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1152 (build-system r-build-system)
1154 `(("r-httpuv" ,r-httpuv)
1155 ("r-jsonlite" ,r-jsonlite)
1157 ("r-xfun" ,r-xfun)))
1158 (home-page "https://github.com/yihui/servr")
1159 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1161 "Servr provides an HTTP server in R to serve static files, or dynamic
1162 documents that can be converted to HTML files (e.g., R Markdown) under a given
1164 (license license:expat)))
1166 (define-public r-htmltools
1168 (name "r-htmltools")
1172 (uri (cran-uri "htmltools" version))
1175 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1176 (build-system r-build-system)
1178 `(("r-base64enc" ,r-base64enc)
1179 ("r-digest" ,r-digest)
1180 ("r-rlang" ,r-rlang)))
1181 (home-page "https://cran.r-project.org/web/packages/htmltools")
1182 (synopsis "R tools for HTML")
1184 "This package provides tools for HTML generation and output in R.")
1185 (license license:expat)))
1187 (define-public r-htmlwidgets
1189 (name "r-htmlwidgets")
1193 (uri (cran-uri "htmlwidgets" version))
1196 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1197 (build-system r-build-system)
1199 `(("r-htmltools" ,r-htmltools)
1200 ("r-jsonlite" ,r-jsonlite)
1201 ("r-yaml" ,r-yaml)))
1203 `(("r-knitr" ,r-knitr)))
1204 (home-page "https://github.com/ramnathv/htmlwidgets")
1205 (synopsis "HTML Widgets for R")
1207 "HTML widgets is a framework for creating HTML widgets that render in
1208 various contexts including the R console, R Markdown documents, and Shiny web
1210 (license license:expat)))
1212 (define-public r-htmltable
1214 (name "r-htmltable")
1219 (uri (cran-uri "htmlTable" version))
1221 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1222 (properties `((upstream-name . "htmlTable")))
1223 (build-system r-build-system)
1225 `(("r-checkmate" ,r-checkmate)
1226 ("r-htmltools" ,r-htmltools)
1227 ("r-htmlwidgets" ,r-htmlwidgets)
1228 ("r-knitr" ,r-knitr)
1229 ("r-magrittr" ,r-magrittr)
1230 ("r-rstudioapi" ,r-rstudioapi)
1231 ("r-stringr" ,r-stringr)))
1233 `(("r-knitr" ,r-knitr)))
1234 (home-page "http://gforge.se/packages/")
1235 (synopsis "Advanced tables for Markdown/HTML")
1237 "This package provides functions to build tables with advanced layout
1238 elements such as row spanners, column spanners, table spanners, zebra
1239 striping, and more. While allowing advanced layout, the underlying
1240 CSS-structure is simple in order to maximize compatibility with word
1241 processors such as LibreOffice. The package also contains a few text
1242 formatting functions that help outputting text compatible with HTML or
1244 (license license:gpl3+)))
1246 (define-public r-curl
1252 (uri (cran-uri "curl" version))
1255 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1256 (build-system r-build-system)
1259 (modify-phases %standard-phases
1260 ;; The environment variable CURL_CA_BUNDLE is only respected when
1261 ;; running Windows, so we disable the platform checks.
1262 ;; This can be removed once the libcurl has been patched.
1263 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1265 (substitute* "R/onload.R"
1266 (("if \\(!grepl\\(\"mingw\".*")
1268 (substitute* "src/handle.c"
1269 (("/\\* Only set" m)
1271 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1272 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1279 `(("pkg-config" ,pkg-config)))
1280 (home-page "https://github.com/jeroenooms/curl")
1281 (synopsis "HTTP client for R")
1283 "The @code{curl()} and @code{curl_download()} functions provide highly
1284 configurable drop-in replacements for base @code{url()} and
1285 @code{download.file()} with better performance, support for encryption, gzip
1286 compression, authentication, and other @code{libcurl} goodies. The core of
1287 the package implements a framework for performing fully customized requests
1288 where data can be processed either in memory, on disk, or streaming via the
1289 callback or connection interfaces.")
1290 (license license:expat)))
1292 (define-public r-hwriter
1299 (uri (cran-uri "hwriter" version))
1302 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1303 (build-system r-build-system)
1304 (home-page "https://cran.r-project.org/web/packages/hwriter")
1305 (synopsis "Output R objects in HTML format")
1307 "This package provides easy-to-use and versatile functions to output R
1308 objects in HTML format.")
1309 (license license:lgpl2.1+)))
1311 (define-public r-rjson
1318 (uri (cran-uri "rjson" version))
1321 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1322 (build-system r-build-system)
1323 (home-page "https://cran.r-project.org/web/packages/rjson")
1324 (synopsis "JSON library for R")
1326 "This package provides functions to convert R objects into JSON objects
1328 (license license:gpl2+)))
1330 (define-public r-fastmap
1337 (uri (cran-uri "fastmap" version))
1340 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1341 (properties `((upstream-name . "fastmap")))
1342 (build-system r-build-system)
1343 (home-page "https://r-lib.github.io/fastmap/")
1344 (synopsis "Fast implementation of a key-value store")
1346 "This package provides a fast implementation of a key-value store.
1347 Environments are commonly used as key-value stores, but every time a new key
1348 is used, it is added to R's global symbol table, causing a small amount of
1349 memory leakage. This can be problematic in cases where many different keys
1350 are used. Fastmap avoids this memory leak issue by implementing the map using
1351 data structures in C++.")
1352 (license license:expat)))
1354 (define-public r-fastghquad
1356 (name "r-fastghquad")
1361 (uri (cran-uri "fastGHQuad" version))
1364 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1365 (properties `((upstream-name . "fastGHQuad")))
1366 (build-system r-build-system)
1368 `(("r-rcpp" ,r-rcpp)))
1369 (home-page "https://github.com/awblocker/fastGHQuad")
1370 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1372 "This package implements numerically-stable Gauss-Hermite quadrature
1373 rules and utility functions for adaptive GH quadrature.")
1374 (license license:expat)))
1376 (define-public r-rstpm2
1383 (uri (cran-uri "rstpm2" version))
1386 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1387 (properties `((upstream-name . "rstpm2")))
1388 (build-system r-build-system)
1390 `(("r-bbmle" ,r-bbmle)
1392 ("r-desolve" ,r-desolve)
1393 ("r-fastghquad" ,r-fastghquad)
1396 ("r-rcpparmadillo" ,r-rcpparmadillo)
1397 ("r-survival" ,r-survival)))
1399 `(("gfortran" ,gfortran)))
1400 (home-page "https://github.com/mclements/rstpm2")
1401 (synopsis "Link-based survival models")
1403 "This package provides R implementations of @dfn{generalized survival
1404 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1405 multi-state models.")
1406 ;; One of these licenses
1407 (license (list license:gpl2 license:gpl3))))
1409 ;; This package includes minified JavaScript files. When upgrading please
1410 ;; check that there are no new minified JavaScript files.
1411 (define-public r-jquerylib
1413 (name "r-jquerylib")
1418 (uri (cran-uri "jquerylib" version))
1421 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1423 '(for-each delete-file
1424 '("inst/lib/jquery-1.12.4.min.js"
1425 "inst/lib/jquery-2.2.4.min.js"
1426 "inst/lib/jquery-3.5.1.min.js")))))
1427 (properties `((upstream-name . "jquerylib")))
1428 (build-system r-build-system)
1430 `(#:modules ((guix build utils)
1431 (guix build r-build-system)
1434 (modify-phases %standard-phases
1435 (add-after 'unpack 'process-javascript
1436 (lambda* (#:key inputs #:allow-other-keys)
1437 (with-directory-excursion "inst/lib/"
1441 `(("jquery-1.12.4.js"
1442 "jquery-1.12.4.min.js")
1444 "jquery-2.2.4.min.js")
1446 "jquery-3.5.1.min.js"))))
1447 (lambda (sources targets)
1448 (for-each (lambda (source target)
1449 (format #t "Processing ~a --> ~a~%"
1451 (invoke "esbuild" source "--minify"
1452 (string-append "--outfile=" target)))
1453 sources targets)))))))))
1455 `(("r-htmltools" ,r-htmltools)))
1457 `(("esbuild" ,esbuild)))
1458 (home-page "https://cran.r-project.org/package=jquerylib")
1459 (synopsis "Obtain jQuery as an HTML dependency object")
1461 "Obtain any major version of jQuery and use it in any webpage generated
1462 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1463 need to use this package directly, but other R packages (e.g. shiny,
1464 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1466 (license license:expat)))
1468 (define-public r-sass
1475 (uri (cran-uri "sass" version))
1478 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1479 (properties `((upstream-name . "sass")))
1480 (build-system r-build-system)
1482 `(("r-digest" ,r-digest)
1484 ("r-htmltools" ,r-htmltools)
1486 ("r-rappdirs" ,r-rappdirs)
1487 ("r-rlang" ,r-rlang)))
1488 (native-inputs `(("r-knitr" ,r-knitr)))
1489 (home-page "https://github.com/rstudio/sass")
1490 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1492 "This package provides an SCSS compiler, powered by the libsass library.
1493 With this, R developers can use variables, inheritance, and functions to
1494 generate dynamic style sheets. The package uses the Sass CSS extension
1495 language, which is stable, powerful, and CSS compatible.")
1496 (license license:expat)))
1498 ;; This package includes minified JavaScript files. When upgrading please
1499 ;; check that there are no new minified JavaScript files.
1500 (define-public r-bslib
1507 (uri (cran-uri "bslib" version))
1510 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1512 '(for-each delete-file
1513 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1514 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1515 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1516 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1517 (properties `((upstream-name . "bslib")))
1518 (build-system r-build-system)
1520 `(#:modules ((guix build utils)
1521 (guix build r-build-system)
1524 (modify-phases %standard-phases
1525 (add-after 'unpack 'process-javascript
1526 (lambda* (#:key inputs #:allow-other-keys)
1527 (with-directory-excursion "inst/lib/"
1531 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1532 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1533 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1534 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1535 ("bs-sass/assets/javascripts/bootstrap.js"
1536 "bs-sass/assets/javascripts/bootstrap.min.js")
1537 (,(assoc-ref inputs "js-bootstrap-bundle")
1538 "bs/dist/js/bootstrap.bundle.min.js"))))
1539 (lambda (sources targets)
1540 (for-each (lambda (source target)
1541 (format #t "Processing ~a --> ~a~%"
1543 (invoke "esbuild" source "--minify"
1544 (string-append "--outfile=" target)))
1545 sources targets)))))))))
1547 `(("r-digest" ,r-digest)
1548 ("r-htmltools" ,r-htmltools)
1549 ("r-jquerylib" ,r-jquerylib)
1550 ("r-jsonlite" ,r-jsonlite)
1551 ("r-magrittr" ,r-magrittr)
1552 ("r-rlang" ,r-rlang)
1553 ("r-sass" ,r-sass)))
1555 `(("esbuild" ,esbuild)
1556 ("js-bootstrap-bundle"
1559 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1562 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1563 (home-page "https://rstudio.github.io/bslib/")
1564 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1566 "This package simplifies custom CSS styling of both shiny and rmarkdown
1567 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1568 various Bootswatch themes. An interactive widget is also provided for
1569 previewing themes in real time.")
1570 (license license:expat)))
1572 ;; This package includes minified JavaScript files. When upgrading please
1573 ;; check that there are no new minified JavaScript files.
1574 (define-public r-shiny
1582 (url "https://github.com/rstudio/shiny")
1583 (commit (string-append "v" version))))
1584 (file-name (git-file-name name version))
1587 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1589 '(for-each delete-file
1590 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1591 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1592 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1593 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1594 "inst/www/shared/highlight/highlight.pack.js"
1595 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1596 "inst/www/shared/jquery.min.js"
1597 "inst/www/shared/jqueryui/jquery-ui.min.js"
1598 "inst/www/shared/legacy/jquery.min.js"
1599 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1600 "inst/www/shared/selectize/js/selectize.min.js"
1601 "inst/www/shared/shiny.min.js"
1602 "inst/www/shared/showdown/compressed/showdown.js"
1603 "inst/www/shared/strftime/strftime-min.js")))))
1604 (build-system r-build-system)
1606 `(#:modules ((guix build r-build-system)
1607 (guix build minify-build-system)
1610 #:imported-modules (,@%r-build-system-modules
1611 (guix build minify-build-system))
1613 (modify-phases (@ (guix build r-build-system) %standard-phases)
1614 (add-after 'unpack 'replace-bundled-minified-JavaScript
1615 (lambda* (#:key inputs #:allow-other-keys)
1616 (let ((replace-file (lambda (old new)
1617 (format #t "replacing ~a with ~a\n" old new)
1618 (symlink new old))))
1619 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1620 ;; contain just data. They are not minified code, so we don't
1622 (with-directory-excursion "inst/www/shared"
1623 (replace-file "strftime/strftime-min.js"
1624 (string-append (assoc-ref inputs "js-strftime")
1625 "/share/javascript/strftime.min.js"))
1626 (replace-file "highlight/highlight.pack.js"
1627 (string-append (assoc-ref inputs "js-highlight")
1628 "/share/javascript/highlight.min.js"))
1629 (replace-file "datatables/js/jquery.dataTables.min.js"
1630 (string-append (assoc-ref inputs "js-datatables")
1631 "/share/javascript/jquery.dataTables.min.js"))
1632 (replace-file "selectize/js/selectize.min.js"
1633 (string-append (assoc-ref inputs "js-selectize")
1634 "/share/javascript/selectize.min.js"))
1635 (for-each (match-lambda
1637 (minify source #:target target)))
1638 `(("jqueryui/jquery-ui.js" .
1639 "jqueryui/jquery-ui.min.js")
1640 ("datepicker/js/bootstrap-datepicker.js" .
1641 "datepicker/js/bootstrap-datepicker.min.js")
1642 ("ionrangeslider/js/ion.rangeSlider.js" .
1643 "ionrangeslider/js/ion.rangeSlider.min.js")
1644 ("bootstrap/js/bootstrap.js" .
1645 "bootstrap/js/bootstrap.min.js")
1646 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1647 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1652 ("legacy/jquery.js" .
1653 "legacy/jquery.min.js")
1654 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1655 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1656 ("showdown/src/showdown.js" .
1657 "showdown/compressed/showdown.js"))))))))))
1659 `(("r-bslib" ,r-bslib)
1660 ("r-cachem" ,r-cachem)
1661 ("r-commonmark" ,r-commonmark)
1662 ("r-crayon" ,r-crayon)
1663 ("r-digest" ,r-digest)
1664 ("r-ellipsis" ,r-ellipsis)
1665 ("r-fastmap" ,r-fastmap)
1667 ("r-htmltools" ,r-htmltools)
1668 ("r-httpuv" ,r-httpuv)
1669 ("r-jsonlite" ,r-jsonlite)
1670 ("r-later" ,r-later)
1671 ("r-lifecycle" ,r-lifecycle)
1673 ("r-promises" ,r-promises)
1675 ("r-rlang" ,r-rlang)
1676 ("r-sourcetools" ,r-sourcetools)
1677 ("r-withr" ,r-withr)
1678 ("r-xtable" ,r-xtable)))
1680 `(("js-datatables" ,js-datatables)
1681 ("js-selectize" ,js-selectize)
1682 ("js-strftime" ,js-strftime)
1683 ("js-highlight" ,js-highlight)))
1685 `(("uglify-js" ,uglify-js)
1686 ("gfortran" ,gfortran)
1687 ("js-bootstrap-accessibility"
1690 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1691 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1694 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1695 (home-page "https://shiny.rstudio.com")
1696 (synopsis "Easy interactive web applications with R")
1698 "Makes it incredibly easy to build interactive web applications
1699 with R. Automatic \"reactive\" binding between inputs and outputs and
1700 extensive prebuilt widgets make it possible to build beautiful,
1701 responsive, and powerful applications with minimal effort.")
1702 (license license:artistic2.0)))
1704 ;; This package includes minified JavaScript files. When upgrading please
1705 ;; check that there are no new minified JavaScript files.
1706 (define-public r-shinytree
1708 (name "r-shinytree")
1713 (uri (cran-uri "shinyTree" version))
1716 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1717 (modules '((guix build utils)))
1720 ;; Delete minified JavaScript
1721 (for-each delete-file
1722 '("inst/www/jsTree-3.3.7/libs/require.js"
1723 "inst/www/jsTree-3.3.7/libs/jquery.js"
1724 "inst/www/jsTree-3.3.7/jstree.min.js"))
1726 (properties `((upstream-name . "shinyTree")))
1727 (build-system r-build-system)
1729 `(#:modules ((guix build utils)
1730 (guix build r-build-system)
1734 (modify-phases %standard-phases
1735 (add-after 'unpack 'replace-minified-javascript
1736 (lambda* (#:key inputs #:allow-other-keys)
1737 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1738 (symlink (string-append (assoc-ref inputs "js-requirejs")
1739 "/share/javascript/require.min.js")
1744 `((,(assoc-ref inputs "js-jquery")
1748 (lambda (sources targets)
1749 (for-each (lambda (source target)
1750 (format #t "Processing ~a --> ~a~%"
1752 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1753 (call-with-output-file target
1755 (dump-port minified port)))))
1759 `(("r-htmlwidgets" ,r-htmlwidgets)
1760 ("r-jsonlite" ,r-jsonlite)
1761 ("r-promises" ,r-promises)
1762 ("r-shiny" ,r-shiny)
1763 ("r-stringr" ,r-stringr)))
1765 `(("js-requirejs" ,js-requirejs)))
1767 `(("uglify-js" ,uglify-js)
1771 (uri "https://code.jquery.com/jquery-3.3.1.js")
1774 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1775 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1776 (synopsis "jsTree bindings for Shiny")
1778 "This package exposes R bindings to jsTree, a JavaScript library that
1779 supports interactive trees, to enable rich, editable trees in Shiny.")
1780 (license license:expat)))
1782 (define-public r-shinydashboard
1784 (name "r-shinydashboard")
1788 (uri (cran-uri "shinydashboard" version))
1791 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1792 (build-system r-build-system)
1793 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1794 ;; Regenerate it from the included sources.
1796 `(#:modules ((guix build utils)
1797 (guix build r-build-system)
1800 (modify-phases %standard-phases
1801 (add-after 'unpack 'generate-minified-javascript
1803 (with-directory-excursion "inst/AdminLTE"
1804 (delete-file "app.min.js")
1805 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1806 (call-with-output-file "app.min.js"
1808 (dump-port minified port))))))))))
1810 `(("r-htmltools" ,r-htmltools)
1811 ("r-promises" ,r-promises)
1812 ("r-shiny" ,r-shiny)))
1814 `(("uglify-js" ,uglify-js)))
1815 (home-page "https://rstudio.github.io/shinydashboard/")
1816 (synopsis "Create dashboards with shiny")
1817 (description "This package provides an extension to the Shiny web
1818 application framework for R, making it easy to create attractive dashboards.")
1819 ;; This package includes software that was released under the Expat
1820 ;; license, but the whole package is released under GPL version 2 or
1822 (license license:gpl2+)))
1824 (define-public r-shinyfiles
1826 (name "r-shinyfiles")
1831 (uri (cran-uri "shinyFiles" version))
1833 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1834 (properties `((upstream-name . "shinyFiles")))
1835 (build-system r-build-system)
1838 ("r-htmltools" ,r-htmltools)
1839 ("r-jsonlite" ,r-jsonlite)
1840 ("r-shiny" ,r-shiny)
1841 ("r-tibble" ,r-tibble)))
1842 (home-page "https://github.com/thomasp85/shinyFiles")
1843 (synopsis "Server-side file system viewer for Shiny")
1845 "This package provides functionality for client-side navigation of the
1846 server side file system in shiny apps. In case the app is running locally
1847 this gives the user direct access to the file system without the need to
1848 \"download\" files to a temporary location. Both file and folder selection as
1849 well as file saving is available.")
1850 (license license:gpl2+)))
1852 (define-public r-shinythemes
1854 (name "r-shinythemes")
1859 (uri (cran-uri "shinythemes" version))
1862 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1863 (properties `((upstream-name . "shinythemes")))
1864 (build-system r-build-system)
1865 (propagated-inputs `(("r-shiny" ,r-shiny)))
1866 (home-page "https://rstudio.github.io/shinythemes/")
1867 (synopsis "Themes for Shiny")
1869 "This package provides themes for use with Shiny. It includes several
1870 Bootstrap themes, which are packaged for use with Shiny applications.")
1871 ;; The package is released under version 3 of the GPL, but it includes
1872 ;; source files that are covered by the Expat license. It also includes
1873 ;; fonts under SIL or the ASL.
1874 (license (list license:gpl3 license:expat
1875 license:silofl1.1 license:asl2.0))))
1877 ;; The package sources include minified variants of d3.js and non-minified
1878 ;; source code of d3-jetpack.
1879 (define-public r-d3r
1886 (uri (cran-uri "d3r" version))
1889 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1890 (build-system r-build-system)
1892 `(#:modules ((guix build utils)
1893 (guix build r-build-system)
1896 (modify-phases %standard-phases
1897 (add-after 'unpack 'process-javascript
1898 (lambda* (#:key inputs #:allow-other-keys)
1899 (with-directory-excursion "inst/www/d3/"
1903 `((,(assoc-ref inputs "d3.v3.js")
1904 "v3/dist/d3.min.js")
1905 (,(assoc-ref inputs "d3.v4.js")
1906 "v4/dist/d3.min.js")
1907 (,(assoc-ref inputs "d3.v5.js")
1908 "v5/dist/d3.min.js")
1909 (,(assoc-ref inputs "d3.v6.js")
1910 "v6/dist/d3.min.js"))))
1911 (lambda (sources targets)
1912 (for-each (lambda (source target)
1913 (format #t "Processing ~a --> ~a~%"
1915 (delete-file target)
1916 (invoke "esbuild" source "--minify"
1917 (string-append "--outfile=" target)))
1921 `(("r-dplyr" ,r-dplyr)
1922 ("r-htmltools" ,r-htmltools)
1923 ("r-rlang" ,r-rlang)
1924 ("r-tidyr" ,r-tidyr)))
1926 `(("esbuild" ,esbuild)
1930 (uri "https://d3js.org/d3.v3.js")
1933 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1937 (uri "https://d3js.org/d3.v4.js")
1940 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1944 (uri "https://d3js.org/d3.v5.js")
1947 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1951 (uri "https://d3js.org/d3.v6.js")
1954 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1955 (home-page "https://github.com/timelyportfolio/d3r")
1956 (synopsis "d3.js utilities for R")
1958 "This package provides a suite of functions to help ease the use of the
1959 d3.js visualization library in R. These helpers include
1960 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1961 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1962 R objects into the JSON format that the d3.js library expects.")
1963 (license license:bsd-3)))
1965 ;; We use the latest commit here because the last release was in 2016 while
1966 ;; the latest commit was in 2018.
1967 (define-public r-sankeyd3
1968 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1972 (version (git-version "0.3.2" revision commit))
1977 (url "https://github.com/fbreitwieser/sankeyD3")
1979 (file-name (git-file-name name version))
1982 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1983 (build-system r-build-system)
1986 ("r-htmlwidgets" ,r-htmlwidgets)
1987 ("r-shiny" ,r-shiny)
1988 ("r-magrittr" ,r-magrittr)))
1989 (home-page "https://github.com/fbreitwieser/sankeyD3")
1990 (synopsis "Sankey network graphs from R")
1992 "This package provides an R library to generate Sankey network graphs
1993 in R and Shiny via the D3 visualization library.")
1994 ;; The R code is licensed under GPLv3+. It includes the non-minified
1995 ;; JavaScript source code of d3-sankey, which is released under the
1996 ;; 3-clause BSD license.
1997 (license (list license:gpl3+ license:bsd-3)))))
1999 (define-public r-wesanderson
2001 (name "r-wesanderson")
2006 (uri (cran-uri "wesanderson" version))
2009 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2010 (properties `((upstream-name . "wesanderson")))
2011 (build-system r-build-system)
2012 (home-page "https://github.com/karthik/wesanderson")
2013 (synopsis "Wes Anderson color palette generator")
2015 "This package provides color palettes that have been generated mostly
2016 from Wes Anderson movies.")
2017 (license license:expat)))
2019 (define-public r-gg-gap
2026 (uri (cran-uri "gg.gap" version))
2029 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2030 (properties `((upstream-name . "gg.gap")))
2031 (build-system r-build-system)
2033 `(("r-cowplot" ,r-cowplot)
2034 ("r-ggplot2" ,r-ggplot2)))
2035 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2036 (synopsis "Define segments on the y-axis for ggplot2")
2038 "The @code{gg.gap} function enables you to define segments for the y-axis
2039 in a ggplot2 plot.")
2040 (license license:gpl3)))
2042 (define-public r-tablerdash
2044 (name "r-tablerdash")
2049 (uri (cran-uri "tablerDash" version))
2052 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2055 ;; Delete minified JavaScript
2056 (for-each delete-file
2057 '("inst/tablerDash-0.1.0/require.min.js"
2058 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2060 (properties `((upstream-name . "tablerDash")))
2061 (build-system r-build-system)
2063 `(#:modules ((guix build utils)
2064 (guix build r-build-system)
2067 (modify-phases %standard-phases
2068 (add-after 'unpack 'process-javascript
2069 (lambda* (#:key inputs #:allow-other-keys)
2070 (with-directory-excursion "inst"
2074 `((,(assoc-ref inputs "js-requirejs")
2075 "tablerDash-0.1.0/require.min.js")
2076 (,(assoc-ref inputs "js-bootstrap")
2077 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2078 (lambda (sources targets)
2079 (for-each (lambda (source target)
2080 (format #t "Processing ~a --> ~a~%"
2082 (invoke "esbuild" source "--minify"
2083 (string-append "--outfile=" target)))
2087 `(("r-htmltools" ,r-htmltools)
2088 ("r-knitr" ,r-knitr)
2089 ("r-shiny" ,r-shiny)))
2091 `(("esbuild" ,esbuild)
2095 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2098 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2102 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2103 v4.0.0/dist/js/bootstrap.bundle.js")
2106 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2107 (home-page "https://rinterface.github.io/tablerDash/")
2108 (synopsis "Tabler API for Shiny")
2110 "This package provides an R interface to the
2111 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2112 4 dashboard template. There are different layouts available such as a one
2113 page dashboard or a multi-page template, where the navigation menu is
2114 contained in the navigation bar.")
2115 (license license:gpl2+)))
2117 (define-public r-spelling
2124 (uri (cran-uri "spelling" version))
2127 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2128 (properties `((upstream-name . "spelling")))
2129 (build-system r-build-system)
2131 `(("r-commonmark" ,r-commonmark)
2132 ("r-hunspell" ,r-hunspell)
2133 ("r-knitr" ,r-knitr)
2134 ("r-xml2" ,r-xml2)))
2135 (home-page "https://docs.ropensci.org/spelling/")
2136 (synopsis "Tools for spell checking in R")
2138 "This is an R package for spell checking common document formats
2139 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2140 utilities to automate checking of documentation and vignettes as a unit test
2141 during @code{R CMD check}. Both British and American English are supported
2142 out of the box and other languages can be added. In addition, packages may
2143 define a wordlist to allow custom terminology without having to abuse
2145 (license license:expat)))
2147 (define-public r-crosstalk
2149 (name "r-crosstalk")
2154 (uri (cran-uri "crosstalk" version))
2157 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2158 (build-system r-build-system)
2160 `(("r-htmltools" ,r-htmltools)
2161 ("r-jsonlite" ,r-jsonlite)
2162 ("r-lazyeval" ,r-lazyeval)
2164 (home-page "https://rstudio.github.io/crosstalk/")
2165 (synopsis "Inter-widget interactivity for HTML widgets")
2167 "This package provides building blocks for allowing HTML widgets to
2168 communicate with each other, with Shiny or without (i.e. static @code{.html}
2169 files). It currently supports linked brushing and filtering.")
2170 (license license:expat)))
2172 (define-public r-rook
2179 (uri (cran-uri "Rook" version))
2182 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2183 (properties `((upstream-name . "Rook")))
2184 (build-system r-build-system)
2185 (propagated-inputs `(("r-brew" ,r-brew)))
2186 (home-page "https://cran.r-project.org/web/packages/Rook")
2187 (synopsis "Web server interface for R")
2189 "This package contains the Rook specification and convenience software
2190 for building and running Rook applications. A Rook application is an R
2191 reference class object that implements a @code{call} method or an R closure
2192 that takes exactly one argument, an environment, and returns a list with three
2193 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2194 (license license:gpl2)))
2196 (define-public r-miniui
2203 (uri (cran-uri "miniUI" version))
2206 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2207 (properties `((upstream-name . "miniUI")))
2208 (build-system r-build-system)
2210 `(("r-htmltools" ,r-htmltools)
2211 ("r-shiny" ,r-shiny)))
2212 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2213 (synopsis "Shiny UI widgets for small screens")
2215 "This package provides UI widget and layout functions for writing Shiny apps that
2216 work well on small screens.")
2217 (license license:gpl3)))
2219 (define-public r-feather
2226 (uri (cran-uri "feather" version))
2229 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2230 (build-system r-build-system)
2234 ("r-tibble" ,r-tibble)))
2235 (home-page "https://github.com/wesm/feather")
2236 (synopsis "R Bindings to the Feather API")
2237 (description "Read and write feather files, a lightweight binary columnar
2238 data store designed for maximum speed.")
2239 (license license:asl2.0)))
2241 (define-public r-maps
2248 (uri (cran-uri "maps" version))
2251 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2252 (build-system r-build-system)
2253 (home-page "https://cran.r-project.org/web/packages/maps")
2254 (synopsis "Draw geographical maps")
2255 (description "This package provides an R module for display of maps.
2256 Projection code and larger maps are in separate packages (@code{mapproj} and
2258 (license license:gpl2)))
2260 (define-public r-mapproj
2267 (uri (cran-uri "mapproj" version))
2270 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2271 (build-system r-build-system)
2272 (propagated-inputs `(("r-maps" ,r-maps)))
2273 (home-page "https://cran.r-project.org/web/packages/mapproj")
2274 (synopsis "Map projection in R")
2275 (description "This package converts latitude/longitude into projected
2277 (license (list license:gpl2 ; The R interface
2278 (license:non-copyleft ; The C code
2279 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2280 "Lucent Public License Version 1.02")))))
2282 (define-public r-rgooglemaps
2284 (name "r-rgooglemaps")
2289 (uri (cran-uri "RgoogleMaps" version))
2292 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2293 (properties `((upstream-name . "RgoogleMaps")))
2294 (build-system r-build-system)
2298 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2299 (synopsis "Use Google Maps in R")
2300 (description "This package serves two purposes:
2302 @item Provide a comfortable R interface to query the Google server for static
2304 @item Use the map as a background image to overlay plots within R. This
2305 requires proper coordinate scaling.
2307 (license license:gpl2+)))
2309 (define-public r-geosphere
2311 (name "r-geosphere")
2316 (uri (cran-uri "geosphere" version))
2319 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2320 (build-system r-build-system)
2321 (propagated-inputs `(("r-sp" ,r-sp)))
2322 (home-page "https://cran.r-project.org/web/packages/geosphere")
2323 (synopsis "Spherical trigonometry")
2324 (description "This package computes spherical trigonometry for geographic
2325 applications. That is, compute distances and related measures for angular
2326 (longitude/latitude) locations.")
2327 (license license:gpl3+)))
2329 (define-public r-jpeg
2336 (uri (cran-uri "jpeg" version))
2339 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2340 (build-system r-build-system)
2341 (inputs `(("libjpeg" ,libjpeg-turbo)))
2342 (home-page "https://www.rforge.net/jpeg/")
2343 (synopsis "Read and write JPEG images with R")
2344 (description "This package provides a way to read, write and display
2345 bitmap images stored in the JPEG format with R. It can read and write both
2346 files and in-memory raw vectors.")
2347 (license license:gpl2+)))
2349 (define-public r-ggmap
2356 (uri (cran-uri "ggmap" version))
2359 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2360 (build-system r-build-system)
2362 `(("r-bitops" ,r-bitops)
2363 ("r-digest" ,r-digest)
2364 ("r-dplyr" ,r-dplyr)
2365 ("r-ggplot2" ,r-ggplot2)
2369 ("r-magrittr" ,r-magrittr)
2372 ("r-purrr" ,r-purrr)
2373 ("r-rgooglemaps" ,r-rgooglemaps)
2374 ("r-rjson" ,r-rjson)
2375 ("r-scales" ,r-scales)
2376 ("r-stringr" ,r-stringr)
2377 ("r-tibble" ,r-tibble)
2378 ("r-tidyr" ,r-tidyr)))
2379 (home-page "https://github.com/dkahle/ggmap")
2380 (synopsis "Spatial visualization with ggplot2")
2381 (description "This package provides a collection of functions to visualize
2382 spatial data and models on top of static maps from various online sources (e.g
2383 Google Maps and Stamen Maps). It includes tools common to those tasks,
2384 including functions for geolocation and routing.")
2385 (license license:gpl2)))
2387 (define-public r-haven
2394 (uri (cran-uri "haven" version))
2397 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2398 (modules '((guix build utils)))
2401 ;; unvendor readstat
2402 (delete-file-recursively "src/readstat")
2404 (build-system r-build-system)
2407 (modify-phases %standard-phases
2408 (add-after 'unpack 'unbundle-readstat
2410 ;; Not required, since we’re not building readstat.
2411 (substitute* "src/Makevars"
2412 (("-lz") "-lreadstat"))
2415 `(("readstat" ,readstat)))
2417 `(("r-knitr" ,r-knitr)))
2419 `(("r-forcats" ,r-forcats)
2422 ("r-rlang" ,r-rlang)
2423 ("r-readr" ,r-readr)
2424 ("r-tibble" ,r-tibble)
2425 ("r-tidyselect" ,r-tidyselect)
2426 ("r-vctrs" ,r-vctrs)))
2427 (home-page "https://haven.tidyverse.org")
2428 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2430 "This package lets you mport foreign statistical formats into R via the
2431 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2432 (license license:expat)))
2434 (define-public r-amap
2440 (uri (cran-uri "amap" version))
2443 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2444 (build-system r-build-system)
2446 `(("gfortran" ,gfortran)))
2447 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2448 (synopsis "Another multidimensional analysis package")
2449 (description "This package provides tools for clustering and principal
2450 component analysis (with robust methods, and parallelized functions).")
2451 (license license:gpl2+)))
2453 (define-public r-ape
2460 (uri (cran-uri "ape" version))
2463 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2464 (build-system r-build-system)
2466 `(("r-lattice" ,r-lattice)
2468 ("r-rcpp" ,r-rcpp)))
2469 (home-page "http://ape-package.ird.fr/")
2470 (synopsis "Analyses of phylogenetics and evolution")
2472 "This package provides functions for reading, writing, plotting, and
2473 manipulating phylogenetic trees, analyses of comparative data in a
2474 phylogenetic framework, ancestral character analyses, analyses of
2475 diversification and macroevolution, computing distances from DNA sequences,
2476 and several other tools.")
2477 (license license:gpl2+)))
2479 (define-public r-abbyyr
2486 (uri (cran-uri "abbyyR" version))
2489 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2490 (properties `((upstream-name . "abbyyR")))
2491 (build-system r-build-system)
2493 `(("r-curl" ,r-curl)
2496 ("r-progress" ,r-progress)
2497 ("r-readr" ,r-readr)
2499 (home-page "https://github.com/soodoku/abbyyR")
2500 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2502 "This package provides tools to get text from images of text using Abbyy
2503 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2504 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2505 passports and get the results in a variety of formats including plain text and
2506 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2507 (license license:expat)))
2509 (define-public r-colorspace
2511 (name "r-colorspace")
2516 (uri (cran-uri "colorspace" version))
2518 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2519 (build-system r-build-system)
2521 `(("r-knitr" ,r-knitr)))
2522 (home-page "https://cran.r-project.org/web/packages/colorspace")
2523 (synopsis "Color space manipulation")
2525 "This package carries out a mapping between assorted color spaces
2526 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2527 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2528 colors are provided.")
2529 (license license:bsd-3)))
2531 (define-public r-glue
2538 (uri (cran-uri "glue" version))
2541 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2542 (build-system r-build-system)
2543 ;; knitr depends on glue, so we can't add knitr here to build the
2547 `(("r-knitr" ,r-knitr)))
2548 (home-page "https://github.com/tidyverse/glue")
2549 (synopsis "Interpreted string literals")
2551 "This package provides an implementation of interpreted string literals,
2552 inspired by Python's Literal String Interpolation (PEP-0498) and
2553 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2554 (license license:expat)))
2556 (define-public r-palmerpenguins
2558 (name "r-palmerpenguins")
2563 (uri (cran-uri "palmerpenguins" version))
2566 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2568 `((upstream-name . "palmerpenguins")))
2569 (build-system r-build-system)
2570 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2571 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2573 "This package includes size measurements, clutch observations, and blood
2574 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2575 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2576 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2577 Station Long Term Ecological Research (LTER) Program.")
2578 (license license:cc0)))
2580 (define-public r-pastecs
2586 (uri (cran-uri "pastecs" version))
2589 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2590 (build-system r-build-system)
2592 `(("r-boot" ,r-boot)))
2593 (home-page "https://github.com/phgrosjean/pastecs")
2594 (synopsis "Analysis of space-time ecological series")
2596 "This package provides functions for regulation, decomposition and analysis
2597 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2598 initiative to bring PASSTEC 2000 functionalities to R.")
2599 (license license:gpl2+)))
2601 (define-public r-partykit
2607 (uri (cran-uri "partykit" version))
2610 "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4"))))
2611 (build-system r-build-system)
2613 `(("r-formula" ,r-formula)
2615 ("r-libcoin" ,r-libcoin)
2616 ("r-mvtnorm" ,r-mvtnorm)
2617 ("r-rpart" ,r-rpart)
2618 ("r-survival" ,r-survival)))
2619 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2620 (synopsis "Toolkit for recursive partytioning")
2622 "This package provides a toolkit with infrastructure for representing,
2623 summarizing, and visualizing tree-structured regression and classification
2625 (license license:gpl2+)))
2627 (define-public r-plogr
2634 (uri (cran-uri "plogr" version))
2637 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2638 (build-system r-build-system)
2639 (home-page "https://github.com/krlmlr/plogr")
2640 (synopsis "R bindings for the plog C++ logging library")
2642 "This package provides the header files for a stripped-down version of
2643 the plog header-only C++ logging library, and a method to log to R's standard
2645 (license license:expat)))
2647 (define-public r-pls
2654 (uri (cran-uri "pls" version))
2656 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2657 (build-system r-build-system)
2658 (home-page "https://mevik.net/work/software/pls.html")
2659 (synopsis "Partial Least Squares and Principal Component Regression")
2661 "The pls package implements multivariate regression methods: Partial Least
2662 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2663 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2666 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2667 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2668 @item multi-response models (or @dfn{PLS2})
2669 @item flexible cross-validation
2670 @item Jackknife variance estimates of regression coefficients
2671 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2672 (R)MSEP, R², and correlation loadings
2673 @item formula interface, modelled after @code{lm()}, with methods for predict,
2674 print, summary, plot, update, etc.
2675 @item extraction functions for coefficients, scores, and loadings
2676 @item MSEP, RMSEP, and R² estimates
2677 @item multiplicative scatter correction (@dfn{MSC})
2679 (license license:gpl2)))
2688 (uri (cran-uri "ps" version))
2690 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
2691 (build-system r-build-system)
2692 (home-page "https://ps.r-lib.org")
2693 (synopsis "List, query, and manipulate system processes")
2695 "The ps package implements an API to list, query, and manipulate system
2696 processes. Most of its code is based on the @code{psutil} Python package.")
2697 (license license:bsd-3)))
2699 (define-public r-pkgbuild
2706 (uri (cran-uri "pkgbuild" version))
2708 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2709 (build-system r-build-system)
2711 `(("r-callr" ,r-callr)
2713 ("r-crayon" ,r-crayon)
2715 ("r-prettyunits" ,r-prettyunits)
2717 ("r-rprojroot" ,r-rprojroot)
2718 ("r-withr" ,r-withr)))
2719 (home-page "https://github.com/r-pkgs/pkgbuild")
2720 (synopsis "Find tools needed to build R packages")
2722 "This package provides functions used to build R packages. It locates
2723 compilers needed to build R packages on various platforms and ensures the PATH
2724 is configured appropriately so R can use them.")
2725 (license license:gpl3)))
2727 (define-public r-pkgload
2734 (uri (cran-uri "pkgload" version))
2737 "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v"))))
2738 (build-system r-build-system)
2741 ("r-crayon" ,r-crayon)
2743 ("r-pkgbuild" ,r-pkgbuild)
2744 ("r-rlang" ,r-rlang)
2745 ("r-rprojroot" ,r-rprojroot)
2746 ("r-rstudioapi" ,r-rstudioapi)
2747 ("r-withr" ,r-withr)))
2748 (home-page "https://github.com/r-lib/pkgload")
2749 (synopsis "Simulate package installation and attach")
2751 "This package simulates the process of installing a package and then
2752 attaching it. This is a key part of the @code{devtools} package as it allows
2753 you to rapidly iterate while developing a package.")
2754 (license license:gpl3)))
2756 (define-public r-rcpp
2763 (uri (cran-uri "Rcpp" version))
2765 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2766 (build-system r-build-system)
2767 (home-page "http://www.rcpp.org")
2768 (synopsis "Seamless R and C++ integration")
2770 "The Rcpp package provides R functions as well as C++ classes which offer
2771 a seamless integration of R and C++. Many R data types and objects can be
2772 mapped back and forth to C++ equivalents which facilitates both writing of new
2773 code as well as easier integration of third-party libraries. Documentation
2774 about Rcpp is provided by several vignettes included in this package, via the
2775 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2776 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2777 @code{citation(\"Rcpp\")} for details on these last two.")
2778 (license license:gpl2+)))
2780 (define-public r-rcppthread
2782 (name "r-rcppthread")
2787 (uri (cran-uri "RcppThread" version))
2790 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2791 (properties `((upstream-name . "RcppThread")))
2792 (build-system r-build-system)
2794 "https://github.com/tnagler/RcppThread")
2795 (synopsis "R threading in C++")
2797 "This package provides a C++11-style thread class and thread pool that can
2798 safely be interrupted from R.")
2799 (license license:expat)))
2801 (define-public r-bindr
2808 (uri (cran-uri "bindr" version))
2811 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2812 (build-system r-build-system)
2813 (home-page "https://github.com/krlmlr/bindr")
2814 (synopsis "Parametrized active bindings")
2816 "This package provides a simple interface for creating active bindings
2817 where the bound function accepts additional arguments.")
2818 (license license:expat)))
2820 (define-public r-bindrcpp
2827 (uri (cran-uri "bindrcpp" version))
2830 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2831 (build-system r-build-system)
2833 `(("r-bindr" ,r-bindr)
2834 ("r-plogr" ,r-plogr)
2835 ("r-rcpp" ,r-rcpp)))
2836 (home-page "https://github.com/krlmlr/bindrcpp")
2837 (synopsis "Rcpp interface to active bindings")
2839 "This package provides an easy way to fill an environment with active
2840 bindings that call a C++ function.")
2841 (license license:expat)))
2843 (define-public r-auc
2850 (uri (cran-uri "AUC" version))
2853 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2854 (properties `((upstream-name . "AUC")))
2855 (build-system r-build-system)
2856 (home-page "https://cran.r-project.org/web/packages/AUC")
2857 (synopsis "Compute the area under the curve of selected measures")
2859 "This package includes functions to compute the area under the curve of
2860 selected measures: the area under the sensitivity curve (AUSEC), the area
2861 under the specificity curve (AUSPC), the area under the accuracy
2862 curve (AUACC), and the area under the receiver operating characteristic
2863 curve (AUROC). The curves can also be visualized. Support for partial areas
2865 (license license:gpl2+)))
2867 (define-public r-calibrate
2869 (name "r-calibrate")
2874 (uri (cran-uri "calibrate" version))
2876 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2877 (build-system r-build-system)
2879 `(("r-mass" ,r-mass)))
2880 (home-page "https://cran.r-project.org/web/packages/calibrate")
2881 (synopsis "Calibration of scatterplot and biplot axes")
2883 "This is a package for drawing calibrated scales with tick marks
2884 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2885 (license license:gpl2)))
2887 (define-public r-shape
2894 (uri (cran-uri "shape" version))
2897 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2898 (build-system r-build-system)
2899 (home-page "https://cran.r-project.org/web/packages/shape")
2900 (synopsis "Functions for plotting graphical shapes")
2902 "This package provides functions for plotting graphical shapes such as
2903 ellipses, circles, cylinders, arrows, ...")
2904 (license license:gpl3+)))
2906 (define-public r-globaloptions
2908 (name "r-globaloptions")
2913 (uri (cran-uri "GlobalOptions" version))
2915 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2916 (properties `((upstream-name . "GlobalOptions")))
2917 (build-system r-build-system)
2919 `(("r-knitr" ,r-knitr)))
2920 (home-page "https://github.com/jokergoo/GlobalOptions")
2921 (synopsis "Generate functions to get or set global options")
2923 "This package provides more controls on the option values such as
2924 validation and filtering on the values, making options invisible or private.")
2925 (license license:gpl2+)))
2927 (define-public r-circlize
2934 (uri (cran-uri "circlize" version))
2937 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2938 (build-system r-build-system)
2940 `(("r-colorspace" ,r-colorspace)
2941 ("r-globaloptions" ,r-globaloptions)
2942 ("r-shape" ,r-shape)))
2944 `(("r-knitr" ,r-knitr)))
2945 (home-page "https://github.com/jokergoo/circlize")
2946 (synopsis "Circular visualization")
2948 "Circular layout is an efficient way to visualise huge amounts of
2949 information. This package provides an implementation of circular layout
2950 generation in R as well as an enhancement of available software. Its
2951 flexibility is based on the usage of low-level graphics functions such that
2952 self-defined high-level graphics can be easily implemented by users for
2953 specific purposes. Together with the seamless connection between the powerful
2954 computational and visual environment in R, it gives users more convenience and
2955 freedom to design figures for better understanding complex patterns behind
2956 multi-dimensional data.")
2957 (license license:gpl2+)))
2959 (define-public r-powerlaw
2966 (uri (cran-uri "poweRlaw" version))
2968 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2969 (properties `((upstream-name . "poweRlaw")))
2970 (build-system r-build-system)
2972 `(("r-pracma" ,r-pracma)))
2974 `(("r-knitr" ,r-knitr)))
2975 (home-page "https://github.com/csgillespie/poweRlaw")
2976 (synopsis "Tools for the analysis of heavy tailed distributions")
2978 "This package provides an implementation of maximum likelihood estimators
2979 for a variety of heavy tailed distributions, including both the discrete and
2980 continuous power law distributions. Additionally, a goodness-of-fit based
2981 approach is used to estimate the lower cut-off for the scaling region.")
2982 ;; Any of these GPL versions.
2983 (license (list license:gpl2 license:gpl3))))
2985 (define-public r-compare
2992 (uri (cran-uri "compare" version))
2995 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2996 (build-system r-build-system)
2997 (home-page "https://cran.r-project.org/web/packages/compare")
2998 (synopsis "Comparing objects for differences")
3000 "This package provides functions to compare a model object to a
3001 comparison object. If the objects are not identical, the functions can be
3002 instructed to explore various modifications of the objects (e.g., sorting
3003 rows, dropping names) to see if the modified versions are identical.")
3004 (license license:gpl2+)))
3006 (define-public r-dendextend
3008 (name "r-dendextend")
3013 (uri (cran-uri "dendextend" version))
3016 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3017 (build-system r-build-system)
3019 `(("r-ggplot2" ,r-ggplot2)
3020 ("r-magrittr" ,r-magrittr)
3021 ("r-viridis" ,r-viridis)))
3023 `(("r-knitr" ,r-knitr)))
3024 (home-page "https://cran.r-project.org/web/packages/dendextend")
3025 (synopsis "Extending 'dendrogram' functionality in R")
3027 "This package offers a set of functions for extending @code{dendrogram}
3028 objects in R, letting you visualize and compare trees of hierarchical
3029 clusterings. You can adjust a tree's graphical parameters (the color, size,
3030 type, etc of its branches, nodes and labels) and visually and statistically
3031 compare different dendrograms to one another.")
3032 ;; Any of these versions
3033 (license (list license:gpl2 license:gpl3))))
3035 (define-public r-getoptlong
3037 (name "r-getoptlong")
3042 (uri (cran-uri "GetoptLong" version))
3045 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3046 (properties `((upstream-name . "GetoptLong")))
3047 (build-system r-build-system)
3051 `(("r-crayon" ,r-crayon)
3052 ("r-globaloptions" ,r-globaloptions)
3053 ("r-rjson" ,r-rjson)))
3055 `(("r-knitr" ,r-knitr)))
3056 (home-page "https://github.com/jokergoo/GetoptLong")
3057 (synopsis "Parsing command-line arguments and variable interpolation")
3059 "This is yet another command-line argument parser which wraps the
3060 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3061 use in R. It also provides a simple way for variable interpolation in R.")
3062 (license license:gpl2+)))
3064 (define-public r-fastmatch
3066 (name "r-fastmatch")
3071 (uri (cran-uri "fastmatch" version))
3074 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3075 (build-system r-build-system)
3076 (home-page "https://www.rforge.net/fastmatch")
3077 (synopsis "Fast match function")
3079 "This package provides a fast @code{match} replacement for cases that
3080 require repeated look-ups. It is slightly faster that R's built-in
3081 @code{match} function on first match against a table, but extremely fast on
3082 any subsequent lookup as it keeps the hash table in memory.")
3083 (license license:gpl2)))
3092 (uri (cran-uri "ff" version))
3095 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3096 (build-system r-build-system)
3097 (propagated-inputs `(("r-bit" ,r-bit)))
3098 (home-page "http://ff.r-forge.r-project.org/")
3099 (synopsis "Memory-efficient storage of large data on disk and access functions")
3101 "This package provides data structures that are stored on disk but
3102 behave (almost) as if they were in RAM by transparently mapping only a section
3104 ;; error Architecture not supported.
3105 (supported-systems (delete "aarch64-linux" %supported-systems))
3106 (license license:gpl2)))
3108 (define-public r-ffbase
3115 (uri (cran-uri "ffbase" version))
3118 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3119 (build-system r-build-system)
3122 ("r-fastmatch" ,r-fastmatch)
3124 (home-page "https://github.com/edwindj/ffbase")
3125 (synopsis "Basic statistical functions for package 'ff'")
3127 "This package extends the out of memory vectors of @code{ff} with
3128 statistical functions and other utilities to ease their usage.")
3129 (license license:gpl3)))
3131 (define-public r-prettyunits
3133 (name "r-prettyunits")
3138 (uri (cran-uri "prettyunits" version))
3141 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3142 (build-system r-build-system)
3143 (home-page "https://github.com/gaborcsardi/prettyunits")
3144 (synopsis "Pretty, human readable formatting of quantities")
3146 "This package provides tools for pretty, human readable formatting of
3148 (license license:expat)))
3150 (define-public r-reshape
3157 (uri (cran-uri "reshape" version))
3160 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3161 (build-system r-build-system)
3163 `(("r-plyr" ,r-plyr)
3164 ("r-rcpp" ,r-rcpp)))
3165 (home-page "http://had.co.nz/reshape")
3166 (synopsis "Flexibly reshape data")
3168 "Flexibly restructure and aggregate data using just two functions:
3169 @code{melt} and @code{cast}. This package provides them.")
3170 (license license:expat)))
3172 (define-public r-restrserve
3174 (name "r-restrserve")
3179 (uri (cran-uri "RestRserve" version))
3181 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3182 (build-system r-build-system)
3184 `(("r-checkmate" ,r-checkmate)
3185 ("r-jsonlite" ,r-jsonlite)
3189 ("r-rserve" ,r-rserve)
3190 ("r-uuid" ,r-uuid)))
3192 `(("r-knitr" ,r-knitr)))
3193 (home-page "https://restrserve.org")
3194 (synopsis "R web API framework")
3196 "RestRserve is an R web API framework for building high-performance AND
3197 robust microservices and app backends. With Rserve backend on UNIX-like
3198 systems it is parallel by design. It will handle incoming requests in
3199 parallel - each request in a separate fork.")
3200 (license license:gpl2+)))
3202 (define-public r-progress
3209 (uri (cran-uri "progress" version))
3212 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3213 (build-system r-build-system)
3215 `(("r-crayon" ,r-crayon)
3217 ("r-prettyunits" ,r-prettyunits)
3219 (home-page "https://github.com/gaborcsardi/progress")
3220 (synopsis "Terminal progress bars")
3222 "This package provides configurable progress bars. They may include
3223 percentage, elapsed time, and/or the estimated completion time. They work in
3224 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3225 package also provides a C++ API, that works with or without Rcpp.")
3226 (license license:expat)))
3228 (define-public r-ggally
3235 (uri (cran-uri "GGally" version))
3238 "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p"))))
3239 (properties `((upstream-name . "GGally")))
3240 (build-system r-build-system)
3242 `(("openssl" ,openssl)))
3244 `(("r-dplyr" ,r-dplyr)
3245 ("r-forcats" ,r-forcats)
3246 ("r-ggplot2" ,r-ggplot2)
3247 ("r-gtable" ,r-gtable)
3248 ("r-lifecycle" ,r-lifecycle)
3250 ("r-progress" ,r-progress)
3251 ("r-rcolorbrewer" ,r-rcolorbrewer)
3252 ("r-reshape" ,r-reshape)
3253 ("r-rlang" ,r-rlang)
3254 ("r-scales" ,r-scales)
3255 ("r-tidyr" ,r-tidyr)))
3256 (home-page "https://ggobi.github.io/ggally")
3257 (synopsis "Extension to ggplot2")
3259 "The R package ggplot2 is a plotting system based on the grammar of
3260 graphics. GGally extends ggplot2 by adding several functions to reduce the
3261 complexity of combining geometric objects with transformed data. Some of
3262 these functions include a pairwise plot matrix, a two group pairwise plot
3263 matrix, a parallel coordinates plot, a survival plot, and several functions to
3265 (license license:gpl2+)))
3267 (define-public r-proxy
3274 (uri (cran-uri "proxy" version))
3277 "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f"))))
3278 (build-system r-build-system)
3279 (home-page "https://cran.r-project.org/web/packages/proxy")
3280 (synopsis "Distance and similarity measures")
3282 "This package provides an extensible framework for the efficient
3283 calculation of auto- and cross-proximities, along with implementations of the
3284 most popular ones.")
3285 (license license:gpl2)))
3294 (uri (cran-uri "sp" version))
3296 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3297 (build-system r-build-system)
3299 `(("r-lattice" ,r-lattice)))
3300 (home-page "https://cran.r-project.org/web/packages/sp")
3301 (synopsis "Classes and methods for spatial data")
3303 "This package provides classes and methods for spatial data; the classes
3304 document where the spatial location information resides, for 2D or 3D data.
3305 Utility functions are provided, e.g. for plotting data as maps, spatial
3306 selection, as well as methods for retrieving coordinates, for subsetting,
3307 print, summary, etc.")
3308 (license license:gpl2+)))
3310 (define-public r-laplacesdemon
3312 (name "r-laplacesdemon")
3317 (uri (cran-uri "LaplacesDemon" version))
3319 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3320 (properties `((upstream-name . "LaplacesDemon")))
3321 (build-system r-build-system)
3322 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3323 (synopsis "Complete environment for Bayesian inference")
3325 "This package provides a complete environment for Bayesian inference using
3326 a variety of different samplers.")
3327 (license license:expat)))
3329 (define-public r-rmtstat
3336 (uri (cran-uri "RMTstat" version))
3339 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3340 (properties `((upstream-name . "RMTstat")))
3341 (build-system r-build-system)
3342 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3343 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3345 "This package provides functions for working with the Tracy-Widom laws
3346 and other distributions related to the eigenvalues of large Wishart
3348 (license license:bsd-3)))
3350 (define-public r-rmpi
3356 (uri (cran-uri "Rmpi" version))
3359 "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r"))))
3360 (properties `((upstream-name . "Rmpi")))
3361 (build-system r-build-system)
3363 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3364 #:phases (modify-phases %standard-phases
3365 (add-before 'install 'mpi-setup
3368 `(("openmpi" ,openmpi)))
3370 `(("pkg-config" ,pkg-config)))
3371 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3372 (synopsis "R interface to message-passing interface (MPI)")
3374 "This package provides an interface (wrapper) to MPI APIs. It also
3375 provides an interactive R manager and worker environment.")
3376 (license license:gpl2+)))
3378 (define-public r-lmoments
3385 (uri (cran-uri "Lmoments" version))
3388 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3389 (properties `((upstream-name . "Lmoments")))
3390 (build-system r-build-system)
3392 `(("r-rcpp" ,r-rcpp)
3393 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3394 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3395 (synopsis "L-moments and quantile mixtures")
3397 "This package contains functions to estimate L-moments and trimmed
3398 L-moments from the data. It also contains functions to estimate the
3399 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3400 quantile mixture from L-moments and trimmed L-moments.")
3401 (license license:gpl2)))
3403 (define-public r-distillery
3405 (name "r-distillery")
3410 (uri (cran-uri "distillery" version))
3413 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3414 (build-system r-build-system)
3415 (home-page "https://ral.ucar.edu/staff/ericg/")
3416 (synopsis "Functions for confidence intervals and object information")
3418 "This package provides some very simple method functions for confidence
3419 interval calculation and to distill pertinent information from a potentially
3420 complex object; primarily used in common with the packages extRemes and
3422 (license license:gpl2+)))
3424 (define-public r-etrunct
3430 (uri (cran-uri "etrunct" version))
3433 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3434 (properties `((upstream-name . "etrunct")))
3435 (build-system r-build-system)
3436 (home-page "https://cran.r-project.org/web/packages/etrunct")
3437 (synopsis "Computes moments of univariate truncated T distribution")
3438 (description "This package computes moments of univariate truncated
3439 T distribution. There is only one exported function, @code{e_trunct},
3440 which should be seen for details.")
3441 (license license:expat)))
3443 (define-public r-extremes
3450 (uri (cran-uri "extRemes" version))
3453 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3454 (properties `((upstream-name . "extRemes")))
3455 (build-system r-build-system)
3457 `(("r-distillery" ,r-distillery)
3458 ("r-lmoments" ,r-lmoments)))
3459 (home-page "https://www.assessment.ucar.edu/toolkit/")
3460 (synopsis "Extreme value analysis")
3462 "ExtRemes is a suite of functions for carrying out analyses on the
3463 extreme values of a process of interest; be they block maxima over long blocks
3464 or excesses over a high threshold.")
3465 (license license:gpl2+)))
3467 (define-public r-lmtest
3474 (uri (cran-uri "lmtest" version))
3477 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3478 (build-system r-build-system)
3480 `(("r-zoo" ,r-zoo)))
3482 `(("gfortran" ,gfortran)))
3483 (home-page "https://cran.r-project.org/web/packages/lmtest")
3484 (synopsis "Testing linear regression models")
3486 "This package provides a collection of tests, data sets, and examples for
3487 diagnostic checking in linear regression models. Furthermore, some generic
3488 tools for inference in parametric models are provided.")
3489 ;; Either version is okay
3490 (license (list license:gpl2 license:gpl3))))
3492 (define-public r-idr
3498 (uri (cran-uri "idr" version))
3501 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3502 (build-system r-build-system)
3503 (home-page "https://cran.r-project.org/web/packages/idr/")
3504 (synopsis "Irreproducible discovery rate")
3506 "This is a package for estimating the copula mixture model and plotting
3507 correspondence curves in \"Measuring reproducibility of high-throughput
3508 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3509 by Li, Brown, Huang, and Bickel")
3510 (license license:gpl2+)))
3512 (define-public r-inline
3518 (uri (cran-uri "inline" version))
3521 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3522 (build-system r-build-system)
3523 (home-page "https://cran.r-project.org/web/packages/inline")
3524 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3526 "This package provides functionality to dynamically define R functions
3527 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3528 @code{.Call} calling conventions.")
3529 ;; Any version of the LGPL.
3530 (license license:lgpl3+)))
3532 (define-public r-inum
3538 (uri (cran-uri "inum" version))
3541 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3542 (build-system r-build-system)
3544 `(("r-libcoin" ,r-libcoin)))
3545 (home-page "https://cran.r-project.org/web/packages/inum/")
3546 (synopsis "Interval and enum-type representation of vectors")
3548 "This package provides an enum-type representation of vectors and
3549 representation of intervals, including a method of coercing variables
3551 (license license:gpl2)))
3552 (define-public r-invgamma
3558 (uri (cran-uri "invgamma" version))
3561 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3562 (properties `((upstream-name . "invgamma")))
3563 (build-system r-build-system)
3564 (home-page "https://github.com/dkahle/invgamma")
3565 (synopsis "Inverse gamma distribution")
3566 (description "This package provides a light weight implementation of the
3567 standard distribution functions for the inverse gamma distribution, wrapping
3568 those for the gamma distribution in the @code{stats} package.")
3569 (license license:gpl2)))
3571 (define-public r-bdsmatrix
3573 (name "r-bdsmatrix")
3578 (uri (cran-uri "bdsmatrix" version))
3581 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3582 (properties `((upstream-name . "bdsmatrix")))
3583 (build-system r-build-system)
3584 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3585 (synopsis "Routines for block diagonal symmetric matrices")
3587 "This package provides procedures to work with block diagonal symmetric
3588 matrices, a special case of sparse matrices.")
3589 (license license:lgpl2.0)))
3591 (define-public r-bbmle
3594 (version "1.0.23.1")
3598 (uri (cran-uri "bbmle" version))
3601 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3602 (build-system r-build-system)
3604 `(("r-bdsmatrix" ,r-bdsmatrix)
3605 ("r-lattice" ,r-lattice)
3607 ("r-matrix" ,r-matrix)
3608 ("r-mvtnorm" ,r-mvtnorm)
3609 ("r-numderiv" ,r-numderiv)))
3610 (home-page "https://cran.r-project.org/web/packages/bbmle")
3611 (synopsis "Tools for General Maximum Likelihood Estimation")
3613 "This package provides methods and functions for fitting maximum
3614 likelihood models in R. This package modifies and extends the @code{mle}
3615 classes in the @code{stats4} package.")
3616 ;; Any version of the GPL
3617 (license license:gpl2+)))
3619 (define-public r-emdbook
3626 (uri (cran-uri "emdbook" version))
3629 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3630 (build-system r-build-system)
3632 `(("r-bbmle" ,r-bbmle)
3634 ("r-lattice" ,r-lattice)
3636 ("r-plyr" ,r-plyr)))
3637 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3638 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3640 "This package provides auxiliary functions and data sets for \"Ecological
3641 Models and Data\", a book presenting maximum likelihood estimation and related
3642 topics for ecologists (ISBN 978-0-691-12522-0).")
3644 (license (list license:gpl2 license:gpl3))))
3646 (define-public r-lpsolve
3653 (uri (cran-uri "lpSolve" version))
3656 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3657 (properties `((upstream-name . "lpSolve")))
3658 (build-system r-build-system)
3659 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3660 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3662 "Lp_solve is software for solving linear, integer and mixed integer
3663 programs. This implementation supplies a \"wrapper\" function in C and some R
3664 functions that solve general linear/integer problems, assignment problems, and
3665 transportation problems.")
3666 (license license:lgpl2.0)))
3668 (define-public r-limsolve
3675 (uri (cran-uri "limSolve" version))
3678 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3679 (properties `((upstream-name . "limSolve")))
3680 (build-system r-build-system)
3682 `(("r-lpsolve" ,r-lpsolve)
3684 ("r-quadprog" ,r-quadprog)))
3685 (native-inputs `(("gfortran" ,gfortran)))
3686 (home-page "https://cran.r-project.org/web/packages/limSolve")
3687 (synopsis "Solving linear inverse models")
3689 "This package provides functions that:
3692 @item find the minimum/maximum of a linear or quadratic function,
3693 @item sample an underdetermined or overdetermined system,
3694 @item solve a linear system Ax=B for the unknown x.
3697 It includes banded and tridiagonal linear systems. The package calls Fortran
3698 functions from LINPACK.")
3700 (license (list license:gpl2+ license:gpl3+))))
3702 (define-public r-fitdistrplus
3704 (name "r-fitdistrplus")
3709 (uri (cran-uri "fitdistrplus" version))
3712 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3713 (build-system r-build-system)
3715 `(("r-mass" ,r-mass)
3716 ("r-survival" ,r-survival)))
3718 `(("r-knitr" ,r-knitr)))
3719 (home-page "http://riskassessment.r-forge.r-project.org")
3720 (synopsis "Fitting a parametric distribution from data")
3722 "This package extends the @code{fitdistr} function of the MASS package
3723 with several functions to help the fit of a parametric distribution to
3724 non-censored or censored data. Censored data may contain left-censored,
3725 right-censored and interval-censored values, with several lower and upper
3726 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3727 provides moment matching (MME), quantile matching (QME) and maximum
3728 goodness-of-fit estimation (MGE) methods (available only for non-censored
3729 data). Weighted versions of MLE, MME and QME are available.")
3730 (license license:gpl2+)))
3732 (define-public r-energy
3739 (uri (cran-uri "energy" version))
3742 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
3743 (build-system r-build-system)
3745 `(("r-boot" ,r-boot)
3747 ("r-rcpp" ,r-rcpp)))
3748 (home-page "https://cran.r-project.org/web/packages/energy")
3749 (synopsis "Multivariate inference via the energy of data")
3751 "This package provides e-statistics (energy) tests and statistics for
3752 multivariate and univariate inference, including distance correlation,
3753 one-sample, two-sample, and multi-sample tests for comparing multivariate
3754 distributions, are implemented. Measuring and testing multivariate
3755 independence based on distance correlation, partial distance correlation,
3756 multivariate goodness-of-fit tests, clustering based on energy distance,
3757 testing for multivariate normality, distance components (disco) for
3758 non-parametric analysis of structured data, and other energy
3759 statistics/methods are implemented.")
3760 (license license:gpl2+)))
3762 (define-public r-suppdists
3764 (name "r-suppdists")
3769 (uri (cran-uri "SuppDists" version))
3772 "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8"))))
3773 (properties `((upstream-name . "SuppDists")))
3774 (build-system r-build-system)
3775 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3776 (synopsis "Supplementary distributions")
3778 "This package provides ten distributions supplementing those built into
3779 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3780 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3781 coefficient, Johnson distributions, normal scores and generalized
3782 hypergeometric distributions. In addition two random number generators of
3783 George Marsaglia are included.")
3784 (license license:gpl2+)))
3786 (define-public r-ksamples
3793 (uri (cran-uri "kSamples" version))
3796 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3797 (properties `((upstream-name . "kSamples")))
3798 (build-system r-build-system)
3800 `(("r-suppdists" ,r-suppdists)))
3801 (home-page "https://cran.r-project.org/web/packages/kSamples")
3802 (synopsis "K-Sample rank tests and their combinations")
3804 "This package provides tools to compares k samples using the
3805 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3806 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3807 test. It computes asymptotic, simulated or (limited) exact P-values, all
3808 valid under randomization, with or without ties, or conditionally under random
3809 sampling from populations, given the observed tie pattern. Except for Steel's
3810 test and the JT test it also combines these tests across several blocks of
3812 (license license:gpl2+)))
3814 (define-public r-cvst
3821 (uri (cran-uri "CVST" version))
3824 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3825 (properties `((upstream-name . "CVST")))
3826 (build-system r-build-system)
3828 `(("r-kernlab" ,r-kernlab)
3829 ("r-matrix" ,r-matrix)))
3830 (home-page "https://cran.r-project.org/web/packages/CVST")
3831 (synopsis "Fast cross-validation via sequential testing")
3833 "This package implements the fast cross-validation via sequential
3834 testing (CVST) procedure. CVST is an improved cross-validation procedure
3835 which uses non-parametric testing coupled with sequential analysis to
3836 determine the best parameter set on linearly increasing subsets of the data.
3837 Additionally to the CVST the package contains an implementation of the
3838 ordinary k-fold cross-validation with a flexible and powerful set of helper
3839 objects and methods to handle the overall model selection process. The
3840 implementations of the Cochran's Q test with permutations and the sequential
3841 testing framework of Wald are generic and can therefore also be used in other
3843 (license license:gpl2+)))
3845 (define-public r-squarem
3852 (uri (cran-uri "SQUAREM" version))
3855 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3856 (properties `((upstream-name . "SQUAREM")))
3857 (build-system r-build-system)
3858 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3859 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3861 "This package provides algorithms for accelerating the convergence of
3862 slow, monotone sequences from smooth, contraction mapping such as the EM
3863 algorithm. It can be used to accelerate any smooth, linearly convergent
3864 acceleration scheme. A tutorial style introduction to this package is
3865 available in a vignette.")
3866 (license license:gpl2+)))
3868 (define-public r-lava
3875 (uri (cran-uri "lava" version))
3878 "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83"))))
3879 (build-system r-build-system)
3881 `(("r-numderiv" ,r-numderiv)
3882 ("r-squarem" ,r-squarem)
3883 ("r-survival" ,r-survival)))
3885 `(("r-knitr" ,r-knitr)))
3886 (home-page "https://github.com/kkholst/lava")
3887 (synopsis "Latent variable models")
3889 "This package provides tools for the estimation and simulation of latent
3891 (license license:gpl3)))
3893 (define-public r-drr
3900 (uri (cran-uri "DRR" version))
3903 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3904 (properties `((upstream-name . "DRR")))
3905 (build-system r-build-system)
3907 `(("r-cvst" ,r-cvst)
3908 ("r-kernlab" ,r-kernlab)
3909 ("r-matrix" ,r-matrix)))
3910 (home-page "https://cran.r-project.org/web/packages/DRR")
3911 (synopsis "Dimensionality reduction via regression")
3913 "This package provides an implementation of dimensionality reduction via
3914 regression using Kernel Ridge Regression.")
3915 (license license:gpl3)))
3917 (define-public r-prodlim
3920 (version "2019.11.13")
3924 (uri (cran-uri "prodlim" version))
3927 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3928 (build-system r-build-system)
3930 `(("r-kernsmooth" ,r-kernsmooth)
3933 ("r-survival" ,r-survival)))
3934 (home-page "https://cran.r-project.org/web/packages/prodlim")
3935 (synopsis "Product-limit estimation for censored event history analysis")
3937 "This package provides a fast and user-friendly implementation of
3938 nonparametric estimators for censored event history (survival) analysis with
3939 the Kaplan-Meier and Aalen-Johansen methods.")
3940 (license license:gpl2+)))
3942 (define-public r-dimred
3949 (uri (cran-uri "dimRed" version))
3952 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3953 (properties `((upstream-name . "dimRed")))
3954 (build-system r-build-system)
3957 ("r-magrittr" ,r-magrittr)))
3958 (home-page "https://github.com/gdkrmr/dimRed")
3959 (synopsis "Framework for dimensionality reduction")
3961 "This package provides a collection of dimensionality reduction
3962 techniques from R packages and provides a common interface for calling the
3964 (license license:gpl3)))
3966 (define-public r-timedate
3969 (version "3043.102")
3973 (uri (cran-uri "timeDate" version))
3976 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3977 (properties `((upstream-name . "timeDate")))
3978 (build-system r-build-system)
3979 (home-page "https://www.rmetrics.org")
3980 (synopsis "Chronological and calendar objects")
3982 "This package provides an environment for teaching \"Financial
3983 Engineering and Computational Finance\" and for managing chronological and
3985 (license license:gpl2+)))
3987 (define-public r-magic
3994 (uri (cran-uri "magic" version))
3997 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3998 (build-system r-build-system)
4000 `(("r-abind" ,r-abind)))
4001 (home-page "https://github.com/RobinHankin/magic.git")
4002 (synopsis "Create and investigate magic squares")
4004 "This package provides a collection of efficient, vectorized algorithms
4005 for the creation and investigation of magic squares and hypercubes, including
4006 a variety of functions for the manipulation and analysis of arbitrarily
4007 dimensioned arrays.")
4008 (license license:gpl2)))
4010 (define-public r-rmysql
4017 (uri (cran-uri "RMySQL" version))
4020 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4021 (properties `((upstream-name . "RMySQL")))
4022 (build-system r-build-system)
4024 `(("mariadb-dev" ,mariadb "dev")
4027 `(("r-dbi" ,r-dbi)))
4028 (home-page "https://github.com/r-dbi/RMySQL")
4029 (synopsis "Database interface and MySQL driver for R")
4031 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4032 package contains an old implementation based on legacy code from S-PLUS which
4033 is being phased out. A modern MySQL client based on Rcpp is available from
4034 the RMariaDB package.")
4035 (license license:gpl2)))
4037 (define-public r-rpostgresql
4039 (name "r-rpostgresql")
4044 (uri (cran-uri "RPostgreSQL" version))
4047 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4048 (properties `((upstream-name . "RPostgreSQL")))
4049 (build-system r-build-system)
4051 `(("postgresql" ,postgresql)))
4053 `(("r-dbi" ,r-dbi)))
4054 (home-page "https://github.com/tomoakin/RPostgreSQL")
4055 (synopsis "R interface to the PostgreSQL database system")
4057 "This package provides a Database Interface (DBI) compliant driver for R
4058 to access PostgreSQL database systems.")
4059 ;; The whole package is released under GPL version 2. It includes code
4060 ;; under the PostgreSQL license.
4061 (license license:gpl2)))
4063 (define-public r-linprog
4070 (uri (cran-uri "linprog" version))
4073 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4074 (build-system r-build-system)
4075 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4076 (home-page "http://linprog.r-forge.r-project.org/")
4077 (synopsis "Linear programming and optimization")
4079 "This package can be used to solve Linear Programming / Linear
4080 Optimization problems by using the simplex algorithm.")
4081 (license license:gpl2+)))
4083 (define-public r-geometry
4090 (uri (cran-uri "geometry" version))
4093 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4094 (build-system r-build-system)
4096 `(("r-magic" ,r-magic)
4097 ("r-linprog" ,r-linprog)
4098 ("r-lpsolve" ,r-lpsolve)
4100 ("r-rcppprogress" ,r-rcppprogress)))
4101 (home-page "http://geometry.r-forge.r-project.org/")
4102 (synopsis "Mesh generator and surface tessellator")
4104 "This package makes the qhull library available in R, in a similar manner
4105 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4106 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4107 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4108 and higher dimensions. It implements the Quickhull algorithm for computing
4109 the convex hull. Qhull does not support constrained Delaunay triangulations,
4110 or mesh generation of non-convex objects, but the package does include some R
4111 functions that allow for this. Currently the package only gives access to
4112 Delaunay triangulation and convex hull computation.")
4113 ;; The Qhull sources are included and are distributed under a custom
4114 ;; non-copyleft license. The R sources are released under GPL version 2.
4115 (license (list license:gpl2
4116 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4118 (define-public r-ddalpha
4125 (uri (cran-uri "ddalpha" version))
4128 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4129 (build-system r-build-system)
4132 ("r-class" ,r-class)
4133 ("r-geometry" ,r-geometry)
4136 ("r-robustbase" ,r-robustbase)
4137 ("r-sfsmisc" ,r-sfsmisc)))
4139 `(("gfortran" ,gfortran)))
4140 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4141 (synopsis "Depth-Based classification and calculation of data depth")
4143 "This package contains procedures for depth-based supervised learning,
4144 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4145 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4146 statistical depth function to a compact low-dimensional space, where the final
4147 classification is done. It also offers an extension to functional data and
4148 routines for calculating certain notions of statistical depth functions. 50
4149 multivariate and 5 functional classification problems are included.")
4150 (license license:gpl2)))
4152 (define-public r-gower
4159 (uri (cran-uri "gower" version))
4162 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4163 (build-system r-build-system)
4164 (home-page "https://github.com/markvanderloo/gower")
4165 (synopsis "Gower's distance")
4167 "This package provides tools to compute Gower's distance (or similarity)
4168 coefficient between records, and to compute the top-n matches between records.
4169 Core algorithms are executed in parallel on systems supporting OpenMP.")
4170 (license license:gpl3)))
4172 (define-public r-rcpproll
4179 (uri (cran-uri "RcppRoll" version))
4182 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4183 (properties `((upstream-name . "RcppRoll")))
4184 (build-system r-build-system)
4186 `(("r-rcpp" ,r-rcpp)))
4187 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4188 (synopsis "Efficient rolling and windowed operations")
4190 "This package provides fast and efficient routines for common rolling /
4191 windowed operations. Routines for the efficient computation of windowed mean,
4192 median, sum, product, minimum, maximum, standard deviation and variance are
4194 (license license:gpl2+)))
4196 (define-public r-ipred
4203 (uri (cran-uri "ipred" version))
4206 "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp"))))
4207 (build-system r-build-system)
4209 `(("r-class" ,r-class)
4212 ("r-prodlim" ,r-prodlim)
4213 ("r-rpart" ,r-rpart)
4214 ("r-survival" ,r-survival)))
4215 (home-page "https://cran.r-project.org/web/packages/ipred")
4216 (synopsis "Improved predictors")
4218 "This package provides improved predictive models by indirect
4219 classification and bagging for classification, regression and survival
4220 problems as well as resampling based estimators of prediction error.")
4221 (license license:gpl2+)))
4223 (define-public r-psych
4230 (uri (cran-uri "psych" version))
4233 "1ibh1ivr280wpmk3qjgm715dk79wx0ikjl9jjjcqs03q6vz4wmdx"))))
4234 (build-system r-build-system)
4236 `(("r-lattice" ,r-lattice)
4237 ("r-mnormt" ,r-mnormt)
4238 ("r-nlme" ,r-nlme)))
4240 `(("r-knitr" ,r-knitr)))
4241 (home-page "https://cran.r-project.org/web/packages/psych/")
4242 (synopsis "Procedures for psychological, psychometric, and personality research")
4244 "This package provides a general purpose toolbox for personality,
4245 psychometric theory and experimental psychology. Functions are primarily for
4246 multivariate analysis and scale construction using factor analysis, principal
4247 component analysis, cluster analysis and reliability analysis, although others
4248 provide basic descriptive statistics. Item Response Theory is done using
4249 factor analysis of tetrachoric and polychoric correlations. Functions for
4250 analyzing data at multiple levels include within and between group statistics,
4251 including correlations and factor analysis. Functions for simulating and
4252 testing particular item and test structures are included. Several functions
4253 serve as a useful front end for structural equation modeling. Graphical
4254 displays of path diagrams, factor analysis and structural equation models are
4255 created using basic graphics.")
4256 (license license:gpl2+)))
4258 (define-public r-generics
4265 (uri (cran-uri "generics" version))
4268 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4269 (build-system r-build-system)
4270 (home-page "https://github.com/r-lib/generics")
4271 (synopsis "Common S3 generics not provided by base R methods")
4273 "In order to reduce potential package dependencies and conflicts,
4274 generics provides a number of commonly used S3 generics that are not provided
4275 by base R methods related to model fitting.")
4276 (license license:gpl2)))
4278 (define-public r-broom
4285 (uri (cran-uri "broom" version))
4288 "1ljcl8mh0yqxw3qxzar482qwbxbcaim1x6y1wm82ws12pfdw0j8n"))))
4289 (build-system r-build-system)
4291 `(("r-backports" ,r-backports)
4292 ("r-dplyr" ,r-dplyr)
4293 ("r-ellipsis" ,r-ellipsis)
4294 ("r-generics" ,r-generics)
4296 ("r-purrr" ,r-purrr)
4297 ("r-rlang" ,r-rlang)
4298 ("r-stringr" ,r-stringr)
4299 ("r-tibble" ,r-tibble)
4300 ("r-tidyr" ,r-tidyr)))
4302 `(("r-knitr" ,r-knitr)))
4303 (home-page "https://github.com/tidyverse/broom")
4304 (synopsis "Convert statistical analysis objects into tidy data frames")
4306 "This package provides tools to convert statistical analysis objects from
4307 R into tidy data frames, so that they can more easily be combined, reshaped
4308 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4309 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4310 summarizes a model's statistical findings such as coefficients of a
4311 regression; @code{augment}, which adds columns to the original data such as
4312 predictions, residuals and cluster assignments; and @code{glance}, which
4313 provides a one-row summary of model-level statistics.")
4314 (license license:expat)))
4316 (define-public r-recipes
4323 (uri (cran-uri "recipes" version))
4326 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4327 (build-system r-build-system)
4329 `(("r-dplyr" ,r-dplyr)
4330 ("r-generics" ,r-generics)
4332 ("r-gower" ,r-gower)
4333 ("r-ipred" ,r-ipred)
4334 ("r-lifecycle" ,r-lifecycle)
4335 ("r-lubridate" ,r-lubridate)
4336 ("r-magrittr" ,r-magrittr)
4337 ("r-matrix" ,r-matrix)
4338 ("r-purrr" ,r-purrr)
4339 ("r-rlang" ,r-rlang)
4340 ("r-tibble" ,r-tibble)
4341 ("r-tidyr" ,r-tidyr)
4342 ("r-tidyselect" ,r-tidyselect)
4343 ("r-timedate" ,r-timedate)
4344 ("r-withr" ,r-withr)))
4346 `(("r-knitr" ,r-knitr)))
4347 (home-page "https://github.com/topepo/recipes")
4348 (synopsis "Preprocessing tools to create design matrices")
4350 "Recipes is an extensible framework to create and preprocess design
4351 matrices. Recipes consist of one or more data manipulation and analysis
4352 \"steps\". Statistical parameters for the steps can be estimated from an
4353 initial data set and then applied to other data sets. The resulting design
4354 matrices can then be used as inputs into statistical or machine learning
4356 (license license:gpl2)))
4358 (define-public r-pdist
4365 (uri (cran-uri "pdist" version))
4368 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4369 (build-system r-build-system)
4370 (home-page "https://github.com/jeffwong/pdist")
4371 (synopsis "Partitioned distance function")
4373 "Pdist computes the euclidean distance between rows of a matrix X and
4374 rows of another matrix Y. Previously, this could be done by binding the two
4375 matrices together and calling @code{dist}, but this creates unnecessary
4376 computation by computing the distances between a row of X and another row of
4377 X, and likewise for Y. Pdist strictly computes distances across the two
4378 matrices, not within the same matrix, making computations significantly faster
4379 for certain use cases.")
4380 (license license:gpl3+)))
4382 (define-public r-ggrepel
4389 (uri (cran-uri "ggrepel" version))
4392 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4393 (build-system r-build-system)
4395 `(("r-ggplot2" ,r-ggplot2)
4397 ("r-rlang" ,r-rlang)
4398 ("r-scales" ,r-scales)))
4400 `(("r-knitr" ,r-knitr))) ; for vignettes
4401 (home-page "https://github.com/slowkow/ggrepel")
4402 (synopsis "Repulsive text and label geometries for ggplot2")
4404 "This package provides text and label geometries for ggplot2 that help to
4405 avoid overlapping text labels. Labels repel away from each other and away
4406 from the data points.")
4407 (license license:gpl3)))
4409 (define-public r-corrplot
4416 (uri (cran-uri "corrplot" version))
4419 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4420 (build-system r-build-system)
4421 (home-page "https://github.com/taiyun/corrplot")
4422 (synopsis "Visualization of a correlation matrix")
4424 "This package provides a graphical display of a correlation matrix or
4425 general matrix. It also contains some algorithms to do matrix reordering. In
4426 addition, corrplot is good at details, including choosing color, text labels,
4427 color labels, layout, etc.")
4428 ;; Any version of the GPL
4429 (license license:gpl2+)))
4431 (define-public r-stringdist
4433 (name "r-stringdist")
4438 (uri (cran-uri "stringdist" version))
4440 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4441 (build-system r-build-system)
4442 (home-page "https://github.com/markvanderloo/stringdist")
4443 (synopsis "Approximate string matching and string distance functions")
4445 "This package implements an approximate string matching version of R's
4446 native @code{match} function. It can calculate various string distances based
4447 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4448 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4449 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4450 can be computed between character vectors while taking proper care of encoding
4451 or between integer vectors representing generic sequences.")
4452 (license license:gpl3+)))
4454 (define-public r-ucminf
4461 (uri (cran-uri "ucminf" version))
4464 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4465 (build-system r-build-system)
4466 (native-inputs `(("gfortran" ,gfortran)))
4467 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4468 (synopsis "General-purpose unconstrained non-linear optimization")
4470 "This package provides an implementation of an algorithm for
4471 general-purpose unconstrained non-linear optimization. The algorithm is of
4472 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4473 search with a trust region type monitoring of the input to the line search
4474 algorithm. The interface of @code{ucminf} is designed for easy interchange
4475 with the package @code{optim}.")
4476 (license license:gpl2+)))
4478 (define-public r-useful
4484 (uri (cran-uri "useful" version))
4487 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4488 (properties `((upstream-name . "useful")))
4489 (build-system r-build-system)
4491 `(("r-assertthat" ,r-assertthat)
4492 ("r-dplyr" ,r-dplyr)
4493 ("r-ggplot2" ,r-ggplot2)
4494 ("r-magrittr" ,r-magrittr)
4495 ("r-matrix" ,r-matrix)
4497 ("r-purrr" ,r-purrr)
4498 ("r-scales" ,r-scales)))
4499 (home-page "https://github.com/jaredlander/useful")
4500 (synopsis "Collection of handy, useful functions")
4501 (description "This package provides a set of little functions that have been
4502 found useful to do little odds and ends such as plotting the results of K-means
4503 clustering, substituting special text characters, viewing parts of a
4504 @code{data.frame}, constructing formulas from text and building design and
4505 response matrices.")
4506 (license license:bsd-3)))
4508 (define-public r-ordinal
4511 (version "2019.12-10")
4515 (uri (cran-uri "ordinal" version))
4518 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4519 (build-system r-build-system)
4521 `(("r-mass" ,r-mass)
4522 ("r-matrix" ,r-matrix)
4523 ("r-numderiv" ,r-numderiv)
4524 ("r-ucminf" ,r-ucminf)))
4525 (home-page "https://github.com/runehaubo/ordinal")
4526 (synopsis "Regression models for ordinal data")
4528 "This package provides an implementation of cumulative link (mixed)
4529 models also known as ordered regression models, proportional odds models,
4530 proportional hazards models for grouped survival times and ordered models.
4531 Estimation is via maximum likelihood and mixed models are fitted with the
4532 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4533 (license license:gpl2+)))
4535 (define-public r-jomo
4542 (uri (cran-uri "jomo" version))
4545 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4546 (build-system r-build-system)
4548 `(("r-lme4" ,r-lme4)
4550 ("r-ordinal" ,r-ordinal)
4551 ("r-survival" ,r-survival)))
4552 (home-page "https://cran.r-project.org/web/packages/jomo/")
4553 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4555 "Similarly to Schafer's package pan, jomo is a package for multilevel
4556 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4557 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4558 possibility of handling binary and categorical data through latent normal
4559 variables, the option to use cluster-specific covariance matrices and to
4560 impute compatibly with the substantive model.")
4561 (license license:gpl2)))
4563 (define-public r-pan
4570 (uri (cran-uri "pan" version))
4573 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4574 (build-system r-build-system)
4575 (native-inputs `(("gfortran" ,gfortran)))
4576 (home-page "https://cran.r-project.org/web/packages/pan/")
4577 (synopsis "Multiple imputation for multivariate panel or clustered data")
4579 "This package implements multiple imputation for multivariate panel or
4581 (license license:gpl3)))
4583 (define-public r-mitml
4590 (uri (cran-uri "mitml" version))
4593 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4594 (build-system r-build-system)
4596 `(("r-haven" ,r-haven)
4600 `(("r-knitr" ,r-knitr)))
4601 (home-page "https://cran.r-project.org/web/packages/mitml/")
4602 (synopsis "Tools for multiple imputation in multilevel modeling")
4604 "This package provides tools for multiple imputation of missing data in
4605 multilevel modeling. It includes a user-friendly interface to the packages
4606 pan and jomo, and several functions for visualization, data management and the
4607 analysis of multiply imputed data sets.")
4608 (license license:gpl2+)))
4610 (define-public r-mice
4617 (uri (cran-uri "mice" version))
4620 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4621 (build-system r-build-system)
4623 `(("r-broom" ,r-broom)
4624 ("r-cpp11" ,r-cpp11)
4625 ("r-dplyr" ,r-dplyr)
4626 ("r-generics" ,r-generics)
4627 ("r-lattice" ,r-lattice)
4629 ("r-rlang" ,r-rlang)
4630 ("r-tidyr" ,r-tidyr)))
4631 (home-page "https://cran.r-project.org/web/packages/mice/")
4632 (synopsis "Multivariate imputation by chained equations")
4634 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4635 implemented by the MICE algorithm as described in @url{Van Buuren and
4636 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4637 variable has its own imputation model. Built-in imputation models are
4638 provided for continuous data (predictive mean matching, normal), binary
4639 data (logistic regression), unordered categorical data (polytomous logistic
4640 regression) and ordered categorical data (proportional odds). MICE can also
4641 impute continuous two-level data (normal model, pan, second-level variables).
4642 Passive imputation can be used to maintain consistency between variables.
4643 Various diagnostic plots are available to inspect the quality of the
4645 ;; Any of these two versions.
4646 (license (list license:gpl2 license:gpl3))))
4648 (define-public r-truncnorm
4650 (name "r-truncnorm")
4655 (uri (cran-uri "truncnorm" version))
4658 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4659 (build-system r-build-system)
4660 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4661 (synopsis "Truncated normal distribution")
4662 (description "This package provides functions for the truncated normal
4663 distribution with mean equal to @code{mean} and standard deviation equal to
4664 @code{sd}. It includes density, distribution, quantile, and expected value
4665 functions, as well as a random generation function.")
4666 (license license:gpl2)))
4668 (define-public r-rsolnp
4675 (uri (cran-uri "Rsolnp" version))
4678 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4679 (properties `((upstream-name . "Rsolnp")))
4680 (build-system r-build-system)
4682 `(("r-truncnorm" ,r-truncnorm)))
4683 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4684 (synopsis "General non-linear optimization")
4685 (description "The Rsolnp package implements a general non-linear augmented
4686 Lagrange multiplier method solver, a @dfn{sequential quadratic
4687 programming} (SQP) based solver).")
4688 ;; Any version of the GPL.
4689 (license license:gpl2+)))
4691 (define-public r-hardyweinberg
4693 (name "r-hardyweinberg")
4698 (uri (cran-uri "HardyWeinberg" version))
4701 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4702 (properties `((upstream-name . "HardyWeinberg")))
4703 (build-system r-build-system)
4705 `(("r-mice" ,r-mice)
4707 ("r-rsolnp" ,r-rsolnp)))
4708 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4709 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4711 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4712 diallelic genetic marker data. All classical tests (chi-square, exact,
4713 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4714 included in the package, as well as functions for power computation and for
4715 the simulation of marker data under equilibrium and disequilibrium. Routines
4716 for dealing with markers on the X-chromosome are included. Functions for
4717 testing equilibrium in the presence of missing data by using multiple
4718 imputation are also provided. Implements several graphics for exploring the
4719 equilibrium status of a large set of diallelic markers: ternary plots with
4720 acceptance regions, log-ratio plots and Q-Q plots.")
4721 (license license:gpl2+)))
4730 (uri (cran-uri "sm" version))
4733 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4734 (build-system r-build-system)
4735 (native-inputs `(("gfortran" ,gfortran)))
4736 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4737 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4739 "This is software accompanying the book 'Applied Smoothing Techniques for
4740 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4741 University Press. It provides smoothing methods for nonparametric regression
4742 and density estimation")
4743 (license license:gpl2+)))
4745 (define-public r-venndiagram
4747 (name "r-venndiagram")
4751 (uri (cran-uri "VennDiagram" version))
4754 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4755 (properties `((upstream-name . "VennDiagram")))
4756 (build-system r-build-system)
4758 `(("r-futile-logger" ,r-futile-logger)))
4759 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4760 (synopsis "Generate High-Resolution Venn and Euler Plots")
4762 "This package provides a set of functions to generate high-resolution
4763 Venn and Euler plots. It includes handling for several special cases,
4764 including two-case scaling, and extensive customization of plot shape and
4766 (license license:gpl2+)))
4768 (define-public r-vioplot
4775 (uri (cran-uri "vioplot" version))
4778 "15vmrm9gwdhfg8mnq8rsg7m59kzc9h53cv96am4ds1dkm56w4n6p"))))
4779 (build-system r-build-system)
4784 `(("r-knitr" ,r-knitr)))
4785 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4786 (synopsis "Violin plot")
4788 "This package provides a violin plot, which is a combination of a box
4789 plot and a kernel density plot.")
4790 (license license:bsd-3)))
4792 (define-public r-rsofia
4798 ;; This package has been removed from CRAN, so we can
4799 ;; only fetch it from the archives.
4800 (uri (string-append "https://cran.r-project.org/src/"
4801 "contrib/Archive/RSofia/RSofia_"
4805 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4806 (properties `((upstream-name . "RSofia")))
4807 (build-system r-build-system)
4809 `(("r-rcpp" ,r-rcpp)))
4810 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4811 (synopsis "Port of sofia-ml to R")
4812 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4813 suite of fast incremental algorithms for machine learning that can be used for
4814 training models for classification or ranking.")
4815 (license license:asl2.0)))
4817 (define-public r-xts
4824 (uri (cran-uri "xts" version))
4827 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4828 (build-system r-build-system)
4829 (propagated-inputs `(("r-zoo" ,r-zoo)))
4830 (home-page "https://github.com/joshuaulrich/xts")
4831 (synopsis "Extensible time series")
4833 "This package provides for uniform handling of R's different time-based
4834 data classes by extending @code{zoo}, maximizing native format information
4835 preservation and allowing for user-level customization and extension, while
4836 simplifying cross-class interoperability.")
4837 (license license:gpl2+)))
4839 (define-public r-performanceanalytics
4841 (name "r-performanceanalytics")
4846 (uri (cran-uri "PerformanceAnalytics" version))
4849 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4851 `((upstream-name . "PerformanceAnalytics")))
4852 (build-system r-build-system)
4854 `(("r-quadprog" ,r-quadprog)
4857 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4858 (synopsis "Econometric tools for performance and risk analysis")
4859 (description "This is a collection of econometric functions for
4860 performance and risk analysis. This package aims to aid practitioners and
4861 researchers in utilizing the latest research in analysis of non-normal return
4862 streams. In general, it is most tested on return (rather than price) data on
4863 a regular scale, but most functions will work with irregular return data as
4864 well, and increasing numbers of functions will work with P&L or price data
4866 ;; Either version may be picked.
4867 (license (list license:gpl2 license:gpl3))))
4869 (define-public r-laeken
4876 (uri (cran-uri "laeken" version))
4879 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4880 (build-system r-build-system)
4882 `(("r-boot" ,r-boot)
4883 ("r-mass" ,r-mass)))
4884 (home-page "https://cran.r-project.org/web/packages/laeken/")
4885 (synopsis "Estimation of indicators on social exclusion and poverty")
4886 (description "This package provides tools for the estimation of indicators
4887 on social exclusion and poverty, as well as an implementation of Pareto tail
4888 modeling for empirical income distributions.")
4889 (license license:gpl2+)))
4891 (define-public r-vcd
4898 (uri (cran-uri "vcd" version))
4901 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4902 (build-system r-build-system)
4904 `(("r-colorspace" ,r-colorspace)
4905 ("r-lmtest" ,r-lmtest)
4906 ("r-mass" ,r-mass)))
4907 (home-page "https://cran.r-project.org/web/packages/vcd/")
4908 (synopsis "Visualizing categorical data")
4909 (description "This package provides visualization techniques, data sets,
4910 summary and inference procedures aimed particularly at categorical data.
4911 Special emphasis is given to highly extensible grid graphics. The package was
4912 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4913 Friendly and is now the main support package for a new book, \"Discrete Data
4914 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4915 (license license:gpl2)))
4917 (define-public r-ica
4924 (uri (cran-uri "ica" version))
4927 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4928 (build-system r-build-system)
4929 (home-page "https://cran.r-project.org/web/packages/ica/")
4930 (synopsis "Independent component analysis")
4931 (description "This package provides tools for @dfn{Independent Component
4932 Analysis} (ICA) using various algorithms: FastICA,
4933 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4934 of Eigenmatrices} (JADE).")
4935 (license license:gpl2+)))
4937 (define-public r-dtw
4944 (uri (cran-uri "dtw" version))
4947 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4948 (build-system r-build-system)
4949 (propagated-inputs `(("r-proxy" ,r-proxy)))
4950 (home-page "http://dtw.r-forge.r-project.org/")
4951 (synopsis "Dynamic Time Warping Algorithms")
4952 (description "This package provides a comprehensive implementation of
4953 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4954 optimal (least cumulative distance) alignment between points of two time
4955 series. Common DTW variants covered include local (slope) and global (window)
4956 constraints, subsequence matches, arbitrary distance definitions,
4957 normalizations, minimum variance matching, and so on.")
4958 (license license:gpl2+)))
4960 (define-public r-sdmtools
4963 (version "1.1-221.2")
4967 (uri (cran-uri "SDMTools" version))
4970 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4971 (properties `((upstream-name . "SDMTools")))
4972 (build-system r-build-system)
4973 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4974 (home-page "https://www.rforge.net/SDMTools/")
4975 (synopsis "Species distribution modelling tools")
4976 (description "This package provides a set of tools for post processing
4977 the outcomes of species distribution modeling exercises. It includes novel
4978 methods for comparing models and tracking changes in distributions through
4979 time. It further includes methods for visualizing outcomes, selecting
4980 thresholds, calculating measures of accuracy and landscape fragmentation
4982 (license license:gpl3+)))
4984 (define-public r-scatterplot3d
4986 (name "r-scatterplot3d")
4991 (uri (cran-uri "scatterplot3d" version))
4994 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4995 (build-system r-build-system)
4996 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4997 (synopsis "3D scatter plot")
4998 (description "This package provides an implementation of scatter plots for
4999 plotting. a three dimensional point cloud.")
5000 (license license:gpl2)))
5002 (define-public r-ggridges
5009 (uri (cran-uri "ggridges" version))
5012 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5013 (build-system r-build-system)
5015 `(("r-ggplot2" ,r-ggplot2)
5017 ("r-scales" ,r-scales)
5018 ("r-withr" ,r-withr)))
5020 `(("r-knitr" ,r-knitr)))
5021 (home-page "https://github.com/clauswilke/ggridges")
5022 (synopsis "Ridgeline plots in ggplot2")
5024 "Ridgeline plots provide a convenient way of visualizing changes in
5025 distributions over time or space. This package enables the creation of such
5026 plots in @code{ggplot2}.")
5027 (license license:gpl2)))
5029 (define-public r-ggjoy
5036 (uri (cran-uri "ggjoy" version))
5039 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5040 (build-system r-build-system)
5042 `(("r-ggplot2" ,r-ggplot2)
5043 ("r-ggridges" ,r-ggridges)))
5044 (home-page "https://github.com/clauswilke/ggjoy")
5045 (synopsis "Joyplots in ggplot2")
5046 (description "Joyplots provide a convenient way of visualizing changes in
5047 distributions over time or space. This package enables the creation of such
5048 plots in @code{ggplot2}.")
5049 (license license:gpl2)))
5051 (define-public r-cli
5058 (uri (cran-uri "cli" version))
5061 "0l1s9yv23bc7mm0hfdlamgz4wjfrisv8aylr65ihjs98jsynrkg3"))))
5062 (build-system r-build-system)
5064 `(("r-glue" ,r-glue)))
5065 (home-page "https://github.com/r-lib/cli#readme")
5066 (synopsis "Helpers for developing command line interfaces")
5067 (description "This package provides a suite of tools designed to build
5068 attractive command line interfaces (CLIs). It includes tools for drawing
5069 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5070 (license license:expat)))
5072 (define-public r-argparser
5074 (name "r-argparser")
5079 (uri (cran-uri "argparser" version))
5082 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5083 (build-system r-build-system)
5084 (home-page "https://bitbucket.org/djhshih/argparser")
5085 (synopsis "Command-line argument parser")
5087 "This package provides a cross-platform command-line argument parser
5088 written purely in R with no external dependencies. It is useful with the
5089 Rscript front-end and facilitates turning an R script into an executable
5091 (license license:gpl3+)))
5093 (define-public r-debugme
5100 (uri (cran-uri "debugme" version))
5103 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5104 (build-system r-build-system)
5105 (propagated-inputs `(("r-crayon" ,r-crayon)))
5106 (home-page "https://github.com/r-lib/debugme#readme")
5107 (synopsis "Debug R packages")
5109 "This package allows the user to specify debug messages as special string
5110 constants, and control debugging of packages via environment variables.")
5111 (license license:expat)))
5113 (define-public r-processx
5120 (uri (cran-uri "processx" version))
5122 (base32 "1z7zag7g041xlhzhkdfl33y2phc877h1pwj9k69p69b967qi6p6k"))))
5123 (build-system r-build-system)
5127 (home-page "https://github.com/r-lib/processx3")
5128 (synopsis "Execute and control system processes")
5130 "This package provides portable tools to run system processes in the
5131 background. It can check if a background process is running; wait on a
5132 background process to finish; get the exit status of finished processes; kill
5133 background processes and their children; restart processes. It can read the
5134 standard output and error of the processes, using non-blocking connections.
5135 @code{processx} can poll a process for standard output or error, with a
5136 timeout. It can also poll several processes at once.")
5137 (license license:expat)))
5139 (define-public r-tsp
5146 (uri (cran-uri "TSP" version))
5149 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5150 (properties `((upstream-name . "TSP")))
5151 (build-system r-build-system)
5152 (propagated-inputs `(("r-foreach" ,r-foreach)))
5153 (home-page "https://cran.r-project.org/web/packages/TSP/")
5154 (synopsis "Traveling salesperson problem (TSP)")
5155 (description "This package provides basic infrastructure and some
5156 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5157 traveling salesman problem).")
5158 (license license:gpl3)))
5160 (define-public r-qap
5167 (uri (cran-uri "qap" version))
5170 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5171 (build-system r-build-system)
5172 (native-inputs `(("gfortran" ,gfortran)))
5173 (home-page "https://cran.r-project.org/web/packages/qap/")
5174 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5175 (description "This package implements heuristics for the @dfn{quadratic
5176 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5178 (license license:gpl3)))
5180 (define-public r-gclus
5187 (uri (cran-uri "gclus" version))
5190 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5191 (build-system r-build-system)
5192 (propagated-inputs `(("r-cluster" ,r-cluster)))
5193 (home-page "https://cran.r-project.org/web/packages/gclus/")
5194 (synopsis "Clustering graphics")
5195 (description "This package orders panels in scatterplot matrices and
5196 parallel coordinate displays by some merit index. It contains various indices
5197 of merit, ordering functions, and enhanced versions of @code{pairs} and
5198 @code{parcoord} which color panels according to their merit level.")
5199 (license license:gpl2+)))
5201 (define-public r-webshot
5208 (uri (cran-uri "webshot" version))
5211 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5212 (build-system r-build-system)
5214 `(("r-callr" ,r-callr)
5215 ("r-jsonlite" ,r-jsonlite)
5216 ("r-magrittr" ,r-magrittr)))
5217 (home-page "https://github.com/wch/webshot/")
5218 (synopsis "Take screenshots of web pages")
5220 "Webshot makes it easy to take screenshots of web pages from within R.
5221 It can also run Shiny applications locally and take screenshots of the
5222 application; and it can render and screenshot static as well as interactive R
5223 Markdown documents.")
5224 (license license:gpl2)))
5226 (define-public r-seriation
5228 (name "r-seriation")
5233 (uri (cran-uri "seriation" version))
5236 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5237 (build-system r-build-system)
5239 `(("r-cluster" ,r-cluster)
5240 ("r-colorspace" ,r-colorspace)
5241 ("r-dendextend" ,r-dendextend)
5242 ("r-gclus" ,r-gclus)
5243 ("r-gplots" ,r-gplots)
5246 ("r-registry" ,r-registry)
5248 (native-inputs `(("gfortran" ,gfortran)))
5249 (home-page "https://s2.smu.edu/IDA/seriation/")
5250 (synopsis "Infrastructure for ordering objects using seriation")
5252 "This package provides infrastructure for seriation with an
5253 implementation of several seriation/sequencing techniques to reorder matrices,
5254 dissimilarity matrices, and dendrograms. It also provides (optimally)
5255 reordered heatmaps, color images and clustering visualizations like
5256 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5258 (license license:gpl3)))
5260 (define-public r-xfun
5267 (uri (cran-uri "xfun" version))
5269 (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y"))))
5270 (build-system r-build-system)
5271 ;; knitr itself depends on xfun
5274 `(("r-knitr" ,r-knitr)))
5275 (home-page "https://github.com/yihui/xfun")
5276 (synopsis "Miscellaneous functions")
5278 "This package provides miscellaneous functions commonly used in other
5279 packages maintained by Yihui Xie.")
5280 (license license:expat)))
5282 (define-public r-utf8
5289 (uri (cran-uri "utf8" version))
5292 "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk"))))
5293 (build-system r-build-system)
5295 `(("r-knitr" ,r-knitr)))
5296 (home-page "https://github.com/patperry/r-utf8")
5297 (synopsis "Unicode text processing")
5299 "This package provides tools to process and print UTF-8 encoded
5300 international text (Unicode). Input, validate, normalize, encode, format, and
5302 (license license:asl2.0)))
5304 (define-public r-zeallot
5311 (uri (cran-uri "zeallot" version))
5314 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5315 (build-system r-build-system)
5316 (home-page "https://github.com/nteetor/zeallot")
5317 (synopsis "Multiple, unpacking, and destructuring assignment")
5319 "This package provides a @code{%<-%} operator to perform multiple,
5320 unpacking, and destructuring assignment in R. The operator unpacks the
5321 right-hand side of an assignment into multiple values and assigns these values
5322 to variables on the left-hand side of the assignment.")
5323 (license license:expat)))
5325 (define-public r-vctrs
5332 (uri (cran-uri "vctrs" version))
5335 "03hyxk3x635xfdn2x707gygdb2xk0cayl1nl44zib9bwqyyb7nas"))))
5336 (build-system r-build-system)
5338 `(("r-ellipsis" ,r-ellipsis)
5340 ("r-rlang" ,r-rlang)))
5342 `(("r-knitr" ,r-knitr)))
5343 (home-page "https://github.com/r-lib/vctrs")
5344 (synopsis "Vector helpers")
5346 "There are three main goals to the @code{vctrs} package:
5349 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5350 @code{length()} and @code{class()}. These definitions are paired with a
5351 framework for type-coercion and size-recycling.
5352 @item To define type- and size-stability as desirable function properties, use
5353 them to analyse existing base function, and to propose better alternatives.
5354 This work has been particularly motivated by thinking about the ideal
5355 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5356 @item To provide a new @code{vctr} base class that makes it easy to create new
5357 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5358 a few new @code{vctrs} generics, making implementation considerably simpler
5361 (license license:gpl3)))
5363 (define-public r-pillar
5370 (uri (cran-uri "pillar" version))
5373 "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c"))))
5374 (build-system r-build-system)
5377 ("r-crayon" ,r-crayon)
5378 ("r-ellipsis" ,r-ellipsis)
5379 ("r-fansi" ,r-fansi)
5380 ("r-lifecycle" ,r-lifecycle)
5381 ("r-rlang" ,r-rlang)
5383 ("r-vctrs" ,r-vctrs)))
5385 `(("r-knitr" ,r-knitr)))
5386 (home-page "https://github.com/r-lib/pillar")
5387 (synopsis "Coloured formatting for columns")
5389 "This package provides a @code{pillar} generic designed for formatting
5390 columns of data using the full range of colours provided by modern
5392 (license license:gpl3)))
5394 (define-public r-uuid
5401 (uri (cran-uri "uuid" version))
5404 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5405 (build-system r-build-system)
5406 (home-page "https://www.rforge.net/uuid")
5407 (synopsis "Tools for generating and handling of UUIDs")
5409 "This package provides tools for generating and handling of
5410 @dfn{Universally Unique Identifiers} (UUIDs).")
5411 (license license:expat)))
5413 (define-public r-tinytex
5420 (uri (cran-uri "tinytex" version))
5423 "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p"))))
5424 (build-system r-build-system)
5426 `(("r-xfun" ,r-xfun)))
5427 (home-page "https://github.com/yihui/tinytex")
5428 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5430 "This package provides helper functions to install and maintain the LaTeX
5431 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5432 easy-to-maintain version of TeX Live. This package also contains helper
5433 functions to compile LaTeX documents, and install missing LaTeX packages
5435 (license license:expat)))
5437 (define-public r-tinytest
5444 (uri (cran-uri "tinytest" version))
5447 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5448 (properties `((upstream-name . "tinytest")))
5449 (build-system r-build-system)
5450 (home-page "https://github.com/markvanderloo/tinytest")
5451 (synopsis "Lightweight unit testing framework")
5453 "This package provides a lightweight unit testing framework. Main
5457 @item install tests with the package;
5458 @item test results are treated as data that can be stored and manipulated;
5459 @item test files are R scripts interspersed with test commands, that can be
5461 @item fully automated build-install-test sequence for packages;
5462 @item skip tests when not run locally (e.g. on CRAN);
5463 @item flexible and configurable output printing;
5464 @item compare computed output with output stored with the package;
5465 @item run tests in parallel;
5466 @item extensible by other packages;
5467 @item report side effects.
5470 (license license:gpl3)))
5472 (define-public r-network
5479 (uri (cran-uri "network" version))
5482 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5483 (build-system r-build-system)
5485 `(("r-magrittr" ,r-magrittr)
5486 ("r-tibble" ,r-tibble)))
5487 (home-page "https://statnet.org/")
5488 (synopsis "Classes for relational data")
5490 "This package provides tools to create and modify network objects. The
5491 @code{network} class can represent a range of relational data types, and
5492 supports arbitrary vertex/edge/graph attributes.")
5493 (license license:gpl2+)))
5495 (define-public r-stabs
5502 (uri (cran-uri "stabs" version))
5505 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5506 (build-system r-build-system)
5508 `(("r-knitr" ,r-knitr)))
5509 (home-page "https://github.com/hofnerb/stabs")
5510 (synopsis "Stability selection with error control")
5512 "This package provides resampling procedures to assess the stability of
5513 selected variables with additional finite sample error control for
5514 high-dimensional variable selection procedures such as Lasso or boosting.
5515 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5516 complementary pairs stability selection with improved error bounds
5517 (Shah & Samworth, 2013) are implemented. The package can be combined with
5518 arbitrary user specified variable selection approaches.")
5519 (license license:gpl2)))
5521 (define-public r-rle
5528 (uri (cran-uri "rle" version))
5531 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5532 (properties `((upstream-name . "rle")))
5533 (build-system r-build-system)
5534 (home-page "https://cran.r-project.org/web/packages/rle/")
5535 (synopsis "Common functions for run-length encoded vectors")
5537 "This package provides common @code{base} and @code{stats} methods for
5538 @code{rle} objects, aiming to make it possible to treat them transparently as
5540 (license license:gpl3)))
5542 (define-public r-statnet-common
5544 (name "r-statnet-common")
5549 (uri (cran-uri "statnet.common" version))
5552 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5554 `((upstream-name . "statnet.common")))
5555 (build-system r-build-system)
5557 `(("r-coda" ,r-coda)
5559 (home-page "https://statnet.org")
5560 (synopsis "R scripts and utilities used by the Statnet software")
5561 (description "This package provides non-statistical utilities used by the
5562 software developed by the Statnet Project.")
5563 (license license:gpl3)))
5565 (define-public r-statcheck
5567 (name "r-statcheck")
5572 (uri (cran-uri "statcheck" version))
5575 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5576 (build-system r-build-system)
5578 `(("r-ggplot2" ,r-ggplot2)
5580 ("r-rmarkdown" ,r-rmarkdown)))
5581 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5582 (synopsis "Extract statistics from articles and recompute p-values")
5583 (description "This package can automatically extract statistical
5584 null-hypothesis significant testing (NHST) results from articles and recompute
5585 the p-values based on the reported test statistic and degrees of freedom to
5586 detect possible inconsistencies.")
5587 (license license:gpl2)))
5589 (define-public r-sna
5596 (uri (cran-uri "sna" version))
5599 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5600 (build-system r-build-system)
5602 `(("r-network" ,r-network)
5603 ("r-statnet-common" ,r-statnet-common)))
5604 (home-page "https://statnet.org")
5605 (synopsis "Tools for social network analysis")
5607 "This package provides a range of tools for social network analysis,
5608 including node and graph-level indices, structural distance and covariance
5609 methods, structural equivalence detection, network regression, random graph
5610 generation, and 2D/3D network visualization.")
5611 (license license:gpl2+)))
5613 (define-public r-tfisher
5620 (uri (cran-uri "TFisher" version))
5623 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5624 (properties `((upstream-name . "TFisher")))
5625 (build-system r-build-system)
5627 `(("r-matrix" ,r-matrix)
5628 ("r-mvtnorm" ,r-mvtnorm)
5630 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5631 (synopsis "Optimal thresholding Fisher's p-value combination method")
5633 "This package provides the @dfn{cumulative distribution function} (CDF),
5634 quantile, and statistical power calculator for a collection of thresholding
5635 Fisher's p-value combination methods, including Fisher's p-value combination
5636 method, truncated product method and, in particular, soft-thresholding
5637 Fisher's p-value combination method which is proven to be optimal in some
5638 context of signal detection. The p-value calculator for the omnibus version
5639 of these tests are also included.")
5640 (license license:gpl2)))
5642 (define-public r-ttr
5649 (uri (cran-uri "TTR" version))
5652 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5653 (properties `((upstream-name . "TTR")))
5654 (build-system r-build-system)
5656 `(("r-curl" ,r-curl)
5659 (home-page "https://github.com/joshuaulrich/TTR")
5660 (synopsis "Technical trading rules")
5662 "This package provides functions and data to construct technical trading
5664 (license license:gpl2)))
5666 (define-public r-leaps
5673 (uri (cran-uri "leaps" version))
5676 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5677 (build-system r-build-system)
5678 (native-inputs `(("gfortran" ,gfortran)))
5679 (home-page "https://cran.r-project.org/web/packages/leaps/")
5680 (synopsis "Regression subset selection")
5682 "This package provides tools for regression subset selection, including
5683 exhaustive search.")
5684 (license license:gpl2+)))
5686 (define-public r-splus2r
5693 (uri (cran-uri "splus2R" version))
5696 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5697 (properties `((upstream-name . "splus2R")))
5698 (build-system r-build-system)
5699 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5700 (synopsis "Supplemental S-PLUS functionality in R")
5702 "Currently there are many functions in S-PLUS that are missing in R. To
5703 facilitate the conversion of S-PLUS packages to R packages, this package
5704 provides some missing S-PLUS functionality in R.")
5705 (license license:gpl2)))
5707 (define-public r-ifultools
5709 (name "r-ifultools")
5714 (uri (cran-uri "ifultools" version))
5717 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5718 (build-system r-build-system)
5720 `(("r-mass" ,r-mass)
5721 ("r-splus2r" ,r-splus2r)))
5722 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5723 (synopsis "Insightful research tools")
5724 (description "This package provides C code used by the wmtsa, fractal, and
5726 (license license:gpl2)))
5728 (define-public r-sapa
5735 (uri (cran-uri "sapa" version))
5738 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
5739 (build-system r-build-system)
5741 `(("r-ifultools" ,r-ifultools)
5742 ("r-splus2r" ,r-splus2r)))
5743 (home-page "https://cran.r-project.org/web/packages/sapa/")
5744 (synopsis "Spectral analysis for physical applications")
5745 (description "This package provides software for the book Spectral
5746 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5747 Cambridge University Press, 1993.")
5748 (license license:gpl2)))
5750 (define-public r-aggregation
5752 (name "r-aggregation")
5757 (uri (cran-uri "aggregation" version))
5760 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5761 (build-system r-build-system)
5762 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5763 (synopsis "Methods for p-value aggregation")
5765 "This package contains functionality for performing the following methods
5766 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5767 Fisher's method), and Sidak correction.")
5768 (license license:gpl3)))
5770 (define-public r-quantmod
5777 (uri (cran-uri "quantmod" version))
5780 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5781 (build-system r-build-system)
5783 `(("r-curl" ,r-curl)
5787 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5788 (synopsis "Quantitative financial modelling framework")
5789 (description "This package provides a quantitative financial modelling
5790 framework to allow users to specify, build, trade, and analyse quantitative
5791 financial trading strategies.")
5792 (license license:gpl3)))
5794 (define-public r-tseries
5801 (uri (cran-uri "tseries" version))
5804 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5805 (build-system r-build-system)
5807 `(("r-quadprog" ,r-quadprog)
5808 ("r-quantmod" ,r-quantmod)
5811 `(("gfortran" ,gfortran)))
5812 (home-page "https://cran.r-project.org/web/packages/tseries/")
5813 (synopsis "Time series analysis and computational finance")
5815 "This package provides functions relating to time series analysis and
5816 computational finance.")
5817 (license license:gpl2)))
5819 (define-public r-wmtsa
5826 (uri (cran-uri "wmtsa" version))
5829 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5830 (build-system r-build-system)
5832 `(("r-ifultools" ,r-ifultools)
5834 ("r-splus2r" ,r-splus2r)))
5835 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5836 (synopsis "Wavelet methods for time series analysis")
5838 "This package provides software to accompany the book \"Wavelet Methods
5839 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5840 University Press, 2000.")
5841 (license license:gpl2)))
5843 (define-public r-tsa
5850 (uri (cran-uri "TSA" version))
5853 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5854 (properties `((upstream-name . "TSA")))
5855 (build-system r-build-system)
5857 `(("r-leaps" ,r-leaps)
5858 ("r-locfit" ,r-locfit)
5860 ("r-tseries" ,r-tseries)))
5861 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5862 (synopsis "Time series analysis")
5864 "This package contains R functions and datasets detailed in the book
5865 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5866 Cryer and Kung-Sik Chan.")
5867 (license license:gpl2+)))
5869 (define-public r-extradistr
5871 (name "r-extradistr")
5876 (uri (cran-uri "extraDistr" version))
5879 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5880 (properties `((upstream-name . "extraDistr")))
5881 (build-system r-build-system)
5883 `(("r-rcpp" ,r-rcpp)))
5884 (home-page "https://github.com/twolodzko/extraDistr")
5885 (synopsis "Additional univariate and multivariate distributions")
5887 "This package implements density, distribution functions, quantile
5888 functions and random generation functions for a large number of univariate and
5889 multivariate distributions.")
5890 (license license:gpl2)))
5892 (define-public r-fractal
5899 (uri (cran-uri "fractal" version))
5902 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5903 (build-system r-build-system)
5905 `(("r-ifultools" ,r-ifultools)
5908 ("r-scatterplot3d" ,r-scatterplot3d)
5909 ("r-splus2r" ,r-splus2r)
5910 ("r-wmtsa" ,r-wmtsa)))
5911 (home-page "https://cran.r-project.org/web/packages/fractal/")
5912 (synopsis "Fractal time series modeling and analysis")
5914 "This package provides tools for stochastic fractal and deterministic
5915 chaotic time series analysis.")
5916 (license license:gpl2)))
5918 (define-public r-urca
5925 (uri (cran-uri "urca" version))
5928 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5929 (build-system r-build-system)
5930 (propagated-inputs `(("r-nlme" ,r-nlme)))
5931 (native-inputs `(("gfortran" ,gfortran)))
5932 (home-page "https://cran.r-project.org/web/packages/urca/")
5933 (synopsis "Unit root and cointegration tests for time series data")
5935 "This package provides unit root and cointegration tests encountered in
5936 applied econometric analysis.")
5937 (license license:gpl2+)))
5939 (define-public r-cubature
5946 (uri (cran-uri "cubature" version))
5949 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5950 (build-system r-build-system)
5952 `(("r-rcpp" ,r-rcpp)))
5954 `(("r-knitr" ,r-knitr)))
5955 (home-page "https://github.com/bnaras/cubature")
5956 (synopsis "Adaptive multivariate integration over hypercubes")
5958 "This package is an R wrapper around the cubature C library for adaptive
5959 multivariate integration over hypercubes. This version provides both
5960 @code{hcubature} and @code{pcubature} routines in addition to a vector
5962 ;; The included cubature C library is released under GPLv2+, but the
5963 ;; wrapper declares the license to be GPLv3+.
5964 (license (list license:gpl2+ license:gpl3+))))
5966 (define-public r-trend
5973 (uri (cran-uri "trend" version))
5976 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5977 (build-system r-build-system)
5979 `(("r-extradistr" ,r-extradistr)))
5981 `(("gfortran" ,gfortran)))
5982 (home-page "https://cran.r-project.org/web/packages/trend/")
5983 (synopsis "Non-parametric trend tests and change-point detection")
5985 "The analysis of environmental data often requires the detection of
5986 trends and change-points. This package includes tests for trend
5987 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5988 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5989 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5990 correlation trend test), change-point detection (Lanzante's test procedures,
5991 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5992 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5993 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5994 sample Robust Rank-Order Distributional Test.")
5995 (license license:gpl3)))
5997 (define-public r-expm
6004 (uri (cran-uri "expm" version))
6007 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6008 (build-system r-build-system)
6009 (propagated-inputs `(("r-matrix" ,r-matrix)))
6010 (native-inputs `(("gfortran" ,gfortran)))
6011 (home-page "https://r-forge.r-project.org/projects/expm/")
6012 (synopsis "Tools for matrix exponentials and related quantities")
6014 "This package provides tools for the computation of the matrix
6015 exponential, logarithm, square root, and related quantities.")
6016 (license license:gpl2+)))
6018 (define-public r-complexplus
6020 (name "r-complexplus")
6025 (uri (cran-uri "complexplus" version))
6028 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6029 (build-system r-build-system)
6031 `(("r-expm" ,r-expm)
6032 ("r-matrix" ,r-matrix)))
6033 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6034 (synopsis "Functions of complex or real variables")
6036 "This package extends several functions to the complex domain, including
6037 the matrix exponential and logarithm, and the determinant.")
6038 (license license:gpl2)))
6040 (define-public r-phontools
6042 (name "r-phontools")
6047 (uri (cran-uri "phonTools" version))
6050 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6051 (properties `((upstream-name . "phonTools")))
6052 (build-system r-build-system)
6053 (home-page "http://www.santiagobarreda.com/rscripts.html")
6054 (synopsis "Tools for phonetic and acoustic analyses")
6056 "This package contains tools for the organization, display, and analysis
6057 of the sorts of data frequently encountered in phonetics research and
6058 experimentation, including the easy creation of IPA vowel plots, and the
6059 creation and manipulation of WAVE audio files.")
6060 (license license:bsd-2)))
6069 (uri (cran-uri "np" version))
6072 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6073 (build-system r-build-system)
6075 `(("r-boot" ,r-boot)
6076 ("r-cubature" ,r-cubature)
6077 ("r-quadprog" ,r-quadprog)
6078 ("r-quantreg" ,r-quantreg)))
6079 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6080 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6081 (description "This package provides non-parametric (and semi-parametric)
6082 kernel methods that seamlessly handle a mix of continuous, unordered, and
6083 ordered factor data types.")
6084 ;; Any version of the GPL.
6085 (license license:gpl3+)))
6087 (define-public r-powerplus
6089 (name "r-powerplus")
6094 (uri (cran-uri "powerplus" version))
6097 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6098 (build-system r-build-system)
6100 `(("r-complexplus" ,r-complexplus)
6103 ("r-matrix" ,r-matrix)
6104 ("r-phontools" ,r-phontools)))
6105 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6106 (synopsis "Exponentiation operations")
6108 "This package provides tools for the computation of matrix and scalar
6110 (license license:gpl2)))
6112 (define-public r-egg
6119 (uri (cran-uri "egg" version))
6122 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6123 (properties `((upstream-name . "egg")))
6124 (build-system r-build-system)
6126 `(("r-ggplot2" ,r-ggplot2)
6127 ("r-gridextra" ,r-gridextra)
6128 ("r-gtable" ,r-gtable)))
6129 (home-page "https://cran.r-project.org/web/packages/egg")
6130 (synopsis "Extensions for ggplot2")
6132 "This package provides miscellaneous functions to help customize ggplot2
6133 objects. High-level functions are provided to post-process ggplot2 layouts
6134 and allow alignment between plot panels, as well as setting panel sizes to
6135 fixed values. Other functions include a custom @code{geom}, and helper
6136 functions to enforce symmetric scales or add tags to facetted plots.")
6137 (license license:gpl3)))
6139 (define-public r-heatmaply
6141 (name "r-heatmaply")
6146 (uri (cran-uri "heatmaply" version))
6149 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6150 (build-system r-build-system)
6152 `(("r-assertthat" ,r-assertthat)
6153 ("r-colorspace" ,r-colorspace)
6154 ("r-dendextend" ,r-dendextend)
6156 ("r-ggplot2" ,r-ggplot2)
6157 ("r-htmlwidgets" ,r-htmlwidgets)
6158 ("r-magrittr" ,r-magrittr)
6159 ("r-plotly" ,r-plotly)
6160 ("r-rcolorbrewer" ,r-rcolorbrewer)
6161 ("r-reshape2" ,r-reshape2)
6162 ("r-scales" ,r-scales)
6163 ("r-seriation" ,r-seriation)
6164 ("r-viridis" ,r-viridis)
6165 ("r-webshot" ,r-webshot)))
6167 `(("r-knitr" ,r-knitr)))
6168 (home-page "https://cran.r-project.org/package=heatmaply")
6169 (synopsis "Interactive cluster heat maps using plotly")
6171 "This package enables you to create interactive cluster heatmaps that can
6172 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6173 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6174 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6175 a popular graphical method for visualizing high-dimensional data, in which a
6176 table of numbers is encoded as a grid of colored cells. The rows and columns
6177 of the matrix are ordered to highlight patterns and are often accompanied by
6179 ;; Either version of the license.
6180 (license (list license:gpl2 license:gpl3))))
6189 (uri (cran-uri "h5" version))
6192 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6193 (build-system r-build-system)
6198 `(("which" ,which)))
6200 `(("r-rcpp" ,r-rcpp)))
6201 (home-page "https://github.com/mannau/h5")
6202 (synopsis "Interface to the HDF5 Library")
6204 "This package provides an S4 interface to the HDF5 library supporting
6205 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6206 binary files in a language independent format. The HDF5 format can therefore
6207 be used as an alternative to R's save/load mechanism. Since h5 is able to
6208 access only subsets of stored data it can also handle data sets which do not
6210 (license license:bsd-2)))
6212 (define-public r-cgdsr
6219 (uri (cran-uri "cgdsr" version))
6222 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6223 (build-system r-build-system)
6225 `(("r-httr" ,r-httr)
6226 ("r-r-methodss3" ,r-r-methodss3)
6227 ("r-r-oo" ,r-r-oo)))
6228 (home-page "https://github.com/cBioPortal/cgdsr")
6229 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6231 "This package provides a basic set of R functions for querying the Cancer
6232 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6233 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6234 (license license:lgpl3)))
6236 (define-public r-import
6243 (uri (cran-uri "import" version))
6246 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6247 (build-system r-build-system)
6249 `(("r-knitr" ,r-knitr)))
6250 (home-page "https://github.com/smbache/import")
6251 (synopsis "Import mechanism for R")
6253 "This is an alternative mechanism for importing objects from packages.
6254 The syntax allows for importing multiple objects from a package with a single
6255 command in an expressive way. The import package bridges some of the gap
6256 between using @code{library} (or @code{require}) and direct (single-object)
6257 imports. Furthermore the imported objects are not placed in the current
6258 environment. It is also possible to import objects from stand-alone @code{.R}
6260 (license license:expat)))
6262 (define-public r-shinyace
6269 (uri (cran-uri "shinyAce" version))
6272 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6273 (properties `((upstream-name . "shinyAce")))
6274 (build-system r-build-system)
6276 `(("r-shiny" ,r-shiny)
6277 ("r-jsonlite" ,r-jsonlite)))
6278 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6279 (synopsis "Ace editor bindings for Shiny")
6281 "This package provides Ace editor bindings to enable a rich text editing
6282 environment within Shiny.")
6283 (license license:expat)))
6285 (define-public r-randomizr
6287 (name "r-randomizr")
6292 (uri (cran-uri "randomizr" version))
6295 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6296 (properties `((upstream-name . "randomizr")))
6297 (build-system r-build-system)
6299 `(("r-knitr" ,r-knitr)))
6300 (home-page "https://declaredesign.org/r/randomizr/")
6301 (synopsis "Tools for common forms of random assignment and sampling")
6303 "This package provides tools for generating random assignments for common
6304 experimental designs and random samples for common sampling designs.")
6305 (license license:expat)))
6307 (define-public r-base64url
6309 (name "r-base64url")
6314 (uri (cran-uri "base64url" version))
6317 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6318 (build-system r-build-system)
6320 `(("r-backports" ,r-backports)))
6321 (home-page "https://github.com/mllg/base64url")
6322 (synopsis "Fast and URL-safe base64 encoder and decoder")
6324 "This package provides a URL-safe base64 encoder and decoder. In
6325 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6326 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6327 encoder does not fill the string with trailing @code{=}. The resulting
6328 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6329 and thus are safe to use in URLs or for file names. The package also comes
6330 with a simple base32 encoder/decoder suited for case insensitive file
6332 (license license:gpl3)))
6334 (define-public r-radiant-data
6336 (name "r-radiant-data")
6341 (uri (cran-uri "radiant.data" version))
6344 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6345 (modules '((guix build utils)))
6348 ;; Delete files that are under CC-NC-SA.
6349 (delete-file-recursively "inst/app/tools/help")
6351 (properties `((upstream-name . "radiant.data")))
6352 (build-system r-build-system)
6354 `(("r-base64enc" ,r-base64enc)
6355 ("r-broom" ,r-broom)
6358 ("r-dplyr" ,r-dplyr)
6361 ("r-ggplot2" ,r-ggplot2)
6362 ("r-import" ,r-import)
6363 ("r-jsonlite" ,r-jsonlite)
6364 ("r-knitr" ,r-knitr)
6365 ("r-lubridate" ,r-lubridate)
6366 ("r-magrittr" ,r-magrittr)
6367 ("r-markdown" ,r-markdown)
6369 ("r-patchwork" ,r-patchwork)
6370 ("r-plotly" ,r-plotly)
6371 ("r-psych" ,r-psych)
6372 ("r-randomizr" ,r-randomizr)
6373 ("r-readr" ,r-readr)
6374 ("r-readxl" ,r-readxl)
6375 ("r-rlang" ,r-rlang)
6376 ("r-rmarkdown" ,r-rmarkdown)
6377 ("r-rstudioapi" ,r-rstudioapi)
6378 ("r-scales" ,r-scales)
6379 ("r-shiny" ,r-shiny)
6380 ("r-shinyfiles" ,r-shinyfiles)
6381 ("r-shinyace" ,r-shinyace)
6382 ("r-stringi" ,r-stringi)
6383 ("r-tibble" ,r-tibble)
6384 ("r-tidyr" ,r-tidyr)
6385 ("r-writexl" ,r-writexl)))
6386 (home-page "https://github.com/radiant-rstats/radiant.data")
6387 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6389 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6390 visualizing, summarizing, transforming, and combining data. It also contains
6391 functionality to generate reproducible reports of the analyses conducted in
6393 (license license:agpl3)))
6395 (define-public r-algdesign
6397 (name "r-algdesign")
6402 (uri (cran-uri "AlgDesign" version))
6404 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6405 (properties `((upstream-name . "AlgDesign")))
6406 (build-system r-build-system)
6407 (home-page "https://github.com/jvbraun/AlgDesign")
6408 (synopsis "Algorithmic experimental design")
6410 "This package provides tools to calculate exact and approximate theory
6411 experimental designs for D, A, and I criteria. Very large designs may be
6412 created. Experimental designs may be blocked or blocked designs created from
6413 a candidate list, using several criteria. The blocking can be done when whole
6414 and within plot factors interact.")
6415 (license license:gpl2+)))
6417 (define-public r-signal
6424 (uri (cran-uri "signal" version))
6427 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6428 (build-system r-build-system)
6429 (propagated-inputs `(("r-mass" ,r-mass)))
6430 (native-inputs `(("gfortran" ,gfortran)))
6431 (home-page "https://cran.r-project.org/web/packages/signal/")
6432 (synopsis "Signal processing")
6434 "This package provides a set of signal processing functions originally
6435 written for Matlab and GNU Octave. It includes filter generation utilities,
6436 filtering functions, resampling routines, and visualization of filter models.
6437 It also includes interpolation functions.")
6438 (license license:gpl2)))
6440 (define-public r-gsubfn
6447 (uri (cran-uri "gsubfn" version))
6450 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6451 (build-system r-build-system)
6452 (propagated-inputs `(("r-proto" ,r-proto)))
6453 (home-page "https://code.google.com/archive/p/gsubfn/")
6454 (synopsis "Utilities for strings and function arguments.")
6456 "This package provides @code{gsubfn} which is like @code{gsub} but can
6457 take a replacement function or certain other objects instead of the
6458 replacement string. Matches and back references are input to the replacement
6459 function and replaced by the function output. @code{gsubfn} can be used to
6460 split strings based on content rather than delimiters and for quasi-perl-style
6461 string interpolation. The package also has facilities for translating
6462 formulas to functions and allowing such formulas in function calls instead of
6464 (license license:gpl2+)))
6466 (define-public r-sqldf
6473 (uri (cran-uri "sqldf" version))
6476 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6477 (build-system r-build-system)
6479 `(("r-chron" ,r-chron)
6481 ("r-gsubfn" ,r-gsubfn)
6482 ("r-proto" ,r-proto)
6483 ("r-rsqlite" ,r-rsqlite)))
6484 (home-page "https://github.com/ggrothendieck/sqldf")
6485 (synopsis "Manipulate R data frames using SQL")
6487 "The @code{sqldf} function is typically passed a single argument which is
6488 an SQL select statement where the table names are ordinary R data frame names.
6489 @code{sqldf} transparently sets up a database, imports the data frames into
6490 that database, performs the SQL statement and returns the result using a
6491 heuristic to determine which class to assign to each column of the returned
6492 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6493 used to read filtered files into R even if the original files are larger than
6494 R itself can handle.")
6495 (license license:gpl2)))
6497 (define-public r-abind
6504 (uri (cran-uri "abind" version))
6507 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6508 (build-system r-build-system)
6509 (home-page "https://cran.r-project.org/web/packages/abind/")
6510 (synopsis "Combine multidimensional arrays")
6512 "This package provides tools to combine multidimensional arrays into a
6513 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6514 works with vectors, matrices, and higher-dimensional arrays. It also provides
6515 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6516 extracting and replacing data in arrays.")
6517 (license license:lgpl2.0+)))
6519 (define-public r-prroc
6526 (uri (cran-uri "PRROC" version))
6529 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6530 (properties `((upstream-name . "PRROC")))
6531 (build-system r-build-system)
6532 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6533 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6535 "This package computes the areas under the @dfn{precision-recall} (PR)
6536 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6537 contrast to other implementations, the interpolation between points of the PR
6538 curve is done by a non-linear piecewise function. In addition to the areas
6539 under the curves, the curves themselves can also be computed and plotted by a
6540 specific S3-method.")
6541 (license license:gpl3)))
6543 (define-public r-vim
6550 (uri (cran-uri "VIM" version))
6553 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6554 (properties `((upstream-name . "VIM")))
6555 (build-system r-build-system)
6558 ("r-colorspace" ,r-colorspace)
6559 ("r-data-table" ,r-data-table)
6560 ("r-e1071" ,r-e1071)
6561 ("r-laeken" ,r-laeken)
6562 ("r-magrittr" ,r-magrittr)
6565 ("r-ranger" ,r-ranger)
6567 ("r-robustbase" ,r-robustbase)
6571 `(("r-knitr" ,r-knitr)))
6572 (home-page "https://github.com/alexkowa/VIM")
6573 (synopsis "Visualization and imputation of missing values")
6575 "This package provides tools for the visualization of missing and/or
6576 imputed values are introduced, which can be used for exploring the data and
6577 the structure of the missing and/or imputed values. Depending on this
6578 structure of the missing values, the corresponding methods may help to
6579 identify the mechanism generating the missing values and explore the
6580 data including missing values. In addition, the quality of imputation can be
6581 visually explored using various univariate, bivariate, multiple and
6582 multivariate plot methods.")
6583 (license license:gpl2+)))
6585 (define-public r-fnn
6592 (uri (cran-uri "FNN" version))
6595 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6596 (properties `((upstream-name . "FNN")))
6597 (build-system r-build-system)
6598 (home-page "https://cran.r-project.org/web/packages/FNN")
6599 (synopsis "Fast nearest neighbor search algorithms and applications")
6601 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6602 search algorithms. Related applications including KNN classification,
6603 regression and information measures are implemented.")
6604 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6605 ;; later can be used.
6606 (license license:gpl2+)))
6608 (define-public r-smoother
6615 (uri (cran-uri "smoother" version))
6618 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6619 (build-system r-build-system)
6621 `(("r-ttr" ,r-ttr)))
6622 (home-page "https://cran.r-project.org/web/packages/smoother")
6623 (synopsis "Functions relating to the smoothing of numerical data")
6625 "This package provides a collection of methods for smoothing numerical
6626 data, commencing with a port of the Matlab gaussian window smoothing function.
6627 In addition, several functions typically used in smoothing of financial data
6629 (license license:gpl2)))
6631 (define-public r-riverplot
6633 (name "r-riverplot")
6638 (uri (cran-uri "riverplot" version))
6641 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6642 (build-system r-build-system)
6644 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6646 `(("r-knitr" ,r-knitr)))
6647 (home-page "https://logfc.wordpress.com")
6648 (synopsis "Sankey or ribbon plots")
6650 "Sankey plots are a type of diagram that is convenient to illustrate how
6651 flow of information, resources etc. separates and joins, much like observing
6652 how rivers split and merge. For example, they can be used to compare
6653 different clusterings. This package provides an implementation of Sankey
6655 (license license:gpl2+)))
6657 (define-public r-dyn
6664 (uri (cran-uri "dyn" version))
6667 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6668 (build-system r-build-system)
6670 `(("r-zoo" ,r-zoo)))
6671 (home-page "https://cran.r-project.org/web/packages/dyn")
6672 (synopsis "Time series regression")
6674 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6675 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6676 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6677 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6678 @code{randomForest::randomForest()} and other regression functions, allowing
6679 those functions to be used with time series including specifications that may
6680 contain lags, diffs and missing values.")
6682 (license license:gpl2+)))
6684 (define-public r-catdap
6691 (uri (cran-uri "catdap" version))
6694 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6695 (build-system r-build-system)
6697 `(("gfortran" ,gfortran)))
6698 (home-page "https://cran.r-project.org/web/packages/catdap/")
6699 (synopsis "Tools for categorical data analysis")
6701 "This package provides functions for analyzing multivariate data.
6702 Dependencies of the distribution of the specified variable (response
6703 variable) to other variables (explanatory variables) are derived and
6704 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6705 (license license:gpl2+)))
6707 (define-public r-arules
6714 (uri (cran-uri "arules" version))
6717 "0m80kndfbannw8h53nqdd5wl8h33q2z259aa1cp1nwadaxf9fc1q"))))
6718 (build-system r-build-system)
6720 `(("r-matrix" ,r-matrix)))
6721 (home-page "https://github.com/mhahsler/arules")
6722 (synopsis "Mining association rules and frequent itemsets")
6724 "This package provides an infrastructure for representing, manipulating
6725 and analyzing transaction data and patterns (frequent itemsets and association rules).
6726 It also provides C implementations of the association mining algorithms Apriori
6728 (license license:gpl3)))
6730 (define-public r-parsedate
6732 (name "r-parsedate")
6737 (uri (cran-uri "parsedate" version))
6740 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6741 (build-system r-build-system)
6743 `(("r-rematch2" ,r-rematch2)))
6744 (home-page "https://github.com/gaborcsardi/parsedate")
6746 "Recognize and parse dates in various formats")
6748 "This package provides three functions for dealing with dates:
6749 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6750 time formats, @code{parse_date} parses dates in unspecified formats,
6751 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6752 (license license:gpl2)))
6754 (define-public r-abc-data
6761 (uri (cran-uri "abc.data" version))
6764 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6765 (properties `((upstream-name . "abc.data")))
6766 (build-system r-build-system)
6767 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6768 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6770 "This package contains data which are used by functions of the abc
6771 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6772 algorithms for performing parameter estimation, model selection, and
6774 (license license:gpl3+)))
6776 (define-public r-abc
6783 (uri (cran-uri "abc" version))
6786 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6787 (build-system r-build-system)
6789 `(("r-abc-data" ,r-abc-data)
6790 ("r-locfit" ,r-locfit)
6793 ("r-quantreg" ,r-quantreg)))
6794 (home-page "https://cran.r-project.org/web/packages/abc/")
6795 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6797 "This package implements several @dfn{Approximate Bayesian
6798 Computation} (ABC) algorithms for performing parameter estimation, model
6799 selection, and goodness-of-fit. Cross-validation tools are also available for
6800 measuring the accuracy of ABC estimates, and to calculate the
6801 misclassification probabilities of different models.")
6802 (license license:gpl3+)))
6804 (define-public r-zip
6811 (uri (cran-uri "zip" version))
6814 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6815 (build-system r-build-system)
6816 (home-page "https://github.com/gaborcsardi/zip")
6817 (synopsis "Cross-platform Zip compression")
6819 "This package provides a cross-platform Zip compression library for R.
6820 It is a replacement for the @code{zip} function, that does not require any
6821 additional external tools on any platform.")
6822 (license license:cc0)))
6824 (define-public r-openxlsx
6831 (uri (cran-uri "openxlsx" version))
6834 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6835 (build-system r-build-system)
6837 `(("r-rcpp" ,r-rcpp)
6838 ("r-stringi" ,r-stringi)
6841 `(("r-knitr" ,r-knitr)))
6842 (home-page "https://github.com/awalker89/openxlsx")
6843 (synopsis "Read, write and edit XLSX files")
6845 "This package simplifies the creation of Excel @code{.xlsx} files by
6846 providing a high level interface to writing, styling and editing worksheets.
6847 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6848 and @code{XLConnect} packages with the added benefit of removing the
6849 dependency on Java.")
6850 (license license:gpl3)))
6852 (define-public r-rio
6859 (uri (cran-uri "rio" version))
6862 "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d"))))
6863 (build-system r-build-system)
6865 `(("r-curl" ,r-curl)
6866 ("r-data-table" ,r-data-table)
6867 ("r-foreign" ,r-foreign)
6868 ("r-haven" ,r-haven)
6869 ("r-openxlsx" ,r-openxlsx)
6870 ("r-readxl" ,r-readxl)
6871 ("r-tibble" ,r-tibble)))
6873 `(("r-knitr" ,r-knitr)))
6874 (home-page "https://github.com/leeper/rio")
6875 (synopsis "Swiss-army knife for data I/O")
6877 "This package provides streamlined data import and export infrastructure
6878 by making assumptions that the user is probably willing to make: @code{import}
6879 and @code{export} determine the data structure from the file extension,
6880 reasonable defaults are used for data import and export (e.g.,
6881 @code{stringsAsFactors=FALSE}), web-based import is natively
6882 supported (including from SSL/HTTPS), compressed files can be read directly
6883 without explicit decompression, and fast import packages are used where
6884 appropriate. An additional convenience function, @code{convert}, provides a
6885 simple method for converting between file types.")
6886 (license license:gpl2)))
6888 (define-public r-maptools
6895 (uri (cran-uri "maptools" version))
6898 "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l"))))
6899 (build-system r-build-system)
6901 `(("r-foreign" ,r-foreign)
6902 ("r-lattice" ,r-lattice)
6904 (home-page "https://r-forge.r-project.org/projects/maptools/")
6905 (synopsis "Tools for reading and handling spatial objects")
6907 "This package provides a set of tools for manipulating and reading
6908 geographic data, in particular ESRI Shapefiles. It includes binary access to
6909 GSHHG shoreline files. The package also provides interface wrappers for
6910 exchanging spatial objects with other R packages.")
6911 ;; The C source files from shapelib are released under the Expat license.
6912 ;; The R code is released under GPL version 2 or later.
6913 (license (list license:gpl2+
6916 (define-public r-later
6923 (uri (cran-uri "later" version))
6926 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6927 (build-system r-build-system)
6931 ("r-rlang" ,r-rlang)))
6933 `(("r-knitr" ,r-knitr)))
6934 (home-page "https://github.com/r-lib/later")
6935 (synopsis "Utilities for delaying function execution")
6937 "This package provides tools to execute arbitrary R or C functions some
6938 time after the current time, after the R execution stack has emptied.")
6939 (license license:gpl2+)))
6941 (define-public r-promises
6948 (uri (cran-uri "promises" version))
6951 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
6952 (build-system r-build-system)
6954 `(("r-later" ,r-later)
6955 ("r-magrittr" ,r-magrittr)
6958 ("r-rlang" ,r-rlang)))
6960 `(("r-knitr" ,r-knitr)))
6961 (home-page "https://rstudio.github.io/promises")
6962 (synopsis "Abstractions for promise-based asynchronous programming")
6964 "This package provides fundamental abstractions for doing asynchronous
6965 programming in R using promises. Asynchronous programming is useful for
6966 allowing a single R process to orchestrate multiple tasks in the background
6967 while also attending to something else. Semantics are similar to JavaScript
6968 promises, but with a syntax that is idiomatic R.")
6969 (license license:expat)))
6971 (define-public r-dosnow
6978 (uri (cran-uri "doSNOW" version))
6981 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6982 (properties `((upstream-name . "doSNOW")))
6983 (build-system r-build-system)
6985 `(("r-foreach" ,r-foreach)
6986 ("r-iterators" ,r-iterators)
6987 ("r-snow" ,r-snow)))
6988 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6989 (synopsis "Foreach parallel adaptor for the snow package")
6991 "This package provides a parallel backend for the @code{%dopar%} function
6992 using the @code{snow} package.")
6993 (license license:gpl2)))
6995 (define-public r-fst
7002 (uri (cran-uri "fst" version))
7005 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7006 (properties `((upstream-name . "fst")))
7007 (build-system r-build-system)
7008 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7009 (home-page "http://www.fstpackage.org")
7010 (synopsis "Fast serialization of data frames")
7012 "The fst package for R provides a fast, easy and flexible way to
7013 serialize data frames. With access speeds of multiple GB/s, fst is
7014 specifically designed to unlock the potential of high speed solid state disks.
7015 Data frames stored in the fst format have full random access, both in column
7016 and rows. The fst format allows for random access of stored data and
7017 compression with the LZ4 and ZSTD compressors.")
7018 (license license:agpl3)))
7020 (define-public r-snowfall
7023 (version "1.84-6.1")
7026 (uri (cran-uri "snowfall" version))
7028 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7029 (build-system r-build-system)
7031 `(("r-snow" ,r-snow)))
7032 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7033 (synopsis "Easier cluster computing")
7034 (description "This package is a usability wrapper around snow for easier
7035 development of parallel R programs. This package offers e.g. extended error
7036 checks, and additional functions. All functions work in sequential mode, too,
7037 if no cluster is present or wished. The package is also designed as connector
7038 to the cluster management tool @code{sfCluster}, but can also used without
7040 (license license:gpl2+)))
7042 (define-public r-rgexf
7049 (uri (cran-uri "rgexf" version))
7052 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7055 ;; Delete minified JavaScript files
7056 (for-each delete-file
7057 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7058 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7059 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7061 (properties `((upstream-name . "rgexf")))
7062 (build-system r-build-system)
7064 `(#:modules ((guix build utils)
7065 (guix build r-build-system)
7069 (modify-phases %standard-phases
7070 (add-after 'unpack 'process-javascript
7071 (lambda* (#:key inputs #:allow-other-keys)
7072 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7073 (with-directory-excursion "inst/gexf-js/js/"
7077 `((,(assoc-ref inputs "js-jquery")
7078 "jquery-2.0.2.min.js")
7079 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7080 "jquery-ui-1.10.3.custom.min.js")
7081 (,(assoc-ref inputs "js-jquery-mousewheel")
7082 "jquery.mousewheel.min.js"))))
7083 (lambda (sources targets)
7084 (for-each (lambda (source target)
7085 (format #true "Processing ~a --> ~a~%"
7087 (invoke "esbuild" source "--minify"
7088 (string-append "--outfile=" target)))
7092 `(("r-igraph" ,r-igraph)
7093 ("r-servr" ,r-servr)
7096 `(("r-knitr" ,r-knitr)
7097 ("esbuild" ,esbuild)
7102 (uri "https://code.jquery.com/jquery-2.0.2.js")
7105 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7109 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7112 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7113 ("js-jquery-mousewheel"
7116 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7117 3.0.6/jquery.mousewheel.js")
7120 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7121 (home-page "https://gvegayon.github.io/rgexf")
7122 (synopsis "Build, import and export GEXF graph files")
7124 "Create, read and write GEXF (Graph Exchange XML Format) graph
7125 files (used in Gephi and others). It allows the user to easily build/read
7126 graph files including attributes, GEXF visual attributes (such as color, size,
7127 and position), network dynamics (for both edges and nodes) and edge weighting.
7128 Users can build/handle graphs element-by-element or massively through
7129 data-frames, visualize the graph on a web browser through gexf-js (a
7130 JavaScript library) and interact with the igraph package.")
7131 (license license:expat)))
7133 (define-public r-data-tree
7135 (name "r-data-tree")
7140 (uri (cran-uri "data.tree" version))
7143 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7144 (properties `((upstream-name . "data.tree")))
7145 (build-system r-build-system)
7148 ("r-stringi" ,r-stringi)))
7150 `(("r-knitr" ,r-knitr)))
7151 (home-page "https://github.com/gluc/data.tree")
7152 (synopsis "General purpose hierarchical data structure")
7154 "Create tree structures from hierarchical data, and traverse the tree in
7155 various orders. Aggregate, cumulate, print, plot, convert to and from
7156 data.frame and more. This is useful for decision trees, machine learning,
7157 finance, conversion from and to JSON, and many other applications.")
7158 (license license:gpl2+)))
7160 (define-public r-collapsibletree
7162 (name "r-collapsibletree")
7167 (uri (cran-uri "collapsibleTree" version))
7170 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7173 ;; Delete minified JavaScript file
7174 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7177 `((upstream-name . "collapsibleTree")))
7178 (build-system r-build-system)
7181 (modify-phases %standard-phases
7182 (add-after 'unpack 'process-javascript
7183 (lambda* (#:key inputs #:allow-other-keys)
7184 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7185 (let ((source (assoc-ref inputs "d3.v4.js"))
7186 (target "d3.min.js"))
7187 (format #t "Processing ~a --> ~a~%"
7189 (invoke "esbuild" source "--minify"
7190 (string-append "--outfile=" target)))))))))
7192 `(("r-data-tree" ,r-data-tree)
7193 ("r-htmlwidgets" ,r-htmlwidgets)))
7195 `(("esbuild" ,esbuild)
7199 (uri "https://d3js.org/d3.v4.js")
7202 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7203 (home-page "https://github.com/AdeelK93/collapsibleTree")
7204 (synopsis "Interactive collapsible tree diagrams using D3.js")
7206 "This is a package for interactive Reingold-Tilford tree diagrams created
7207 using D3.js, where every node can be expanded and collapsed by clicking on it.
7208 Tooltips and color gradients can be mapped to nodes using a numeric column in
7209 the source data frame.")
7210 (license license:gpl3+)))
7212 (define-public r-rappdirs
7219 (uri (cran-uri "rappdirs" version))
7222 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7223 (build-system r-build-system)
7224 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7225 (synopsis "Determine where to save data, caches, and logs")
7227 "This package provides an easy way to determine which directories on the
7228 user's computer should be used to save data, caches and logs. It is a port of
7229 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7230 (license license:expat)))
7232 (define-public r-rastervis
7234 (name "r-rastervis")
7239 (uri (cran-uri "rasterVis" version))
7242 "1fkmyllydnmk3j2cmgf86r91wyxf2kh573x8bkck7wgkfniw4h7w"))))
7243 (properties `((upstream-name . "rasterVis")))
7244 (build-system r-build-system)
7246 `(("r-hexbin" ,r-hexbin)
7247 ("r-lattice" ,r-lattice)
7248 ("r-latticeextra" ,r-latticeextra)
7249 ("r-raster" ,r-raster)
7250 ("r-rcolorbrewer" ,r-rcolorbrewer)
7252 ("r-terra" ,r-terra)
7253 ("r-viridislite" ,r-viridislite)
7255 (home-page "https://oscarperpinan.github.io/rastervis/")
7256 (synopsis "Visualization methods for raster data")
7258 "This package provides methods for enhanced visualization and interaction
7259 with raster data. It implements visualization methods for quantitative data
7260 and categorical data, both for univariate and multivariate rasters. It also
7261 provides methods to display spatiotemporal rasters, and vector fields.")
7262 (license license:gpl3)))
7264 (define-public r-rentrez
7271 (uri (cran-uri "rentrez" version))
7274 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7275 (properties `((upstream-name . "rentrez")))
7276 (build-system r-build-system)
7278 `(("r-httr" ,r-httr)
7279 ("r-jsonlite" ,r-jsonlite)
7282 `(("r-knitr" ,r-knitr)))
7283 (home-page "https://docs.ropensci.org/rentrez/")
7284 (synopsis "Entrez in R")
7286 "This package provides an R interface to the NCBI's EUtils API,
7287 allowing users to search databases like GenBank PubMed, process the results of
7288 those searches and pull data into their R sessions.")
7289 (license license:expat)))
7291 (define-public r-renv
7298 (uri (cran-uri "renv" version))
7301 "0jlsf6vfvqhr4i35xy3xf1ixkfillivzy3wbpl6ca9vyjpnhiwj1"))))
7302 (properties `((upstream-name . "renv")))
7303 (build-system r-build-system)
7305 `(("r-knitr" ,r-knitr)))
7306 (home-page "https://rstudio.github.io/renv")
7307 (synopsis "Project environments")
7309 "This package provides a dependency management toolkit for R. Using
7310 renv, you can create and manage project-local R libraries, save the state of
7311 these libraries to a lockfile, and later restore your library as required.
7312 Together, these tools can help make your projects more isolated, portable, and
7314 (license license:expat)))
7316 (define-public r-learnr
7323 (uri (cran-uri "learnr" version))
7326 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7327 (build-system r-build-system)
7329 `(("r-checkmate" ,r-checkmate)
7330 ("r-ellipsis" ,r-ellipsis)
7331 ("r-evaluate" ,r-evaluate)
7332 ("r-htmltools" ,r-htmltools)
7333 ("r-htmlwidgets" ,r-htmlwidgets)
7334 ("r-jsonlite" ,r-jsonlite)
7335 ("r-knitr" ,r-knitr)
7336 ("r-markdown" ,r-markdown)
7337 ("r-rappdirs" ,r-rappdirs)
7339 ("r-rmarkdown" ,r-rmarkdown)
7340 ("r-rprojroot" ,r-rprojroot)
7341 ("r-shiny" ,r-shiny)
7342 ("r-withr" ,r-withr)))
7343 (home-page "https://rstudio.github.io/learnr/")
7344 (synopsis "Interactive tutorials for R")
7346 "This package provides tools to create interactive tutorials using R
7347 Markdown. Use a combination of narrative, figures, videos, exercises, and
7348 quizzes to create self-paced tutorials for learning about R and R packages.")
7349 (license license:asl2.0)))
7351 (define-public r-analytics
7353 (name "r-analytics")
7358 (uri (cran-uri "analytics" version))
7361 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7362 (build-system r-build-system)
7365 ("r-cluster" ,r-cluster)
7366 ("r-fractal" ,r-fractal)
7367 ("r-lmtest" ,r-lmtest)
7370 ("r-powerplus" ,r-powerplus)
7371 ("r-robust" ,r-robust)
7372 ("r-trend" ,r-trend)
7376 (home-page "https://cran.r-project.org/web/packages/analytics/")
7377 (synopsis "Collection of data analysis tools")
7379 "This package is a collection of data analysis tools. It includes tools
7380 for regression outlier detection in a fitted linear model, stationary
7381 bootstrap using a truncated geometric distribution, a comprehensive test for
7382 weak stationarity, column means by group, weighted biplots, and a heuristic to
7383 obtain a better initial configuration in non-metric MDS.")
7384 (license license:gpl2)))
7386 (define-public r-reticulate
7388 (name "r-reticulate")
7393 (uri (cran-uri "reticulate" version))
7396 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7397 (build-system r-build-system)
7398 (inputs `(("python" ,python)))
7400 `(("r-rappdirs" ,r-rappdirs)
7401 ("r-jsonlite" ,r-jsonlite)
7402 ("r-matrix" ,r-matrix)
7403 ("r-rcpp" ,r-rcpp)))
7405 `(("r-knitr" ,r-knitr)))
7406 (home-page "https://github.com/rstudio/reticulate")
7407 (synopsis "R interface to Python")
7409 "This package provides an interface from R to Python modules, classes,
7410 and functions. When calling into Python, R data types are automatically
7411 converted to their equivalent Python types. When values are returned from
7412 Python to R they are converted back to R types.")
7413 (license license:asl2.0)))
7415 (define-public r-bibtex
7422 (uri (cran-uri "bibtex" version))
7425 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7426 (build-system r-build-system)
7427 (propagated-inputs `(("r-stringr" ,r-stringr)))
7428 (home-page "https://github.com/romainfrancois/bibtex")
7429 (synopsis "Bibtex parser")
7430 (description "This package provides a utility for R to parse a bibtex
7432 (license license:gpl2+)))
7434 (define-public r-ggseqlogo
7436 (name "r-ggseqlogo")
7441 (uri (cran-uri "ggseqlogo" version))
7444 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7445 (build-system r-build-system)
7446 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7447 (home-page "https://github.com/omarwagih/ggseqlogo")
7448 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7450 "The range of functions provided by this package makes it possible to
7451 draw highly versatile genomic sequence logos. Features include, but are not
7452 limited to, modifying colour schemes and fonts used to draw the logo,
7453 generating multiple logo plots, and aiding the visualisation with annotations.
7454 Sequence logos can easily be combined with other ggplot2 plots.")
7455 ;; Unspecified version of the LGPL.
7456 (license license:lgpl3+)))
7458 (define-public r-ggsci
7465 (uri (cran-uri "ggsci" version))
7468 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7469 (build-system r-build-system)
7471 `(("r-ggplot2" ,r-ggplot2)
7472 ("r-scales" ,r-scales)))
7473 (home-page "https://nanx.me/ggsci/")
7474 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7476 "This package provides a collection of ggplot2 color palettes inspired by
7477 plots in scientific journals, data visualization libraries, science fiction
7478 movies, and TV shows.")
7479 (license license:gpl3)))
7481 (define-public r-ggsignif
7488 (uri (cran-uri "ggsignif" version))
7491 "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh"))))
7492 (build-system r-build-system)
7494 `(("r-knitr" ,r-knitr)))
7496 `(("r-ggplot2" ,r-ggplot2)))
7497 (home-page "https://github.com/const-ae/ggsignif")
7498 (synopsis "Significance brackets for ggplot2")
7500 "Enrich your ggplots with group-wise comparisons. This package provides
7501 an easy way to indicate if two groups are significantly different. Commonly
7502 this is shown by a bracket on top connecting the groups of interest which
7503 itself is annotated with the level of significance. The package provides a
7504 single layer that takes the groups for comparison and the test as arguments
7505 and adds the annotation to the plot.")
7506 (license license:gpl3)))
7508 (define-public r-rstatix
7515 (uri (cran-uri "rstatix" version))
7518 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
7519 (properties `((upstream-name . "rstatix")))
7520 (build-system r-build-system)
7522 `(("r-broom" ,r-broom)
7524 ("r-corrplot" ,r-corrplot)
7525 ("r-dplyr" ,r-dplyr)
7526 ("r-generics" ,r-generics)
7527 ("r-magrittr" ,r-magrittr)
7528 ("r-purrr" ,r-purrr)
7529 ("r-rlang" ,r-rlang)
7530 ("r-tibble" ,r-tibble)
7531 ("r-tidyr" ,r-tidyr)
7532 ("r-tidyselect" ,r-tidyselect)))
7533 (home-page "https://rpkgs.datanovia.com/rstatix/")
7534 (synopsis "Pipe-friendly framework for basic statistical tests")
7536 "This package provides a simple and intuitive pipe-friendly framework,
7537 coherent with the @code{tidyverse} design philosophy, for performing basic
7538 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7539 correlation analyses. The output of each test is automatically transformed
7540 into a tidy data frame to facilitate visualization. Additional functions are
7541 available for reshaping, reordering, manipulating and visualizing correlation
7543 (license license:gpl2)))
7545 (define-public r-ggpubr
7552 (uri (cran-uri "ggpubr" version))
7555 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7556 (build-system r-build-system)
7558 `(("r-cowplot" ,r-cowplot)
7559 ("r-dplyr" ,r-dplyr)
7560 ("r-ggplot2" ,r-ggplot2)
7561 ("r-ggrepel" ,r-ggrepel)
7562 ("r-ggsci" ,r-ggsci)
7563 ("r-ggsignif" ,r-ggsignif)
7565 ("r-gridextra" ,r-gridextra)
7566 ("r-magrittr" ,r-magrittr)
7567 ("r-polynom" ,r-polynom)
7568 ("r-purrr" ,r-purrr)
7569 ("r-rlang" ,r-rlang)
7570 ("r-scales" ,r-scales)
7571 ("r-rstatix" ,r-rstatix)
7572 ("r-tibble" ,r-tibble)
7573 ("r-tidyr" ,r-tidyr)))
7574 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7575 (synopsis "ggplot2-based publication-ready plots")
7577 "The ggplot2 package is an excellent and flexible package for elegant
7578 data visualization in R. However the default generated plots require some
7579 formatting before we can send them for publication. The ggpubr package
7580 provides some easy-to-use functions for creating and customizing ggplot2-based
7581 publication-ready plots.")
7582 (license license:gpl2)))
7584 (define-public r-ellipse
7591 (uri (cran-uri "ellipse" version))
7594 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7595 (build-system r-build-system)
7596 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7597 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7599 "This package contains various routines for drawing ellipses and
7600 ellipse-like confidence regions, implementing the plots described in Murdoch
7601 and Chow (1996), A graphical display of large correlation matrices, The
7602 American Statistician 50, 178-180. There are also routines implementing the
7603 profile plots described in Bates and Watts (1988), Nonlinear Regression
7604 Analysis and its Applications.")
7605 (license license:gpl2+)))
7607 (define-public r-flashclust
7609 (name "r-flashclust")
7614 (uri (cran-uri "flashClust" version))
7617 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7618 (properties `((upstream-name . "flashClust")))
7619 (build-system r-build-system)
7620 (native-inputs `(("gfortran" ,gfortran)))
7621 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7622 (synopsis "Implementation of optimal hierarchical clustering")
7624 "This package provides a fast implementation of hierarchical
7626 (license license:gpl2+)))
7628 (define-public r-factominer
7630 (name "r-factominer")
7635 (uri (cran-uri "FactoMineR" version))
7638 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7639 (properties `((upstream-name . "FactoMineR")))
7640 (build-system r-build-system)
7643 ("r-cluster" ,r-cluster)
7645 ("r-ellipse" ,r-ellipse)
7646 ("r-flashclust" ,r-flashclust)
7647 ("r-ggplot2" ,r-ggplot2)
7648 ("r-ggrepel" ,r-ggrepel)
7649 ("r-lattice" ,r-lattice)
7650 ("r-leaps" ,r-leaps)
7652 ("r-scatterplot3d" ,r-scatterplot3d)))
7654 `(("r-knitr" ,r-knitr)))
7655 (home-page "http://factominer.free.fr")
7656 (synopsis "Multivariate exploratory data analysis and data mining")
7658 "This package provides exploratory data analysis methods to summarize,
7659 visualize and describe datasets. The main principal component methods are
7660 available, those with the largest potential in terms of applications:
7661 principal component analysis (PCA) when variables are quantitative,
7662 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7663 variables are categorical, Multiple Factor Analysis when variables are
7664 structured in groups, etc. and hierarchical cluster analysis.")
7665 (license license:gpl2+)))
7667 (define-public r-factoextra
7669 (name "r-factoextra")
7674 (uri (cran-uri "factoextra" version))
7677 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7678 (build-system r-build-system)
7680 `(("r-abind" ,r-abind)
7681 ("r-cluster" ,r-cluster)
7682 ("r-dendextend" ,r-dendextend)
7683 ("r-factominer" ,r-factominer)
7684 ("r-ggplot2" ,r-ggplot2)
7685 ("r-ggpubr" ,r-ggpubr)
7686 ("r-ggrepel" ,r-ggrepel)
7687 ("r-reshape2" ,r-reshape2)
7688 ("r-tidyr" ,r-tidyr)))
7689 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7690 (synopsis "Extract and visualize the results of multivariate data analyses")
7692 "This package provides some easy-to-use functions to extract and
7693 visualize the output of multivariate data analyses, including
7694 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7695 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7696 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7697 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7698 packages. It contains also functions for simplifying some clustering analysis
7699 steps and provides ggplot2-based elegant data visualization.")
7700 (license license:gpl2)))
7702 (define-public r-fansi
7709 (uri (cran-uri "fansi" version))
7712 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7713 (build-system r-build-system)
7715 `(("r-knitr" ,r-knitr))) ; for vignettes
7716 (home-page "https://github.com/brodieG/fansi")
7717 (synopsis "ANSI control sequence aware string functions")
7719 "This package provides counterparts to R string manipulation functions
7720 that account for the effects of ANSI text formatting control sequences.")
7721 (license license:gpl2+)))
7723 (define-public r-nbclust
7730 (uri (cran-uri "NbClust" version))
7733 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7734 (properties `((upstream-name . "NbClust")))
7735 (build-system r-build-system)
7736 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7737 (synopsis "Determine the best number of clusters in a data set")
7739 "NbClust provides 30 indexes for determining the optimal number of
7740 clusters in a data set and offers the best clustering scheme from different
7741 results to the user.")
7742 (license license:gpl2)))
7744 (define-public r-hdf5r
7751 (uri (cran-uri "hdf5r" version))
7754 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7755 (build-system r-build-system)
7760 `(("r-bit64" ,r-bit64)
7763 `(("r-knitr" ,r-knitr)))
7764 (home-page "https://hhoeflin.github.io/hdf5r")
7765 (synopsis "Interface to the HDF5 binary data format")
7767 "HDF5 is a data model, library and file format for storing and managing
7768 large amounts of data. This package provides a nearly feature complete,
7769 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7770 functionality is added so that HDF5 objects behave very similar to their
7771 corresponding R counterparts.")
7772 (license license:asl2.0)))
7774 (define-public r-itertools
7776 (name "r-itertools")
7781 (uri (cran-uri "itertools" version))
7784 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7785 (build-system r-build-system)
7787 `(("r-iterators" ,r-iterators)))
7788 (home-page "https://cran.r-project.org/web/packages/itertools/")
7789 (synopsis "Iterator tools")
7791 "This package provides various tools for creating iterators, many
7792 patterned after functions in the Python @code{itertools} module, and others
7793 patterned after functions in the snow package.")
7794 (license license:gpl2)))
7796 (define-public r-polynom
7803 (uri (cran-uri "polynom" version))
7806 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7807 (build-system r-build-system)
7808 (home-page "https://cran.r-project.org/web/packages/polynom/")
7809 (synopsis "Functions for univariate polynomial manipulations")
7811 "This package provides a collection of functions to implement a class for
7812 univariate polynomial manipulations.")
7813 (license license:gpl2)))
7815 (define-public r-gbrd
7822 (uri (cran-uri "gbRd" version))
7825 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7826 (properties `((upstream-name . "gbRd")))
7827 (build-system r-build-system)
7828 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7829 (synopsis "Utilities for processing Rd objects and files")
7831 "This package provides utilities for processing Rd objects and files.
7832 Extract argument descriptions and other parts of the help pages of
7834 (license license:gpl2+)))
7836 (define-public r-rjags
7843 (uri (cran-uri "rjags" version))
7846 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7847 (build-system r-build-system)
7849 `(("r-coda" ,r-coda)))
7853 `(("pkg-config" ,pkg-config)))
7854 (home-page "http://mcmc-jags.sourceforge.net")
7855 (synopsis "Bayesian graphical models using MCMC")
7857 "This package provides an R interface to the JAGS MCMC library. JAGS is
7858 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7859 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7860 (license license:gpl2)))
7862 (define-public r-rbibutils
7864 (name "r-rbibutils")
7869 (uri (cran-uri "rbibutils" version))
7872 "13phw0dk3p3s1z45ff7dbqnn27zws1209mp3d4763zh7xnsdsl44"))))
7873 (properties `((upstream-name . "rbibutils")))
7874 (build-system r-build-system)
7875 (home-page "https://geobosh.github.io/rbibutils/")
7876 (synopsis "Convert between bibliography formats")
7878 "This package converts between a number of bibliography formats,
7879 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7880 utilities and supports all bibliography formats and character encodings
7881 implemented in bibutils.")
7882 (license license:gpl2)))
7884 (define-public r-rdpack
7891 (uri (cran-uri "Rdpack" version))
7894 "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
7895 (properties `((upstream-name . "Rdpack")))
7896 (build-system r-build-system)
7898 `(("r-rbibutils" ,r-rbibutils)))
7899 (home-page "https://github.com/GeoBosh/Rdpack")
7900 (synopsis "Update and manipulate Rd documentation objects")
7902 "This package provides functions for manipulation of R documentation
7903 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7904 updating Rd documentation for functions, methods and classes; it also includes
7905 Rd macros for citations and import of references from bibtex files for use in
7906 Rd files and roxygen2 comments, as well as many functions for manipulation of
7907 references and Rd files.")
7908 (license license:gpl2+)))
7910 (define-public r-officer
7917 (uri (cran-uri "officer" version))
7920 "1j3bv4j8x5ijj0j447vpdsk4p8pl3ncwdwnns6n3plfrqgsf3vsg"))))
7921 (build-system r-build-system)
7928 `(("r-knitr" ,r-knitr)))
7929 (home-page "https://davidgohel.github.io/officer")
7930 (synopsis "Manipulation of Word and PowerPoint documents")
7932 "This package provides tools to access and manipulate Word and PowerPoint
7933 documents from R. The package focuses on tabular and graphical reporting from
7934 R; it also provides two functions that let users get document content into
7935 data objects. A set of functions lets add and remove images, tables and
7936 paragraphs of text in new or existing documents. When working with PowerPoint
7937 presentations, slides can be added or removed; shapes inside slides can also
7938 be added or removed. When working with Word documents, a cursor can be used
7939 to help insert or delete content at a specific location in the document.")
7940 (license license:gpl3)))
7942 (define-public r-profilemodel
7944 (name "r-profilemodel")
7949 (uri (cran-uri "profileModel" version))
7952 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7953 (properties `((upstream-name . "profileModel")))
7954 (build-system r-build-system)
7955 (home-page "https://github.com/ikosmidis/profileModel")
7956 (synopsis "Profiling inference functions for various model classes")
7958 "This package provides tools that can be used to calculate, evaluate,
7959 plot and use for inference the profiles of *arbitrary* inference functions for
7960 arbitrary @code{glm}-like fitted models with linear predictors. More information
7961 on the methods that are implemented can be found in Kosmidis (2008)
7962 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7963 (license license:gpl2+)))
7965 (define-public r-brglm
7972 (uri (cran-uri "brglm" version))
7975 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7976 (properties `((upstream-name . "brglm")))
7977 (build-system r-build-system)
7979 `(("r-profilemodel" ,r-profilemodel)))
7980 (home-page "https://github.com/ikosmidis/brglm")
7981 (synopsis "Bias reduction in binomial-response generalized linear models")
7983 "Fit generalized linear models with binomial responses using either an
7984 adjusted-score approach to bias reduction or maximum penalized likelihood
7985 where penalization is by Jeffreys invariant prior. These procedures return
7986 estimates with improved frequentist properties (bias, mean squared error) that
7987 are always finite even in cases where the maximum likelihood estimates are
7988 infinite (data separation). Fitting takes place by fitting generalized linear
7989 models on iteratively updated pseudo-data. The interface is essentially the
7990 same as @code{glm}. More flexibility is provided by the fact that custom
7991 pseudo-data representations can be specified and used for model fitting.
7992 Functions are provided for the construction of confidence intervals for the
7993 reduced-bias estimates.")
7994 (license license:gpl2+)))
7996 (define-public r-entropy
8003 (uri (cran-uri "entropy" version))
8006 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8007 (properties `((upstream-name . "entropy")))
8008 (build-system r-build-system)
8009 (home-page "https://www.strimmerlab.org/software/entropy/")
8010 (synopsis "Estimation of entropy, mutual information and related quantities")
8012 "This package implements various estimators of entropy, such as the
8013 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8014 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8015 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8016 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8017 mutual information, and chi-squared statistic of independence. In addition
8018 there are functions for discretizing continuous random variables.")
8019 (license license:gpl3+)))
8021 (define-public r-abn
8028 (uri (cran-uri "abn" version))
8031 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8032 (build-system r-build-system)
8036 `(("r-lme4" ,r-lme4)
8039 ("r-rcpparmadillo" ,r-rcpparmadillo)
8040 ("r-rjags" ,r-rjags)))
8041 (home-page "https://r-bayesian-networks.org/")
8042 (synopsis "Modelling multivariate data with additive bayesian networks")
8044 "Bayesian network analysis is a form of probabilistic graphical models
8045 which derives from empirical data a directed acyclic graph, DAG, describing
8046 the dependency structure between random variables. An additive Bayesian
8047 network model consists of a form of a DAG where each node comprises a
8048 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8049 equivalent to Bayesian multivariate regression using graphical modelling, they
8050 generalises the usual multivariable regression, GLM, to multiple dependent
8051 variables. This package provides routines to help determine optimal Bayesian
8052 network models for a given data set, where these models are used to identify
8053 statistical dependencies in messy, complex data.")
8054 (license license:gpl2+)))
8056 (define-public r-acd
8063 (uri (cran-uri "ACD" version))
8066 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8067 (properties `((upstream-name . "ACD")))
8068 (build-system r-build-system)
8069 (home-page "https://cran.r-project.org/web/packages/ACD/")
8070 (synopsis "Categorical data analysis with complete or missing responses")
8072 "This package provides tools for categorical data analysis with complete
8073 or missing responses.")
8074 (license license:gpl2+)))
8076 (define-public r-acdm
8083 (uri (cran-uri "ACDm" version))
8086 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8087 (properties `((upstream-name . "ACDm")))
8088 (build-system r-build-system)
8090 `(("r-dplyr" ,r-dplyr)
8091 ("r-ggplot2" ,r-ggplot2)
8093 ("r-rsolnp" ,r-rsolnp)
8095 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8096 (synopsis "Tools for Autoregressive Conditional Duration Models")
8098 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8099 and Russell, 1998) models. It creates trade, price or volume durations from
8100 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8102 (license license:gpl2+)))
8104 (define-public r-overlap
8111 (uri (cran-uri "overlap" version))
8114 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8115 (build-system r-build-system)
8116 (home-page "https://cran.r-project.org/web/packages/overlap/")
8117 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8119 "This package provides functions to fit kernel density functions to data
8120 on temporal activity patterns of animals; estimate coefficients of overlapping
8121 of densities for two species; and calculate bootstrap estimates of confidence
8123 (license license:gpl3+)))
8125 (define-public r-snakecase
8127 (name "r-snakecase")
8132 (uri (cran-uri "snakecase" version))
8135 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8136 (build-system r-build-system)
8138 `(("r-stringi" ,r-stringi)
8139 ("r-stringr" ,r-stringr)))
8140 (home-page "https://github.com/Tazinho/snakecase")
8141 (synopsis "Convert strings into any case")
8143 "This package provides a consistent, flexible and easy to use tool to
8144 parse and convert strings into cases like snake or camel among others.")
8145 (license license:gpl3)))
8147 (define-public r-prediction
8149 (name "r-prediction")
8154 (uri (cran-uri "prediction" version))
8157 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8158 (build-system r-build-system)
8160 `(("r-data-table" ,r-data-table)))
8161 (home-page "https://github.com/leeper/prediction")
8162 (synopsis "Tidy, type-safe prediction methods")
8164 "This package provides the @code{prediction()} function, a type-safe
8165 alternative to @code{predict()} that always returns a data frame. The package
8166 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8167 from the @code{stats} package, as well as numerous other model classes from
8168 other add-on packages.")
8169 (license license:expat)))
8171 (define-public r-insight
8178 (uri (cran-uri "insight" version))
8181 "03b7kd17h25mi1si40ibcp3jpasyqpj51mr8js0ywywyfw7909j1"))))
8182 (build-system r-build-system)
8184 `(("r-knitr" ,r-knitr)))
8185 (home-page "https://easystats.github.io/insight/")
8186 (synopsis "Easy access to model information for various model objects")
8188 "This package provides a tool to provide an easy, intuitive and
8189 consistent access to information contained in various R models, like model
8190 formulas, model terms, information about random effects, data that was used to
8191 fit the model or data from response variables. The package mainly revolves
8192 around two types of functions: Functions that find (the names of) information,
8193 starting with @code{find_}, and functions that get the underlying data,
8194 starting with @code{get_}. The package has a consistent syntax and works with
8195 many different model objects, where otherwise functions to access these
8196 information are missing.")
8197 (license license:gpl3)))
8199 (define-public r-sjlabelled
8201 (name "r-sjlabelled")
8206 (uri (cran-uri "sjlabelled" version))
8209 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8210 (build-system r-build-system)
8212 `(("r-insight" ,r-insight)))
8214 `(("r-knitr" ,r-knitr)))
8215 (home-page "https://github.com/strengejacke/sjlabelled")
8216 (synopsis "Labelled data utility functions")
8218 "This package provides a collection of functions dealing with labelled
8219 data, like reading and writing data between R and other statistical software
8220 packages. This includes easy ways to get, set or change value and variable
8221 label attributes, to convert labelled vectors into factors or numeric (and
8222 vice versa), or to deal with multiple declared missing values.")
8223 (license license:gpl3)))
8225 (define-public r-sjmisc
8232 (uri (cran-uri "sjmisc" version))
8235 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8236 (build-system r-build-system)
8238 `(("r-dplyr" ,r-dplyr)
8239 ("r-insight" ,r-insight)
8240 ("r-magrittr" ,r-magrittr)
8241 ("r-purrr" ,r-purrr)
8242 ("r-rlang" ,r-rlang)
8243 ("r-sjlabelled" ,r-sjlabelled)
8244 ("r-tidyselect" ,r-tidyselect)))
8246 `(("r-knitr" ,r-knitr)))
8247 (home-page "https://github.com/strengejacke/sjmisc")
8248 (synopsis "Data and variable transformation functions")
8250 "This package is a collection of miscellaneous utility functions,
8251 supporting data transformation tasks like recoding, dichotomizing or grouping
8252 variables, setting and replacing missing values. The data transformation
8253 functions also support labelled data, and all integrate seamlessly into a
8254 tidyverse workflow.")
8255 (license license:gpl3)))
8257 (define-public r-nortest
8264 (uri (cran-uri "nortest" version))
8267 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8268 (build-system r-build-system)
8269 (home-page "https://cran.r-project.org/web/packages/nortest/")
8270 (synopsis "Tests for normality")
8272 "This package provides five omnibus tests for testing the composite
8273 hypothesis of normality.")
8274 (license license:gpl2+)))
8276 (define-public r-moonbook
8283 (uri (cran-uri "moonBook" version))
8286 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8287 (properties `((upstream-name . "moonBook")))
8288 (build-system r-build-system)
8290 `(("r-magrittr" ,r-magrittr)
8291 ("r-nortest" ,r-nortest)
8292 ("r-sjmisc" ,r-sjmisc)
8293 ("r-stringr" ,r-stringr)
8294 ("r-survival" ,r-survival)
8295 ("r-ztable" ,r-ztable)))
8297 `(("r-knitr" ,r-knitr)))
8298 (home-page "https://github.com/cardiomoon/moonBook")
8299 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8301 "This package provides several analysis-related functions for the book
8302 entitled \"R statistics and graph for medical articles\" (written in Korean),
8303 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8305 (license license:gpl2)))
8307 (define-public r-flextable
8309 (name "r-flextable")
8314 (uri (cran-uri "flextable" version))
8317 "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma"))))
8318 (build-system r-build-system)
8320 `(("r-base64enc" ,r-base64enc)
8321 ("r-data-table" ,r-data-table)
8322 ("r-gdtools" ,r-gdtools)
8323 ("r-htmltools" ,r-htmltools)
8324 ("r-knitr" ,r-knitr)
8325 ("r-officer" ,r-officer)
8326 ("r-rlang" ,r-rlang)
8327 ("r-rmarkdown" ,r-rmarkdown)
8329 ("r-xml2" ,r-xml2)))
8331 `(("r-knitr" ,r-knitr)))
8332 (home-page "https://davidgohel.github.io/flextable")
8333 (synopsis "Functions for tabular reporting")
8335 "This package provides tools to create pretty tables for HTML documents
8336 and other formats. Functions are provided to let users create tables, modify
8337 and format their content. It extends the @code{officer} package and can be
8338 used within R markdown documents when rendering to HTML and to Word
8340 (license license:gpl3)))
8342 (define-public r-writexl
8349 (uri (cran-uri "writexl" version))
8352 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8353 (build-system r-build-system)
8354 (inputs `(("zlib" ,zlib)))
8355 (home-page "https://github.com/ropensci/writexl")
8356 (synopsis "Export data frames to xlsx format")
8358 "This package provides a data frame to xlsx exporter based on
8360 (license license:bsd-2)))
8362 (define-public r-biasedurn
8364 (name "r-biasedurn")
8369 (uri (cran-uri "BiasedUrn" version))
8372 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8373 (properties `((upstream-name . "BiasedUrn")))
8374 (build-system r-build-system)
8375 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8376 (synopsis "Biased Urn model distributions")
8378 "This package provides statistical models of biased sampling in the form
8379 of univariate and multivariate noncentral hypergeometric distributions,
8380 including Wallenius' noncentral hypergeometric distribution and Fisher's
8381 noncentral hypergeometric distribution (also called extended hypergeometric
8383 (license license:gpl3)))
8385 (define-public r-goplot
8392 (uri (cran-uri "GOplot" version))
8395 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8396 (properties `((upstream-name . "GOplot")))
8397 (build-system r-build-system)
8399 `(("r-ggdendro" ,r-ggdendro)
8400 ("r-ggplot2" ,r-ggplot2)
8401 ("r-gridextra" ,r-gridextra)
8402 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8403 (home-page "https://github.com/wencke/wencke.github.io")
8404 (synopsis "Visualization of functional analysis data")
8406 "This package provides an implementation of multilayered visualizations
8407 for enhanced graphical representation of functional analysis data. It
8408 combines and integrates omics data derived from expression and functional
8409 annotation enrichment analyses. Its plotting functions have been developed
8410 with an hierarchical structure in mind: starting from a general overview to
8411 identify the most enriched categories (modified bar plot, bubble plot) to a
8412 more detailed one displaying different types of relevant information for the
8413 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8414 Venn diagram, heatmap).")
8415 (license license:gpl2)))
8417 (define-public r-getopt
8424 (uri (cran-uri "getopt" version))
8427 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8428 (build-system r-build-system)
8429 (home-page "https://github.com/trevorld/getopt")
8430 (synopsis "Command-line option processor for R")
8432 "This package is designed to be used with Rscript to write shebang
8433 scripts that accept short and long options. Many users will prefer to
8434 use the packages @code{optparse} or @code{argparse} which add extra
8435 features like automatically generated help options and usage texts,
8436 support for default values, positional argument support, etc.")
8437 (license license:gpl2+)))
8439 (define-public r-findpython
8441 (name "r-findpython")
8446 (uri (cran-uri "findpython" version))
8449 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8450 (build-system r-build-system)
8451 (home-page "https://github.com/trevorld/findpython")
8452 (synopsis "Functions to find an acceptable Python binary")
8454 "This package was designed to find an acceptable Python binary that
8455 matches version and feature constraints.")
8456 (license license:expat)))
8458 ;; This in not the same as "r-argparser"
8459 (define-public r-argparse
8466 (uri (cran-uri "argparse" version))
8469 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8470 (build-system r-build-system)
8471 (inputs `(("python" ,python)))
8473 `(("r-findpython" ,r-findpython)
8474 ("r-jsonlite" ,r-jsonlite)
8477 `(("r-knitr" ,r-knitr)))
8478 (home-page "https://github.com/trevorld/argparse")
8479 (synopsis "Command line optional and positional argument parser")
8481 "This package provides a command line parser to be used with Rscript to
8482 write shebang scripts that gracefully accept positional and optional arguments
8483 and automatically generate usage notices.")
8484 (license license:gpl2+)))
8486 (define-public r-hash
8493 (uri (cran-uri "hash" version))
8496 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8497 (build-system r-build-system)
8498 (home-page "https://cran.r-project.org/web/packages/hash/")
8499 (synopsis "Implementation of hash/associated arrays/dictionaries")
8501 "This package implements a data structure similar to hashes in Perl and
8502 dictionaries in Python but with a purposefully R flavor. For objects of
8503 appreciable size, access using hashes outperforms native named lists and
8505 (license license:gpl2+)))
8507 (define-public r-orddom
8514 (uri (cran-uri "orddom" version))
8517 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8518 (build-system r-build-system)
8519 (propagated-inputs `(("r-psych" ,r-psych)))
8520 (home-page "https://cran.r-project.org/web/packages/orddom/")
8521 (synopsis "Ordinal dominance statistics")
8523 "This package provides tools to compute ordinal, statistics and effect
8524 sizes as an alternative to mean comparison: Cliff's delta or success rate
8525 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8526 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8527 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8528 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8529 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8530 Group (Non-)Overlap considerations.")
8531 (license license:gpl2)))
8533 (define-public r-deriv
8540 (uri (cran-uri "Deriv" version))
8543 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
8544 (properties `((upstream-name . "Deriv")))
8545 (build-system r-build-system)
8546 (home-page "https://cran.r-project.org/web/packages/Deriv")
8547 (synopsis "Symbolic differentiation")
8549 "This package provides an R-based solution for symbolic differentiation.
8550 It admits user-defined functions as well as function substitution in arguments
8551 of functions to be differentiated. Some symbolic simplification is part of
8553 (license license:gpl3+)))
8555 (define-public r-doby
8562 (uri (cran-uri "doBy" version))
8565 "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00"))))
8566 (properties `((upstream-name . "doBy")))
8567 (build-system r-build-system)
8569 `(("r-broom" ,r-broom)
8570 ("r-deriv" ,r-deriv)
8571 ("r-dplyr" ,r-dplyr)
8572 ("r-ggplot2" ,r-ggplot2)
8573 ("r-magrittr" ,r-magrittr)
8575 ("r-matrix" ,r-matrix)
8576 ("r-pbkrtest" ,r-pbkrtest)
8577 ("r-tibble" ,r-tibble)))
8579 `(("r-knitr" ,r-knitr)))
8580 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8581 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8583 "This package contains:
8586 @item facilities for working with grouped data: @code{do}
8587 something to data stratified @code{by} some variables.
8588 @item implementations of least-squares means, general linear contrasts, and
8589 @item miscellaneous other utilities.
8591 (license license:gpl2+)))
8593 (define-public r-refgenome
8595 (name "r-refgenome")
8600 (uri (cran-uri "refGenome" version))
8603 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8604 (properties `((upstream-name . "refGenome")))
8605 (build-system r-build-system)
8609 ("r-rsqlite" ,r-rsqlite)))
8610 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8612 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8614 "This package contains functionality for importing and managing of
8615 downloaded genome annotation data from the Ensembl genome browser (European
8616 Bioinformatics Institute) and from the UCSC genome browser (University of
8617 California, Santa Cruz) and annotation routines for genomic positions and
8618 splice site positions.")
8619 (license license:gpl2)))
8621 (define-public r-basix
8628 (uri (cran-uri "BASIX" version))
8631 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8632 (properties `((upstream-name . "BASIX")))
8633 (build-system r-build-system)
8634 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8635 (synopsis "Efficient C/C++ toolset for R")
8637 "BASIX provides some efficient C/C++ implementations of native R
8638 procedures to speed up calculations in R.")
8639 (license license:gpl2)))
8641 (define-public r-blockfest
8643 (name "r-blockfest")
8648 (uri (cran-uri "BlockFeST" version))
8651 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
8652 (properties `((upstream-name . "BlockFeST")))
8653 (build-system r-build-system)
8654 (propagated-inputs `(("r-basix" ,r-basix)))
8655 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8656 (synopsis "Bayesian calculation of region-specific fixation index")
8658 "This package provides an R implementation of an extension of the
8659 BayeScan software for codominant markers, adding the option to group
8660 individual SNPs into pre-defined blocks. A typical application of this new
8661 approach is the identification of genomic regions, genes, or gene sets
8662 containing one or more SNPs that evolved under directional selection.")
8663 (license license:gpl2)))
8665 (define-public r-proc
8668 (version "1.17.0.1")
8672 (uri (cran-uri "pROC" version))
8675 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8676 (properties `((upstream-name . "pROC")))
8677 (build-system r-build-system)
8679 `(("r-plyr" ,r-plyr)
8680 ("r-rcpp" ,r-rcpp)))
8681 (home-page "https://web.expasy.org/pROC/")
8682 (synopsis "Display and analyze ROC curves")
8684 "This package provides tools for visualizing, smoothing and comparing
8685 receiver operating characteristic (ROC curves). The area under the
8686 curve (AUC) can be compared with statistical tests based on U-statistics or
8687 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8688 (license license:gpl3+)))
8690 (define-public r-rootsolve
8692 (name "r-rootsolve")
8697 (uri (cran-uri "rootSolve" version))
8700 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8701 (properties `((upstream-name . "rootSolve")))
8702 (build-system r-build-system)
8703 (native-inputs `(("gfortran" ,gfortran)))
8704 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8705 (synopsis "Tools for the analysis of ordinary differential equations")
8707 "This package provides routines to find the root of nonlinear functions,
8708 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8709 differential equations} (ODE). It includes routines that:
8712 @item generate gradient and jacobian matrices (full and banded),
8713 @item find roots of non-linear equations by the Newton-Raphson method,
8714 @item estimate steady-state conditions of a system of (differential) equations
8715 in full, banded or sparse form, using the Newton-Raphson method, or by
8716 dynamically running,
8717 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8718 and 3-D partial differential equations, that have been converted to ordinary
8719 differential equations by numerical differencing (using the method-of-lines
8722 (license license:gpl2+)))
8724 (define-public r-abcanalysis
8726 (name "r-abcanalysis")
8731 (uri (cran-uri "ABCanalysis" version))
8733 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8734 (properties `((upstream-name . "ABCanalysis")))
8735 (build-system r-build-system)
8736 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8737 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8738 (synopsis "Computed ABC Analysis")
8740 "Multivariate data sets often differ in several factors or derived statistical
8741 parameters, which have to be selected for a valid interpretation. Basing this
8742 selection on traditional statistical limits leads occasionally to the perception
8743 of losing information from a data set. This package provides tools to calculate
8744 these limits on the basis of the mathematical properties of the distribution of
8745 the analyzed items.")
8746 (license license:gpl3)))
8748 (define-public r-slam
8755 (uri (cran-uri "slam" version))
8757 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8758 (build-system r-build-system)
8759 (home-page "https://cran.r-project.org/web/packages/slam/")
8760 (synopsis "Sparse lightweight arrays and matrices")
8762 "This package contains data structures and algorithms for sparse arrays and matrices,
8763 based on index arrays and simple triplet representations, respectively.")
8764 (license license:gpl2)))
8766 (define-public r-manipulatewidget
8768 (name "r-manipulatewidget")
8773 (uri (cran-uri "manipulateWidget" version))
8775 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8777 `((upstream-name . "manipulateWidget")))
8778 (build-system r-build-system)
8780 `(("r-base64enc" ,r-base64enc)
8781 ("r-codetools" ,r-codetools)
8782 ("r-htmltools" ,r-htmltools)
8783 ("r-htmlwidgets" ,r-htmlwidgets)
8784 ("r-knitr" ,r-knitr)
8785 ("r-miniui" ,r-miniui)
8786 ("r-shiny" ,r-shiny)
8787 ("r-webshot" ,r-webshot)))
8788 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8789 (synopsis "Add even more interactivity to interactive charts")
8791 "This package lets you create in just a few lines of R code a nice user interface to
8792 modify the data or the graphical parameters of one or multiple interactive
8793 charts. It is useful to quickly explore visually some data or for package
8794 developers to generate user interfaces easy to maintain.")
8795 (license license:gpl2+)))
8804 (uri (cran-uri "A3" version))
8806 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8807 (properties `((upstream-name . "A3")))
8808 (build-system r-build-system)
8810 `(("r-pbapply" ,r-pbapply)
8811 ("r-xtable" ,r-xtable)))
8812 (home-page "https://cran.r-project.org/web/packages/A3/")
8813 (synopsis "Error metrics for predictive models")
8815 "This package supplies tools for tabulating and analyzing the results of predictive
8816 models. The methods employed are applicable to virtually any predictive model
8817 and make comparisons between different methodologies straightforward.")
8818 (license license:gpl2+)))
8820 (define-public r-infotheo
8827 (uri (cran-uri "infotheo" version))
8830 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8831 (build-system r-build-system)
8832 (home-page "http://homepage.meyerp.com/software")
8833 (synopsis "Information-theoretic measures")
8835 "This package implements various measures of information theory based on
8836 several entropy estimators.")
8837 (license license:gpl3+)))
8839 (define-public r-abcoptim
8846 (uri (cran-uri "ABCoptim" version))
8848 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8849 (properties `((upstream-name . "ABCoptim")))
8850 (build-system r-build-system)
8851 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8852 (home-page "https://github.com/gvegayon/ABCoptim/")
8853 (synopsis "Optimization of Artificial Bee Colony algorithm")
8855 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8856 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8857 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8858 algorithms, and uses only common control parameters such as colony size and
8859 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8860 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8861 This version is a work-in-progress and is written in R code.")
8862 (license license:expat)))
8864 (define-public r-abcp2
8871 (uri (cran-uri "ABCp2" version))
8873 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8874 (properties `((upstream-name . "ABCp2")))
8875 (build-system r-build-system)
8876 (propagated-inputs `(("r-mass" ,r-mass)))
8877 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8878 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8880 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8881 Poisson, and Gamma distribution and estimates the proportional paternity of the
8882 second male (P2) based on the best fit distribution.")
8883 (license license:gpl2)))
8885 (define-public r-abcrf
8892 (uri (cran-uri "abcrf" version))
8894 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8895 (build-system r-build-system)
8897 `(("r-doparallel" ,r-doparallel)
8898 ("r-foreach" ,r-foreach)
8900 ("r-matrixstats" ,r-matrixstats)
8901 ("r-ranger" ,r-ranger)
8903 ("r-rcpparmadillo" ,r-rcpparmadillo)
8904 ("r-readr" ,r-readr)
8905 ("r-stringr" ,r-stringr)))
8906 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8907 (synopsis "Approximate bayesian computation via random forests")
8909 "This package performs approximate bayesian computation (ABC) model choice and
8910 parameter inference via random forests. This machine learning tool named random
8911 forests (RF) can conduct selection among the highly complex models covered by
8913 (license license:gpl2+)))
8915 (define-public r-abctools
8922 (uri (cran-uri "abctools" version))
8924 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8925 (build-system r-build-system)
8928 ("r-abind" ,r-abind)
8929 ("r-hmisc" ,r-hmisc)
8930 ("r-plyr" ,r-plyr)))
8931 (home-page "https://github.com/dennisprangle/abctools/")
8932 (synopsis "Tools for ABC analyses")
8934 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8935 including summary statistic selection and assessing coverage. This includes
8936 recent dimension reduction algorithms to tune the choice of summary statistics,
8937 and coverage methods to tune the choice of threshold.")
8938 (license license:gpl2+)))
8940 (define-public r-ggstance
8947 (uri (cran-uri "ggstance" version))
8949 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8950 (build-system r-build-system)
8952 `(("r-ggplot2" ,r-ggplot2)
8954 ("r-rlang" ,r-rlang)
8955 ("r-withr" ,r-withr)))
8956 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8957 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8959 "This package is a @code{r-ggplot2} extension that provides flipped components:
8961 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8962 @item vertical versions of @code{r-ggplot2} positions.
8964 (license license:gpl3)))
8966 (define-public r-mosaiccore
8968 (name "r-mosaiccore")
8973 (uri (cran-uri "mosaicCore" version))
8975 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8976 (properties `((upstream-name . "mosaicCore")))
8977 (build-system r-build-system)
8979 `(("r-dplyr" ,r-dplyr)
8981 ("r-rlang" ,r-rlang)
8982 ("r-tidyr" ,r-tidyr)))
8983 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8984 (synopsis "Common utilities for mosaic family packages")
8986 "Common utilities used in other Mosaic family packages are collected here.")
8987 (license license:gpl2+)))
8989 (define-public r-labelled
8996 (uri (cran-uri "labelled" version))
8999 "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg"))))
9000 (properties `((upstream-name . "labelled")))
9001 (build-system r-build-system)
9003 `(("r-dplyr" ,r-dplyr)
9004 ("r-haven" ,r-haven)
9005 ("r-lifecycle" ,r-lifecycle)
9006 ("r-rlang" ,r-rlang)
9007 ("r-stringr" ,r-stringr)
9008 ("r-tidyr" ,r-tidyr)
9009 ("r-vctrs" ,r-vctrs)))
9011 `(("r-knitr" ,r-knitr)))
9012 (home-page "http://larmarange.github.io/labelled/")
9013 (synopsis "Manipulating labelled data")
9015 "This package provides useful functions to deal with the
9016 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9018 (license license:gpl3)))
9020 (define-public r-ggformula
9022 (name "r-ggformula")
9027 (uri (cran-uri "ggformula" version))
9029 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9030 (build-system r-build-system)
9032 `(("r-ggforce" ,r-ggforce)
9033 ("r-ggplot2" ,r-ggplot2)
9034 ("r-ggridges" ,r-ggridges)
9035 ("r-ggstance" ,r-ggstance)
9036 ("r-labelled" ,r-labelled)
9037 ("r-magrittr" ,r-magrittr)
9038 ("r-mosaiccore" ,r-mosaiccore)
9039 ("r-rlang" ,r-rlang)
9040 ("r-scales" ,r-scales)
9041 ("r-stringr" ,r-stringr)
9042 ("r-tibble" ,r-tibble)))
9044 `(("r-knitr" ,r-knitr)))
9045 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9046 (synopsis "Formula interface for the @code{r-ggplot2}")
9048 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9049 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9050 and extends the excellent simplicity of the lattice-graphics formula interface,
9051 while providing the intuitive capabilities of @code{r-ggplot2}.")
9052 (license license:expat)))
9054 (define-public r-mosaicdata
9056 (name "r-mosaicdata")
9061 (uri (cran-uri "mosaicData" version))
9063 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9064 (properties `((upstream-name . "mosaicData")))
9065 (build-system r-build-system)
9066 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9067 (synopsis "Data sets for project Mosaic")
9069 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9070 used to teach mathematics, statistics, computation and modeling.")
9071 (license license:gpl2+)))
9073 (define-public r-raster
9080 (uri (cran-uri "raster" version))
9083 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9084 (build-system r-build-system)
9086 `(("r-rcpp" ,r-rcpp)
9088 (home-page "https://www.rspatial.org/")
9089 (synopsis "Geographic data analysis and modeling")
9091 "The package implements basic and high-level functions for reading,
9092 writing, manipulating, analyzing and modeling of gridded spatial data.
9093 Processing of very large files is supported.")
9094 (license license:gpl3+)))
9096 (define-public r-mosaic
9103 (uri (cran-uri "mosaic" version))
9105 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9106 (build-system r-build-system)
9108 `(("r-broom" ,r-broom)
9109 ("r-dplyr" ,r-dplyr)
9110 ("r-ggdendro" ,r-ggdendro)
9111 ("r-ggformula" ,r-ggformula)
9112 ("r-ggplot2" ,r-ggplot2)
9113 ("r-ggrepel" ,r-ggrepel)
9115 ("r-gridextra" ,r-gridextra)
9116 ("r-lattice" ,r-lattice)
9117 ("r-latticeextra" ,r-latticeextra)
9118 ("r-lazyeval" ,r-lazyeval)
9120 ("r-matrix" ,r-matrix)
9121 ("r-mosaiccore" ,r-mosaiccore)
9122 ("r-mosaicdata" ,r-mosaicdata)
9123 ("r-readr" ,r-readr)
9124 ("r-tidyr" ,r-tidyr)))
9126 `(("r-knitr" ,r-knitr)))
9127 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9128 (synopsis "Mathematics, statistics, and computation teaching utilities")
9130 "This package contain data sets and utilities from
9131 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9132 statistics, computation and modeling. Project MOSAIC is a community of
9133 educators working to tie together aspects of quantitative work that students
9134 in science, technology, engineering and mathematics will need in their
9135 professional lives, but which are usually taught in isolation, if at all.")
9136 (license license:gpl2+)))
9138 (define-public r-abd
9145 (uri (cran-uri "abd" version))
9147 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9148 (build-system r-build-system)
9150 `(("r-lattice" ,r-lattice)
9151 ("r-mosaic" ,r-mosaic)
9152 ("r-nlme" ,r-nlme)))
9153 (home-page "https://cran.r-project.org/web/packages/abd/")
9154 (synopsis "Analysis of biological data")
9156 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9157 biological data by Michael Whitlock and Dolph Schluter.")
9158 (license license:gpl2)))
9160 (define-public r-svgui
9167 (uri (cran-uri "svGUI" version))
9169 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9170 (properties `((upstream-name . "svGUI")))
9171 (build-system r-build-system)
9172 (home-page "https://github.com/SciViews/svGUI/")
9173 (synopsis "Functions for managing GUI clients in R")
9175 "The SciViews @code{svGUI} package eases the management of Graphical User
9176 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9177 centralizes info about GUI elements currently used, and it dispatches GUI
9178 calls to the particular toolkits in use in function of the context.")
9179 (license license:gpl2)))
9181 (define-public r-svdialogs
9183 (name "r-svdialogs")
9188 (uri (cran-uri "svDialogs" version))
9190 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9191 (properties `((upstream-name . "svDialogs")))
9192 (build-system r-build-system)
9195 ("zenity" ,zenity)))
9197 `(("r-rstudioapi" ,r-rstudioapi)
9198 ("r-svgui" ,r-svgui)))
9199 (home-page "https://github.com/SciViews/svDialogs/")
9200 (synopsis "Portable dialog boxes")
9202 "This package helps to construct standard dialog boxes for your GUI, including
9203 message boxes, input boxes, list, file or directory selection, and others. In
9204 case R cannot display GUI dialog boxes, a simpler command line version of these
9205 interactive elements is also provided as a fallback solution.")
9206 (license license:gpl2)))
9208 (define-public r-abe
9215 (uri (cran-uri "abe" version))
9218 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9219 (build-system r-build-system)
9220 (home-page "https://cran.r-project.org/web/packages/abe/")
9221 (synopsis "Augmented backward elimination")
9223 "This package performs augmented backward elimination and checks the
9224 stability of the obtained model. Augmented backward elimination combines
9225 significance or information based criteria with the change in estimate to
9226 either select the optimal model for prediction purposes or to serve as a tool
9227 to obtain a practically sound, highly interpretable model.")
9228 (license license:gpl2+)))
9230 (define-public r-abf2
9237 (uri (cran-uri "abf2" version))
9239 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9240 (build-system r-build-system)
9241 (home-page "https://cran.r-project.org/web/packages/abf2/")
9242 (synopsis "Load gap-free axon @code{r-abf2} files")
9244 "This package loads electrophysiology data from ABF2 files, as created by
9245 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9246 mode are currently supported.")
9247 (license license:artistic2.0)))
9249 (define-public r-abhgenotyper
9251 (name "r-abhgenotyper")
9256 (uri (cran-uri "ABHgenotypeR" version))
9258 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9259 (properties `((upstream-name . "ABHgenotypeR")))
9260 (build-system r-build-system)
9262 `(("r-ggplot2" ,r-ggplot2)
9263 ("r-reshape2" ,r-reshape2)))
9264 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9265 (synopsis "Visualize and manipulate ABH genotypes")
9267 "The @code{r-abhgenotyper} package provides simple imputation,
9268 error-correction and plotting capacities for genotype data. The package is
9269 supposed to serve as an intermediate but independent analysis tool between the
9270 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9271 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9272 genotypes as \"graphical genotypes\".")
9273 (license license:gpl3)))
9275 (define-public r-furrr
9282 (uri (cran-uri "furrr" version))
9285 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9286 (build-system r-build-system)
9288 `(("r-ellipsis" ,r-ellipsis)
9289 ("r-future" ,r-future)
9290 ("r-globals" ,r-globals)
9291 ("r-lifecycle" ,r-lifecycle)
9292 ("r-purrr" ,r-purrr)
9293 ("r-rlang" ,r-rlang)
9294 ("r-vctrs" ,r-vctrs)))
9295 (home-page "https://github.com/DavisVaughan/furrr")
9296 (synopsis "Apply mapping functions in parallel using futures")
9298 "This package provides implementations of the family of @code{map()}
9299 functions from the @code{purrr} package that can be resolved using any
9300 @code{future}-supported backend, e.g. parallel on the local machine or
9301 distributed on a compute cluster.")
9302 (license license:lgpl2.1+)))
9304 (define-public r-abjutils
9311 (uri (cran-uri "abjutils" version))
9313 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9314 (build-system r-build-system)
9316 `(("r-dplyr" ,r-dplyr)
9317 ("r-magrittr" ,r-magrittr)
9318 ("r-purrr" ,r-purrr)
9319 ("r-rlang" ,r-rlang)
9320 ("r-rstudioapi" ,r-rstudioapi)
9321 ("r-stringi" ,r-stringi)
9322 ("r-stringr" ,r-stringr)
9323 ("r-tidyr" ,r-tidyr)))
9324 (home-page "https://github.com/abjur/abjutils/")
9325 (synopsis "Collection of tools for jurimetrical analysis")
9327 "This package implements general purpose tools, such as functions for
9328 sampling and basic manipulation of Brazilian lawsuits identification number.
9329 It also implements functions for text cleaning, such as accentuation
9331 (license license:expat)))
9333 (define-public r-abnormality
9335 (name "r-abnormality")
9340 (uri (cran-uri "abnormality" version))
9342 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9343 (build-system r-build-system)
9345 `(("r-mass" ,r-mass)
9346 ("r-matrix" ,r-matrix)))
9347 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9348 (synopsis "Measure a subject's abnormality with respect to a reference population")
9350 "This package contains functions to implement the methodology and
9351 considerations laid out by Marks et al. in the article \"Measuring abnormality
9352 in high dimensional spaces: applications in biomechanical gait analysis\".
9353 Using high-dimensional datasets to measure a subject's overall level of
9354 abnormality as compared to a reference population is often needed in outcomes
9356 (license license:expat)))
9358 (define-public r-abodoutlier
9360 (name "r-abodoutlier")
9365 (uri (cran-uri "abodOutlier" version))
9367 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9368 (properties `((upstream-name . "abodOutlier")))
9369 (build-system r-build-system)
9371 `(("r-cluster" ,r-cluster)))
9372 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9373 (synopsis "Angle-based outlier detection")
9375 "This package performs angle-based outlier detection on a given data
9376 frame. It offers three methods to process data:
9378 @item full but slow implementation using all the data that has cubic
9380 @item a fully randomized method;
9381 @item a method using k-nearest neighbours.
9383 These algorithms are well suited for high dimensional data outlier
9385 (license license:expat)))
9387 (define-public r-abps
9394 (uri (cran-uri "ABPS" version))
9396 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9397 (properties `((upstream-name . "ABPS")))
9398 (build-system r-build-system)
9399 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9400 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9401 (synopsis "Abnormal blood profile score to detect blood doping")
9403 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9404 The ABPS is a part of the Athlete biological passport program of the World
9405 anti-doping agency, which combines several blood parameters into a single
9406 score in order to detect blood doping. The package also contains functions to
9407 calculate other scores used in anti-doping programs, such as the ratio of
9408 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9409 (license license:gpl2+)))
9411 (define-public r-parmigene
9413 (name "r-parmigene")
9418 (uri (cran-uri "parmigene" version))
9421 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9422 (build-system r-build-system)
9423 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9424 (synopsis "Mutual information estimation for gene network reconstruction")
9426 "This package provides a parallel estimation of the mutual information
9427 based on entropy estimates from k-nearest neighbors distances and algorithms
9428 for the reconstruction of gene regulatory networks.")
9429 (license license:agpl3+)))
9431 (define-public r-pscl
9438 (uri (cran-uri "pscl" version))
9440 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9441 (build-system r-build-system)
9443 `(("r-mass" ,r-mass)))
9444 (home-page "https://github.com/atahk/pscl/")
9445 (synopsis "Political science computational laboratory")
9447 "The @code{pscl} is an R package providing classes and methods for:
9449 @item Bayesian analysis of roll call data (item-response models);
9450 @item elementary Bayesian statistics;
9451 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9453 @item utility functions.
9455 (license license:gpl2)))
9457 (define-public r-accelmissing
9459 (name "r-accelmissing")
9464 (uri (cran-uri "accelmissing" version))
9466 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9467 (build-system r-build-system)
9469 `(("r-mice" ,r-mice)
9470 ("r-pscl" ,r-pscl)))
9471 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9472 (synopsis "Missing value imputation for accelerometer data")
9474 "This package provides a statistical method to impute the missing values in
9475 accelerometer data. The methodology includes both parametric and
9476 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9477 model. It also provides multiple functions to preprocess the accelerometer data
9478 previous to the missing data imputation. These include detecting the wearing
9479 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9480 (license license:gpl2+)))
9482 (define-public r-mhsmm
9489 (uri (cran-uri "mhsmm" version))
9491 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9492 (build-system r-build-system)
9493 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9494 (home-page "https://github.com/jaredo/mhsmm/")
9495 (synopsis "Inference for hidden Markov and semi-Markov models")
9497 "The @code{r-mhsmm} package implements estimation and prediction methods for
9498 hidden Markov and semi-Markov models for multiple observation sequences. Such
9499 techniques are of interest when observed data is thought to be dependent on some
9500 unobserved (or hidden) state. Also, this package is suitable for equidistant
9501 time series data, with multivariate and/or missing data. Allows user defined
9502 emission distributions.")
9503 (license license:gpl2+)))
9505 (define-public r-nleqslv
9512 (uri (cran-uri "nleqslv" version))
9514 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9515 (build-system r-build-system)
9516 (native-inputs `(("gfortran" ,gfortran)))
9517 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9518 (synopsis "Solve systems of nonlinear equations")
9520 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9521 Broyden or a Newton method with a choice of global strategies such as line
9522 search and trust region. There are options for using a numerical or user
9523 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9524 singular or ill-conditioned Jacobian.")
9525 (license license:gpl2+)))
9527 (define-public r-physicalactivity
9529 (name "r-physicalactivity")
9534 (uri (cran-uri "PhysicalActivity" version))
9536 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9538 `((upstream-name . "PhysicalActivity")))
9539 (build-system r-build-system)
9540 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9541 (synopsis "Procesing accelerometer data for physical activity measurement")
9543 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9544 for classification of monitor wear and nonwear time intervals in accelerometer
9545 data collected to assess physical activity. The package also contains functions
9546 for making plots of accelerometer data and obtaining the summary of various
9547 information including daily monitor wear time and the mean monitor wear time
9548 during valid days. The revised package version 0.2-1 improved the functions
9549 regarding speed, robustness and add better support for time zones and daylight
9550 saving. In addition, several functions were added:
9552 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9553 @item the @code{markPAI} can categorize physical activity intensity level based
9554 on user-defined cut-points of accelerometer counts.
9556 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9557 @code{queryActigraph} functions.")
9558 (license license:gpl3+)))
9560 (define-public r-acc
9567 (uri (cran-uri "acc" version))
9569 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9570 (build-system r-build-system)
9572 `(("r-circlize" ,r-circlize)
9574 ("r-ggplot2" ,r-ggplot2)
9575 ("r-iterators" ,r-iterators)
9576 ("r-mhsmm" ,r-mhsmm)
9577 ("r-nleqslv" ,r-nleqslv)
9578 ("r-physicalactivity" ,r-physicalactivity)
9580 ("r-r-utils" ,r-r-utils)
9582 ("r-rcpparmadillo" ,r-rcpparmadillo)
9583 ("r-rsqlite" ,r-rsqlite)
9585 (home-page "https://cran.r-project.org/web/packages/acc/")
9586 (synopsis "Exploring accelerometer data")
9588 "This package processes accelerometer data from uni-axial and tri-axial devices
9589 and generates data summaries. Also, includes functions to plot, analyze, and
9590 simulate accelerometer data.")
9591 (license license:gpl2+)))
9593 (define-public r-rbenchmark
9595 (name "r-rbenchmark")
9600 (uri (cran-uri "rbenchmark" version))
9602 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9603 (build-system r-build-system)
9604 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9605 (synopsis "Benchmarking routine for R")
9607 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9608 and is intended to facilitate benchmarking of arbitrary R code. The library
9609 consists of just one function, benchmark, which is a simple wrapper around
9610 system.time. Given a specification of the benchmarking process (counts of
9611 replications, evaluation environment) and an arbitrary number of expressions,
9612 benchmark evaluates each of the expressions in the specified environment,
9613 replicating the evaluation as many times as specified, and returning the results
9614 conveniently wrapped into a data frame.")
9615 (license license:gpl2+)))
9617 (define-public r-mitools
9624 (uri (cran-uri "mitools" version))
9627 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9628 (build-system r-build-system)
9629 (propagated-inputs `(("r-dbi" ,r-dbi)))
9630 (home-page "https://cran.r-project.org/web/packages/mitools/")
9631 (synopsis "Tools for multiple imputation of missing data")
9633 "This package provides tools to perform analyses and combine results from
9634 multiple-imputation datasets.")
9635 (license license:gpl2)))
9637 (define-public r-mixsqp
9643 (uri (cran-uri "mixsqp" version))
9646 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9647 (properties `((upstream-name . "mixsqp")))
9648 (build-system r-build-system)
9650 `(("r-irlba" ,r-irlba)
9652 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9654 `(("r-knitr" ,r-knitr)))
9655 (home-page "https://github.com/stephenslab/mixsqp")
9657 "Sequential quadratic programming for maximum-likelihood estimation")
9659 "This package provides an optimization method based on sequential
9660 quadratic programming for maximum likelihood estimation of the mixture
9661 proportions in a finite mixture model where the component densities are
9662 known. The algorithm is expected to obtain solutions that are at least
9663 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9664 are expected to arrive at solutions more quickly when the number of
9665 samples is large and the number of mixture components is not too large.")
9666 (license license:expat)))
9668 (define-public r-magick
9675 (uri (cran-uri "magick" version))
9678 "16svy84dq25g69axqgympsrh8dzssa1w3zz08zc8m6nprr3jqwqf"))))
9679 (build-system r-build-system)
9681 `(("imagemagick" ,imagemagick)
9684 `(("r-curl" ,r-curl)
9685 ("r-magrittr" ,r-magrittr)
9686 ("r-rcpp" ,r-rcpp)))
9688 `(("pkg-config" ,pkg-config)
9689 ("r-knitr" ,r-knitr)))
9690 (home-page "https://github.com/ropensci/magick")
9691 (synopsis "Advanced graphics and image-processing in R")
9693 "This package provides bindings to ImageMagick, a comprehensive image
9694 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9695 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9696 operations are vectorized via the Magick++ STL meaning they operate either on
9697 a single frame or a series of frames for working with layers, collages, or
9698 animation. In RStudio, images are automatically previewed when printed to the
9699 console, resulting in an interactive editing environment.")
9700 (license license:expat)))
9702 (define-public r-survey
9709 (uri (cran-uri "survey" version))
9712 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9713 (build-system r-build-system)
9715 `(("r-lattice" ,r-lattice)
9716 ("r-matrix" ,r-matrix)
9717 ("r-minqa" ,r-minqa)
9718 ("r-mitools" ,r-mitools)
9719 ("r-numderiv" ,r-numderiv)
9720 ("r-survival" ,r-survival)))
9721 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9722 (synopsis "Analysis of complex survey samples")
9724 "This package provides tools for the analysis of complex survey samples.
9725 The provided features include: summary statistics, two-sample tests, rank
9726 tests, generalised linear models, cumulative link models, Cox models,
9727 loglinear models, and general maximum pseudolikelihood estimation for
9728 multistage stratified, cluster-sampled, unequally weighted survey samples;
9729 variances by Taylor series linearisation or replicate weights;
9730 post-stratification, calibration, and raking; two-phase subsampling designs;
9731 graphics; PPS sampling without replacement; principal components, and factor
9733 ;; Either version of the GPL.
9734 (license (list license:gpl2 license:gpl3))))
9736 (define-public r-gee
9743 (uri (cran-uri "gee" version))
9746 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9747 (properties `((upstream-name . "gee")))
9748 (build-system r-build-system)
9750 `(("gfortran" ,gfortran)))
9751 (home-page "https://cran.r-project.org/web/packages/gee/")
9752 (synopsis "Generalized estimation equation solver")
9754 "This package provides a solver for generalized estimation equations.")
9755 (license license:gpl2)))
9757 (define-public r-tab
9764 (uri (cran-uri "tab" version))
9767 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9768 (properties `((upstream-name . "tab")))
9769 (build-system r-build-system)
9771 `(("r-dplyr" ,r-dplyr)
9773 ("r-knitr" ,r-knitr)
9775 ("r-survey" ,r-survey)
9776 ("r-survival" ,r-survival)
9777 ("r-xtable" ,r-xtable)))
9778 (home-page "https://cran.r-project.org/web/packages/tab/")
9779 (synopsis "Create summary tables for statistical reports")
9781 "This package contains functions for creating various types of summary
9782 tables, e.g. comparing characteristics across levels of a categorical variable
9783 and summarizing fitted generalized linear models, generalized estimating
9784 equations, and Cox proportional hazards models. Functions are available to
9785 handle data from simple random samples as well as complex surveys.")
9786 (license license:gpl3+)))
9788 (define-public r-dvmisc
9795 (uri (cran-uri "dvmisc" version))
9797 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9798 (build-system r-build-system)
9800 `(("r-cubature" ,r-cubature)
9801 ("r-data-table" ,r-data-table)
9802 ("r-dplyr" ,r-dplyr)
9803 ("r-ggplot2" ,r-ggplot2)
9805 ("r-mvtnorm" ,r-mvtnorm)
9806 ("r-pracma" ,r-pracma)
9807 ("r-rbenchmark" ,r-rbenchmark)
9809 ("r-survey" ,r-survey)
9811 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9812 (synopsis "Faster computation of common statistics and miscellaneous functions")
9814 "This package implements faster versions of base R functions (e.g. mean, standard
9815 deviation, covariance, weighted mean), mostly written in C++, along with
9816 miscellaneous functions for various purposes (e.g. create the histogram with
9817 fitted probability density function or probability mass function curve, create
9818 the body mass index groups, assess the linearity assumption in logistic
9820 (license license:gpl2)))
9822 (define-public r-accelerometry
9824 (name "r-accelerometry")
9829 (uri (cran-uri "accelerometry" version))
9831 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9832 (build-system r-build-system)
9834 `(("r-dvmisc" ,r-dvmisc)
9835 ("r-rcpp" ,r-rcpp)))
9836 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9837 (synopsis "Functions for processing accelerometer data")
9839 "This package provides a collection of functions that perform operations on
9840 time-series accelerometer data, such as identify the non-wear time, flag minutes
9841 that are part of an activity bout, and find the maximum 10-minute average count
9842 value. The functions are generally very flexible, allowing for a variety of
9843 algorithms to be implemented.")
9844 (license license:gpl3)))
9846 (define-public r-absim
9853 (uri (cran-uri "AbSim" version))
9855 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9856 (properties `((upstream-name . "AbSim")))
9857 (build-system r-build-system)
9860 ("r-powerlaw" ,r-powerlaw)))
9861 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9862 (synopsis "Time resolved simulations of antibody repertoires")
9864 "This package provides simulation methods for the evolution of antibody repertoires.
9865 The heavy and light chain variable region of both human and C57BL/6 mice can
9866 be simulated in a time-dependent fashion. Both single lineages using one set of
9867 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9868 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9869 Upon completion, the main loop of the algorithm begins, with each iteration
9870 representing one simulated time step. Various mutation events are possible at
9871 each time step, contributing to a diverse final repertoire.")
9872 (license license:gpl2)))
9874 (define-public r-quic
9881 (uri (cran-uri "QUIC" version))
9883 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9884 (properties `((upstream-name . "QUIC")))
9885 (build-system r-build-system)
9886 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9887 (synopsis "Regularized sparse inverse covariance matrix estimation")
9889 "This package implements the regularized Gaussian maximum likelihood
9890 estimation of the inverse of a covariance matrix. It uses Newton's method and
9891 coordinate descent to solve the regularized inverse covariance matrix
9892 estimation problem.")
9893 ;; The project home page states that the release is under GPLv3 or later.
9894 ;; The CRAN page only says GPL-3.
9895 (license license:gpl3+)))
9897 (define-public r-abundant
9904 (uri (cran-uri "abundant" version))
9906 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9907 (build-system r-build-system)
9909 `(("r-quic" ,r-quic)))
9910 (home-page "https://cran.r-project.org/web/packages/abundant/")
9911 (synopsis "Abundant regression and high-dimensional principal fitted components")
9913 "This package provides tools to fit and predict with the high-dimensional
9914 principal fitted components model. This model is described by Cook, Forzani,
9915 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9916 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9917 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9918 (license license:gpl2+)))
9920 (define-public r-ac3net
9927 (uri (cran-uri "Ac3net" version))
9929 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9930 (properties `((upstream-name . "Ac3net")))
9931 (build-system r-build-system)
9933 `(("r-data-table" ,r-data-table)))
9934 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9935 (synopsis "Inferring directional conservative causal core gene networks")
9936 (description "This package infers directional Conservative causal core
9937 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9938 directional network.")
9939 (license license:gpl3+)))
9941 (define-public r-aca
9948 (uri (cran-uri "ACA" version))
9950 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9951 (properties `((upstream-name . "ACA")))
9952 (build-system r-build-system)
9953 (home-page "https://cran.r-project.org/web/packages/ACA/")
9954 (synopsis "Abrupt change-point or aberration detection in point series")
9956 "This package offers an interactive function for the detection of breakpoints in
9958 ;; Any version of the GPL
9959 (license (list license:gpl2+ license:gpl3+))))
9961 (define-public r-acceptancesampling
9963 (name "r-acceptancesampling")
9968 (uri (cran-uri "AcceptanceSampling" version))
9970 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9972 `((upstream-name . "AcceptanceSampling")))
9973 (build-system r-build-system)
9974 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9975 (synopsis "Creation and evaluation of acceptance sampling plans")
9977 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9978 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9979 in quality control and improvement. International standards of acceptance
9980 sampling provide sampling plans for specific circumstances. The aim of this
9981 package is to provide an easy-to-use interface to visualize single, double or
9982 multiple sampling plans. In addition, methods have been provided to enable the
9983 user to assess sampling plans against pre-specified levels of performance, as
9984 measured by the probability of acceptance for a given level of quality in the
9986 (license license:gpl3+)))
9988 (define-public r-acclma
9995 (uri (cran-uri "ACCLMA" version))
9997 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
9998 (properties `((upstream-name . "ACCLMA")))
9999 (build-system r-build-system)
10000 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10001 (synopsis "ACC & LMA graph plotting")
10003 "This package contains a function that imports data from a @acronym{CSV,
10004 Comma-Separated Values} file, or uses manually entered data from the format (x,
10005 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10006 Curve} vs @acronym{LOI, Line of Independence} graph and
10007 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10008 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10009 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10010 string) was passed, a manual data entry window is opened. The header parameter
10011 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10012 a header row or not. The dataset should contain only one independent variable
10013 (x) and one dependent variable (y) and can contain a weight for each
10015 (license license:gpl2)))
10017 (define-public r-aspi
10024 (uri (cran-uri "aspi" version))
10026 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10027 (build-system r-build-system)
10029 "https://cran.r-project.org/web/packages/aspi/")
10031 "Analysis of symmetry of parasitic infections")
10033 "This package provides tools for the analysis and visualization of bilateral
10034 asymmetry in parasitic infections.")
10035 (license license:gpl3+)))
10037 (define-public r-sandwich
10039 (name "r-sandwich")
10044 (uri (cran-uri "sandwich" version))
10047 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10048 (build-system r-build-system)
10050 `(("r-zoo" ,r-zoo)))
10051 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10052 (synopsis "Robust Covariance Matrix Estimators")
10054 "This package provides model-robust standard error estimators for
10055 cross-sectional, time series, clustered, panel, and longitudinal data.")
10056 ;; Either version of the license.
10057 (license (list license:gpl2 license:gpl3))))
10059 (define-public r-th-data
10066 (uri (cran-uri "TH.data" version))
10069 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10070 (properties `((upstream-name . "TH.data")))
10071 (build-system r-build-system)
10073 `(("r-mass" ,r-mass)
10074 ("r-survival" ,r-survival)))
10075 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10076 (synopsis "Shared data sets")
10078 "This package contains supporting data sets that are used in other
10079 packages maintained by Torsten Hothorn.")
10080 (license license:gpl3)))
10082 (define-public r-multcomp
10084 (name "r-multcomp")
10089 (uri (cran-uri "multcomp" version))
10092 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10093 (build-system r-build-system)
10095 `(("r-codetools" ,r-codetools)
10096 ("r-mvtnorm" ,r-mvtnorm)
10097 ("r-sandwich" ,r-sandwich)
10098 ("r-survival" ,r-survival)
10099 ("r-th-data" ,r-th-data)))
10100 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10101 (synopsis "Simultaneous inference in general parametric models")
10103 "Simultaneous tests and confidence intervals for general linear
10104 hypotheses in parametric models, including linear, generalized linear, linear
10105 mixed effects, and survival models. The package includes demos reproducing
10106 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10107 Hothorn, Westfall, 2010, CRC Press).")
10108 (license license:gpl2)))
10110 (define-public r-emmeans
10113 (version "1.5.5-1")
10117 (uri (cran-uri "emmeans" version))
10120 "0l5dd71ihhs7zy6ygniy07iisgy7a1ai1w41hqf84swb0j3cl6iz"))))
10121 (build-system r-build-system)
10123 `(("r-estimability" ,r-estimability)
10124 ("r-mvtnorm" ,r-mvtnorm)
10125 ("r-numderiv" ,r-numderiv)
10127 ("r-xtable" ,r-xtable)))
10129 `(("r-knitr" ,r-knitr)))
10130 (home-page "https://github.com/rvlenth/emmeans")
10131 (synopsis "Estimated marginal means, aka least-squares means")
10133 "This package provides tools to obtain @dfn{estimated marginal
10134 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10135 be used to compute contrasts or linear functions of EMMs, trends, and
10136 comparisons of slopes.")
10137 ;; Either version of the license.
10138 (license (list license:gpl2 license:gpl3))))
10140 (define-public r-pwr
10147 (uri (cran-uri "pwr" version))
10150 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10151 (build-system r-build-system)
10153 `(("r-knitr" ,r-knitr)))
10154 (home-page "https://github.com/heliosdrm/pwr")
10155 (synopsis "Basic functions for power analysis")
10157 "This package provides power analysis functions along the lines of
10159 (license license:gpl3+)))
10161 (define-public r-libcoin
10168 (uri (cran-uri "libcoin" version))
10170 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10171 (build-system r-build-system)
10172 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10173 (home-page "https://cran.r-project.org/web/packages/libcoin")
10174 (synopsis "Linear test statistics for permutation inference")
10176 "This package provides basic infrastructure for linear test statistics
10177 and permutation inference in the framework of Strasser and Weber (1999).")
10178 (license license:gpl2)))
10180 (define-public r-coin
10187 (uri (cran-uri "coin" version))
10190 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10191 (build-system r-build-system)
10193 `(("r-libcoin" ,r-libcoin)
10194 ("r-matrixstats" ,r-matrixstats)
10195 ("r-modeltools" ,r-modeltools)
10196 ("r-multcomp" ,r-multcomp)
10197 ("r-mvtnorm" ,r-mvtnorm)
10198 ("r-survival" ,r-survival)))
10199 (home-page "http://coin.r-forge.r-project.org")
10200 (synopsis "Conditional inference procedures in a permutation test framework")
10202 "This package provides conditional inference procedures for the general
10203 independence problem including two-sample, K-sample (non-parametric ANOVA),
10204 correlation, censored, ordered and multivariate problems.")
10205 (license license:gpl2)))
10207 (define-public r-bayesplot
10209 (name "r-bayesplot")
10214 (uri (cran-uri "bayesplot" version))
10217 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10218 (build-system r-build-system)
10220 `(("pandoc" ,pandoc)
10221 ("pandoc-citeproc" ,pandoc-citeproc)))
10223 `(("r-knitr" ,r-knitr)))
10225 `(("r-dplyr" ,r-dplyr)
10226 ("r-ggplot2" ,r-ggplot2)
10227 ("r-ggridges" ,r-ggridges)
10229 ("r-reshape2" ,r-reshape2)
10230 ("r-rlang" ,r-rlang)
10231 ("r-tibble" ,r-tibble)
10232 ("r-tidyselect" ,r-tidyselect)))
10233 (home-page "https://mc-stan.org/bayesplot")
10234 (synopsis "Plotting for Bayesian models")
10236 "This package provides plotting functions for posterior analysis, model
10237 checking, and MCMC diagnostics. The package is designed not only to provide
10238 convenient functionality for users, but also a common set of functions that
10239 can be easily used by developers working on a variety of R packages for
10240 Bayesian modeling.")
10241 (license license:gpl3+)))
10243 (define-public r-tmb
10250 (uri (cran-uri "TMB" version))
10253 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10254 (properties `((upstream-name . "TMB")))
10255 (build-system r-build-system)
10257 `(("r-matrix" ,r-matrix)
10258 ("r-rcppeigen" ,r-rcppeigen)))
10259 (home-page "http://tmb-project.org")
10260 (synopsis "Template model builder: a general random effect tool")
10262 "With this tool, a user should be able to quickly implement complex
10263 random effect models through simple C++ templates. The package combines
10264 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10265 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10266 from R) to obtain an efficient implementation of the applied Laplace
10267 approximation with exact derivatives. Key features are: Automatic sparseness
10268 detection, parallelism through BLAS and parallel user templates.")
10269 (license license:gpl2)))
10271 (define-public r-sjstats
10278 (uri (cran-uri "sjstats" version))
10280 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10281 (build-system r-build-system)
10283 `(("r-bayestestr" ,r-bayestestr)
10284 ("r-broom" ,r-broom)
10285 ("r-dplyr" ,r-dplyr)
10286 ("r-effectsize" ,r-effectsize)
10287 ("r-emmeans" ,r-emmeans)
10288 ("r-insight" ,r-insight)
10290 ("r-magrittr" ,r-magrittr)
10292 ("r-modelr" ,r-modelr)
10293 ("r-parameters" ,r-parameters)
10294 ("r-performance" ,r-performance)
10295 ("r-purrr" ,r-purrr)
10296 ("r-rlang" ,r-rlang)
10297 ("r-sjlabelled" ,r-sjlabelled)
10298 ("r-sjmisc" ,r-sjmisc)
10299 ("r-tidyr" ,r-tidyr)))
10300 (home-page "https://github.com/strengejacke/sjstats")
10301 (synopsis "Functions for common statistical computations")
10303 "This package provides a collection of convenient functions for common
10304 statistical computations, which are not directly provided by R's @code{base}
10305 or @code{stats} packages. This package aims at providing, first, shortcuts
10306 for statistical measures, which otherwise could only be calculated with
10307 additional effort. Second, these shortcut functions are generic, and can be
10308 applied not only to vectors, but also to other objects as well. The focus of
10309 most functions lies on summary statistics or fit measures for regression
10310 models, including generalized linear models, mixed effects models and Bayesian
10312 (license license:gpl3)))
10314 (define-public r-glmmtmb
10317 (version "1.0.2.1")
10321 (uri (cran-uri "glmmTMB" version))
10324 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10325 (properties `((upstream-name . "glmmTMB")))
10326 (build-system r-build-system)
10328 `(("r-lme4" ,r-lme4)
10329 ("r-matrix" ,r-matrix)
10331 ("r-rcppeigen" ,r-rcppeigen)
10334 `(("r-knitr" ,r-knitr))) ; for vignettes
10335 (home-page "https://github.com/glmmTMB")
10336 (synopsis "Generalized linear mixed models")
10338 "Fit linear and generalized linear mixed models with various extensions,
10339 including zero-inflation. The models are fitted using maximum likelihood
10340 estimation via the Template Model Builder. Random effects are assumed to be
10341 Gaussian on the scale of the linear predictor and are integrated out using the
10342 Laplace approximation. Gradients are calculated using automatic
10344 (license license:agpl3+)))
10346 (define-public r-bayestestr
10348 (name "r-bayestestr")
10353 (uri (cran-uri "bayestestR" version))
10356 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10357 (properties `((upstream-name . "bayestestR")))
10358 (build-system r-build-system)
10360 `(("r-insight" ,r-insight)))
10362 `(("r-knitr" ,r-knitr)))
10363 (home-page "https://github.com/easystats/bayestestR")
10364 (synopsis "Describe Bayesian models and posterior distributions")
10366 "This package provides utilities to understand and describe posterior
10367 distributions and Bayesian models. It includes point-estimates such as
10368 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10369 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10370 ROPE percentage and pd).")
10371 (license license:gpl3)))
10373 (define-public r-performance
10375 (name "r-performance")
10380 (uri (cran-uri "performance" version))
10383 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10384 (build-system r-build-system)
10386 `(("r-bayestestr" ,r-bayestestr)
10387 ("r-insight" ,r-insight)))
10388 (home-page "https://easystats.github.io/performance/")
10389 (synopsis "Assessment of regression models performance")
10391 "This package provides utilities for computing measures to assess model
10392 quality, which are not directly provided by R's @code{base} or @code{stats}
10393 packages. These include e.g. measures like r-squared, intraclass correlation
10394 coefficient, root mean squared error or functions to check models for
10395 overdispersion, singularity or zero-inflation and more. Functions apply to a
10396 large variety of regression models, including generalized linear models, mixed
10397 effects models and Bayesian models.")
10398 (license license:gpl3)))
10400 (define-public r-ggeffects
10402 (name "r-ggeffects")
10407 (uri (cran-uri "ggeffects" version))
10410 "0qh8x8yi8gkb5x7zfxmb1c689k7bhc1f5947yymny34j7xdsb9s8"))))
10411 (build-system r-build-system)
10413 `(("r-insight" ,r-insight)
10415 ("r-sjlabelled" ,r-sjlabelled)))
10417 `(("r-knitr" ,r-knitr)))
10418 (home-page "https://github.com/strengejacke/ggeffects")
10419 (synopsis "Create tidy data frames of marginal effects for ggplot")
10421 "This package provides tools to compute marginal effects from statistical
10422 models and return the result as tidy data frames. These data frames are ready
10423 to use with the @code{ggplot2} package. Marginal effects can be calculated
10424 for many different models. Interaction terms, splines and polynomial terms
10425 are also supported. The two main functions are @code{ggpredict()} and
10426 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10427 results using @code{ggplot2}.")
10428 (license license:gpl3)))
10430 (define-public r-effectsize
10432 (name "r-effectsize")
10433 (version "0.4.4-1")
10437 (uri (cran-uri "effectsize" version))
10440 "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb"))))
10441 (properties `((upstream-name . "effectsize")))
10442 (build-system r-build-system)
10444 `(("r-bayestestr" ,r-bayestestr)
10445 ("r-insight" ,r-insight)
10446 ("r-parameters" ,r-parameters)))
10448 `(("r-knitr" ,r-knitr)))
10449 (home-page "https://github.com/easystats/effectsize")
10450 (synopsis "Indices of effect size and standardized parameters")
10452 "This package provides utilities to work with indices of effect size and
10453 standardized parameters for a wide variety of models, allowing computation and
10454 conversion of indices such as Cohen's d, r, odds, etc.")
10455 (license license:gpl3)))
10457 (define-public r-sjplot
10464 (uri (cran-uri "sjPlot" version))
10466 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10467 (properties `((upstream-name . "sjPlot")))
10468 (build-system r-build-system)
10470 `(("r-bayestestr" ,r-bayestestr)
10471 ("r-dplyr" ,r-dplyr)
10472 ("r-effectsize" ,r-effectsize)
10473 ("r-ggeffects" ,r-ggeffects)
10474 ("r-ggplot2" ,r-ggplot2)
10475 ("r-insight" ,r-insight)
10476 ("r-knitr" ,r-knitr)
10478 ("r-parameters" ,r-parameters)
10479 ("r-performance" ,r-performance)
10480 ("r-purrr" ,r-purrr)
10481 ("r-rlang" ,r-rlang)
10482 ("r-scales" ,r-scales)
10483 ("r-sjlabelled" ,r-sjlabelled)
10484 ("r-sjmisc" ,r-sjmisc)
10485 ("r-sjstats" ,r-sjstats)
10486 ("r-tidyr" ,r-tidyr)))
10488 `(("r-knitr" ,r-knitr)))
10489 (home-page "https://strengejacke.github.io/sjPlot/")
10490 (synopsis "Data visualization for statistics in social science")
10492 "This package represents a collection of plotting and table output
10493 functions for data visualization. Results of various statistical
10494 analyses (that are commonly used in social sciences) can be visualized using
10495 this package, including simple and cross tabulated frequencies, histograms,
10496 box plots, (generalized) linear models, mixed effects models, principal
10497 component analysis and correlation matrices, cluster analyses, scatter plots,
10498 stacked scales, effects plots of regression models (including interaction
10499 terms) and much more. This package supports labelled data.")
10500 (license license:gpl3)))
10502 (define-public r-ini
10509 (uri (cran-uri "ini" version))
10512 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10513 (build-system r-build-system)
10514 (home-page "https://github.com/dvdscripter/ini")
10515 (synopsis "Read and write configuration files")
10517 "This package provides tools to parse simple @code{.ini} configuration
10518 files to an structured list. Users can manipulate this resulting list with
10519 @code{lapply()} functions. This same structured list can be used to write
10520 back to file after modifications.")
10521 (license license:gpl3)))
10523 (define-public r-gitcreds
10525 (name "r-gitcreds")
10530 (uri (cran-uri "gitcreds" version))
10533 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10534 (properties `((upstream-name . "gitcreds")))
10535 (build-system r-build-system)
10536 (inputs `(("git" ,git-minimal)))
10537 (native-inputs `(("r-knitr" ,r-knitr)))
10538 (home-page "https://github.com/r-lib/gitcreds")
10539 (synopsis "Query git credentials from R")
10541 "Query, set, and delete credentials from the git credential store.
10542 Manage GitHub tokens and other git credentials. This package is to be used by
10543 other packages that need to authenticate to GitHub and/or other git
10545 (license license:expat)))
10547 (define-public r-gh
10554 (uri (cran-uri "gh" version))
10557 "16xa1qb1r28f8yc6ybjrxiq2zigxj886dp9k29jpsn5091xbzkq0"))))
10558 (build-system r-build-system)
10561 ("r-gitcreds" ,r-gitcreds)
10564 ("r-jsonlite" ,r-jsonlite)))
10566 `(("r-knitr" ,r-knitr)))
10567 (home-page "https://github.com/r-lib/gh#readme")
10568 (synopsis "Access the GitHub API via R")
10570 "This package provides a minimal R client to access the GitHub API.")
10571 (license license:expat)))
10573 (define-public r-fs
10580 (uri (cran-uri "fs" version))
10583 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10584 (build-system r-build-system)
10586 `(("r-knitr" ,r-knitr)))
10587 (home-page "https://fs.r-lib.org")
10588 (synopsis "Cross-platform file system operations based on libuv")
10590 "This package provides a cross-platform interface to file system
10591 operations, built on top of the libuv C library.")
10592 (license license:gpl3)))
10594 (define-public r-clisymbols
10596 (name "r-clisymbols")
10601 (uri (cran-uri "clisymbols" version))
10604 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10605 (build-system r-build-system)
10606 (home-page "https://github.com/gaborcsardi/clisymbols")
10607 (synopsis "Unicode symbols at the R prompt")
10609 "This package provides a small subset of Unicode symbols, that are useful
10610 when building command line applications. They fall back to alternatives on
10611 terminals that do not support Unicode.")
10612 (license license:expat)))
10614 (define-public r-credentials
10616 (name "r-credentials")
10621 (uri (cran-uri "credentials" version))
10624 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10625 (properties `((upstream-name . "credentials")))
10626 (build-system r-build-system)
10629 (modify-phases %standard-phases
10630 (add-after 'unpack 'setenv-HOME
10632 ;; This is necessary because git looks for $HOME/.gitconfig
10633 (setenv "HOME" "/tmp")
10636 `(("git" ,git-minimal)))
10638 `(("r-askpass" ,r-askpass)
10640 ("r-jsonlite" ,r-jsonlite)
10641 ("r-openssl" ,r-openssl)
10644 `(("r-knitr" ,r-knitr)))
10645 (home-page "https://docs.ropensci.org/credentials/")
10646 (synopsis "Tools for managing SSH and Git credentials")
10648 "This package assists you in setting up and retrieving of HTTPS and SSH
10649 credentials for use with git and other services. For HTTPS remotes the
10650 package interfaces the @command{git-credential} utility which @command{git}
10651 uses to store HTTP usernames and passwords. For SSH remotes this package
10652 provides convenient functions to find or generate appropriate SSH keys. The
10653 package both helps the user to setup a local git installation, and also
10654 provides a back-end for git/ssh client libraries to authenticate with existing
10655 user credentials.")
10656 (license license:expat)))
10658 (define-public r-gert
10665 (uri (cran-uri "gert" version))
10668 "1fh72p92wj83yv1ch77jms6k1gjqfji8cmgw23vpxd0p8l9jj4h7"))))
10669 (properties `((upstream-name . "gert")))
10670 (build-system r-build-system)
10672 `(("libgit2" ,libgit2)
10675 `(("r-askpass" ,r-askpass)
10676 ("r-credentials" ,r-credentials)
10677 ("r-openssl" ,r-openssl)
10678 ("r-rstudioapi" ,r-rstudioapi)
10682 `(("pkg-config" ,pkg-config)
10683 ("r-knitr" ,r-knitr)))
10684 (home-page "https://docs.ropensci.org/gert/")
10685 (synopsis "Simple Git client for R")
10687 "This package provides a simple git client for R based on libgit2 with
10688 support for SSH and HTTPS remotes. All functions in gert use basic R data
10689 types (such as vectors and data-frames) for their arguments and return values.
10690 User credentials are shared with command line git through the
10691 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10692 (license license:expat)))
10694 (define-public r-usethis
10701 (uri (cran-uri "usethis" version))
10704 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10705 (build-system r-build-system)
10708 ("r-clipr" ,r-clipr)
10709 ("r-crayon" ,r-crayon)
10716 ("r-jsonlite" ,r-jsonlite)
10717 ("r-lifecycle" ,r-lifecycle)
10718 ("r-purrr" ,r-purrr)
10719 ("r-rappdirs" ,r-rappdirs)
10720 ("r-rlang" ,r-rlang)
10721 ("r-rprojroot" ,r-rprojroot)
10722 ("r-rstudioapi" ,r-rstudioapi)
10723 ("r-whisker" ,r-whisker)
10724 ("r-withr" ,r-withr)
10725 ("r-yaml" ,r-yaml)))
10726 (home-page "https://github.com/r-lib/usethis")
10727 (synopsis "Automate R package and project setup")
10729 "This package helps you to automate R package and project setup tasks
10730 that are otherwise performed manually. This includes setting up unit testing,
10731 test coverage, continuous integration, Git, GitHub integration, licenses,
10732 Rcpp, RStudio projects, and more.")
10733 (license license:gpl3)))
10735 (define-public r-sessioninfo
10737 (name "r-sessioninfo")
10742 (uri (cran-uri "sessioninfo" version))
10745 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10746 (build-system r-build-system)
10749 ("r-withr" ,r-withr)))
10750 (home-page "https://github.com/r-lib/sessioninfo#readme")
10751 (synopsis "R session information")
10753 "This package provides tools to query and print information about the
10754 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10755 more information about packages, and where they were installed from.")
10756 (license license:gpl2)))
10758 (define-public r-remotes
10765 (uri (cran-uri "remotes" version))
10768 "0f35648bdxhvplcfj80r4hfj5w21f1s01kcz6b29d098c1mnfzb7"))))
10769 (build-system r-build-system)
10771 `(("r-knitr" ,r-knitr)))
10772 (home-page "https://github.com/r-lib/remotes#readme")
10773 (synopsis "R package installation from remote repositories")
10775 "Download and install R packages stored in GitHub, BitBucket, or plain
10776 subversion or git repositories. This package is a lightweight replacement of
10777 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10778 the code was copied over from @code{devtools}.")
10779 (license license:gpl2+)))
10781 (define-public r-xopen
10788 (uri (cran-uri "xopen" version))
10791 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10792 (build-system r-build-system)
10794 `(("r-processx" ,r-processx)))
10795 (home-page "https://github.com/r-lib/xopen#readme")
10796 (synopsis "Open system files, URLs, anything")
10798 "This package provides a cross-platform solution to open files,
10799 directories or URLs with their associated programs.")
10800 (license license:expat)))
10802 (define-public r-rcmdcheck
10804 (name "r-rcmdcheck")
10809 (uri (cran-uri "rcmdcheck" version))
10812 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10813 (build-system r-build-system)
10815 `(("r-callr" ,r-callr)
10817 ("r-crayon" ,r-crayon)
10819 ("r-digest" ,r-digest)
10820 ("r-pkgbuild" ,r-pkgbuild)
10821 ("r-prettyunits" ,r-prettyunits)
10823 ("r-rprojroot" ,r-rprojroot)
10824 ("r-sessioninfo" ,r-sessioninfo)
10825 ("r-withr" ,r-withr)
10826 ("r-xopen" ,r-xopen)))
10827 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10828 (synopsis "Run R CMD check from R and capture results")
10830 "Run @code{R CMD check} from R programmatically, and capture the results
10831 of the individual checks.")
10832 (license license:expat)))
10834 (define-public r-rapportools
10836 (name "r-rapportools")
10841 (uri (cran-uri "rapportools" version))
10844 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10845 (build-system r-build-system)
10847 `(("r-pander" ,r-pander)
10849 ("r-reshape" ,r-reshape)))
10850 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10851 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10853 "This package provides helper functions that act as wrappers to more
10854 advanced statistical methods with the advantage of having sane defaults for
10856 (license license:agpl3+)))
10858 (define-public r-pander
10865 (uri (cran-uri "pander" version))
10868 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10869 (build-system r-build-system)
10871 `(("r-digest" ,r-digest)
10872 ("r-rcpp" ,r-rcpp)))
10873 (home-page "https://rapporter.github.io/pander")
10874 (synopsis "Render R objects into Pandoc's markdown")
10876 "The main aim of the pander R package is to provide a minimal and easy
10877 tool for rendering R objects into Pandoc's markdown. The package is also
10878 capable of exporting/converting complex Pandoc documents (reports) in various
10880 ;; This package is licensed under either the AGPLv3+ or the very rarely
10882 (license license:agpl3+)))
10884 (define-public r-summarytools
10886 (name "r-summarytools")
10891 (uri (cran-uri "summarytools" version))
10894 "0ig7vgjvldbndwhky1bsi38zifr9ji8xvvfqbfffplac08llvrbr"))))
10895 (build-system r-build-system)
10897 `(("r-base64enc" ,r-base64enc)
10898 ("r-checkmate" ,r-checkmate)
10899 ("r-dplyr" ,r-dplyr)
10900 ("r-htmltools" ,r-htmltools)
10901 ("r-lubridate" ,r-lubridate)
10902 ("r-magick" ,r-magick)
10903 ("r-matrixstats" ,r-matrixstats)
10904 ("r-pander" ,r-pander)
10906 ("r-rapportools" ,r-rapportools)
10907 ("r-tibble" ,r-tibble)
10908 ("r-tidyr" ,r-tidyr)))
10910 `(("r-knitr" ,r-knitr)))
10911 (home-page "https://github.com/dcomtois/summarytools")
10912 (synopsis "Tools to quickly and neatly summarize data")
10914 "This package provides tools for data frame summaries, cross-tabulations,
10915 weight-enabled frequency tables and common univariate statistics in concise
10916 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10917 good point-of-entry for exploring data, both for experienced and new R
10919 (license license:gpl2)))
10921 (define-public r-lsei
10928 (uri (cran-uri "lsei" version))
10931 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10932 (build-system r-build-system)
10934 `(("gfortran" ,gfortran)))
10935 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10936 (synopsis "Solve regression problems under equality/inequality constraints")
10938 "It contains functions that solve least squares linear regression
10939 problems under linear equality/inequality constraints. Functions for solving
10940 quadratic programming problems are also available, which transform such
10941 problems into least squares ones first.")
10942 (license license:gpl2+)))
10944 (define-public r-npsurv
10951 (uri (cran-uri "npsurv" version))
10954 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10955 (build-system r-build-system)
10957 `(("r-lsei" ,r-lsei)))
10958 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10959 (synopsis "Nonparametric survival analysis")
10961 "This package contains functions for non-parametric survival analysis of
10962 exact and interval-censored observations.")
10963 (license license:gpl2+)))
10965 (define-public r-clusteval
10967 (name "r-clusteval")
10972 (uri (cran-uri "clusteval" version))
10975 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10976 (build-system r-build-system)
10978 `(("r-mvtnorm" ,r-mvtnorm)
10979 ("r-rcpp" ,r-rcpp)))
10980 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10981 (synopsis "Evaluation of clustering algorithms")
10983 "This R package provides a suite of tools to evaluate clustering
10984 algorithms, clusterings, and individual clusters.")
10985 (license license:expat)))
10987 (define-public r-tweedie
10994 (uri (cran-uri "tweedie" version))
10997 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
10998 (build-system r-build-system)
10999 (native-inputs `(("gfortran" ,gfortran)))
11000 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11001 (synopsis "Evaluation of Tweedie exponential family models")
11003 "Maximum likelihood computations for Tweedie families, including the
11004 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11005 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11006 and related methods.")
11007 (license license:gpl2+)))
11009 (define-public r-rcppgsl
11016 (uri (cran-uri "RcppGSL" version))
11018 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11019 (properties `((upstream-name . "RcppGSL")))
11020 (build-system r-build-system)
11022 `(("r-rcpp" ,r-rcpp)
11024 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11025 (synopsis "Rcpp integration for GSL vectors and matrices")
11027 "The GNU Scientific Library (or GSL) is a collection of numerical
11028 routines for scientific computing. It is particularly useful for C and C++
11029 programs as it provides a standard C interface to a wide range of mathematical
11030 routines. There are over 1000 functions in total with an extensive test
11031 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11032 structures and R using concepts from Rcpp which is itself a package that eases
11033 the interfaces between R and C++.")
11034 (license license:gpl2+)))
11036 (define-public r-mvabund
11043 (uri (cran-uri "mvabund" version))
11046 "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
11047 (build-system r-build-system)
11049 `(("r-mass" ,r-mass)
11051 ("r-rcppgsl" ,r-rcppgsl)
11052 ("r-statmod" ,r-statmod)
11053 ("r-tweedie" ,r-tweedie)))
11054 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11055 (synopsis "Statistical methods for analysing multivariate abundance data")
11057 "This package provides a set of tools for displaying, modeling and
11058 analysing multivariate abundance data in community ecology.")
11059 (license license:lgpl2.1+)))
11061 (define-public r-afex
11068 (uri (cran-uri "afex" version))
11071 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11072 (build-system r-build-system)
11076 ("r-lmertest" ,r-lmertest)
11077 ("r-pbkrtest" ,r-pbkrtest)
11078 ("r-reshape2" ,r-reshape2)))
11080 `(("r-knitr" ,r-knitr)))
11081 (home-page "https://afex.singmann.science/")
11082 (synopsis "Analysis of factorial experiments")
11084 "This package provides convenience functions for analyzing factorial
11085 experiments using ANOVA or mixed models.")
11086 (license license:gpl2+)))
11088 (define-public r-lmertest
11090 (name "r-lmertest")
11095 (uri (cran-uri "lmerTest" version))
11098 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11099 (properties `((upstream-name . "lmerTest")))
11100 (build-system r-build-system)
11102 `(("r-ggplot2" ,r-ggplot2)
11105 ("r-numderiv" ,r-numderiv)))
11106 (home-page "https://github.com/runehaubo/lmerTestR")
11107 (synopsis "Tests in linear mixed effects models")
11109 "This package provides p-values in type I, II or III anova and summary
11110 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11111 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11112 package. Model selection methods include step, drop1 and anova-like tables
11113 for random effects (ranova). Methods for Least-Square means (LS-means) and
11114 tests of linear contrasts of fixed effects are also available.")
11115 (license license:gpl2+)))
11117 (define-public r-r2glmm
11124 (uri (cran-uri "r2glmm" version))
11127 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11128 (build-system r-build-system)
11130 `(("r-afex" ,r-afex)
11131 ("r-data-table" ,r-data-table)
11132 ("r-dplyr" ,r-dplyr)
11133 ("r-ggplot2" ,r-ggplot2)
11134 ("r-gridextra" ,r-gridextra)
11135 ("r-lmertest" ,r-lmertest)
11137 ("r-matrix" ,r-matrix)
11139 ("r-pbkrtest" ,r-pbkrtest)))
11140 (home-page "https://github.com/bcjaeger/r2glmm")
11141 (synopsis "Compute R squared for mixed (multilevel) models")
11143 "This package computes model and semi partial R squared with confidence
11144 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11145 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11146 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11148 (license license:gpl2)))
11150 (define-public r-weights
11157 (uri (cran-uri "weights" version))
11160 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11161 (build-system r-build-system)
11163 `(("r-gdata" ,r-gdata)
11164 ("r-hmisc" ,r-hmisc)
11165 ("r-mice" ,r-mice)))
11167 "https://cran.r-project.org/web/packages/weights/")
11168 (synopsis "Weighting and weighted statistics")
11169 (description "This package Provides a variety of functions for producing
11170 simple weighted statistics, such as weighted Pearson's correlations, partial
11171 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11172 includes some software for quickly recoding survey data and plotting point
11173 estimates from interaction terms in regressions (and multiply imputed
11174 regressions). NOTE: Weighted partial correlation calculations pulled to
11176 (license license:gpl2+)))
11178 (define-public r-rcppannoy
11180 (name "r-rcppannoy")
11185 (uri (cran-uri "RcppAnnoy" version))
11188 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11189 (properties `((upstream-name . "RcppAnnoy")))
11190 (build-system r-build-system)
11192 `(("r-rcpp" ,r-rcpp)))
11193 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11194 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11196 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11197 for efficient memory usage as well an ability to load from and save to disk.
11198 This package provides an R interface.")
11199 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11201 (license (list license:gpl2+ license:asl2.0))))
11203 (define-public r-rcpphnsw
11205 (name "r-rcpphnsw")
11210 (uri (cran-uri "RcppHNSW" version))
11213 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11214 (properties `((upstream-name . "RcppHNSW")))
11215 (build-system r-build-system)
11216 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11217 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11218 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11220 "Hnswlib is a C++ library for approximate nearest neighbors. This
11221 package provides a minimal R interface by relying on the Rcpp package.")
11222 ;; hnswlib is released under Version 2.0 of the Apache License.
11223 (license (list license:gpl3 license:asl2.0))))
11225 (define-public r-rcppparallel
11227 (name "r-rcppparallel")
11232 (uri (cran-uri "RcppParallel" version))
11235 "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki"))))
11236 (properties `((upstream-name . "RcppParallel")))
11237 (build-system r-build-system)
11238 (home-page "https://rcppcore.github.io/RcppParallel/")
11239 (synopsis "Parallel programming tools for Rcpp")
11241 "This package provides high level functions for parallel programming with
11242 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11243 the work of a standard serial @code{for} loop into a parallel one and the
11244 @code{parallelReduce()} function can be used for accumulating aggregates or
11246 (license license:gpl2)))
11248 (define-public r-ncdf4
11255 (uri (cran-uri "ncdf4" version))
11258 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11259 (build-system r-build-system)
11261 `(("netcdf" ,netcdf)
11263 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11264 (synopsis "R interface to Unidata netCDF format data files")
11266 "This package provides a high-level R interface to data files written
11267 using Unidata's netCDF library (version 4 or earlier), which are binary data
11268 files that are portable across platforms and include metadata information in
11269 addition to the data sets. Using this package, netCDF files can be opened and
11270 data sets read in easily. It is also easy to create new netCDF dimensions,
11271 variables, and files, in either version 3 or 4 format, and manipulate existing
11273 (license license:gpl3+)))
11275 (define-public r-biocmanager
11277 (name "r-biocmanager")
11278 (version "1.30.12")
11282 (uri (cran-uri "BiocManager" version))
11284 (base32 "0c2anza01pc36manj3cvycbq8p57qpq18dsimk3y3gpks70hhqf3"))))
11285 (properties `((upstream-name . "BiocManager")))
11286 (build-system r-build-system)
11288 `(("r-knitr" ,r-knitr)))
11289 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11290 (synopsis "Access the Bioconductor project package repository")
11292 "This package provides a convenient tool to install and update
11293 Bioconductor packages.")
11294 (license license:artistic2.0)))
11296 (define-public r-rgl
11299 (version "0.105.22")
11303 (uri (cran-uri "rgl" version))
11306 "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz"))))
11307 (build-system r-build-system)
11309 `(("pkg-config" ,pkg-config)
11310 ("r-knitr" ,r-knitr)))
11312 `(("freetype" ,freetype)
11319 `(("r-crosstalk" ,r-crosstalk)
11320 ("r-htmltools" ,r-htmltools)
11321 ("r-htmlwidgets" ,r-htmlwidgets)
11322 ("r-jsonlite" ,r-jsonlite)
11323 ("r-knitr" ,r-knitr)
11324 ("r-magrittr" ,r-magrittr)
11325 ("r-manipulatewidget" ,r-manipulatewidget)
11326 ("r-shiny" ,r-shiny)))
11327 (home-page "https://r-forge.r-project.org/projects/rgl/")
11328 (synopsis "3D visualization using OpenGL")
11330 "This package provides medium to high level functions for 3D interactive graphics,
11331 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11332 as functions for constructing representations of geometric
11333 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11334 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11335 image formats, including PNG, Postscript, SVG, PGF.")
11336 ;; Any version of the GPL.
11337 (license (list license:gpl2+ license:gpl3+))))
11339 (define-public r-multicool
11341 (name "r-multicool")
11346 (uri (cran-uri "multicool" version))
11349 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11350 (build-system r-build-system)
11351 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11352 (home-page "https://cran.r-project.org/web/packages/multicool/")
11353 (synopsis "Permutations of multisets in cool-lex order")
11355 "This package provides a set of tools to permute multisets without loops
11356 or hash tables and to generate integer partitions. Cool-lex order is similar
11357 to colexicographical order.")
11358 (license license:gpl2)))
11360 (define-public r-misc3d
11367 (uri (cran-uri "misc3d" version))
11370 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11371 (build-system r-build-system)
11372 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11373 (synopsis "Miscellaneous 3D Plots")
11375 "This package provides a collection of miscellaneous 3d plots, including
11377 ;; Any version of the GPL.
11378 (license (list license:gpl2+ license:gpl3+))))
11380 (define-public r-ks
11387 (uri (cran-uri "ks" version))
11389 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11390 (build-system r-build-system)
11393 ("r-kernlab" ,r-kernlab)
11394 ("r-kernsmooth" ,r-kernsmooth)
11395 ("r-matrix" ,r-matrix)
11396 ("r-mclust" ,r-mclust)
11398 ("r-multicool" ,r-multicool)
11399 ("r-mvtnorm" ,r-mvtnorm)
11400 ("r-plot3d" ,r-plot3d)))
11401 (home-page "https://www.mvstat.net/tduong/")
11402 (synopsis "Kernel smoothing")
11404 "This package provides kernel smoothers for univariate and multivariate
11405 data, including density functions, density derivatives, cumulative
11406 distributions, modal clustering, discriminant analysis, and two-sample
11407 hypothesis testing.")
11408 ;; Either version of the GPL.
11409 (license (list license:gpl2 license:gpl3))))
11411 (define-public r-feature
11418 (uri (cran-uri "feature" version))
11421 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11422 (build-system r-build-system)
11425 ("r-plot3d" ,r-plot3d)))
11427 `(("r-knitr" ,r-knitr)))
11428 (home-page "https://www.mvstat.net/tduong/")
11429 (synopsis "Inferential feature significance for kernel density estimation")
11431 "The feature package contains functions to display and compute kernel
11432 density estimates, significant gradient and significant curvature regions.
11433 Significant gradient and/or curvature regions often correspond to significant
11434 features (e.g. local modes).")
11435 ;; Either version of the GPL.
11436 (license (list license:gpl2 license:gpl3))))
11438 (define-public r-arm
11445 (uri (cran-uri "arm" version))
11448 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11449 (build-system r-build-system)
11451 `(("r-abind" ,r-abind)
11453 ("r-hmisc" ,r-hmisc)
11456 ("r-matrix" ,r-matrix)
11457 ("r-nlme" ,r-nlme)))
11458 (home-page "https://cran.r-project.org/web/packages/arm/")
11459 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11461 "This package provides functions to accompany A. Gelman and J. Hill,
11462 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11463 University Press, 2007.")
11464 (license license:gpl3+)))
11466 (define-public r-circular
11468 (name "r-circular")
11473 (uri (cran-uri "circular" version))
11476 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11477 (build-system r-build-system)
11479 `(("r-boot" ,r-boot)
11480 ("r-mvtnorm" ,r-mvtnorm)))
11482 `(("gfortran" ,gfortran)))
11483 (home-page "https://cran.r-project.org/web/packages/circular/")
11484 (synopsis "Circular statistics")
11486 "This package provides tools for circular statistics, from \"Topics in
11487 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11489 (license license:gpl2+)))
11491 (define-public r-activity
11493 (name "r-activity")
11498 (uri (cran-uri "activity" version))
11501 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
11502 (build-system r-build-system)
11504 `(("r-circular" ,r-circular)
11505 ("r-insol" ,r-insol)
11506 ("r-pbapply" ,r-pbapply)))
11507 (home-page "https://cran.r-project.org/web/packages/activity/")
11508 (synopsis "Animal activity statistics")
11510 "This package provides functions to fit kernel density functions to
11511 animal activity time data; plot activity distributions; quantify overall
11512 levels of activity; statistically compare activity metrics through
11513 bootstrapping; and evaluate variation in linear variables with time (or other
11514 circular variables).")
11515 (license license:gpl3)))
11517 (define-public r-ouch
11524 (uri (cran-uri "ouch" version))
11527 "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q"))))
11528 (build-system r-build-system)
11529 (propagated-inputs `(("r-subplex" ,r-subplex)))
11530 (home-page "https://kingaa.github.io/ouch/")
11531 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11533 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11534 for evolution along a phylogenetic tree.")
11535 (license license:gpl2+)))
11537 (define-public r-fmsb
11544 (uri (cran-uri "fmsb" version))
11547 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11548 (build-system r-build-system)
11549 (home-page "http://minato.sip21c.org/msb/")
11550 (synopsis "Functions for medical statistics book with demographic data")
11552 "This package provides several utility functions for the book entitled
11553 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11554 Japan, 2007) with Japanese demographic data and some demographic analysis
11555 related functions.")
11556 (license license:gpl2+)))
11558 (define-public r-stabledist
11560 (name "r-stabledist")
11565 (uri (cran-uri "stabledist" version))
11568 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11569 (build-system r-build-system)
11570 (home-page "https://www.rmetrics.org")
11571 (synopsis "Stable distribution functions")
11573 "This package provides density, probability and quantile functions, and
11574 random number generation for (skew) stable distributions, using the
11575 parametrizations of Nolan.")
11576 (license license:gpl2+)))
11578 (define-public r-gsl
11585 (uri (cran-uri "gsl" version))
11588 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11589 (build-system r-build-system)
11592 (home-page "https://cran.r-project.org/web/packages/gsl")
11593 (synopsis "Wrapper for the GNU Scientific Library")
11595 "This package provides an R wrapper for the special functions and quasi
11596 random number generators of the GNU Scientific Library.")
11597 (license license:gpl2+)))
11599 (define-public r-adgoftest
11601 (name "r-adgoftest")
11606 (uri (cran-uri "ADGofTest" version))
11609 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11610 (properties `((upstream-name . "ADGofTest")))
11611 (build-system r-build-system)
11612 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11613 (synopsis "Anderson-Darling GoF test")
11615 "This package provides an implementation of the Anderson-Darling GoF test
11616 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11617 Anderson-Darling Distribution\".")
11618 ;; Any version of the GPL.
11619 (license license:gpl3+)))
11621 (define-public r-sodium
11628 (uri (cran-uri "sodium" version))
11631 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11632 (properties `((upstream-name . "sodium")))
11633 (build-system r-build-system)
11635 `(("libsodium" ,libsodium)))
11637 `(("pkg-config" ,pkg-config)
11638 ("r-knitr" ,r-knitr)))
11639 (home-page "https://github.com/jeroen/sodium")
11640 (synopsis "R bindings to the libsodium crypto library")
11642 "This package provides bindings to libsodium: a library for encryption,
11643 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11644 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11645 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11646 (license license:expat)))
11648 (define-public r-softimpute
11650 (name "r-softimpute")
11655 (uri (cran-uri "softImpute" version))
11658 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11659 (properties `((upstream-name . "softImpute")))
11660 (build-system r-build-system)
11662 `(("r-matrix" ,r-matrix)))
11664 `(("gfortran" ,gfortran)))
11665 (home-page "https://cran.r-project.org/web/packages/softImpute")
11666 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11668 "This package provides iterative methods for matrix completion that use
11669 nuclear-norm regularization. The package includes procedures for centering
11670 and scaling rows, columns or both, and for computing low-rank @dfn{single
11671 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11673 (license license:gpl2)))
11675 (define-public r-fftwtools
11677 (name "r-fftwtools")
11682 (uri (cran-uri "fftwtools" version))
11685 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
11686 (build-system r-build-system)
11687 (inputs `(("fftw" ,fftw)))
11689 `(("pkg-config" ,pkg-config)))
11690 (home-page "https://github.com/krahim/fftwtools")
11691 (synopsis "Wrapper for FFTW3")
11693 "This package provides a wrapper for several FFTW functions. It provides
11694 access to the two-dimensional FFT, the multivariate FFT, and the
11695 one-dimensional real to complex FFT using the FFTW3 library. The package
11696 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11697 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11698 The FFT functions have a parameter that allows them to not return the
11699 redundant complex conjugate when the input is real data.")
11700 (license license:gpl2+)))
11702 (define-public r-tiff
11709 (uri (cran-uri "tiff" version))
11712 "18m17g5q3nz4v4wrqxnb129b1j02873g2vknddczkklf1pvq4x2b"))))
11713 (build-system r-build-system)
11715 `(("libtiff" ,libtiff)
11716 ("libjpeg" ,libjpeg-turbo)
11719 `(("pkg-config" ,pkg-config)))
11720 (home-page "https://www.rforge.net/tiff/")
11721 (synopsis "Read and write TIFF images")
11723 "This package provides an easy and simple way to read, write and display
11724 bitmap images stored in the TIFF format. It can read and write both files and
11725 in-memory raw vectors.")
11726 ;; Either of these two license versions.
11727 (license (list license:gpl2 license:gpl3))))
11729 (define-public r-nlp
11736 (uri (cran-uri "NLP" version))
11739 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11740 (properties `((upstream-name . "NLP")))
11741 (build-system r-build-system)
11742 (home-page "https://cran.r-project.org/web/packages/NLP/")
11743 (synopsis "Natural language processing infrastructure")
11745 "This package provides basic classes and methods for Natural Language
11747 (license license:gpl3)))
11749 (define-public r-tm
11756 (uri (cran-uri "tm" version))
11759 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11760 (properties `((upstream-name . "tm")))
11761 (build-system r-build-system)
11767 ("r-xml2" ,r-xml2)))
11768 (home-page "http://tm.r-forge.r-project.org/")
11769 (synopsis "Text mining package")
11771 "This package provides a framework for text mining applications within R.")
11772 (license license:gpl3)))
11774 (define-public r-waveslim
11776 (name "r-waveslim")
11781 (uri (cran-uri "waveslim" version))
11784 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11785 (build-system r-build-system)
11787 `(("gfortran" ,gfortran)))
11788 (home-page "http://waveslim.blogspot.com")
11789 (synopsis "Basic wavelet routines for signal processing")
11791 "This package provides basic wavelet routines for time series (1D),
11792 image (2D) and array (3D) analysis. The code provided here is based on
11793 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11794 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11795 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11796 pairs (Selesnick 2001, 2002).")
11797 (license license:bsd-3)))
11799 (define-public r-wordcloud
11801 (name "r-wordcloud")
11806 (uri (cran-uri "wordcloud" version))
11809 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11810 (build-system r-build-system)
11812 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11814 ;; The "tm" package is only "suggested" according to CRAN, but the
11815 ;; wordcloud package cannot be loaded without it.
11817 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11818 (synopsis "Word clouds")
11820 "This package provides functionality to create pretty word clouds,
11821 visualize differences and similarity between documents, and avoid
11822 over-plotting in scatter plots with text.")
11823 (license license:lgpl2.1)))
11825 (define-public r-colorramps
11827 (name "r-colorramps")
11832 (uri (cran-uri "colorRamps" version))
11835 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11836 (properties `((upstream-name . "colorRamps")))
11837 (build-system r-build-system)
11838 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11839 (synopsis "Build color tables")
11840 (description "This package provides features to build gradient color
11842 ;; Any version of the GPL
11843 (license license:gpl3+)))
11845 (define-public r-tidytree
11847 (name "r-tidytree")
11852 (uri (cran-uri "tidytree" version))
11854 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11855 (build-system r-build-system)
11858 ("r-dplyr" ,r-dplyr)
11859 ("r-lazyeval" ,r-lazyeval)
11860 ("r-magrittr" ,r-magrittr)
11861 ("r-rlang" ,r-rlang)
11862 ("r-tibble" ,r-tibble)))
11864 `(("r-knitr" ,r-knitr)))
11865 (home-page "https://github.com/GuangchuangYu/tidytree")
11866 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11868 "Phylogenetic trees generally contain multiple components including nodes,
11869 edges, branches and associated data. This package provides an approach to
11870 convert tree objects to tidy data frames. It also provides tidy interfaces to
11871 manipulate tree data.")
11872 (license license:artistic2.0)))
11874 (define-public r-rvcheck
11881 (uri (cran-uri "rvcheck" version))
11883 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11884 (build-system r-build-system)
11886 `(("r-biocmanager" ,r-biocmanager)
11887 ("r-rlang" ,r-rlang)))
11888 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11889 (synopsis "R package version check")
11891 "This package provides tools to check the latest release version of R and
11892 R packages (on CRAN, Bioconductor or Github).")
11893 (license license:artistic2.0)))
11895 (define-public r-docopt
11902 (uri (cran-uri "docopt" version))
11905 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11906 (build-system r-build-system)
11907 (home-page "https://github.com/docopt/docopt.R")
11908 (synopsis "Command-line interface specification language")
11910 "This package enables you to define a command-line interface by just
11911 giving it a description in the specific format.")
11912 (license license:expat)))
11914 (define-public r-sparsesvd
11916 (name "r-sparsesvd")
11921 (uri (cran-uri "sparsesvd" version))
11924 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11925 (build-system r-build-system)
11926 (propagated-inputs `(("r-matrix" ,r-matrix)))
11927 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11928 (synopsis "Sparse truncated singular value decomposition")
11930 "This package provides a Wrapper around the SVDLIBC library
11931 for (truncated) singular value decomposition of a sparse matrix. Currently,
11932 only sparse real matrices in Matrix package format are supported.")
11933 ;; SVDLIBC is released under BSD-2. The R interface is released under
11935 (license (list license:bsd-3 license:bsd-2))))
11937 (define-public r-speedglm
11939 (name "r-speedglm")
11944 (uri (cran-uri "speedglm" version))
11947 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11948 (build-system r-build-system)
11950 `(("r-mass" ,r-mass)
11951 ("r-matrix" ,r-matrix)))
11952 (home-page "https://cran.r-project.org/web/packages/speedglm")
11953 (synopsis "Fit linear and generalized linear models to large data sets")
11955 "This package provides tools for fitting linear models and generalized
11956 linear models to large data sets by updating algorithms.")
11957 ;; Any version of the GPL
11958 (license license:gpl2+)))
11960 (define-public r-densityclust
11962 (name "r-densityclust")
11967 (uri (cran-uri "densityClust" version))
11970 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11971 (properties `((upstream-name . "densityClust")))
11972 (build-system r-build-system)
11975 ("r-ggplot2" ,r-ggplot2)
11976 ("r-ggrepel" ,r-ggrepel)
11977 ("r-gridextra" ,r-gridextra)
11978 ("r-rcolorbrewer" ,r-rcolorbrewer)
11980 ("r-rtsne" ,r-rtsne)))
11981 (home-page "https://cran.r-project.org/web/packages/densityClust")
11982 (synopsis "Clustering by fast search and find of density peaks")
11984 "This package provides an improved implementation (based on k-nearest
11985 neighbors) of the density peak clustering algorithm, originally described by
11986 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11987 large datasets (> 100,000 samples) very efficiently.")
11988 (license license:gpl2+)))
11990 (define-public r-combinat
11992 (name "r-combinat")
11997 (uri (cran-uri "combinat" version))
12000 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
12001 (build-system r-build-system)
12002 (home-page "https://cran.r-project.org/web/packages/combinat")
12003 (synopsis "Combinatorics utilities")
12004 (description "This package provides assorted routines for combinatorics.")
12005 (license license:gpl2)))
12007 (define-public r-qlcmatrix
12009 (name "r-qlcmatrix")
12014 (uri (cran-uri "qlcMatrix" version))
12017 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12018 (properties `((upstream-name . "qlcMatrix")))
12019 (build-system r-build-system)
12021 `(("r-docopt" ,r-docopt)
12022 ("r-matrix" ,r-matrix)
12024 ("r-sparsesvd" ,r-sparsesvd)))
12025 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12026 (synopsis "Sparse matrix functions for quantitative language comparison")
12028 "This package provides an extension of the functionality of the Matrix
12029 package for using sparse matrices. Some of the functions are very general,
12030 while other are highly specific for the special data format used for
12031 @dfn{quantitative language comparison} (QLC).")
12032 (license license:gpl3)))
12034 (define-public r-ddrtree
12041 (uri (cran-uri "DDRTree" version))
12044 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12045 (properties `((upstream-name . "DDRTree")))
12046 (build-system r-build-system)
12049 ("r-irlba" ,r-irlba)
12051 ("r-rcppeigen" ,r-rcppeigen)))
12052 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12053 (synopsis "Learning principal graphs with DDRTree")
12055 "This package provides an implementation of the framework of
12056 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12057 dimensional space while constructs a principal tree which passes through the
12058 middle of the data simultaneously. DDRTree shows superiority to
12059 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12060 intrinsic structure of single cell genomics data. In general, it could be
12061 used to reconstruct the temporal progression as well as the bifurcation
12062 structure of any data type.")
12063 (license license:asl2.0)))
12065 (define-public r-corpcor
12072 (uri (cran-uri "corpcor" version))
12075 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12076 (build-system r-build-system)
12077 (home-page "http://strimmerlab.org/software/corpcor/")
12078 (synopsis "Efficient estimation of covariance and (partial) correlation")
12080 "This package implements a James-Stein-type shrinkage estimator for the
12081 covariance matrix, with separate shrinkage for variances and correlations.
12082 Furthermore, functions are available for fast singular value decomposition,
12083 for computing the pseudoinverse, and for checking the rank and positive
12084 definiteness of a matrix.")
12085 (license license:gpl3+)))
12087 (define-public r-rspectra
12089 (name "r-rspectra")
12094 (uri (cran-uri "RSpectra" version))
12097 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12098 (properties `((upstream-name . "RSpectra")))
12099 (build-system r-build-system)
12101 `(("r-matrix" ,r-matrix)
12103 ("r-rcppeigen" ,r-rcppeigen)))
12104 (home-page "https://github.com/yixuan/RSpectra")
12105 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12107 "This package provides an R interface to the Spectra library for
12108 large-scale eigenvalue and SVD problems. It is typically used to compute a
12109 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12110 which is usually more efficient than @code{eigen()} if k << n.")
12112 (license license:mpl2.0)))
12114 (define-public r-vbsr
12121 (uri (cran-uri "vbsr" version))
12124 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12125 (build-system r-build-system)
12126 (home-page "https://cran.r-project.org/web/packages/vbsr")
12127 (synopsis "Variational Bayes spike regression regularized linear models")
12129 "This package provides an efficient algorithm for solving ultra-sparse
12130 regularized regression models using a variational Bayes algorithm with a spike
12131 prior. The algorithm is solved on a path, with coordinate updates, and is
12132 capable of generating very sparse models. Very general model
12133 diagnostics for controlling type-1 errors are also provided.")
12134 (license license:gpl2)))
12136 (define-public r-flare
12143 (uri (cran-uri "flare" version))
12146 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12147 (build-system r-build-system)
12149 `(("r-igraph" ,r-igraph)
12150 ("r-lattice" ,r-lattice)
12152 ("r-matrix" ,r-matrix)))
12153 (home-page "https://cran.r-project.org/web/packages/flare")
12154 (synopsis "Family of Lasso regression implementations")
12156 "This package provides implementations of a family of Lasso variants
12157 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12158 high dimensional sparse linear models.")
12159 (license license:gpl2)))
12161 (define-public r-lassopv
12168 (uri (cran-uri "lassopv" version))
12171 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12172 (build-system r-build-system)
12173 (propagated-inputs `(("r-lars" ,r-lars)))
12174 (home-page "https://github.com/lingfeiwang/lassopv")
12175 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12177 "This package enables you to estimate the p-values for predictors x
12178 against target variable y in Lasso regression, using the regularization
12179 strength when each predictor enters the active set of regularization path for
12180 the first time as the statistic.")
12181 (license license:gpl3)))
12183 (define-public r-splitstackshape
12185 (name "r-splitstackshape")
12190 (uri (cran-uri "splitstackshape" version))
12193 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12194 (build-system r-build-system)
12196 `(("r-data-table" ,r-data-table)))
12197 (home-page "https://github.com/mrdwab/splitstackshape")
12198 (synopsis "Stack and reshape datasets after splitting concatenated values")
12200 "Online data collection tools like Google Forms often export
12201 multiple-response questions with data concatenated in cells. The
12202 @code{concat.split} (cSplit) family of functions provided by this package
12203 splits such data into separate cells. This package also includes functions to
12204 stack groups of columns and to reshape wide data, even when the data are
12205 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12206 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12208 (license license:gpl3)))
12210 (define-public r-tfmpvalue
12212 (name "r-tfmpvalue")
12217 (uri (cran-uri "TFMPvalue" version))
12220 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12221 (properties `((upstream-name . "TFMPvalue")))
12222 (build-system r-build-system)
12223 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12224 (home-page "https://github.com/ge11232002/TFMPvalue")
12225 (synopsis "P-value computation for position weight matrices")
12227 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12228 identification from sequence/alignments, we are interested in the significance
12229 of certain match scores. TFMPvalue provides the accurate calculation of a
12230 p-value with a score threshold for position weight matrices, or the score with
12231 a given p-value. It is an interface to code originally made available by
12232 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12233 Touzet and Varre (2007).")
12234 (license license:gpl2)))
12236 (define-public r-rnifti
12243 (uri (cran-uri "RNifti" version))
12246 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12247 (properties `((upstream-name . "RNifti")))
12248 (build-system r-build-system)
12249 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12250 (home-page "https://github.com/jonclayden/RNifti")
12251 (synopsis "Fast R and C++ access to NIfTI images")
12253 "This package provides very fast read and write access to images stored
12254 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12255 compiled C and interpreted R code. It also provides a C/C++ API that can be
12256 used by other packages.")
12257 (license license:gpl2)))
12259 (define-public r-shades
12266 (uri (cran-uri "shades" version))
12269 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12270 (build-system r-build-system)
12271 (home-page "https://github.com/jonclayden/shades")
12272 (synopsis "Simple color manipulation")
12274 "This package provides functions for easily manipulating colors,
12275 creating color scales and calculating color distances.")
12276 (license license:bsd-3)))
12278 (define-public r-ore
12285 (uri (cran-uri "ore" version))
12287 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12288 (build-system r-build-system)
12289 (home-page "https://github.com/jonclayden/ore")
12290 (synopsis "R interface to the Onigmo regular expression library")
12292 "This package provides an alternative to R's built-in functionality for
12293 handling regular expressions, based on the Onigmo library. It offers
12294 first-class compiled regex objects, partial matching and function-based
12295 substitutions, amongst other features.")
12296 (license license:bsd-3)))
12298 (define-public r-reportr
12305 (uri (cran-uri "reportr" version))
12308 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12309 (build-system r-build-system)
12310 (propagated-inputs `(("r-ore" ,r-ore)))
12311 (home-page "https://github.com/jonclayden/reportr")
12312 (synopsis "General message and error reporting system")
12314 "This package provides a system for reporting messages, which offers
12315 certain useful features over the standard R system, such as the incorporation
12316 of output consolidation, message filtering, assertions, expression
12317 substitution, automatic generation of stack traces for debugging, and
12318 conditional reporting based on the current \"output level\".")
12319 (license license:gpl2)))
12321 (define-public r-tractor-base
12323 (name "r-tractor-base")
12324 (version "3.3.3.1")
12328 (uri (cran-uri "tractor.base" version))
12331 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12332 (properties `((upstream-name . "tractor.base")))
12333 (build-system r-build-system)
12336 ("r-reportr" ,r-reportr)
12337 ("r-rnifti" ,r-rnifti)
12338 ("r-shades" ,r-shades)))
12339 (home-page "https://www.tractor-mri.org.uk")
12340 (synopsis "Read, manipulate and visualize magnetic resonance images")
12342 "This package provides functions for working with magnetic resonance
12343 images. It supports reading and writing of popular file formats (DICOM,
12344 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12345 visualization; flexible image manipulation; metadata and sparse image
12347 (license license:gpl2)))
12349 (define-public r-grimport
12351 (name "r-grimport")
12356 (uri (cran-uri "grImport" version))
12359 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12360 (properties `((upstream-name . "grImport")))
12361 (build-system r-build-system)
12363 `(("ghostscript" ,ghostscript)))
12365 `(("r-xml" ,r-xml)))
12366 (home-page "https://cran.r-project.org/web/packages/grImport")
12367 (synopsis "Convert, import, and draw PostScript pictures")
12369 "This package provides functions for converting, importing, and drawing
12370 PostScript pictures in R plots.")
12371 (license license:gpl2+)))
12373 (define-public r-grimport2
12375 (name "r-grimport2")
12380 (uri (cran-uri "grImport2" version))
12383 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12384 (properties `((upstream-name . "grImport2")))
12385 (build-system r-build-system)
12387 `(("r-base64enc" ,r-base64enc)
12391 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12392 (synopsis "Import SVG graphics")
12394 "This package provides functions for importing external vector images and
12395 drawing them as part of R plots. This package is different from the
12396 @code{grImport} package because, where that package imports PostScript format
12397 images, this package imports SVG format images. Furthermore, this package
12398 imports a specific subset of SVG, so external images must be preprocessed
12399 using a package like @code{rsvg} to produce SVG that this package can import.
12400 SVG features that are not supported by R graphics, such as gradient fills, can
12401 be imported and then exported via the @code{gridSVG} package.")
12402 (license license:gpl2+)))
12404 (define-public r-kohonen
12411 (uri (cran-uri "kohonen" version))
12414 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12415 (build-system r-build-system)
12417 `(("r-rcpp" ,r-rcpp)))
12418 (home-page "https://cran.r-project.org/web/packages/kohonen")
12419 (synopsis "Supervised and unsupervised self-organising maps")
12421 "This package provides functions to train @dfn{self-organising
12422 maps} (SOMs). Also interrogation of the maps and prediction using trained
12423 maps are supported. The name of the package refers to Teuvo Kohonen, the
12424 inventor of the SOM.")
12425 (license license:gpl2+)))
12427 (define-public r-nnls
12434 (uri (cran-uri "nnls" version))
12437 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12438 (build-system r-build-system)
12439 (native-inputs `(("gfortran" ,gfortran)))
12440 (home-page "https://cran.r-project.org/web/packages/nnls")
12441 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12443 "This package provides an R interface to the Lawson-Hanson implementation
12444 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12445 the combination of non-negative and non-positive constraints.")
12446 (license license:gpl2+)))
12448 (define-public r-iso
12451 (version "0.0-18.1")
12455 (uri (cran-uri "Iso" version))
12458 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12459 (properties `((upstream-name . "Iso")))
12460 (build-system r-build-system)
12461 (native-inputs `(("gfortran" ,gfortran)))
12462 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12463 (synopsis "Functions to perform isotonic regression")
12465 "This package provides support for linear order and unimodal
12466 order (univariate) isotonic regression and bivariate isotonic regression with
12467 linear order on both variables.")
12468 (license license:gpl2+)))
12470 (define-public r-chemometricswithr
12472 (name "r-chemometricswithr")
12477 (uri (cran-uri "ChemometricsWithR" version))
12480 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12482 `((upstream-name . "ChemometricsWithR")))
12483 (build-system r-build-system)
12485 `(("r-devtools" ,r-devtools)
12486 ("r-kohonen" ,r-kohonen)
12489 (home-page "https://github.com/rwehrens/CWR")
12490 (synopsis "Chemometrics with R")
12492 "This package provides functions and scripts used in the book
12493 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12494 Life Sciences\" by Ron Wehrens, Springer (2011).")
12495 (license license:gpl2+)))
12497 (define-public r-als
12504 (uri (cran-uri "ALS" version))
12507 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12508 (properties `((upstream-name . "ALS")))
12509 (build-system r-build-system)
12512 ("r-nnls" ,r-nnls)))
12513 (home-page "https://cran.r-project.org/web/packages/ALS")
12514 (synopsis "Multivariate curve resolution alternating least squares")
12516 "Alternating least squares is often used to resolve components
12517 contributing to data with a bilinear structure; the basic technique may be
12518 extended to alternating constrained least squares. This package provides an
12519 implementation of @dfn{multivariate curve resolution alternating least
12520 squares} (MCR-ALS).
12522 Commonly applied constraints include unimodality, non-negativity, and
12523 normalization of components. Several data matrices may be decomposed
12524 simultaneously by assuming that one of the two matrices in the bilinear
12525 decomposition is shared between datasets.")
12526 (license license:gpl2+)))
12528 (define-public r-strucchange
12530 (name "r-strucchange")
12535 (uri (cran-uri "strucchange" version))
12538 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12539 (build-system r-build-system)
12541 `(("r-sandwich" ,r-sandwich)
12543 (home-page "https://cran.r-project.org/web/packages/strucchange")
12544 (synopsis "Testing, monitoring, and dating structural changes")
12546 "This package provides tools for testing, monitoring and dating
12547 structural changes in (linear) regression models. It features tests/methods
12548 from the generalized fluctuation test framework as well as from the F
12549 test (Chow test) framework. This includes methods to fit, plot and test
12550 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12551 statistics, respectively. It is possible to monitor incoming data online
12552 using fluctuation processes. Finally, the breakpoints in regression models
12553 with structural changes can be estimated together with confidence intervals.
12554 Emphasis is always given to methods for visualizing the data.")
12555 ;; Either of these two GPL versions
12556 (license (list license:gpl2 license:gpl3))))
12558 (define-public r-pixmap
12565 (uri (cran-uri "pixmap" version))
12568 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12569 (build-system r-build-system)
12570 (home-page "https://cran.r-project.org/web/packages/pixmap")
12571 (synopsis "Tools for bitmap images")
12573 "This package provides functions for importing, exporting, plotting and
12574 other manipulations of bitmapped images.")
12575 (license license:gpl2)))
12577 (define-public r-rapidjsonr
12579 (name "r-rapidjsonr")
12584 (uri (cran-uri "rapidjsonr" version))
12587 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12588 (build-system r-build-system)
12589 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12590 (synopsis "JSON parser")
12592 "This package provides JSON parsing capability through the Rapidjson
12594 (license license:expat)))
12596 (define-public r-ontologyindex
12598 (name "r-ontologyindex")
12603 (uri (cran-uri "ontologyIndex" version))
12606 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12607 (properties `((upstream-name . "ontologyIndex")))
12608 (build-system r-build-system)
12610 `(("r-knitr" ,r-knitr)))
12611 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12612 (synopsis "Functions for processing ontologies in R")
12614 "This package provides functions for reading ontologies into R as lists
12615 and manipulating sets of ontological terms.")
12616 (license license:gpl2+)))
12618 (define-public r-gargle
12625 (uri (cran-uri "gargle" version))
12628 "03y29dzz54bw9px5k8a72vmc000lcyrkc5l0izkqcciyi9ijkr3w"))))
12629 (build-system r-build-system)
12635 ("r-jsonlite" ,r-jsonlite)
12636 ("r-rappdirs" ,r-rappdirs)
12637 ("r-rlang" ,r-rlang)
12638 ("r-rstudioapi" ,r-rstudioapi)
12639 ("r-withr" ,r-withr)))
12641 `(("r-knitr" ,r-knitr)))
12642 (home-page "https://gargle.r-lib.org")
12643 (synopsis "Utilities for working with Google APIs")
12645 "This package provides utilities for working with Google APIs. This
12646 includes functions and classes for handling common credential types and for
12647 preparing, executing, and processing HTTP requests.")
12648 (license license:expat)))
12650 (define-public r-bigrquery
12652 (name "r-bigrquery")
12657 (uri (cran-uri "bigrquery" version))
12660 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12661 (build-system r-build-system)
12663 `(("r-assertthat" ,r-assertthat)
12664 ("r-bit64" ,r-bit64)
12667 ("r-gargle" ,r-gargle)
12670 ("r-jsonlite" ,r-jsonlite)
12671 ("r-prettyunits" ,r-prettyunits)
12672 ("r-progress" ,r-progress)
12673 ("r-rapidjsonr" ,r-rapidjsonr)
12675 ("r-rlang" ,r-rlang)
12676 ("r-tibble" ,r-tibble)))
12677 (home-page "https://github.com/rstats-db/bigrquery")
12678 (synopsis "R interface to Google's BigQuery API")
12680 "This package provides an R interface to Google's BigQuery database.")
12681 (license license:gpl3)))
12683 (define-public r-gmp
12690 (uri (cran-uri "gmp" version))
12693 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12694 (build-system r-build-system)
12697 (modify-phases %standard-phases
12698 (add-after 'unpack 'set-CC
12699 (lambda _ (setenv "CC" "gcc") #t)))))
12700 (inputs `(("gmp" ,gmp)))
12701 (home-page "https://cran.r-project.org/web/packages/gmp")
12702 (synopsis "Multiple precision arithmetic")
12704 "This package supports multiple precision arithmetic (big integers and
12705 rationals, prime number tests, matrix computation), \"arithmetic without
12706 limitations\" using the GNU Multiple Precision library.")
12707 ;; Any version of the GPL.
12708 (license license:gpl3+)))
12710 (define-public r-rmpfr
12717 (uri (cran-uri "Rmpfr" version))
12720 "1m9wwwch9wg886147brr2zfih65yfdfs3vmfvim1w6jykycasc9a"))))
12721 (properties `((upstream-name . "Rmpfr")))
12722 (build-system r-build-system)
12727 `(("r-gmp" ,r-gmp)))
12729 `(("pkg-config" ,pkg-config)))
12730 (home-page "http://rmpfr.r-forge.r-project.org/")
12731 (synopsis "R bindings to the MPFR library")
12733 "This package supports arithmetic (via S4 classes and methods) for
12734 arbitrary precision floating point numbers, including transcendental
12735 functions. To this end, the package interfaces with the @dfn{Multiple
12736 Precision Floating-Point Reliable} (MPFR) library.")
12737 (license license:gpl2+)))
12739 (define-public r-assertive-base
12741 (name "r-assertive-base")
12746 (uri (cran-uri "assertive.base" version))
12749 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12751 `((upstream-name . "assertive.base")))
12752 (build-system r-build-system)
12753 (home-page "https://bitbucket.org/richierocks/assertive.base")
12754 (synopsis "Core of the assertive package")
12756 "This package provides a minimal set of predicates and assertions used by
12757 the assertive package. This is mainly for use by other package developers who
12758 want to include run-time testing features in their own packages.")
12759 (license license:gpl3+)))
12761 (define-public r-assertive-properties
12763 (name "r-assertive-properties")
12768 (uri (cran-uri "assertive.properties" version))
12771 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12773 `((upstream-name . "assertive.properties")))
12774 (build-system r-build-system)
12776 `(("r-assertive-base" ,r-assertive-base)))
12777 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12778 (synopsis "Assertions to check properties of variables")
12780 "This package provides a set of predicates and assertions for checking
12781 the properties of variables, such as length, names and attributes. This is
12782 mainly for use by other package developers who want to include run-time
12783 testing features in their own packages.")
12784 (license license:gpl3+)))
12786 (define-public r-assertive-numbers
12788 (name "r-assertive-numbers")
12793 (uri (cran-uri "assertive.numbers" version))
12796 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12798 `((upstream-name . "assertive.numbers")))
12799 (build-system r-build-system)
12801 `(("r-assertive-base" ,r-assertive-base)))
12802 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12803 (synopsis "Assertions to check properties of numbers")
12805 "This package provides a set of predicates and assertions for checking
12806 the properties of numbers. This is mainly for use by other package developers
12807 who want to include run-time testing features in their own packages.")
12808 (license license:gpl3+)))
12810 (define-public r-assertive-sets
12812 (name "r-assertive-sets")
12817 (uri (cran-uri "assertive.sets" version))
12820 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12822 `((upstream-name . "assertive.sets")))
12823 (build-system r-build-system)
12825 `(("r-assertive-base" ,r-assertive-base)))
12826 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12827 (synopsis "Assertions to check properties of sets")
12829 "This package provides a set of predicates and assertions for checking
12830 the properties of sets. This is mainly for use by other package developers
12831 who want to include run-time testing features in their own packages.")
12832 (license license:gpl3+)))
12834 (define-public r-assertive-matrices
12836 (name "r-assertive-matrices")
12841 (uri (cran-uri "assertive.matrices" version))
12844 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12846 `((upstream-name . "assertive.matrices")))
12847 (build-system r-build-system)
12849 `(("r-assertive-base" ,r-assertive-base)))
12850 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12851 (synopsis "Assertions to check properties of matrices")
12853 "This package provides a set of predicates and assertions for checking
12854 the properties of matrices. This is mainly for use by other package
12855 developers who want to include run-time testing features in their own
12857 (license license:gpl3+)))
12859 (define-public r-assertive-models
12861 (name "r-assertive-models")
12866 (uri (cran-uri "assertive.models" version))
12869 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12871 `((upstream-name . "assertive.models")))
12872 (build-system r-build-system)
12874 `(("r-assertive-base" ,r-assertive-base)))
12875 (home-page "https://bitbucket.org/richierocks/assertive.models")
12876 (synopsis "Assertions to check properties of models")
12878 "This package provides a set of predicates and assertions for checking
12879 the properties of models. This is mainly for use by other package developers
12880 who want to include run-time testing features in their own packages.")
12881 (license license:gpl3+)))
12883 (define-public r-assertive-reflection
12885 (name "r-assertive-reflection")
12890 (uri (cran-uri "assertive.reflection" version))
12893 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12895 `((upstream-name . "assertive.reflection")))
12896 (build-system r-build-system)
12898 `(("r-assertive-base" ,r-assertive-base)))
12899 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12900 (synopsis "Assertions for checking the state of R")
12902 "This package provides a set of predicates and assertions for checking
12903 the state and capabilities of R, the operating system it is running on, and
12904 the IDE being used. This is mainly for use by other package developers who
12905 want to include run-time testing features in their own packages.")
12906 (license license:gpl3+)))
12908 (define-public r-assertive-types
12910 (name "r-assertive-types")
12915 (uri (cran-uri "assertive.types" version))
12918 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12920 `((upstream-name . "assertive.types")))
12921 (build-system r-build-system)
12923 `(("r-assertive-base" ,r-assertive-base)
12924 ("r-assertive-properties" ,r-assertive-properties)
12925 ("r-codetools" ,r-codetools)))
12926 (home-page "https://bitbucket.org/richierocks/assertive.types")
12927 (synopsis "Assertions to check types of variables")
12929 "This package provides a set of predicates and assertions for checking
12930 the types of variables. This is mainly for use by other package developers
12931 who want to include run-time testing features in their own packages.")
12932 (license license:gpl3+)))
12934 (define-public r-assertive-files
12936 (name "r-assertive-files")
12941 (uri (cran-uri "assertive.files" version))
12944 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12946 `((upstream-name . "assertive.files")))
12947 (build-system r-build-system)
12949 `(("r-assertive-base" ,r-assertive-base)
12950 ("r-assertive-numbers" ,r-assertive-numbers)))
12951 (home-page "https://bitbucket.org/richierocks/assertive.files")
12952 (synopsis "Assertions to check properties of files")
12954 "This package provides a set of predicates and assertions for checking
12955 the properties of files and connections. This is mainly for use by other
12956 package developers who want to include run-time testing features in their own
12958 (license license:gpl3+)))
12960 (define-public r-assertive-code
12962 (name "r-assertive-code")
12967 (uri (cran-uri "assertive.code" version))
12970 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12972 `((upstream-name . "assertive.code")))
12973 (build-system r-build-system)
12975 `(("r-assertive-base" ,r-assertive-base)
12976 ("r-assertive-properties" ,r-assertive-properties)
12977 ("r-assertive-types" ,r-assertive-types)))
12978 (home-page "https://bitbucket.org/richierocks/assertive.code")
12979 (synopsis "Assertions to check properties of code")
12981 "This package provides a set of predicates and assertions for checking
12982 the properties of code. This is mainly for use by other package developers
12983 who want to include run-time testing features in their own packages.")
12984 (license license:gpl3+)))
12986 (define-public r-assertive-datetimes
12988 (name "r-assertive-datetimes")
12993 (uri (cran-uri "assertive.datetimes" version))
12996 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
12998 `((upstream-name . "assertive.datetimes")))
12999 (build-system r-build-system)
13001 `(("r-assertive-base" ,r-assertive-base)
13002 ("r-assertive-types" ,r-assertive-types)))
13003 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
13004 (synopsis "Assertions to check properties of dates and times")
13006 "This package provides a set of predicates and assertions for checking
13007 the properties of dates and times. This is mainly for use by other package
13008 developers who want to include run-time testing features in their own
13010 (license license:gpl3+)))
13012 (define-public r-assertive-strings
13014 (name "r-assertive-strings")
13019 (uri (cran-uri "assertive.strings" version))
13022 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13024 `((upstream-name . "assertive.strings")))
13025 (build-system r-build-system)
13027 `(("r-assertive-base" ,r-assertive-base)
13028 ("r-assertive-types" ,r-assertive-types)
13029 ("r-stringi" ,r-stringi)))
13030 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13031 (synopsis "Assertions to check properties of strings")
13033 "This package provides a set of predicates and assertions for checking
13034 the properties of strings. This is mainly for use by other package developers
13035 who want to include run-time testing features in their own packages.")
13036 (license license:gpl3+)))
13038 (define-public r-assertive-data-us
13040 (name "r-assertive-data-us")
13045 (uri (cran-uri "assertive.data.us" version))
13048 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13050 `((upstream-name . "assertive.data.us")))
13051 (build-system r-build-system)
13053 `(("r-assertive-base" ,r-assertive-base)
13054 ("r-assertive-strings" ,r-assertive-strings)))
13055 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13056 (synopsis "Assertions to check properties of strings")
13058 "This package provides a set of predicates and assertions for checking
13059 the properties of US-specific complex data types. This is mainly for use by
13060 other package developers who want to include run-time testing features in
13061 their own packages.")
13062 (license license:gpl3+)))
13064 (define-public r-assertive-data-uk
13066 (name "r-assertive-data-uk")
13071 (uri (cran-uri "assertive.data.uk" version))
13074 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13076 `((upstream-name . "assertive.data.uk")))
13077 (build-system r-build-system)
13079 `(("r-assertive-base" ,r-assertive-base)
13080 ("r-assertive-strings" ,r-assertive-strings)))
13081 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13082 (synopsis "Assertions to check properties of strings")
13084 "This package provides a set of predicates and assertions for checking
13085 the properties of UK-specific complex data types. This is mainly for use by
13086 other package developers who want to include run-time testing features in
13087 their own packages.")
13088 (license license:gpl3+)))
13090 (define-public r-assertive-data
13092 (name "r-assertive-data")
13097 (uri (cran-uri "assertive.data" version))
13100 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13102 `((upstream-name . "assertive.data")))
13103 (build-system r-build-system)
13105 `(("r-assertive-base" ,r-assertive-base)
13106 ("r-assertive-strings" ,r-assertive-strings)))
13107 (home-page "https://bitbucket.org/richierocks/assertive.data")
13108 (synopsis "Assertions to check properties of data")
13110 "This package provides a set of predicates and assertions for checking
13111 the properties of (country independent) complex data types. This is mainly
13112 for use by other package developers who want to include run-time testing
13113 features in their own packages.")
13114 (license license:gpl3+)))
13116 (define-public r-assertive
13118 (name "r-assertive")
13123 (uri (cran-uri "assertive" version))
13126 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13127 (build-system r-build-system)
13129 `(("r-assertive-base" ,r-assertive-base)
13130 ("r-assertive-code" ,r-assertive-code)
13131 ("r-assertive-data" ,r-assertive-data)
13132 ("r-assertive-data-uk" ,r-assertive-data-uk)
13133 ("r-assertive-data-us" ,r-assertive-data-us)
13134 ("r-assertive-datetimes" ,r-assertive-datetimes)
13135 ("r-assertive-files" ,r-assertive-files)
13136 ("r-assertive-matrices" ,r-assertive-matrices)
13137 ("r-assertive-models" ,r-assertive-models)
13138 ("r-assertive-numbers" ,r-assertive-numbers)
13139 ("r-assertive-properties" ,r-assertive-properties)
13140 ("r-assertive-reflection" ,r-assertive-reflection)
13141 ("r-assertive-sets" ,r-assertive-sets)
13142 ("r-assertive-strings" ,r-assertive-strings)
13143 ("r-assertive-types" ,r-assertive-types)
13144 ("r-knitr" ,r-knitr)))
13146 `(("r-knitr" ,r-knitr)))
13147 (home-page "https://bitbucket.org/richierocks/assertive")
13148 (synopsis "Readable check functions to ensure code integrity")
13150 "This package provides lots of predicates (@code{is_*} functions) to
13151 check the state of your variables, and assertions (@code{assert_*} functions)
13152 to throw errors if they aren't in the right form.")
13153 (license license:gpl3+)))
13155 (define-public r-dotcall64
13157 (name "r-dotcall64")
13162 (uri (cran-uri "dotCall64" version))
13165 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
13166 (properties `((upstream-name . "dotCall64")))
13167 (build-system r-build-system)
13168 (native-inputs `(("gfortran" ,gfortran)))
13169 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13170 (synopsis "Enhanced foreign function interface supporting long vectors")
13172 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13173 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13174 supports long vectors, arguments of type 64-bit integer, and provides a
13175 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13176 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13177 (license license:gpl2+)))
13179 (define-public r-spam
13186 (uri (cran-uri "spam" version))
13188 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13189 (build-system r-build-system)
13191 `(("r-dotcall64" ,r-dotcall64)))
13193 `(("gfortran" ,gfortran)
13194 ("r-knitr" ,r-knitr)))
13195 (home-page "https://www.math.uzh.ch/pages/spam/")
13196 (synopsis "Sparse matrix algebra")
13198 "This package provides a set of functions for sparse matrix algebra.
13199 Differences with other sparse matrix packages are:
13202 @item it only supports (essentially) one sparse matrix format;
13203 @item it is based on transparent and simple structure(s);
13204 @item it is tailored for MCMC calculations within G(M)RF;
13205 @item and it is fast and scalable (with the extension package @code{spam64}).
13207 ;; Either of these licenses
13208 (license (list license:bsd-3 license:lgpl2.0))))
13210 (define-public r-fields
13217 (uri (cran-uri "fields" version))
13219 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13220 (build-system r-build-system)
13222 `(("r-maps" ,r-maps)
13223 ("r-spam" ,r-spam)))
13225 `(("gfortran" ,gfortran)))
13226 (home-page "https://www.image.ucar.edu/fields")
13227 (synopsis "Tools for spatial data")
13229 "This is a package for curve, surface and function fitting with an
13230 emphasis on splines, spatial data and spatial statistics. The major methods
13231 include cubic, and thin plate splines, Kriging, and compactly supported
13232 covariance functions for large data sets.")
13233 (license license:gpl2+)))
13235 (define-public r-spatialextremes
13237 (name "r-spatialextremes")
13242 (uri (cran-uri "SpatialExtremes" version))
13245 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13247 `((upstream-name . "SpatialExtremes")))
13248 (build-system r-build-system)
13250 `(("r-fields" ,r-fields)
13251 ("r-maps" ,r-maps)))
13252 (home-page "http://spatialextremes.r-forge.r-project.org/")
13253 (synopsis "Modelling spatial extremes")
13255 "This package provides tools for the statistical modelling of spatial
13256 extremes using max-stable processes, copula or Bayesian hierarchical models.
13257 More precisely, this package allows (conditional) simulations from various
13258 parametric max-stable models, analysis of the extremal spatial dependence, the
13259 fitting of such processes using composite likelihoods or least square (simple
13260 max-stable processes only), model checking and selection and prediction.")
13261 (license license:gpl2+)))
13263 (define-public r-drc
13270 (uri (cran-uri "drc" version))
13273 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13274 (build-system r-build-system)
13277 ("r-gtools" ,r-gtools)
13279 ("r-multcomp" ,r-multcomp)
13280 ("r-plotrix" ,r-plotrix)
13281 ("r-scales" ,r-scales)))
13282 (home-page "https://cran.r-project.org/web/packages/drc")
13283 (synopsis "Analysis of dose-response curves")
13285 "This package provides a suite of flexible and versatile model fitting
13286 and after-fitting functions for the analysis of dose-response data.")
13287 (license license:gpl2+)))
13289 (define-public r-rmeta
13296 (uri (cran-uri "rmeta" version))
13299 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13300 (build-system r-build-system)
13301 (home-page "https://cran.r-project.org/web/packages/rmeta")
13302 (synopsis "Tools for meta-analysis")
13304 "This package provides functions for simple fixed and random effects
13305 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13306 draws standard summary plots, funnel plots, and computes summaries and tests
13307 for association and heterogeneity.")
13308 (license license:gpl2)))
13310 (define-public r-bootstrap
13312 (name "r-bootstrap")
13317 (uri (cran-uri "bootstrap" version))
13320 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13321 (build-system r-build-system)
13322 (native-inputs `(("gfortran" ,gfortran)))
13323 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13324 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13326 "This package provides software and data for the book \"An Introduction
13327 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13328 This package is primarily provided for projects already based on it, and for
13329 support of the book. New projects should preferentially use the recommended
13330 package \"boot\".")
13331 (license license:bsd-3)))
13333 (define-public r-survivalroc
13335 (name "r-survivalroc")
13340 (uri (cran-uri "survivalROC" version))
13343 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13344 (properties `((upstream-name . "survivalROC")))
13345 (build-system r-build-system)
13346 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13347 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13349 "Compute time-dependent ROC curve from censored survival data using
13350 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13351 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13352 (license license:gpl2+)))
13354 (define-public r-longitudinal
13356 (name "r-longitudinal")
13361 (uri (cran-uri "longitudinal" version))
13364 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13365 (build-system r-build-system)
13366 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13367 (home-page "http://strimmerlab.org/software/longitudinal/")
13368 (synopsis "Analysis of multiple time course data")
13370 "This package contains general data structures and functions for
13371 longitudinal data with multiple variables, repeated measurements, and
13372 irregularly spaced time points. It also implements a shrinkage estimator of
13373 dynamical correlation and dynamical covariance.")
13374 (license license:gpl3+)))
13376 (define-public r-genenet
13383 (uri (cran-uri "GeneNet" version))
13386 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13387 (properties `((upstream-name . "GeneNet")))
13388 (build-system r-build-system)
13390 `(("r-corpcor" ,r-corpcor)
13391 ("r-fdrtool" ,r-fdrtool)
13392 ("r-longitudinal" ,r-longitudinal)))
13393 (home-page "http://strimmerlab.org/software/genenet/")
13394 (synopsis "Modeling and inferring gene networks")
13396 "This package analyzes gene expression (time series) data with focus on
13397 the inference of gene networks. In particular, GeneNet implements the methods
13398 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13399 for learning large-scale gene association networks (including assignment of
13400 putative directions).")
13401 (license license:gpl3+)))
13403 (define-public r-rbamtools
13405 (name "r-rbamtools")
13406 (version "2.16.17")
13410 (uri (cran-uri "rbamtools" version))
13413 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13414 (build-system r-build-system)
13415 (inputs `(("zlib" ,zlib)))
13417 `(("r-refgenome" ,r-refgenome)))
13418 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13419 (synopsis "Read and write BAM (binary alignment) files")
13421 "This package provides an R interface to functions of the SAMtools
13423 (license license:artistic2.0)))
13425 (define-public r-protviz
13432 (uri (cran-uri "protViz" version))
13435 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13436 (properties `((upstream-name . "protViz")))
13437 (build-system r-build-system)
13438 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13439 (home-page "https://github.com/protViz/protViz/")
13440 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13442 "This package helps with quality checks, visualizations and analysis of
13443 mass spectrometry data, coming from proteomics experiments. The package is
13444 developed, tested and used at the Functional Genomics Center Zurich, where it
13445 is used mainly for prototyping, teaching, and having fun with proteomics data.
13446 But it can also be used to do data analysis for small scale data sets.")
13447 (license license:gpl3)))
13449 (define-public r-cmprsk
13456 (uri (cran-uri "cmprsk" version))
13458 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13459 (build-system r-build-system)
13461 `(("r-survival" ,r-survival)))
13463 `(("gfortran" ,gfortran)))
13464 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13465 (synopsis "Subdistribution analysis of competing risks")
13467 "This package provides tool for estimation, testing and regression
13468 modeling of subdistribution functions in competing risks, as described in
13469 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13470 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13471 A proportional hazards model for the subdistribution of a competing risk,
13472 JASA, 94:496-509.")
13473 (license license:gpl2+)))
13475 (define-public r-etm
13482 (uri (cran-uri "etm" version))
13485 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13486 (build-system r-build-system)
13488 `(("r-data-table" ,r-data-table)
13489 ("r-lattice" ,r-lattice)
13491 ("r-rcpparmadillo" ,r-rcpparmadillo)
13492 ("r-survival" ,r-survival)))
13493 (home-page "https://cran.r-project.org/web/packages/etm")
13494 (synopsis "Empirical transition matrix")
13496 "The @dfn{empirical transition matrix} (etm) package estimates
13497 the matrix of transition probabilities for any time-inhomogeneous multistate
13498 model with finite state space using the Aalen-Johansen estimator.")
13499 (license license:expat)))
13501 (define-public r-epi
13508 (uri (cran-uri "Epi" version))
13511 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
13512 (properties `((upstream-name . "Epi")))
13513 (build-system r-build-system)
13515 `(("r-cmprsk" ,r-cmprsk)
13516 ("r-data-table" ,r-data-table)
13517 ("r-dplyr" ,r-dplyr)
13520 ("r-matrix" ,r-matrix)
13522 ("r-numderiv" ,r-numderiv)
13524 ("r-purrr" ,r-purrr)
13525 ("r-survival" ,r-survival)
13527 (home-page "https://BendixCarstensen.com/Epi/")
13528 (synopsis "Statistical analysis in epidemiology")
13530 "This package provides functions for demographic and epidemiological
13531 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13532 particular representation, manipulation and simulation of multistate data -
13533 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13534 @code{etm} and @code{cmprsk} packages. It also contains functions for
13535 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13536 data and some useful functions for tabulation and plotting, as well as a
13537 number of epidemiological data sets.")
13538 (license license:gpl2)))
13540 (define-public r-ppls
13543 (version "1.6-1.1")
13547 (uri (cran-uri "ppls" version))
13550 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13551 (build-system r-build-system)
13552 (propagated-inputs `(("r-mass" ,r-mass)))
13553 (home-page "https://cran.r-project.org/web/packages/ppls")
13554 (synopsis "Penalized partial least squares")
13556 "This package contains linear and nonlinear regression methods based on
13557 partial least squares and penalization techniques. Model parameters are
13558 selected via cross-validation, and confidence intervals ans tests for the
13559 regression coefficients can be conducted via jackknifing.")
13560 (license license:gpl2+)))
13562 (define-public r-huge
13565 (version "1.3.4.1")
13569 (uri (cran-uri "huge" version))
13571 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13572 (build-system r-build-system)
13574 `(("r-igraph" ,r-igraph)
13576 ("r-matrix" ,r-matrix)
13578 ("r-rcppeigen" ,r-rcppeigen)))
13579 (home-page "https://cran.r-project.org/web/packages/huge")
13580 (synopsis "High-dimensional undirected graph estimation")
13582 "This package provides a general framework for high-dimensional
13583 undirected graph estimation. It integrates data preprocessing, neighborhood
13584 screening, graph estimation, and model selection techniques into a pipeline.")
13585 (license license:gpl2)))
13587 (define-public r-parcor
13594 (uri (cran-uri "parcor" version))
13597 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13598 (build-system r-build-system)
13601 ("r-genenet" ,r-genenet)
13602 ("r-glmnet" ,r-glmnet)
13604 ("r-ppls" ,r-ppls)))
13605 (home-page "https://cran.r-project.org/web/packages/parcor")
13606 (synopsis "Regularized estimation of partial correlation matrices")
13608 "This package estimates the matrix of partial correlations based on
13609 different regularized regression methods: lasso, adaptive lasso, PLS, and
13610 Ridge Regression. In addition, the package provides model selection for
13611 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13612 (license license:gpl2+)))
13614 (define-public r-mcmc
13621 (uri (cran-uri "mcmc" version))
13624 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13625 (build-system r-build-system)
13626 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13627 (synopsis "Markov chain Monte Carlo")
13629 "This package simulates continuous distributions of random vectors using
13630 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13631 function that evaluates the log unnormalized density. Algorithms are random
13632 walk Metropolis algorithm (function @code{metrop}), simulated
13633 tempering (function @code{temper}), and morphometric random walk
13634 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13635 by change of variable.")
13636 (license license:expat)))
13638 (define-public r-listenv
13645 (uri (cran-uri "listenv" version))
13648 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13649 (build-system r-build-system)
13651 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13652 (home-page "https://github.com/HenrikBengtsson/listenv")
13653 (synopsis "Environments behaving (almost) as lists")
13655 "This package implements list environments. List environments are
13656 environments that have list-like properties. For instance, the elements of a
13657 list environment are ordered and can be accessed and iterated over using index
13659 (license license:lgpl2.1+)))
13661 (define-public r-globals
13668 (uri (cran-uri "globals" version))
13671 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13672 (build-system r-build-system)
13674 `(("r-codetools" ,r-codetools)))
13675 (home-page "https://github.com/HenrikBengtsson/globals")
13676 (synopsis "Identify global objects in R expressions")
13678 "This package provides tools to identify global (\"unknown\" or \"free\")
13679 objects in R expressions by code inspection using various strategies, e.g.
13680 conservative or liberal. The objective of this package is to make it as
13681 simple as possible to identify global objects for the purpose of exporting
13682 them in distributed compute environments.")
13683 (license license:lgpl2.1+)))
13685 (define-public r-parallelly
13687 (name "r-parallelly")
13692 (uri (cran-uri "parallelly" version))
13695 "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6"))))
13696 (properties `((upstream-name . "parallelly")))
13697 (build-system r-build-system)
13698 (home-page "https://github.com/HenrikBengtsson/parallelly")
13699 (synopsis "Enhancements of the parallel package")
13701 "This package provides utility functions that enhance the @code{parallel}
13702 package and support the built-in parallel backends of the @code{future}
13703 package. For example, @code{availableCores} gives the number of CPU cores
13704 available to your R process as given by R options and environment variables,
13705 including those set by job schedulers on high-performance compute clusters.
13706 If none is set, it will fall back to @code{parallel::detectCores}. Another
13707 example is @code{makeClusterPSOCK}, which is backward compatible with
13708 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13709 remote cluster workers without the need for configuring the firewall to do
13710 port-forwarding to your local computer.")
13711 (license license:lgpl2.1+)))
13713 (define-public r-future
13720 (uri (cran-uri "future" version))
13723 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13724 (build-system r-build-system)
13726 `(("r-digest" ,r-digest)
13727 ("r-globals" ,r-globals)
13728 ("r-listenv" ,r-listenv)
13729 ("r-parallelly" ,r-parallelly)))
13731 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13732 (home-page "https://github.com/HenrikBengtsson/future")
13733 (synopsis "Unified parallel and distributed processing in R")
13735 "The purpose of this package is to provide a lightweight and unified
13736 Future API for sequential and parallel processing of R expression via futures.
13737 This package implements sequential, multicore, multisession, and cluster
13738 futures. With these, R expressions can be evaluated on the local machine, in
13739 parallel a set of local machines, or distributed on a mix of local and remote
13740 machines. Extensions to this package implement additional backends for
13741 processing futures via compute cluster schedulers etc. Because of its unified
13742 API, there is no need to modify any code in order to switch from sequential on
13743 the local machine to, say, distributed processing on a remote compute cluster.")
13744 (license license:lgpl2.1+)))
13746 (define-public r-future-apply
13748 (name "r-future-apply")
13753 (uri (cran-uri "future.apply" version))
13756 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13757 (properties `((upstream-name . "future.apply")))
13758 (build-system r-build-system)
13760 `(("r-future" ,r-future)
13761 ("r-globals" ,r-globals)))
13763 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13764 (home-page "https://github.com/HenrikBengtsson/future.apply")
13765 (synopsis "Apply function to elements in parallel using futures")
13767 "This package provides implementations of @code{apply()},
13768 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13769 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13770 can be resolved using any future-supported backend, e.g. parallel on the local
13771 machine or distributed on a compute cluster.")
13772 (license license:gpl2+)))
13774 (define-public r-rsvd
13781 (uri (cran-uri "rsvd" version))
13784 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13785 (build-system r-build-system)
13787 `(("r-matrix" ,r-matrix)))
13788 (home-page "https://github.com/erichson/rSVD")
13789 (synopsis "Randomized singular value decomposition")
13791 "Low-rank matrix decompositions are fundamental tools and widely used for
13792 data analysis, dimension reduction, and data compression. Classically, highly
13793 accurate deterministic matrix algorithms are used for this task. However, the
13794 emergence of large-scale data has severely challenged our computational
13795 ability to analyze big data. The concept of randomness has been demonstrated
13796 as an effective strategy to quickly produce approximate answers to familiar
13797 problems such as the @dfn{singular value decomposition} (SVD). This package
13798 provides several randomized matrix algorithms such as the randomized singular
13799 value decomposition (@code{rsvd}), randomized principal component
13800 analysis (@code{rpca}), randomized robust principal component
13801 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13802 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13803 functions are provided.")
13804 (license license:gpl3+)))
13806 (define-public r-sloop
13813 (uri (cran-uri "sloop" version))
13816 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13817 (build-system r-build-system)
13819 `(("r-codetools" ,r-codetools)
13820 ("r-crayon" ,r-crayon)
13821 ("r-purrr" ,r-purrr)
13822 ("r-rlang" ,r-rlang)
13823 ("r-tibble" ,r-tibble)))
13824 (home-page "https://github.com/r-lib/sloop")
13825 (synopsis "Helpers for object-oriented programming in R")
13827 "This package provides a collection of helper functions designed to
13828 help you to better understand object oriented programming in R, particularly
13830 (license license:gpl3)))
13832 (define-public r-capushe
13839 (uri (cran-uri "capushe" version))
13842 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13843 (build-system r-build-system)
13844 (propagated-inputs `(("r-mass" ,r-mass)))
13845 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13846 (synopsis "Calibrating penalties using slope heuristics")
13848 "This package provides tools for the calibration of penalized criteria
13849 for model selection. The calibration methods available are based on the slope
13851 (license license:gpl2+)))
13853 (define-public r-dorng
13860 (uri (cran-uri "doRNG" version))
13863 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13864 (properties `((upstream-name . "doRNG")))
13865 (build-system r-build-system)
13867 `(("r-foreach" ,r-foreach)
13868 ("r-iterators" ,r-iterators)
13869 ("r-rngtools" ,r-rngtools)))
13870 (home-page "https://renozao.github.io/doRNG/")
13871 (synopsis "Generic reproducible parallel backend for foreach loops")
13873 "This package provides functions to perform reproducible parallel
13874 @code{foreach} loops, using independent random streams as generated by
13875 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13876 convert standard @code{%dopar%} loops into fully reproducible loops,
13877 independently of the number of workers, the task scheduling strategy, or the
13878 chosen parallel environment and associated foreach backend.")
13879 (license license:gpl2+)))
13881 (define-public r-blockmodeling
13883 (name "r-blockmodeling")
13888 (uri (cran-uri "blockmodeling" version))
13891 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13892 (build-system r-build-system)
13894 `(("r-matrix" ,r-matrix)))
13895 (native-inputs `(("gfortran" ,gfortran)))
13896 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13897 (synopsis "Generalized and classical blockmodeling of valued networks")
13899 "This package is primarily meant as an implementation of generalized
13900 blockmodeling for valued networks. In addition, measures of similarity or
13901 dissimilarity based on structural equivalence and regular equivalence (REGE
13902 algorithms) can be computed and partitioned matrices can be plotted.")
13903 (license license:gpl2+)))
13905 (define-public r-upsetr
13912 (uri (cran-uri "UpSetR" version))
13915 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13916 (properties `((upstream-name . "UpSetR")))
13917 (build-system r-build-system)
13919 `(("r-ggplot2" ,r-ggplot2)
13920 ("r-gridextra" ,r-gridextra)
13922 ("r-scales" ,r-scales)))
13923 (home-page "https://github.com/hms-dbmi/UpSetR")
13924 (synopsis "Visualize intersecting sets")
13926 "This package provides a more scalable alternative to Venn and Euler
13927 diagrams for visualizing intersecting sets. Create visualizations of
13928 intersecting sets using a novel matrix design, along with visualizations of
13929 several common set, element and attribute related tasks.")
13930 (license license:expat)))
13932 ;; This package includes a JavaScript file, which is not minified. When
13933 ;; upgrading please check that there are no new minified JavaScript files.
13934 (define-public r-shinybs
13941 (uri (cran-uri "shinyBS" version))
13944 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13945 (properties `((upstream-name . "shinyBS")))
13946 (build-system r-build-system)
13947 ;; The tests spawn Shiny browser apps. They cannot be run
13948 ;; non-interactively.
13949 (arguments '(#:tests? #f))
13951 `(("r-htmltools" ,r-htmltools)
13952 ("r-shiny" ,r-shiny)))
13953 (home-page "https://ebailey78.github.io/shinyBS/")
13954 (synopsis "Twitter Bootstrap components for Shiny")
13956 "This package adds additional Twitter Bootstrap components to Shiny.")
13957 (license license:gpl3)))
13959 (define-public r-shinyjqui
13961 (name "r-shinyjqui")
13966 (uri (cran-uri "shinyjqui" version))
13969 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
13972 (delete-file "inst/www/shinyjqui.min.js")))))
13973 (properties `((upstream-name . "shinyjqui")))
13974 (build-system r-build-system)
13977 (modify-phases %standard-phases
13978 (add-after 'unpack 'process-javascript
13979 (lambda* (#:key inputs #:allow-other-keys)
13980 (with-directory-excursion "inst/www/"
13981 (let ((source "shinyjqui.js")
13982 (target "shinyjqui.min.js"))
13983 (format #true "Processing ~a --> ~a~%"
13985 (invoke "esbuild" source "--minify"
13986 (string-append "--outfile=" target)))))))))
13988 `(("r-htmltools" ,r-htmltools)
13989 ("r-htmlwidgets" ,r-htmlwidgets)
13990 ("r-jsonlite" ,r-jsonlite)
13991 ("r-shiny" ,r-shiny)))
13993 `(("r-knitr" ,r-knitr)
13994 ("esbuild" ,esbuild)))
13995 (home-page "https://github.com/yang-tang/shinyjqui")
13996 (synopsis "jQuery UI interactions and effects for Shiny")
13998 "This is an extension to Shiny that brings interactions and animation
13999 effects from the jQuery UI library.")
14000 (license license:expat)))
14002 (define-public r-outliers
14004 (name "r-outliers")
14009 (uri (cran-uri "outliers" version))
14012 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14013 (build-system r-build-system)
14014 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14015 (synopsis "Tests for outliers")
14017 "This package provides a collection of some tests commonly used for
14018 identifying outliers.")
14019 (license license:gpl2+)))
14021 (define-public r-bayesm
14028 (uri (cran-uri "bayesm" version))
14030 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14031 (build-system r-build-system)
14033 `(("r-rcpp" ,r-rcpp)
14034 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14035 (home-page "http://www.perossi.org/home/bsm-1")
14036 (synopsis "Bayesian inference for marketing/micro-econometrics")
14038 "This package covers many important models used in marketing and
14039 micro-econometrics applications, including Bayes Regression (univariate or
14040 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14041 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14042 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14043 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14044 Estimation with normal base, Hierarchical Linear Models with normal prior and
14045 covariates, Hierarchical Linear Models with a mixture of normals prior and
14046 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14047 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14048 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14049 analysis of choice-based conjoint data, Bayesian treatment of linear
14050 instrumental variables models, Analysis of Multivariate Ordinal survey data
14051 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14052 Coefficient Logit Models.")
14053 (license license:gpl2+)))
14055 (define-public r-tensora
14062 (uri (cran-uri "tensorA" version))
14065 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14066 (properties `((upstream-name . "tensorA")))
14067 (build-system r-build-system)
14068 (home-page "http://www.stat.boogaart.de/tensorA")
14069 (synopsis "Advanced tensor arithmetic with named indices")
14071 "This package provides convenience functions for advanced linear algebra
14072 with tensors and computation with datasets of tensors on a higher level
14073 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14074 co- and contravariate indices, and parallel computations on sequences of
14076 (license license:gpl2+)))
14078 (define-public r-rarpack
14085 (uri (cran-uri "rARPACK" version))
14088 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14089 (properties `((upstream-name . "rARPACK")))
14090 (build-system r-build-system)
14091 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14092 (home-page "https://github.com/yixuan/rARPACK")
14093 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14095 "This package was previously an R wrapper of the ARPACK library, and now
14096 a shell of the R package RSpectra, an R interface to the Spectra library for
14097 solving large scale eigenvalue/vector problems. The current version of
14098 rARPACK simply imports and exports the functions provided by RSpectra. New
14099 users of rARPACK are advised to switch to the RSpectra package.")
14100 (license license:bsd-3)))
14102 (define-public r-compositions
14104 (name "r-compositions")
14109 (uri (cran-uri "compositions" version))
14112 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14113 (build-system r-build-system)
14115 `(("r-bayesm" ,r-bayesm)
14117 ("r-robustbase" ,r-robustbase)
14118 ("r-tensora" ,r-tensora)))
14120 `(("r-knitr" ,r-knitr)))
14121 (home-page "http://www.stat.boogaart.de/compositions")
14122 (synopsis "Compositional data analysis")
14124 "This package provides functions for the consistent analysis of
14125 compositional data (e.g. portions of substances) and positive
14126 numbers (e.g. concentrations).")
14127 (license license:gpl2+)))
14129 (define-public r-cobs
14136 (uri (cran-uri "cobs" version))
14139 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14140 (build-system r-build-system)
14142 `(("r-quantreg" ,r-quantreg)
14143 ("r-sparsem" ,r-sparsem)))
14144 (home-page "https://cran.r-project.org/web/packages/cobs")
14145 (synopsis "Constrained B-Splines (sparse matrix based)")
14147 "This package provides qualitatively constrained (regression) smoothing
14148 splines via linear programming and sparse matrices.")
14149 (license license:gpl2+)))
14151 (define-public r-drimpute
14153 (name "r-drimpute")
14158 (uri (cran-uri "DrImpute" version))
14161 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14162 (properties `((upstream-name . "DrImpute")))
14163 (build-system r-build-system)
14165 `(("r-rcpp" ,r-rcpp)
14166 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14167 (home-page "https://github.com/ikwak2/DrImpute")
14168 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14170 "This is an R package for imputing dropout events. Many statistical
14171 methods in cell type identification, visualization and lineage reconstruction
14172 do not account for dropout events. DrImpute can improve the performance of
14173 such software by imputing dropout events.")
14174 (license license:gpl3)))
14176 (define-public r-gamlss-dist
14178 (name "r-gamlss-dist")
14183 (uri (cran-uri "gamlss.dist" version))
14185 (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc"))))
14186 (properties `((upstream-name . "gamlss.dist")))
14187 (build-system r-build-system)
14188 (propagated-inputs `(("r-mass" ,r-mass)))
14189 (home-page "http://www.gamlss.org/")
14190 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14192 "This package provides a set of distributions which can be used for
14193 modelling the response variables in Generalized Additive Models for Location
14194 Scale and Shape. The distributions can be continuous, discrete or mixed
14195 distributions. Extra distributions can be created, by transforming, any
14196 continuous distribution defined on the real line, to a distribution defined on
14197 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14198 transformation, respectively.")
14199 ;; Either version of the GPL.
14200 (license (list license:gpl2 license:gpl3))))
14202 ;; This package includes JavaScript files, which are not minified. When
14203 ;; upgrading please check that there are no new minified JavaScript files.
14204 (define-public r-shinyjs
14211 (uri (cran-uri "shinyjs" version))
14214 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14215 (build-system r-build-system)
14217 `(("r-digest" ,r-digest)
14218 ("r-htmltools" ,r-htmltools)
14219 ("r-jsonlite" ,r-jsonlite)
14220 ("r-shiny" ,r-shiny)))
14222 `(("r-knitr" ,r-knitr)))
14223 (home-page "https://deanattali.com/shinyjs")
14224 (synopsis "Improve the user experience of your Shiny apps")
14226 "Perform common useful JavaScript operations in Shiny apps that will
14227 greatly improve your apps without having to know any JavaScript. Examples
14228 include: hiding an element, disabling an input, resetting an input back to its
14229 original value, delaying code execution by a few seconds, and many more useful
14230 functions for both the end user and the developer. Shinyjs can also be used
14231 to easily call your own custom JavaScript functions from R.")
14232 (license license:agpl3+)))
14234 ;; This package includes minified JavaScript files. When upgrading please
14235 ;; check that there are no new minified JavaScript files.
14236 (define-public r-colourpicker
14238 (name "r-colourpicker")
14243 (uri (cran-uri "colourpicker" version))
14246 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14247 (build-system r-build-system)
14249 `(#:modules ((guix build utils)
14250 (guix build r-build-system)
14254 (modify-phases %standard-phases
14255 (add-after 'unpack 'process-javascript
14256 (lambda* (#:key inputs #:allow-other-keys)
14257 (with-directory-excursion "inst"
14261 `((,(assoc-ref inputs "js-salvattore")
14262 "examples/colourInput/www/salvattore.min.js")
14263 (,(assoc-ref inputs "js-jquery")
14264 "htmlwidgets/lib/jquery/jquery.min.js")
14265 ("www/shared/colourpicker/js/colourpicker.js"
14266 "www/shared/colourpicker/js/colourpicker.min.js"))))
14267 (lambda (sources targets)
14268 (for-each (lambda (source target)
14269 (format #t "Processing ~a --> ~a~%"
14271 (delete-file target)
14272 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14273 (call-with-output-file target
14275 (dump-port minified port)))))
14276 sources targets))))
14279 `(("r-ggplot2" ,r-ggplot2)
14280 ("r-htmltools" ,r-htmltools)
14281 ("r-htmlwidgets" ,r-htmlwidgets)
14282 ("r-jsonlite" ,r-jsonlite)
14283 ("r-miniui" ,r-miniui)
14284 ("r-shiny" ,r-shiny)
14285 ("r-shinyjs" ,r-shinyjs)))
14287 `(("r-knitr" ,r-knitr)
14288 ("uglify-js" ,uglify-js)
14292 (uri "https://code.jquery.com/jquery-3.3.1.js")
14295 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14299 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14302 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14303 (home-page "https://github.com/daattali/colourpicker")
14304 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14306 "This package provides a color picker that can be used as an input in
14307 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14308 custom color palettes, and many more options. A plot color helper tool is
14309 available as an RStudio Addin, which helps you pick colors to use in your
14310 plots. A more generic color picker RStudio Addin is also provided to let you
14311 select colors to use in your R code.")
14312 (license license:expat)))
14314 (define-public r-ggextra
14321 (uri (cran-uri "ggExtra" version))
14324 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14325 (properties `((upstream-name . "ggExtra")))
14326 (build-system r-build-system)
14328 `(("r-colourpicker" ,r-colourpicker)
14329 ("r-ggplot2" ,r-ggplot2)
14330 ("r-gtable" ,r-gtable)
14331 ("r-miniui" ,r-miniui)
14333 ("r-scales" ,r-scales)
14334 ("r-shiny" ,r-shiny)
14335 ("r-shinyjs" ,r-shinyjs)))
14337 `(("r-knitr" ,r-knitr)))
14338 (home-page "https://github.com/daattali/ggExtra")
14339 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14341 "This package is a collection of functions and layers to enhance ggplot2.
14342 The flagship function is @code{ggMarginal()}, which can be used to add
14343 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14344 (license license:expat)))
14346 (define-public r-minpack-lm
14348 (name "r-minpack-lm")
14353 (uri (cran-uri "minpack.lm" version))
14356 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14357 (properties `((upstream-name . "minpack.lm")))
14358 (build-system r-build-system)
14359 (native-inputs `(("gfortran" ,gfortran)))
14360 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14361 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14363 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14364 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14365 problems by a modification of the Levenberg-Marquardt algorithm, with support
14366 for lower and upper parameter bounds. The implementation can be used via
14367 @code{nls}-like calls using the @code{nlsLM} function.")
14368 (license license:gpl3)))
14370 (define-public r-moments
14377 (uri (cran-uri "moments" version))
14380 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14381 (build-system r-build-system)
14382 (home-page "https://cran.r-project.org/web/packages/moments")
14383 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14385 "This package provides functions to calculate: moments, Pearson's
14386 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14387 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14388 (license license:gpl2+)))
14390 (define-public r-msir
14397 (uri (cran-uri "msir" version))
14400 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14401 (build-system r-build-system)
14403 `(("r-mclust" ,r-mclust)))
14405 `(("r-knitr" ,r-knitr)))
14406 (home-page "https://cran.r-project.org/web/packages/msir")
14407 (synopsis "Model-based sliced inverse regression")
14409 "This is an R package for dimension reduction based on finite Gaussian
14410 mixture modeling of inverse regression.")
14411 (license license:gpl2+)))
14413 (define-public r-pbivnorm
14415 (name "r-pbivnorm")
14420 (uri (cran-uri "pbivnorm" version))
14423 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14424 (build-system r-build-system)
14425 (native-inputs `(("gfortran" ,gfortran)))
14426 (home-page "https://github.com/brentonk/pbivnorm")
14427 (synopsis "Vectorized bivariate normal CDF")
14429 "This package provides a vectorized R function for calculating
14430 probabilities from a standard bivariate normal CDF.")
14431 (license license:gpl2+)))
14433 (define-public r-lavaan
14440 (uri (cran-uri "lavaan" version))
14443 "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0"))))
14444 (build-system r-build-system)
14446 `(("r-mass" ,r-mass)
14447 ("r-mnormt" ,r-mnormt)
14448 ("r-numderiv" ,r-numderiv)
14449 ("r-pbivnorm" ,r-pbivnorm)))
14450 (home-page "https://lavaan.ugent.be")
14451 (synopsis "Latent variable analysis")
14453 "This package provides tools to fit a variety of latent variable models,
14454 including confirmatory factor analysis, structural equation modeling and
14455 latent growth curve models.")
14456 (license license:gpl2+)))
14458 (define-public r-nonnest2
14460 (name "r-nonnest2")
14465 (uri (cran-uri "nonnest2" version))
14468 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14469 (build-system r-build-system)
14471 `(("r-compquadform" ,r-compquadform)
14472 ("r-lavaan" ,r-lavaan)
14473 ("r-mvtnorm" ,r-mvtnorm)
14474 ("r-sandwich" ,r-sandwich)))
14476 `(("r-knitr" ,r-knitr)))
14477 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14478 (synopsis "Tests of non-nested models")
14480 "This package allows for testing of non-nested models. It includes tests
14481 of model distinguishability and of model fit that can be applied to both
14482 nested and non-nested models. The package also includes functionality to
14483 obtain confidence intervals associated with AIC and BIC.")
14484 ;; Either version of the GPL.
14485 (license (list license:gpl2 license:gpl3))))
14487 (define-public r-penalized
14489 (name "r-penalized")
14494 (uri (cran-uri "penalized" version))
14497 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14498 (build-system r-build-system)
14500 `(("r-rcpp" ,r-rcpp)
14501 ("r-rcpparmadillo" ,r-rcpparmadillo)
14502 ("r-survival" ,r-survival)))
14503 (home-page "https://cran.r-project.org/web/packages/penalized/")
14504 (synopsis "Penalized estimation in GLMs and in the Cox model")
14506 "This package provides tools for fitting possibly high dimensional
14507 penalized regression models. The penalty structure can be any combination of
14508 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14509 constraint on the regression coefficients. The supported regression models
14510 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14511 model. Cross-validation routines allow optimization of the tuning
14513 (license license:gpl2+)))
14515 (define-public r-zim
14522 (uri (cran-uri "ZIM" version))
14525 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14526 (properties `((upstream-name . "ZIM")))
14527 (build-system r-build-system)
14528 (propagated-inputs `(("r-mass" ,r-mass)))
14529 (home-page "https://github.com/biostatstudio/ZIM")
14530 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14532 "Analyze count time series with excess zeros. Two types of statistical
14533 models are supported: Markov regression and state-space models. They are also
14534 known as observation-driven and parameter-driven models respectively in the
14535 time series literature. The functions used for Markov regression or
14536 observation-driven models can also be used to fit ordinary regression models
14537 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14538 negative binomial (ZINB) assumption. The package also contains miscellaneous
14539 functions to compute density, distribution, quantile, and generate random
14540 numbers from ZIP and ZINB distributions.")
14541 (license license:gpl3)))
14543 (define-public r-nor1mix
14550 (uri (cran-uri "nor1mix" version))
14553 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14554 (build-system r-build-system)
14555 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14556 (synopsis "Normal (1-d) mixture models")
14558 "This package provides S3 classes and methods for one-dimensional normal
14559 mixture models, for, e.g., density estimation or clustering algorithms
14560 research and teaching; it provides the widely used Marron-Wand densities. It
14561 also provides tools for efficient random number generation and graphics.")
14562 (license license:gpl2+)))
14564 (define-public r-beanplot
14566 (name "r-beanplot")
14571 (uri (cran-uri "beanplot" version))
14574 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14575 (build-system r-build-system)
14576 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14577 (synopsis "Visualization via beanplots")
14579 "This package provides beanplots, an alternative to
14580 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14582 (license license:gpl2)))
14584 (define-public r-pbdzmq
14591 (uri (cran-uri "pbdZMQ" version))
14594 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14595 (properties `((upstream-name . "pbdZMQ")))
14596 (build-system r-build-system)
14598 `(("zeromq" ,zeromq)
14601 `(("pkg-config" ,pkg-config)))
14602 (home-page "https://pbdr.org/")
14603 (synopsis "R interface to ZeroMQ")
14605 "ZeroMQ is a well-known library for high-performance asynchronous
14606 messaging in scalable, distributed applications. This package provides high
14607 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14608 interactive client/server programming frameworks. A few wrapper functions
14609 compatible with @code{rzmq} are also provided.")
14610 (license license:gpl3)))
14612 (define-public r-repr
14619 (uri (cran-uri "repr" version))
14622 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14623 (build-system r-build-system)
14625 `(("r-base64enc" ,r-base64enc)
14626 ("r-htmltools" ,r-htmltools)
14627 ("r-jsonlite" ,r-jsonlite)
14628 ("r-pillar" ,r-pillar)))
14629 (home-page "https://cran.r-project.org/web/packages/repr/")
14630 (synopsis "Serializable representations")
14632 "This package provides string and binary representations of objects for
14633 several formats and MIME types.")
14634 (license license:gpl3)))
14636 (define-public r-irdisplay
14638 (name "r-irdisplay")
14643 (uri (cran-uri "IRdisplay" version))
14646 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14647 (properties `((upstream-name . "IRdisplay")))
14648 (build-system r-build-system)
14650 `(("r-repr" ,r-repr)))
14651 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14652 (synopsis "Jupyter display machinery")
14654 "This package provides an interface to the rich display capabilities of
14655 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14656 running IRkernel session.")
14657 (license license:expat)))
14659 (define-public r-irkernel
14661 (name "r-irkernel")
14666 (uri (cran-uri "IRkernel" version))
14669 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14670 (properties `((upstream-name . "IRkernel")))
14671 (build-system r-build-system)
14674 (modify-phases %standard-phases
14675 (add-after 'install 'install-kernelspec
14676 (lambda* (#:key outputs #:allow-other-keys)
14677 (let ((out (assoc-ref outputs "out")))
14678 (setenv "HOME" "/tmp")
14679 (invoke "jupyter" "kernelspec" "install"
14682 (string-append out "/site-library/IRkernel/kernelspec"))
14683 ;; Record the absolute file name of the 'R' executable in
14685 (substitute* (string-append out "/share/jupyter"
14686 "/kernels/ir/kernel.json")
14688 (string-append "[\"" (which "R") "\",")))
14691 `(("jupyter" ,jupyter)))
14693 `(("r-crayon" ,r-crayon)
14694 ("r-digest" ,r-digest)
14695 ("r-evaluate" ,r-evaluate)
14696 ("r-irdisplay" ,r-irdisplay)
14697 ("r-jsonlite" ,r-jsonlite)
14698 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14699 ("r-minimal" ,r-minimal)
14700 ("r-pbdzmq" ,r-pbdzmq)
14702 ("r-uuid" ,r-uuid)))
14703 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14704 (synopsis "Native R kernel for Jupyter")
14706 "The R kernel for the Jupyter environment executes R code which the
14707 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14709 (license license:expat)))
14711 (define-public r-gmodels
14718 (uri (cran-uri "gmodels" version))
14721 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14722 (build-system r-build-system)
14724 `(("r-gdata" ,r-gdata)
14725 ("r-mass" ,r-mass)))
14726 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14727 (synopsis "Various R programming tools for model fitting")
14729 "This package provides various R programming tools for model fitting.")
14730 (license license:gpl2)))
14732 (define-public r-apcluster
14734 (name "r-apcluster")
14739 (uri (cran-uri "apcluster" version))
14742 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14743 (build-system r-build-system)
14745 `(("r-matrix" ,r-matrix)
14746 ("r-rcpp" ,r-rcpp)))
14747 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14748 (synopsis "Affinity propagation clustering")
14750 "This package implements affinity propagation clustering introduced by
14751 Frey and Dueck (2007). The package further provides leveraged affinity
14752 propagation and an algorithm for exemplar-based agglomerative clustering that
14753 can also be used to join clusters obtained from affinity propagation. Various
14754 plotting functions are available for analyzing clustering results.")
14755 (license license:gpl2+)))
14757 (define-public r-valr
14764 (uri (cran-uri "valr" version))
14767 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14768 (build-system r-build-system)
14770 `(("r-broom" ,r-broom)
14771 ("r-dplyr" ,r-dplyr)
14772 ("r-ggplot2" ,r-ggplot2)
14774 ("r-readr" ,r-readr)
14775 ("r-rlang" ,r-rlang)
14776 ("r-stringr" ,r-stringr)
14777 ("r-tibble" ,r-tibble)))
14779 `(("r-knitr" ,r-knitr)))
14780 (home-page "https://github.com/rnabioco/valr")
14781 (synopsis "Genome interval arithmetic in R")
14783 "This package enables you to read and manipulate genome intervals and
14784 signals. It provides functionality similar to command-line tool suites within
14785 R, enabling interactive analysis and visualization of genome-scale data.")
14786 (license license:expat)))
14788 (define-public r-rematch2
14790 (name "r-rematch2")
14795 (uri (cran-uri "rematch2" version))
14798 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14799 (build-system r-build-system)
14801 `(("r-tibble" ,r-tibble)))
14802 (home-page "https://github.com/r-lib/rematch2")
14803 (synopsis "Tidy output from regular expression matching")
14805 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14806 return the match results in tidy data frames.")
14807 (license license:expat)))
14809 (define-public r-picante
14816 (uri (cran-uri "picante" version))
14819 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14820 (build-system r-build-system)
14824 ("r-vegan" ,r-vegan)))
14825 (home-page "https://cran.r-project.org/web/packages/picante/")
14826 (synopsis "Integrating phylogenies and ecology")
14828 "This package provides functions for phylocom integration, community
14829 analyses, null-models, traits and evolution. It implements numerous
14830 ecophylogenetic approaches including measures of community phylogenetic and
14831 trait diversity, phylogenetic signal, estimation of trait values for
14832 unobserved taxa, null models for community and phylogeny randomizations, and
14833 utility functions for data input/output and phylogeny plotting. A full
14834 description of package functionality and methods are provided by Kembel et
14836 (license license:gpl2)))
14838 (define-public r-reinforcelearn
14840 (name "r-reinforcelearn")
14845 (uri (cran-uri "reinforcelearn" version))
14848 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14849 (build-system r-build-system)
14851 `(("r-checkmate" ,r-checkmate)
14853 ("r-purrr" ,r-purrr)
14855 (home-page "https://markusdumke.github.io/reinforcelearn")
14856 (synopsis "Reinforcement learning")
14858 "This package implements reinforcement learning environments and
14859 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14860 can be used with function approximation, eligibility traces (Singh & Sutton,
14861 1996) and experience replay (Mnih et al., 2013).")
14862 (license license:expat)))
14864 (define-public r-lemon
14871 (uri (cran-uri "lemon" version))
14874 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14875 (build-system r-build-system)
14877 `(("r-ggplot2" ,r-ggplot2)
14878 ("r-gridextra" ,r-gridextra)
14879 ("r-gtable" ,r-gtable)
14880 ("r-knitr" ,r-knitr)
14881 ("r-lattice" ,r-lattice)
14883 ("r-rlang" ,r-rlang)
14884 ("r-scales" ,r-scales)))
14886 `(("r-knitr" ,r-knitr)))
14887 (home-page "https://github.com/stefanedwards/lemon")
14888 (synopsis "Freshen up your ggplot2 plots")
14890 "This package provides functions for working with legends and axis lines
14891 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14893 (license license:gpl3)))
14895 (define-public r-wgaim
14902 (uri (cran-uri "wgaim" version))
14904 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14905 (build-system r-build-system)
14907 `(("r-ggplot2" ,r-ggplot2)
14909 (home-page "https://cran.r-project.org/web/packages/wgaim")
14910 (synopsis "Whole genome average interval mapping for QTL detection")
14912 "This package integrates sophisticated mixed modelling methods with a
14913 whole genome approach to detecting significant QTL in linkage maps.")
14914 (license license:gpl2+)))
14916 (define-public r-bedr
14923 (uri (cran-uri "bedr" version))
14926 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14927 (build-system r-build-system)
14929 `(("r-data-table" ,r-data-table)
14930 ("r-r-utils" ,r-r-utils)
14931 ("r-testthat" ,r-testthat)
14932 ("r-venndiagram" ,r-venndiagram)
14935 ("bedtools" ,bedtools)
14936 ("htslib" ,htslib))) ; for tabix
14938 `(("r-knitr" ,r-knitr))) ; for vignettes
14939 (home-page "https://cran.r-project.org/web/packages/bedr")
14940 (synopsis "Genomic region processing")
14942 "This package is for genomic regions processing using command line tools
14943 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14944 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14945 The bedr package's API enhances access to these tools as well as offers
14946 additional utilities for genomic regions processing.")
14947 (license license:gpl2)))
14949 (define-public r-sets
14956 (uri (cran-uri "sets" version))
14959 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14960 (properties `((upstream-name . "sets")))
14961 (build-system r-build-system)
14962 (home-page "https://cran.r-project.org/web/packages/sets")
14963 (synopsis "Sets, generalized sets, customizable sets and intervals")
14965 "This package provides data structures and basic operations for ordinary
14966 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14967 customizable sets, and intervals.")
14968 (license license:gpl2)))
14970 (define-public r-partitions
14972 (name "r-partitions")
14977 (uri (cran-uri "partitions" version))
14980 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14981 (build-system r-build-system)
14984 ("r-polynom" ,r-polynom)
14985 ("r-sets" ,r-sets)))
14986 (home-page "https://cran.r-project.org/web/packages/partitions")
14987 (synopsis "Additive partitions of integers")
14989 "This package provides tools to enumerates the partitions, unequal
14990 partitions, and restricted partitions of an integer; the three corresponding
14991 partition functions are also given.")
14992 ;; Any version of the GPL
14993 (license license:gpl2+)))
14995 (define-public r-brobdingnag
14997 (name "r-brobdingnag")
15002 (uri (cran-uri "Brobdingnag" version))
15005 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
15006 (properties `((upstream-name . "Brobdingnag")))
15007 (build-system r-build-system)
15008 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15009 (synopsis "Very large numbers in R")
15011 "This package handles very large numbers in R. Real numbers are held
15012 using their natural logarithms, plus a logical flag indicating sign. The
15013 package includes a vignette that gives a step-by-step introduction to using S4
15015 ;; Any version of the GPL
15016 (license license:gpl2+)))
15018 (define-public r-untb
15025 (uri (cran-uri "untb" version))
15028 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15029 (build-system r-build-system)
15031 `(("r-brobdingnag" ,r-brobdingnag)
15032 ("r-partitions" ,r-partitions)
15033 ("r-polynom" ,r-polynom)))
15034 (home-page "https://github.com/RobinHankin/untb.git")
15035 (synopsis "Ecological drift under the UNTB")
15037 "This package provides numerical simulations, and visualizations, of
15038 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15039 (license license:gpl2+)))
15041 (define-public r-stepwise
15043 (name "r-stepwise")
15048 (uri (cran-uri "stepwise" version))
15051 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15052 (build-system r-build-system)
15053 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15054 (synopsis "Stepwise detection of recombination breakpoints")
15056 "This package provides a stepwise approach to identifying recombination
15057 breakpoints in a genomic sequence alignment.")
15058 (license license:gpl2+)))
15060 (define-public r-snpmaxsel
15062 (name "r-snpmaxsel")
15067 (uri (cran-uri "SNPmaxsel" version))
15070 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15071 (properties `((upstream-name . "SNPmaxsel")))
15072 (build-system r-build-system)
15074 `(("r-combinat" ,r-combinat)
15075 ("r-mvtnorm" ,r-mvtnorm)))
15076 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15077 (synopsis "Maximally selected statistics for SNP data")
15079 "This package implements asymptotic methods related to maximally selected
15080 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15082 (license license:gpl2+)))
15084 (define-public r-acsnminer
15086 (name "r-acsnminer")
15087 (version "0.16.8.25")
15090 (uri (cran-uri "ACSNMineR" version))
15093 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15094 (properties `((upstream-name . "ACSNMineR")))
15095 (build-system r-build-system)
15097 `(("r-ggplot2" ,r-ggplot2)
15098 ("r-gridextra" ,r-gridextra)))
15099 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15100 (synopsis "Gene enrichment analysis")
15102 "This package provides tools to compute and represent gene set enrichment
15103 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15104 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15105 enrichment can be run with hypergeometric test or Fisher exact test, and can
15106 use multiple corrections. Visualization of data can be done either by
15107 barplots or heatmaps.")
15108 (license license:gpl2+)))
15110 (define-public r-seqinr
15117 (uri (cran-uri "seqinr" version))
15120 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15121 (build-system r-build-system)
15123 `(("r-ade4" ,r-ade4)
15124 ("r-segmented" ,r-segmented)))
15127 (home-page "http://seqinr.r-forge.r-project.org/")
15128 (synopsis "Biological sequences retrieval and analysis")
15130 "This package provides tools for exploratory data analysis and data
15131 visualization of biological sequence (DNA and protein) data. It also includes
15132 utilities for sequence data management under the ACNUC system.")
15133 (license license:gpl2+)))
15135 (define-public r-units
15142 (uri (cran-uri "units" version))
15145 "0kwfcrrbcwl7s50n1wp33vswqzmprh91clvakbd1jpznqpg5m3js"))))
15146 (build-system r-build-system)
15148 `(("udunits" ,udunits)))
15150 `(("r-rcpp" ,r-rcpp)))
15152 `(("r-knitr" ,r-knitr)))
15153 (home-page "https://github.com/r-quantities/units/")
15154 (synopsis "Measurement Units for R Vectors")
15156 "This package provides support for measurement units in R vectors,
15157 matrices and arrays: automatic propagation, conversion, derivation and
15158 simplification of units; raising errors in case of unit incompatibility. It
15159 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15161 (license license:gpl2)))
15163 (define-public r-udunits2
15165 (name "r-udunits2")
15170 (uri (cran-uri "udunits2" version))
15173 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15174 (properties `((upstream-name . "udunits2")))
15175 (build-system r-build-system)
15177 `(("udunits" ,udunits)))
15178 (home-page "https://cran.r-project.org/package=udunits2")
15179 (synopsis "Udunits-2 bindings for R")
15181 "This package provides simple bindings to Unidata's udunits library.")
15182 (license license:gpl2)))
15184 (define-public r-classint
15186 (name "r-classint")
15191 (uri (cran-uri "classInt" version))
15194 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15195 (properties `((upstream-name . "classInt")))
15196 (build-system r-build-system)
15198 `(("r-class" ,r-class)
15199 ("r-e1071" ,r-e1071)
15200 ("r-kernsmooth" ,r-kernsmooth)))
15202 `(("gfortran" ,gfortran)
15203 ("r-knitr" ,r-knitr)))
15204 (home-page "https://github.com/r-spatial/classInt/")
15205 (synopsis "Choose univariate class intervals")
15207 "This package provides selected commonly used methods for choosing
15208 univariate class intervals for mapping or other graphics purposes.")
15209 (license license:gpl2+)))
15211 (define-public r-spdata
15218 (uri (cran-uri "spData" version))
15221 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15222 (properties `((upstream-name . "spData")))
15223 (build-system r-build-system)
15225 `(("r-raster" ,r-raster)
15227 (home-page "https://github.com/Nowosad/spData")
15228 (synopsis "Datasets for spatial analysis")
15230 "This a package containing diverse spatial datasets for demonstrating,
15231 benchmarking and teaching spatial data analysis. It includes R data of class
15232 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15233 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15234 of the datasets are designed to illustrate specific analysis techniques.
15235 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15236 illustrate point pattern analysis techniques.")
15237 (license license:cc0)))
15239 (define-public r-learnbayes
15241 (name "r-learnbayes")
15246 (uri (cran-uri "LearnBayes" version))
15249 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15250 (properties `((upstream-name . "LearnBayes")))
15251 (build-system r-build-system)
15252 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15253 (synopsis "Functions for learning Bayesian inference")
15255 "This package provides a collection of functions helpful in learning the
15256 basic tenets of Bayesian statistical inference. It contains functions for
15257 summarizing basic one and two parameter posterior distributions and predictive
15258 distributions. It contains MCMC algorithms for summarizing posterior
15259 distributions defined by the user. It also contains functions for regression
15260 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15262 (license license:gpl2+)))
15264 (define-public r-deldir
15271 (uri (cran-uri "deldir" version))
15274 "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5"))))
15275 (build-system r-build-system)
15276 (native-inputs `(("gfortran" ,gfortran)))
15277 (home-page "https://cran.r-project.org/web/packages/deldir")
15278 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15280 "This package provides tools for calculating the Delaunay triangulation
15281 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15282 of a planar point set. It plots triangulations and tessellations in various
15283 ways, clips tessellations to sub-windows, calculates perimeters of
15284 tessellations, and summarizes information about the tiles of the
15286 (license license:gpl2+)))
15288 (define-public r-sf
15295 (uri (cran-uri "sf" version))
15298 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
15299 (build-system r-build-system)
15307 `(("r-classint" ,r-classint)
15309 ("r-magrittr" ,r-magrittr)
15311 ("r-units" ,r-units)))
15313 `(("pkg-config" ,pkg-config)
15314 ("r-knitr" ,r-knitr)))
15315 (home-page "https://github.com/r-spatial/sf/")
15316 (synopsis "Simple features for R")
15318 "This package provides support for simple features, a standardized way to
15319 encode spatial vector data. It binds to GDAL for reading and writing data, to
15320 GEOS for geometrical operations, and to PROJ for projection conversions and
15321 datum transformations.")
15322 ;; Either of these licenses
15323 (license (list license:gpl2 license:expat))))
15325 (define-public r-spdep
15332 (uri (cran-uri "spdep" version))
15335 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15336 (build-system r-build-system)
15338 `(("r-boot" ,r-boot)
15340 ("r-deldir" ,r-deldir)
15342 ("r-gmodels" ,r-gmodels)
15343 ("r-learnbayes" ,r-learnbayes)
15345 ("r-matrix" ,r-matrix)
15349 ("r-spdata" ,r-spdata)))
15351 `(("r-knitr" ,r-knitr)))
15352 (home-page "https://github.com/r-spatial/spdep/")
15353 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15355 "This package provides a collection of functions to create spatial
15356 weights matrix objects from polygon contiguities, from point patterns by
15357 distance and tessellations, for summarizing these objects, and for permitting
15358 their use in spatial data analysis, including regional aggregation by minimum
15360 (license license:gpl2+)))
15362 (define-public r-adegenet
15364 (name "r-adegenet")
15369 (uri (cran-uri "adegenet" version))
15372 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15373 (build-system r-build-system)
15375 `(("r-ade4" ,r-ade4)
15378 ("r-dplyr" ,r-dplyr)
15379 ("r-ggplot2" ,r-ggplot2)
15380 ("r-igraph" ,r-igraph)
15382 ("r-reshape2" ,r-reshape2)
15383 ("r-seqinr" ,r-seqinr)
15384 ("r-shiny" ,r-shiny)
15385 ("r-spdep" ,r-spdep)
15386 ("r-vegan" ,r-vegan)))
15387 (home-page "https://github.com/thibautjombart/adegenet")
15388 (synopsis "Exploratory analysis of genetic and genomic data")
15390 "This package provides a toolset for the exploration of genetic and
15391 genomic data. Adegenet provides formal (S4) classes for storing and handling
15392 various genetic data, including genetic markers with varying ploidy and
15393 hierarchical population structure (@code{genind} class), alleles counts by
15394 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15395 also implements original multivariate methods (DAPC, sPCA), graphics,
15396 statistical tests, simulation tools, distance and similarity measures, and
15397 several spatial methods. A range of both empirical and simulated datasets is
15398 also provided to illustrate various methods.")
15399 (license license:gpl2+)))
15401 (define-public r-pegas
15408 (uri (cran-uri "pegas" version))
15410 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15411 (build-system r-build-system)
15413 `(("r-adegenet" ,r-adegenet)
15415 (home-page "http://ape-package.ird.fr/pegas.html")
15416 (synopsis "Population and evolutionary genetics analysis system")
15418 "This package provides functions for reading, writing, plotting,
15419 analysing, and manipulating allelic and haplotypic data, including from VCF
15420 files, and for the analysis of population nucleotide sequences and
15421 micro-satellites including coalescent analyses, linkage disequilibrium,
15422 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15423 minimum spanning tree and network, and median-joining networks.")
15424 (license license:gpl2+)))
15426 (define-public r-rmetasim
15428 (name "r-rmetasim")
15433 (uri (cran-uri "rmetasim" version))
15436 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15437 (build-system r-build-system)
15439 `(("r-ade4" ,r-ade4)
15440 ("r-adegenet" ,r-adegenet)
15441 ("r-gtools" ,r-gtools)
15442 ("r-pegas" ,r-pegas)))
15443 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15444 (synopsis "Individual-based population genetic simulation environment")
15446 "This package provides an interface between R and the metasim simulation
15447 engine. The simulation environment is documented in: Strand, A.(2002),
15448 Metasim 1.0: an individual-based environment for simulating population
15449 genetics of complex population dynamics.")
15451 (license license:gpl2+)))
15453 (define-public r-genetics
15455 (name "r-genetics")
15456 (version "1.3.8.1.3")
15460 (uri (cran-uri "genetics" version))
15463 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
15464 (build-system r-build-system)
15466 `(("r-combinat" ,r-combinat)
15467 ("r-gdata" ,r-gdata)
15468 ("r-gtools" ,r-gtools)
15470 ("r-mvtnorm" ,r-mvtnorm)))
15471 (home-page "https://cran.r-project.org/web/packages/genetics/")
15472 (synopsis "Population genetics")
15474 "This package provides classes and methods for handling genetic data.
15475 It includes classes to represent genotypes and haplotypes at single markers up
15476 to multiple markers on multiple chromosomes. Function include allele
15477 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15478 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15479 and testing for linkage disequilibrium, ...")
15480 ;; Any GPL version.
15481 (license license:gpl2+)))
15483 (define-public r-snp-plotter
15485 (name "r-snp-plotter")
15490 (uri (cran-uri "snp.plotter" version))
15493 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15494 (properties `((upstream-name . "snp.plotter")))
15495 (build-system r-build-system)
15496 (propagated-inputs `(("r-genetics" ,r-genetics)))
15497 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15498 (synopsis "Plot p-values using single SNP and/or haplotype data")
15500 "This package helps you create plots of p-values using single SNP and/or
15501 haplotype data. Main features of the package include options to display a
15502 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15503 datasets simultaneously. Plots can be created using global and/or individual
15504 haplotype p-values along with single SNP p-values. Images are created as
15505 either PDF/EPS files.")
15506 (license license:gpl2+)))
15508 (define-public r-polspline
15510 (name "r-polspline")
15515 (uri (cran-uri "polspline" version))
15517 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15518 (build-system r-build-system)
15519 (native-inputs `(("gfortran" ,gfortran)))
15520 (home-page "https://cran.r-project.org/web/packages/polspline/")
15521 (synopsis "Polynomial spline routines")
15523 "This package provides routines for the polynomial spline fitting
15524 routines hazard regression, hazard estimation with flexible tails, logspline,
15525 lspec, polyclass, and polymars.")
15526 (license license:gpl2+)))
15528 (define-public r-rms
15535 (uri (cran-uri "rms" version))
15537 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15538 (build-system r-build-system)
15540 `(("r-cluster" ,r-cluster)
15541 ("r-digest" ,r-digest)
15542 ("r-ggplot2" ,r-ggplot2)
15543 ("r-hmisc" ,r-hmisc)
15544 ("r-htmltable" ,r-htmltable)
15545 ("r-htmltools" ,r-htmltools)
15546 ("r-lattice" ,r-lattice)
15548 ("r-multcomp" ,r-multcomp)
15550 ("r-polspline" ,r-polspline)
15551 ("r-quantreg" ,r-quantreg)
15552 ("r-rpart" ,r-rpart)
15553 ("r-sparsem" ,r-sparsem)
15554 ("r-survival" ,r-survival)))
15555 (native-inputs `(("gfortran" ,gfortran)))
15556 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15557 (synopsis "Regression modeling strategies")
15559 "This is a package for regression modeling, testing, estimation,
15560 validation, graphics, prediction, and typesetting by storing enhanced model
15561 design attributes in the fit. The rms package is a collection of functions
15562 that assist with and streamline modeling. It also contains functions for
15563 binary and ordinal logistic regression models, ordinal models for continuous Y
15564 with a variety of distribution families, and the Buckley-James multiple
15565 regression model for right-censored responses, and implements penalized
15566 maximum likelihood estimation for logistic and ordinary linear models. The
15567 package works with almost any regression model, but it was especially written
15568 to work with binary or ordinal regression models, Cox regression, accelerated
15569 failure time models, ordinary linear models, the Buckley-James model,
15570 generalized least squares for serially or spatially correlated observations,
15571 generalized linear models, and quantile regression.")
15572 (license license:gpl2+)))
15574 (define-public r-arsenal
15581 (uri (cran-uri "arsenal" version))
15584 "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn"))))
15585 (properties `((upstream-name . "arsenal")))
15586 (build-system r-build-system)
15587 (propagated-inputs `(("r-knitr" ,r-knitr)))
15588 (native-inputs `(("r-knitr" ,r-knitr)))
15589 (home-page "https://github.com/mayoverse/arsenal")
15590 (synopsis "Functions for large-scale statistical summaries")
15592 "This package provides an arsenal of R functions for large-scale
15593 statistical summaries, which are streamlined to work within the latest
15594 reporting tools in R and RStudio and which use formulas and versatile
15595 summary statistics for summary tables and models. The primary functions
15599 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15600 levels of one or more categorical variables;
15601 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15602 across two time points;
15603 @item @code{modelsum}, which performs simple model fits on one or more
15604 endpoints for many variables (univariate or adjusted for covariates);
15605 @item @code{freqlist}, a powerful frequency table across many categorical
15607 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15608 @item @code{write2}, a function to output tables to a document.
15611 (license license:gpl2+)))
15613 (define-public r-haplo-stats
15615 (name "r-haplo-stats")
15620 (uri (cran-uri "haplo.stats" version))
15623 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15624 (properties `((upstream-name . "haplo.stats")))
15625 (build-system r-build-system)
15627 `(("r-arsenal" ,r-arsenal)
15630 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15631 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15632 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15634 "This package provides routines for the analysis of indirectly measured
15635 haplotypes. The statistical methods assume that all subjects are unrelated
15636 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15637 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15638 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15639 examples in the vignette.")
15640 (license license:gpl2+)))
15642 (define-public r-bqtl
15649 (uri (cran-uri "bqtl" version))
15652 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15653 (build-system r-build-system)
15654 (native-inputs `(("gfortran" ,gfortran)))
15655 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15656 (synopsis "Bayesian QTL mapping toolkit")
15658 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15659 lines. It includes maximum likelihood and Bayesian tools.")
15660 (license license:gpl2+)))
15662 (define-public r-ibdreg
15669 (uri (cran-uri "ibdreg" version))
15672 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15673 (build-system r-build-system)
15674 (home-page "https://www.mayo.edu/research/labs/\
15675 statistical-genetics-genetic-epidemiology/software")
15676 (synopsis "Regression methods for IBD linkage with covariates")
15678 "This package provides a method to test genetic linkage with covariates
15679 by regression methods with response IBD sharing for relative pairs. Account
15680 for correlations of IBD statistics and covariates for relative pairs within
15681 the same pedigree.")
15682 (license license:gpl2+)))
15684 (define-public r-dlmap
15691 (uri (cran-uri "dlmap" version))
15694 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15695 (build-system r-build-system)
15697 `(("r-ibdreg" ,r-ibdreg)
15701 ("r-wgaim" ,r-wgaim)))
15702 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15703 (synopsis "Detection localization mapping for QTL")
15705 "This is package for QTL mapping in a mixed model framework with separate
15706 detection and localization stages. The first stage detects the number of QTL
15707 on each chromosome based on the genetic variation due to grouped markers on
15708 the chromosome; the second stage uses this information to determine the most
15709 likely QTL positions. The mixed model can accommodate general fixed and
15710 random effects, including spatial effects in field trials and pedigree
15711 effects. It is applicable to backcrosses, doubled haploids, recombinant
15712 inbred lines, F2 intercrosses, and association mapping populations.")
15713 (license license:gpl2)))
15715 (define-public r-hwde
15722 (uri (cran-uri "hwde" version))
15725 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15726 (build-system r-build-system)
15727 (home-page "https://cran.r-project.org/web/packages/hwde/")
15728 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15730 "This package fits models for genotypic disequilibria, as described in
15731 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15732 terms are available that account for first order interactions between loci.
15733 It also implements, for a single locus in a single population, a conditional
15734 exact test for Hardy-Weinberg equilibrium.")
15735 (license license:gpl2+)))
15737 (define-public r-tdthap
15744 (uri (cran-uri "tdthap" version))
15747 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15748 (build-system r-build-system)
15749 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15750 (synopsis "TDT tests for extended haplotypes")
15752 "Functions and examples are provided for transmission/disequilibrium
15753 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15754 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15755 (license license:artistic2.0)))
15757 (define-public r-sparql
15763 (uri (cran-uri "SPARQL" version))
15766 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15767 (properties `((upstream-name . "SPARQL")))
15768 (build-system r-build-system)
15770 `(("r-rcurl" ,r-rcurl)
15772 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15773 (synopsis "SPARQL client for R")
15774 (description "This package provides an interface to use SPARQL to pose
15775 SELECT or UPDATE queries to an end-point.")
15776 ;; The only license indication is found in the DESCRIPTION file,
15777 ;; which states GPL-3. So we cannot assume GPLv3+.
15778 (license license:gpl3)))
15780 (define-public r-bookdown
15782 (name "r-bookdown")
15786 (uri (cran-uri "bookdown" version))
15789 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15790 (build-system r-build-system)
15792 `(("r-htmltools" ,r-htmltools)
15793 ("r-knitr" ,r-knitr)
15794 ("r-rmarkdown" ,r-rmarkdown)
15795 ("r-tinytex" ,r-tinytex)
15798 ("pandoc" ,pandoc)))
15799 (home-page "https://github.com/rstudio/bookdown")
15800 (synopsis "Authoring books and technical documents with R markdown")
15801 (description "This package provides output formats and utilities for
15802 authoring books and technical documents with R Markdown.")
15803 (license license:gpl3)))
15805 (define-public r-optparse
15807 (name "r-optparse")
15812 (uri (cran-uri "optparse" version))
15815 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15816 (build-system r-build-system)
15818 `(("r-getopt" ,r-getopt)))
15820 `(("r-knitr" ,r-knitr)))
15821 (home-page "https://github.com/trevorld/optparse")
15822 (synopsis "Command line option parser")
15824 "This package provides a command line parser inspired by Python's
15825 @code{optparse} library to be used with Rscript to write shebang scripts
15826 that accept short and long options.")
15827 (license license:gpl2+)))
15829 (define-public r-kernlab
15836 (uri (cran-uri "kernlab" version))
15838 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15839 (build-system r-build-system)
15840 (home-page "https://cran.r-project.org/web/packages/kernlab")
15841 (synopsis "Kernel-based machine learning tools")
15843 "This package provides kernel-based machine learning methods for
15844 classification, regression, clustering, novelty detection, quantile regression
15845 and dimensionality reduction. Among other methods @code{kernlab} includes
15846 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15848 (license license:gpl2)))
15850 (define-public r-hierfstat
15852 (name "r-hierfstat")
15857 (uri (cran-uri "hierfstat" version))
15860 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15861 (build-system r-build-system)
15863 `(("r-ade4" ,r-ade4)
15864 ("r-adegenet" ,r-adegenet)
15865 ("r-gaston" ,r-gaston)
15866 ("r-gtools" ,r-gtools)))
15868 `(("r-knitr" ,r-knitr)))
15869 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15870 (synopsis "Estimation and tests of hierarchical F-statistics")
15872 "This package allows the estimation of hierarchical F-statistics from
15873 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15874 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15875 are also given to test via randomisations the significance of each F and
15876 variance components, using the likelihood-ratio statistics G.")
15877 (license license:gpl2+)))
15879 (define-public r-hapassoc
15881 (name "r-hapassoc")
15886 (uri (cran-uri "hapassoc" version))
15889 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15890 (build-system r-build-system)
15891 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15892 (synopsis "Inference of trait associations with SNP haplotypes")
15894 "Hapassoc performs likelihood inference of trait associations with
15895 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15896 functions are developed primarily for data collected in cohort or
15897 cross-sectional studies. They can accommodate uncertain haplotype phase and
15898 handle missing genotypes at some SNPs.")
15899 (license license:gpl2)))
15901 (define-public r-sampling
15903 (name "r-sampling")
15908 (uri (cran-uri "sampling" version))
15911 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15912 (build-system r-build-system)
15914 `(("r-lpsolve" ,r-lpsolve)
15915 ("r-mass" ,r-mass)))
15916 (home-page "https://cran.r-project.org/web/packages/sampling/")
15917 (synopsis "Survey sampling")
15919 "This package provides functions for drawing and calibrating samples.")
15920 (license license:gpl2+)))
15922 (define-public r-r2html
15929 (uri (cran-uri "R2HTML" version))
15932 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15933 (properties `((upstream-name . "R2HTML")))
15934 (build-system r-build-system)
15935 (home-page "https://github.com/nalimilan/R2HTML")
15936 (synopsis "HTML export for R objects")
15938 "This package includes HTML functions and methods to write in an HTML
15939 file. Thus, making HTML reports is easy. It includes a function that allows
15940 redirection on the fly, which appears to be very useful for teaching purposes,
15941 as the student can keep a copy of the produced output to keep all that they
15942 did during the course. The package comes with a vignette describing how to
15943 write HTML reports for statistical analysis. Finally, a driver for Sweave
15944 parses HTML flat files containing R code and to automatically write
15945 the corresponding outputs (tables and graphs).")
15946 (license license:gpl2+)))
15948 (define-public r-rjava
15955 (uri (cran-uri "rJava" version))
15958 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15959 (properties `((upstream-name . "rJava")))
15960 (build-system r-build-system)
15962 `(#:modules ((guix build utils)
15963 (guix build r-build-system)
15966 (modify-phases %standard-phases
15967 (add-after 'unpack 'set-JAVA_HOME
15968 (lambda* (#:key inputs #:allow-other-keys)
15969 (let ((jdk (assoc-ref inputs "jdk")))
15970 (setenv "JAVA_HOME" jdk)
15971 (setenv "JAVA" (which "java"))
15972 (setenv "JAR" (which "jar"))
15973 (setenv "JAVAC" (which "javac"))
15974 (setenv "JAVAH" (which "javah"))
15975 (setenv "JAVA_CPPFLAGS"
15976 (string-append "-I" jdk "/include "
15977 "-I" jdk "/include/linux"))
15978 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15979 ((lib) (setenv "JAVA_LIBS" lib))
15980 (_ (error "Could not find libjvm.so"))))
15984 ("jdk" ,icedtea-8 "jdk")
15987 (home-page "https://www.rforge.net/rJava/")
15988 (synopsis "Low-Level R to Java interface")
15990 "This package provides a low-level interface to the Java VM very much
15991 like .C/.Call and friends. It allows the creation of objects, calling methods
15992 and accessing fields.")
15993 (license license:gpl2)))
15995 (define-public r-svmisc
16002 (uri (cran-uri "svMisc" version))
16005 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
16006 (properties `((upstream-name . "svMisc")))
16007 (build-system r-build-system)
16008 (home-page "https://github.com/SciViews/svMisc")
16009 (synopsis "Miscellaneous functions for SciViews")
16011 "This package provides miscellaneous functions for SciViews or general
16012 use, including tools to manage a temporary environment attached to the search
16013 path for temporary variables you do not want to @code{save()} or
16014 @code{load()}; test the current platform; showing progress bars, etc.")
16015 (license license:gpl2)))
16017 (define-public r-xyz
16024 (uri (cran-uri "xyz" version))
16027 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16028 (build-system r-build-system)
16030 `(("r-rcpp" ,r-rcpp)))
16031 (home-page "https://cran.r-project.org/web/packages/xyz/")
16032 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16034 "High dimensional interaction search by brute force requires a quadratic
16035 computational cost in the number of variables. The xyz algorithm provably
16036 finds strong interactions in almost linear time. For details of the algorithm
16037 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16038 interaction search in high-dimensional data.")
16039 ;; Any version of the GPL.
16040 (license license:gpl2+)))
16042 (define-public r-rttf2pt1
16044 (name "r-rttf2pt1")
16049 (uri (cran-uri "Rttf2pt1" version))
16052 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16053 (properties `((upstream-name . "Rttf2pt1")))
16054 (build-system r-build-system)
16055 (home-page "https://github.com/wch/Rttf2pt1")
16056 (synopsis "Font conversion utility")
16058 "This package contains the program @code{ttf2pt1}, for use with the
16059 @code{extrafont} package.")
16060 ;; Most of the files are covered under the Expat license. Some files are
16061 ;; covered under BSD-3. Deviations for individual files are recorded in
16062 ;; the LICENSE file.
16063 (license (list license:bsd-3 license:expat
16064 (license:non-copyleft "file://LICENSE")))))
16066 (define-public r-extrafontdb
16068 (name "r-extrafontdb")
16073 (uri (cran-uri "extrafontdb" version))
16076 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16077 (build-system r-build-system)
16078 (home-page "https://github.com/wch/extrafontdb")
16079 (synopsis "Database for the extrafont package")
16081 "This package holds the database for the @code{extrafont} package.")
16082 (license license:gpl2)))
16084 (define-public r-extrafont
16086 (name "r-extrafont")
16091 (uri (cran-uri "extrafont" version))
16094 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16095 (build-system r-build-system)
16097 `(("r-extrafontdb" ,r-extrafontdb)
16098 ("r-rttf2pt1" ,r-rttf2pt1)))
16099 (home-page "https://github.com/wch/extrafont")
16100 (synopsis "Tools for using fonts in R")
16102 "The extrafont package makes it easier to use fonts other than the basic
16103 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16104 used with PDF or PostScript output files. There are two hurdles for using
16105 fonts in PDF (or Postscript) output files:
16108 @item Making R aware of the font and the dimensions of the characters.
16109 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16110 properly on a device that doesn't have the font. This is usually needed if
16111 you want to print the PDF file or share it with others.
16114 The extrafont package makes both of these things easier.")
16115 (license license:gpl2)))
16117 (define-public r-xkcd
16124 (uri (cran-uri "xkcd" version))
16127 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16128 (build-system r-build-system)
16130 `(("r-extrafont" ,r-extrafont)
16131 ("r-ggplot2" ,r-ggplot2)
16132 ("r-hmisc" ,r-hmisc)))
16133 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16134 (synopsis "Plot ggplot2 graphics in the XKCD style")
16136 "This package provides the means to plot ggplot2 graphs in the style of
16137 the XKCD web comic.")
16138 (license license:gpl3)))
16140 (define-public r-msigdbr
16147 (uri (cran-uri "msigdbr" version))
16150 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16151 (build-system r-build-system)
16153 `(("r-dplyr" ,r-dplyr)
16154 ("r-magrittr" ,r-magrittr)
16155 ("r-rlang" ,r-rlang)
16156 ("r-tibble" ,r-tibble)
16157 ("r-tidyselect" ,r-tidyselect)))
16159 `(("r-knitr" ,r-knitr)))
16160 (home-page "https://github.com/igordot/msigdbr")
16161 (synopsis "MSigDB gene sets for multiple organisms")
16163 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16164 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16165 software in a standard R data frame with key-value pairs. Included are the
16166 original human gene symbols and Entrez IDs as well as the equivalents for
16167 various frequently studied model organisms such as mouse, rat, pig, fly, and
16169 ;; The package is covered under the Expat license, but the upstream MSigDB
16170 ;; files are made available under the Creative Commons Attribution 4.0
16171 ;; International license.
16172 (license (list license:expat license:cc-by4.0))))
16174 (define-public r-gridgraphics
16176 (name "r-gridgraphics")
16181 (uri (cran-uri "gridGraphics" version))
16184 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16185 (properties `((upstream-name . "gridGraphics")))
16186 (build-system r-build-system)
16187 (home-page "https://github.com/pmur002/gridgraphics")
16188 (synopsis "Redraw base graphics using @code{grid} graphics")
16190 "This package provides functions to convert a page of plots drawn with
16191 the @code{graphics} package into identical output drawn with the @code{grid}
16192 package. The result looks like the original @code{graphics}-based plot, but
16193 consists of @code{grid} grobs and viewports that can then be manipulated with
16194 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16195 (license license:gpl2+)))
16197 (define-public r-farver
16204 (uri (cran-uri "farver" version))
16207 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
16208 (build-system r-build-system)
16209 (home-page "https://github.com/thomasp85/farver")
16210 (synopsis "Vectorized color conversion and comparison")
16212 "The encoding of color can be handled in many different ways, using
16213 different color spaces. As different color spaces have different uses,
16214 efficient conversion between these representations are important. This
16215 package provides a set of functions that gives access to very fast color space
16216 conversion and comparisons implemented in C++, and offers 100-fold speed
16217 improvements over the @code{convertColor} function in the @code{grDevices}
16219 (license license:expat)))
16221 (define-public r-ggplotify
16223 (name "r-ggplotify")
16228 (uri (cran-uri "ggplotify" version))
16231 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16232 (build-system r-build-system)
16234 `(("r-ggplot2" ,r-ggplot2)
16235 ("r-gridgraphics" ,r-gridgraphics)
16236 ("r-rvcheck" ,r-rvcheck)))
16238 `(("r-knitr" ,r-knitr)))
16239 (home-page "https://github.com/GuangchuangYu/ggplotify")
16240 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16242 "This package provides tools to convert plot function calls (using
16243 expression or formula) to @code{grob} or @code{ggplot} objects that are
16244 compatible with the @code{grid} and @code{ggplot2} environment. With this
16245 package, we are able to e.g. use @code{cowplot} to align plots produced by
16246 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16247 converting them to @code{ggplot} objects.")
16248 (license license:artistic2.0)))
16250 (define-public r-triebeard
16252 (name "r-triebeard")
16257 (uri (cran-uri "triebeard" version))
16260 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16261 (build-system r-build-system)
16262 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16263 (home-page "https://github.com/Ironholds/triebeard/")
16264 (synopsis "Radix trees in Rcpp")
16266 "Radix trees, or tries, are key-value data structures optimized for
16267 efficient lookups, similar in purpose to hash tables. This package provides
16268 an implementation of radix trees for use in R programming and in developing
16269 packages with Rcpp.")
16270 (license license:expat)))
16272 (define-public r-tweenr
16279 (uri (cran-uri "tweenr" version))
16282 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
16283 (build-system r-build-system)
16285 `(("r-farver" ,r-farver)
16286 ("r-magrittr" ,r-magrittr)
16288 ("r-rlang" ,r-rlang)))
16289 (home-page "https://github.com/thomasp85/tweenr")
16290 (synopsis "Interpolate data for smooth animations")
16292 "In order to create smooth animation between states of data, tweening is
16293 necessary. This package provides a range of functions for creating tweened
16294 data that can be used as basis for animation. Furthermore it adds a number of
16295 vectorized interpolaters for common R data types such as numeric, date and
16297 (license license:expat)))
16299 (define-public r-polyclip
16301 (name "r-polyclip")
16306 (uri (cran-uri "polyclip" version))
16309 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16310 (build-system r-build-system)
16311 (native-inputs `(("pkg-config" ,pkg-config)))
16312 (home-page "http://www.angusj.com/delphi/clipper.php")
16313 (synopsis "Polygon clipping")
16315 "This package provides an R port of the library Clipper. It performs
16316 polygon clipping operations (intersection, union, set minus, set difference)
16317 for polygonal regions of arbitrary complexity, including holes. It computes
16318 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16319 dilations) for polygonal regions and polygonal lines. It computes the
16320 Minkowski Sum of general polygons. There is a function for removing
16321 self-intersections from polygon data.")
16322 (license license:boost1.0)))
16324 (define-public r-urltools
16326 (name "r-urltools")
16331 (uri (cran-uri "urltools" version))
16334 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16335 (build-system r-build-system)
16337 `(("r-rcpp" ,r-rcpp)
16338 ("r-triebeard" ,r-triebeard)))
16339 (home-page "https://github.com/Ironholds/urltools/")
16340 (synopsis "Vectorized tools for URL handling and parsing")
16342 "This package provides a toolkit for all URL-handling needs, including
16343 encoding and decoding, parsing, parameter extraction and modification. All
16344 functions are designed to be both fast and entirely vectorized. It is
16345 intended to be useful for people dealing with web-related datasets, such as
16346 server-side logs, although may be useful for other situations involving large
16348 (license license:expat)))
16350 (define-public r-ggforce
16357 (uri (cran-uri "ggforce" version))
16360 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
16361 (build-system r-build-system)
16363 `(("r-ggplot2" ,r-ggplot2)
16364 ("r-gtable" ,r-gtable)
16366 ("r-polyclip" ,r-polyclip)
16368 ("r-rcppeigen" ,r-rcppeigen)
16369 ("r-rlang" ,r-rlang)
16370 ("r-scales" ,r-scales)
16371 ("r-tidyselect" ,r-tidyselect)
16372 ("r-tweenr" ,r-tweenr)
16373 ("r-withr" ,r-withr)))
16374 (home-page "https://ggforce.data-imaginist.com")
16375 (synopsis "Accelerating ggplot2")
16377 "The aim of the ggplot2 package is to aid in visual data investigations.
16378 This focus has led to a lack of facilities for composing specialized plots.
16379 Thi package aims to be a collection of mainly new statistics and geometries
16380 that fills this gap.")
16381 (license license:expat)))
16383 (define-public r-europepmc
16385 (name "r-europepmc")
16390 (uri (cran-uri "europepmc" version))
16393 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16394 (build-system r-build-system)
16396 `(("r-dplyr" ,r-dplyr)
16398 ("r-jsonlite" ,r-jsonlite)
16400 ("r-progress" ,r-progress)
16401 ("r-purrr" ,r-purrr)
16402 ("r-rlang" ,r-rlang)
16403 ("r-tibble" ,r-tibble)
16404 ("r-tidyr" ,r-tidyr)
16405 ("r-urltools" ,r-urltools)
16406 ("r-xml2" ,r-xml2)))
16408 `(("r-knitr" ,r-knitr)))
16409 (home-page "https://github.com/ropensci/europepmc/")
16410 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16412 "This package provides an R Client for the
16413 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16414 Service}. It gives access to both metadata on life science literature and
16415 open access full texts. Europe PMC indexes all PubMed content and other
16416 literature sources including Agricola, a bibliographic database of citations
16417 to the agricultural literature, or Biological Patents. In addition to
16418 bibliographic metadata, the client allows users to fetch citations and
16419 reference lists. Links between life-science literature and other EBI
16420 databases, including ENA, PDB or ChEMBL are also accessible.")
16421 (license license:gpl3)))
16423 (define-public r-ggraph
16430 (uri (cran-uri "ggraph" version))
16433 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
16434 (build-system r-build-system)
16436 `(("r-digest" ,r-digest)
16437 ("r-dplyr" ,r-dplyr)
16438 ("r-ggforce" ,r-ggforce)
16439 ("r-ggplot2" ,r-ggplot2)
16440 ("r-ggrepel" ,r-ggrepel)
16441 ("r-graphlayouts" ,r-graphlayouts)
16442 ("r-gtable" ,r-gtable)
16443 ("r-igraph" ,r-igraph)
16446 ("r-rlang" ,r-rlang)
16447 ("r-scales" ,r-scales)
16448 ("r-tidygraph" ,r-tidygraph)
16449 ("r-viridis" ,r-viridis)
16450 ("r-withr" ,r-withr)))
16452 `(("r-knitr" ,r-knitr)))
16453 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16454 (synopsis "Implementation of grammar of graphics for graphs and networks")
16456 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16457 graph and network visualizations due to its reliance on tabular data input.
16458 The ggraph package is an extension of the ggplot2 API tailored to graph
16459 visualizations and provides the same flexible approach to building up plots
16461 (license license:gpl3)))
16463 (define-public r-gkmsvm
16470 (uri (cran-uri "gkmSVM" version))
16473 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
16474 (properties `((upstream-name . "gkmSVM")))
16475 (build-system r-build-system)
16477 `(("r-kernlab" ,r-kernlab)
16480 ("r-seqinr" ,r-seqinr)))
16481 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
16482 (synopsis "Gapped-kmer support vector machine")
16484 "This R package provides tools for training gapped-kmer SVM classifiers
16485 for DNA and protein sequences. This package supports several sequence
16486 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
16487 (license license:gpl2+)))
16489 (define-public r-varselrf
16491 (name "r-varselrf")
16496 (uri (cran-uri "varSelRF" version))
16499 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16500 (properties `((upstream-name . "varSelRF")))
16501 (build-system r-build-system)
16503 `(("r-randomforest" ,r-randomforest)))
16504 (home-page "https://www.ligarto.org/rdiaz/software/software")
16505 (synopsis "Variable selection using random forests")
16507 "This package provides tools for the variable selection from random
16508 forests using both backwards variable elimination (for the selection of small
16509 sets of non-redundant variables) and selection based on the importance
16510 spectrum (somewhat similar to scree plots; for the selection of large,
16511 potentially highly-correlated variables). The main applications are in
16512 high-dimensional data (e.g., microarray data, and other genomics and
16513 proteomics applications).")
16514 (license license:gpl2+)))
16516 (define-public r-pamr
16523 (uri (cran-uri "pamr" version))
16526 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16527 (build-system r-build-system)
16529 `(("r-cluster" ,r-cluster)
16530 ("r-survival" ,r-survival)))
16531 (native-inputs `(("gfortran" ,gfortran)))
16532 (home-page "https://cran.r-project.org/web/packages/pamr/")
16533 (synopsis "Prediction Analysis for Microarrays")
16535 "This package provides some functions for sample classification in
16537 (license license:gpl2)))
16539 (define-public r-rda
16542 (version "1.0.2-2.1")
16546 (uri (cran-uri "rda" version))
16549 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16550 (build-system r-build-system)
16551 (home-page "https://cran.r-project.org/web/packages/rda/")
16552 (synopsis "Shrunken centroids regularized discriminant analysis")
16554 "This package provides tools for shrunken centroids regularized
16555 discriminant analysis for the purpose of classifying high dimensional data.")
16556 (license license:gpl2+)))
16558 (define-public r-ggvis
16565 (uri (cran-uri "ggvis" version))
16568 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16569 (build-system r-build-system)
16571 `(("r-assertthat" ,r-assertthat)
16572 ("r-dplyr" ,r-dplyr)
16573 ("r-htmltools" ,r-htmltools)
16574 ("r-jsonlite" ,r-jsonlite)
16575 ("r-magrittr" ,r-magrittr)
16576 ("r-rlang" ,r-rlang)
16577 ("r-shiny" ,r-shiny)))
16578 (home-page "https://ggvis.rstudio.com/")
16579 (synopsis "Interactive grammar of graphics")
16581 "This package is a data visualization package for R providing an
16582 implementation of an interactive grammar of graphics, taking the best parts of
16583 ggplot2, combining them with the reactive framework of Shiny and drawing web
16584 graphics using Vega.")
16585 (license license:gpl2)))
16587 (define-public r-gbm
16594 (uri (cran-uri "gbm" version))
16597 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16598 (build-system r-build-system)
16600 `(("r-lattice" ,r-lattice)
16601 ("r-survival" ,r-survival)))
16603 `(("r-knitr" ,r-knitr)))
16604 (home-page "https://github.com/gbm-developers/gbm")
16605 (synopsis "Generalized boosted regression models")
16607 "This package is an implementation of extensions to Freund and Schapire's
16608 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16609 regression methods for least squares, absolute loss, t-distribution loss,
16610 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16611 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16612 and Learning to Rank measures (LambdaMart).")
16613 (license license:gpl2+)))
16615 (define-public r-threejs
16622 (uri (cran-uri "threejs" version))
16625 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16626 (build-system r-build-system)
16628 `(#:modules ((guix build utils)
16629 (guix build r-build-system)
16633 (modify-phases %standard-phases
16634 (add-after 'unpack 'process-javascript
16635 (lambda* (#:key inputs #:allow-other-keys)
16636 (with-directory-excursion "inst"
16640 `((,(assoc-ref inputs "js-jquery")
16641 "htmlwidgets/lib/jquery/jquery.min.js")
16642 (,(assoc-ref inputs "js-threejs-111")
16643 "htmlwidgets/lib/threejs-111/three.min.js"))))
16644 (lambda (sources targets)
16645 (for-each (lambda (source target)
16646 (format #t "Processing ~a --> ~a~%"
16648 (delete-file target)
16649 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16650 (call-with-output-file target
16652 (dump-port minified port)))))
16653 sources targets))))
16656 `(("r-base64enc" ,r-base64enc)
16657 ("r-crosstalk" ,r-crosstalk)
16658 ("r-htmlwidgets" ,r-htmlwidgets)
16659 ("r-igraph" ,r-igraph)))
16661 `(("uglify-js" ,uglify-js)
16665 (uri "https://code.jquery.com/jquery-1.12.4.js")
16668 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16672 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16675 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16676 (home-page "https://bwlewis.github.io/rthreejs")
16677 (synopsis "Interactive 3D scatter plots, networks and globes")
16679 "Create interactive 3D scatter plots, network plots, and globes in R
16680 using the three.js visualization library.")
16681 (license license:expat)))
16683 (define-public r-mlbench
16690 (uri (cran-uri "mlbench" version))
16693 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16694 (build-system r-build-system)
16695 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16696 (synopsis "Machine learning benchmark problems")
16698 "This package provides a collection of artificial and real-world machine
16699 learning benchmark problems, including, e.g., several data sets from the UCI
16701 (license license:gpl2)))
16703 (define-public r-mpm
16710 (uri (cran-uri "mpm" version))
16713 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16714 (build-system r-build-system)
16716 `(("r-kernsmooth" ,r-kernsmooth)
16717 ("r-mass" ,r-mass)))
16718 (home-page "http://mpm.r-forge.r-project.org")
16719 (synopsis "Multivariate projection methods")
16721 "This is a package for exploratory graphical analysis of multivariate
16722 data, specifically gene expression data with different projection methods:
16723 principal component analysis, correspondence analysis, spectral map
16725 (license license:gpl2+)))
16727 (define-public r-png
16733 (uri (cran-uri "png" version))
16736 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16737 (build-system r-build-system)
16739 `(("libpng" ,libpng)
16741 (home-page "https://www.rforge.net/png/")
16742 (synopsis "Read and write PNG images")
16744 "This package provides an easy and simple way to read, write and display
16745 bitmap images stored in the PNG format. It can read and write both files and
16746 in-memory raw vectors.")
16747 ;; Any of these GPL versions.
16748 (license (list license:gpl2 license:gpl3))))
16750 (define-public r-ggcorrplot
16752 (name "r-ggcorrplot")
16757 (uri (cran-uri "ggcorrplot" version))
16760 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16761 (build-system r-build-system)
16763 `(("r-ggplot2" ,r-ggplot2)
16764 ("r-reshape2" ,r-reshape2)))
16765 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16766 (synopsis "Visualization of a correlation matrix using ggplot2")
16768 "The ggcorrplot package can be used to visualize easily a correlation
16769 matrix using ggplot2. It provides a solution for reordering the correlation
16770 matrix and displays the significance level on the plot. It also includes a
16771 function for computing a matrix of correlation p-values.")
16772 (license license:gpl2)))
16774 (define-public r-gridtext
16776 (name "r-gridtext")
16781 (uri (cran-uri "gridtext" version))
16784 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16785 (properties `((upstream-name . "gridtext")))
16786 (build-system r-build-system)
16788 `(("r-jpeg" ,r-jpeg)
16789 ("r-markdown" ,r-markdown)
16792 ("r-rcurl" ,r-rcurl)
16793 ("r-rlang" ,r-rlang)
16794 ("r-stringr" ,r-stringr)
16795 ("r-xml2" ,r-xml2)))
16796 (home-page "https://wilkelab.org/gridtext/")
16797 (synopsis "Improved text rendering support for Grid graphics")
16799 "This package provides support for rendering of formatted text using Grid
16800 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16801 inline CSS directives, and it can be rendered both with and without word
16803 (license license:expat)))
16805 (define-public r-ggtext
16812 (uri (cran-uri "ggtext" version))
16815 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16816 (properties `((upstream-name . "ggtext")))
16817 (build-system r-build-system)
16819 `(("r-ggplot2" ,r-ggplot2)
16820 ("r-gridtext" ,r-gridtext)
16821 ("r-rlang" ,r-rlang)
16822 ("r-scales" ,r-scales)))
16823 (native-inputs `(("r-knitr" ,r-knitr)))
16824 (home-page "https://wilkelab.org/ggtext/")
16825 (synopsis "Improved text rendering support for ggplot2")
16827 "This package provides a ggplot2 extension that enables the rendering of
16828 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16829 etc.). Text boxes with automatic word wrap are also supported.")
16830 (license license:gpl2)))
16832 ;; This package includes minified JavaScript files. When upgrading please
16833 ;; check that there are no new minified JavaScript files.
16834 (define-public r-flexdashboard
16836 (name "r-flexdashboard")
16841 (uri (cran-uri "flexdashboard" version))
16844 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16845 (modules '((guix build utils)))
16848 ;; Delete bundled minified JavaScript files
16849 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16850 (delete-file "inst/www/sly/sly.min.js")
16851 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16852 (delete-file "inst/www/prism/prism.js")
16854 (build-system r-build-system)
16856 `(#:modules ((guix build utils)
16857 (guix build r-build-system)
16861 (ice-9 textual-ports))
16863 (modify-phases %standard-phases
16864 (add-after 'unpack 'process-javascript
16865 (lambda* (#:key inputs #:allow-other-keys)
16866 (with-directory-excursion "inst"
16867 ;; Concatenate all components of prism.js
16868 (let ((contents (string-join
16869 (map (lambda (name)
16870 (call-with-input-file
16871 (assoc-ref inputs name)
16875 "js-prism-line-numbers"))
16877 (call-with-output-file "prism-src.js"
16878 (cut display contents <>)))
16882 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16883 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16885 "www/sly/sly.min.js")
16887 "www/prism/prism.js")
16888 (,(assoc-ref inputs "js-raphael")
16889 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16890 (,(assoc-ref inputs "js-featherlight")
16891 "www/featherlight/featherlight.min.js"))))
16892 (lambda (sources targets)
16893 (for-each (lambda (source target)
16894 (format #t "Processing ~a --> ~a~%"
16896 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16897 (call-with-output-file target
16899 (dump-port minified port)))))
16900 sources targets))))
16903 `(("r-htmltools" ,r-htmltools)
16904 ("r-htmlwidgets" ,r-htmlwidgets)
16905 ("r-jsonlite" ,r-jsonlite)
16906 ("r-knitr" ,r-knitr)
16907 ("r-rmarkdown" ,r-rmarkdown)
16908 ("r-shiny" ,r-shiny)))
16910 `(("uglify-js" ,uglify-js)
16914 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16917 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16921 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16924 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16928 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16931 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16932 ("js-prism-line-numbers"
16935 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16938 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16942 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16945 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16946 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16947 (synopsis "R Markdown format for flexible dashboards")
16949 "This package provides an R Markdown format for converting an R Markdown
16950 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16951 of its components to the containing web page.")
16952 (license license:expat)))
16954 (define-public r-preseqr
16961 (uri (cran-uri "preseqR" version))
16964 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16965 (properties `((upstream-name . "preseqR")))
16966 (build-system r-build-system)
16968 `(("r-polynom" ,r-polynom)))
16969 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16970 (synopsis "Predicting species accumulation curves")
16972 "This package can be used to predict the r-species accumulation
16973 curve (r-SAC), which is the number of species represented at least r times as
16974 a function of the sampling effort. When r = 1, the curve is known as the
16975 species accumulation curve, or the library complexity curve in high-throughput
16976 genomic sequencing. The package includes both parametric and nonparametric
16977 methods, as described by Deng C, et al. (2018).")
16978 (license license:gpl3)))
16980 (define-public r-mapplots
16982 (name "r-mapplots")
16987 (uri (cran-uri "mapplots" version))
16990 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
16991 (build-system r-build-system)
16992 (home-page "https://cran.r-project.org/web/packages/mapplots/")
16993 (synopsis "Data visualization on maps")
16995 "This package helps you create simple maps; add sub-plots like pie plots
16996 to a map or any other plot; format, plot and export gridded data. The package
16997 was developed for displaying fisheries data but most functions can be used for
16998 more generic data visualisation.")
16999 (license license:gpl2+)))
17001 (define-public r-pmcmr
17008 (uri (cran-uri "PMCMR" version))
17011 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
17012 (properties `((upstream-name . "PMCMR")))
17013 (build-system r-build-system)
17014 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
17015 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
17017 "This is a deprecated package for calculating pairwise multiple
17018 comparisons of mean rank sums. This package is superseded by the novel
17019 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
17020 compatibility of dependent packages for some time.")
17021 (license license:gpl3+)))
17023 (define-public r-downloader
17025 (name "r-downloader")
17030 (uri (cran-uri "downloader" version))
17033 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17034 (build-system r-build-system)
17036 `(("r-digest" ,r-digest)))
17037 (home-page "https://github.com/wch/downloader")
17038 (synopsis "Download files over HTTP and HTTPS")
17040 "This package provides a wrapper for the @code{download.file} function,
17041 making it possible to download files over HTTPS across platforms. The
17042 @code{RCurl} package provides this functionality (and much more) but has
17043 external dependencies. This package has is implemented purely in R.")
17044 (license license:gpl2)))
17046 (define-public r-rex
17053 (uri (cran-uri "rex" version))
17056 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17057 (build-system r-build-system)
17059 `(("r-lazyeval" ,r-lazyeval)))
17061 `(("r-knitr" ,r-knitr)))
17062 (home-page "https://github.com/kevinushey/rex")
17063 (synopsis "Friendly regular expressions")
17065 "This package provides a friendly interface for the construction of
17066 regular expressions. Regular expressions are a very powerful feature, however
17067 they are often difficult to interpret. Rex allows you to build complex
17068 regular expressions from human readable expressions")
17069 (license license:expat)))
17071 (define-public r-xmlparsedata
17073 (name "r-xmlparsedata")
17078 (uri (cran-uri "xmlparsedata" version))
17081 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
17082 (properties `((upstream-name . "xmlparsedata")))
17083 (build-system r-build-system)
17084 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17085 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17087 "This package provides tools to convert the output of
17088 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17089 @code{XPath}, and is easier to manipulate in general.")
17090 (license license:expat)))
17092 (define-public r-cyclocomp
17094 (name "r-cyclocomp")
17099 (uri (cran-uri "cyclocomp" version))
17102 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17103 (properties `((upstream-name . "cyclocomp")))
17104 (build-system r-build-system)
17106 `(("r-callr" ,r-callr)
17107 ("r-crayon" ,r-crayon)
17109 ("r-remotes" ,r-remotes)
17110 ("r-withr" ,r-withr)))
17111 (home-page "https://github.com/MangoTheCat/cyclocomp")
17112 (synopsis "Cyclomatic complexity of R code")
17114 "Cyclomatic complexity is a software metric, used to indicate the
17115 complexity of a program. It is a quantitative measure of the number of
17116 linearly independent paths through a program's source code. This package
17117 provides tools to compute this metric.")
17118 (license license:expat)))
17120 (define-public r-lintr
17127 (uri (cran-uri "lintr" version))
17130 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17131 (properties `((upstream-name . "lintr")))
17132 (build-system r-build-system)
17134 `(("r-codetools" ,r-codetools)
17135 ("r-crayon" ,r-crayon)
17136 ("r-cyclocomp" ,r-cyclocomp)
17137 ("r-digest" ,r-digest)
17139 ("r-jsonlite" ,r-jsonlite)
17140 ("r-knitr" ,r-knitr)
17142 ("r-rstudioapi" ,r-rstudioapi)
17143 ("r-testthat" ,r-testthat)
17145 ("r-xmlparsedata" ,r-xmlparsedata)))
17146 (home-page "https://github.com/jimhester/lintr")
17147 (synopsis "Linter for R code")
17148 (description "This package checks adherence to a given style, syntax
17149 errors and possible semantic issues. It supports on the fly checking of R
17150 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17151 (license license:expat)))
17153 (define-public r-sctransform
17155 (name "r-sctransform")
17160 (uri (cran-uri "sctransform" version))
17163 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17164 (build-system r-build-system)
17166 `(("r-future" ,r-future)
17167 ("r-future-apply" ,r-future-apply)
17168 ("r-ggplot2" ,r-ggplot2)
17169 ("r-gridextra" ,r-gridextra)
17171 ("r-matrix" ,r-matrix)
17172 ("r-matrixstats" ,r-matrixstats)
17174 ("r-rcpparmadillo" ,r-rcpparmadillo)
17175 ("r-reshape2" ,r-reshape2)))
17176 (home-page "https://github.com/ChristophH/sctransform")
17177 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17179 "This package provides a normalization method for single-cell UMI count
17180 data using a variance stabilizing transformation. The transformation is based
17181 on a negative binomial regression model with regularized parameters. As part
17182 of the same regression framework, this package also provides functions for
17183 batch correction, and data correction.")
17184 (license license:gpl3)))
17186 (define-public r-styler
17193 (uri (cran-uri "styler" version))
17196 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
17197 (build-system r-build-system)
17199 `(("r-backports" ,r-backports)
17201 ("r-magrittr" ,r-magrittr)
17202 ("r-purrr" ,r-purrr)
17203 ("r-r-cache" ,r-r-cache)
17204 ("r-rematch2" ,r-rematch2)
17205 ("r-rlang" ,r-rlang)
17206 ("r-rprojroot" ,r-rprojroot)
17207 ("r-tibble" ,r-tibble)
17208 ("r-withr" ,r-withr)
17209 ("r-xfun" ,r-xfun)))
17210 (home-page "https://github.com/r-lib/styler")
17211 (synopsis "Non-invasive pretty printing of R code")
17213 "This is a package for pretty-printing R code without changing the user's
17214 formatting intent.")
17215 (license license:gpl3)))
17217 (define-public r-scrime
17224 (uri (cran-uri "scrime" version))
17227 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17228 (build-system r-build-system)
17229 (home-page "https://cran.r-project.org/web/packages/scrime/")
17230 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17232 "This package provides tools for the analysis of high-dimensional data
17233 developed/implemented at the group \"Statistical Complexity Reduction In
17234 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17235 the functions can also be applied to other types of categorical data.")
17236 (license license:gpl2)))
17238 (define-public r-pbmcapply
17240 (name "r-pbmcapply")
17245 (uri (cran-uri "pbmcapply" version))
17248 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17249 (build-system r-build-system)
17250 (home-page "https://github.com/kvnkuang/pbmcapply")
17251 (synopsis "Track the progress of apply procedures with a progress bar")
17253 "This light-weight package helps you track and visualize the progress of
17254 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17255 (license license:expat)))
17257 (define-public r-blme
17264 (uri (cran-uri "blme" version))
17267 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17268 (build-system r-build-system)
17269 (propagated-inputs `(("r-lme4" ,r-lme4)))
17270 (home-page "https://github.com/vdorie/blme")
17271 (synopsis "Bayesian linear mixed-effects models")
17273 "This package provides tools for maximum a posteriori estimation for
17274 linear and generalized linear mixed-effects models in a Bayesian setting. It
17275 extends the lme4 package.")
17276 (license license:gpl2+)))
17278 (define-public r-batchtools
17280 (name "r-batchtools")
17285 (uri (cran-uri "batchtools" version))
17288 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17289 (build-system r-build-system)
17291 `(("r-backports" ,r-backports)
17292 ("r-base64url" ,r-base64url)
17294 ("r-checkmate" ,r-checkmate)
17295 ("r-data-table" ,r-data-table)
17296 ("r-digest" ,r-digest)
17298 ("r-progress" ,r-progress)
17300 ("r-rappdirs" ,r-rappdirs)
17301 ("r-stringi" ,r-stringi)
17302 ("r-withr" ,r-withr)))
17304 `(("r-knitr" ,r-knitr)))
17305 (home-page "https://github.com/mllg/batchtools")
17306 (synopsis "Tools for computation on batch systems")
17308 "As a successor of the packages BatchJobs and BatchExperiments, this
17309 package provides a parallel implementation of the Map function for high
17310 performance computing systems managed by various schedulers. A multicore and
17311 socket mode allow the parallelization on a local machines, and multiple
17312 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17313 the package provides an abstraction mechanism to define large-scale computer
17314 experiments in a well-organized and reproducible way.")
17315 (license license:lgpl3)))
17317 (define-public r-clue
17324 (uri (cran-uri "clue" version))
17327 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17328 (build-system r-build-system)
17329 (propagated-inputs `(("r-cluster" ,r-cluster)))
17330 (home-page "https://cran.r-project.org/web/packages/clue/")
17331 (synopsis "Tools for analyzing cluster ensembles")
17332 (description "Cluster ensembles are collections of individual solutions to
17333 a given clustering problem which are useful or necessary to consider in a wide
17334 range of applications. This R package provides an extensible computational
17335 environment for creating and analyzing cluster ensembles, with basic data
17336 structures for representing partitions and hierarchies, and facilities for
17337 computing on them, including methods for measuring proximity and obtaining
17338 consensus and secondary clusterings.")
17339 (license license:gpl2)))
17341 (define-public r-sitmo
17348 (uri (cran-uri "sitmo" version))
17351 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17352 (build-system r-build-system)
17353 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17354 (home-page "https://github.com/coatless/sitmo/")
17355 (synopsis "Parallel pseudo random number generator header files")
17357 "This package provides two high quality and fast PPRNGs that may be used
17358 in an OpenMP parallel environment. In addition, there is a generator for one
17359 dimensional low-discrepancy sequence.")
17360 (license license:expat)))
17362 (define-public r-dqrng
17369 (uri (cran-uri "dqrng" version))
17372 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17373 (build-system r-build-system)
17377 ("r-sitmo" ,r-sitmo)))
17378 (home-page "https://www.daqana.org/dqrng")
17379 (synopsis "Fast pseudo random number generators")
17381 "Several fast random number generators are provided as C++ header-only
17382 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17383 Additionally, fast functions for generating random numbers according to a
17384 uniform, normal and exponential distribution are included. The latter two use
17385 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17386 functions are exported to R and as a C++ interface and are enabled for use
17387 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17388 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17389 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17390 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17391 ;; whole is distributed under the terms of the AGPL 3.
17392 (license license:agpl3)))
17394 (define-public r-ingredients
17396 (name "r-ingredients")
17401 (uri (cran-uri "ingredients" version))
17404 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17405 (properties `((upstream-name . "ingredients")))
17406 (build-system r-build-system)
17408 `(("r-ggplot2" ,r-ggplot2)
17409 ("r-gridextra" ,r-gridextra)
17410 ("r-scales" ,r-scales)))
17411 (native-inputs `(("r-knitr" ,r-knitr)))
17412 (home-page "https://ModelOriented.github.io/ingredients/")
17413 (synopsis "Effects and importances of model ingredients")
17415 "This is a collection of tools for assessment of feature importance and
17416 feature effects. Key functions are:
17419 @item @code{feature_importance()} for assessment of global level feature
17421 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17422 @item @code{partial_dependence()} for partial dependence plots,
17423 @item @code{conditional_dependence()} for conditional dependence plots,
17424 @item @code{accumulated_dependence()} for accumulated local effects plots,
17425 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17426 aggregation of ceteris paribus profiles,
17427 @item generic @code{print()} and @code{plot()} for better usability of
17428 selected explainers,
17429 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17430 @item generic @code{describe()} for explanations in natural language.
17432 (license license:gpl3)))
17434 (define-public r-ibreakdown
17436 (name "r-ibreakdown")
17441 (uri (cran-uri "iBreakDown" version))
17444 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17445 (properties `((upstream-name . "iBreakDown")))
17446 (build-system r-build-system)
17447 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17448 (native-inputs `(("r-knitr" ,r-knitr)))
17449 (home-page "https://ModelOriented.github.io/iBreakDown/")
17450 (synopsis "Model agnostic instance level variable attributions")
17452 "This package provides a model agnostic tool for decomposition of
17453 predictions from black boxes. It supports additive attributions and
17454 attributions with interactions. The Break Down Table shows contributions of
17455 every variable to a final prediction. The Break Down Plot presents variable
17456 contributions in a concise graphical way. This package works for
17457 classification and regression models.")
17458 (license license:gpl3)))
17460 (define-public r-dae
17467 (uri (cran-uri "dae" version))
17470 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17471 (build-system r-build-system)
17473 `(("r-ggplot2" ,r-ggplot2)
17474 ("r-plyr" ,r-plyr)))
17476 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17477 (home-page "http://chris.brien.name")
17478 (synopsis "Functions useful in the design and ANOVA of experiments")
17480 "This package provides functions useful in the design and ANOVA of
17481 experiments. The content falls into the following groupings:
17485 @item factor manipulation functions,
17486 @item design functions,
17487 @item ANOVA functions,
17488 @item matrix functions,
17489 @item projector and canonical efficiency functions, and
17490 @item miscellaneous functions.
17493 There is a vignette called @code{DesignNotes} describing how to use the design
17494 functions for randomizing and assessing designs. The ANOVA functions
17495 facilitate the extraction of information when the @code{Error} function has
17496 been used in the call to @code{aov}.")
17497 (license license:gpl2)))
17499 (define-public r-dalex
17506 (uri (cran-uri "DALEX" version))
17509 "1dnqsml94s648w8swsrq8spddnd4mj5pl3q6xxr917w6a1jxgyfz"))))
17510 (properties `((upstream-name . "DALEX")))
17511 (build-system r-build-system)
17513 `(("r-ggplot2" ,r-ggplot2)
17514 ("r-ibreakdown" ,r-ibreakdown)
17515 ("r-ingredients" ,r-ingredients)))
17516 (home-page "https://pbiecek.github.io/DALEX/")
17517 (synopsis "Descriptive machine learning explanations")
17519 "Machine Learning models are widely used and have various applications in
17520 classification or regression. Models created with boosting, bagging, stacking
17521 or similar techniques are often used due to their high performance, but such
17522 black-box models usually lack interpretability. The DALEX package contains
17523 various explainers that help to understand the link between input variables
17524 and model output.")
17525 ;; Any version of the GPL
17526 (license license:gpl3+)))
17528 (define-public r-enrichr
17535 (uri (cran-uri "enrichR" version))
17538 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17539 (properties `((upstream-name . "enrichR")))
17540 (build-system r-build-system)
17542 `(("r-ggplot2" ,r-ggplot2)
17544 ("r-rjson" ,r-rjson)))
17546 `(("r-knitr" ,r-knitr)))
17547 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17548 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17550 "This package provides an R interface to all Enrichr databases, a
17551 web-based tool for analyzing gene sets and returns any enrichment of common
17552 annotated biological functions.")
17553 (license license:gpl2+)))
17555 (define-public r-plot3d
17562 (uri (cran-uri "plot3D" version))
17565 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17566 (properties `((upstream-name . "plot3D")))
17567 (build-system r-build-system)
17568 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17569 (home-page "https://cran.r-project.org/web/packages/plot3D")
17570 (synopsis "Plot multi-dimensional data")
17572 "This package provides functions for viewing 2D and 3D data, including
17573 perspective plots, slice plots, surface plots, scatter plots, etc. It
17574 includes data sets from oceanography.")
17575 (license license:gpl3+)))
17577 (define-public r-ggfortify
17579 (name "r-ggfortify")
17584 (uri (cran-uri "ggfortify" version))
17587 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17588 (build-system r-build-system)
17590 `(("r-dplyr" ,r-dplyr)
17591 ("r-ggplot2" ,r-ggplot2)
17592 ("r-gridextra" ,r-gridextra)
17593 ("r-scales" ,r-scales)
17594 ("r-stringr" ,r-stringr)
17595 ("r-tibble" ,r-tibble)
17596 ("r-tidyr" ,r-tidyr)))
17598 `(("r-knitr" ,r-knitr)))
17599 (home-page "https://github.com/sinhrks/ggfortify")
17600 (synopsis "Data visualization tools for statistical analysis results")
17602 "This package provides unified plotting tools for statistics commonly
17603 used, such as GLM, time series, PCA families, clustering and survival
17604 analysis. The package offers a single plotting interface for these analysis
17605 results and plots in a unified style using the @code{ggplot2} package.")
17606 (license license:gpl2)))
17608 (define-public r-refmanager
17610 (name "r-refmanager")
17615 (uri (cran-uri "RefManageR" version))
17618 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17619 (properties `((upstream-name . "RefManageR")))
17620 (build-system r-build-system)
17622 `(("r-httr" ,r-httr)
17623 ("r-jsonlite" ,r-jsonlite)
17624 ("r-lubridate" ,r-lubridate)
17626 ("r-stringr" ,r-stringr)
17627 ("r-xml2" ,r-xml2)))
17629 `(("r-knitr" ,r-knitr)))
17630 (home-page "https://github.com/ropensci/RefManageR/")
17631 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17633 "This package provides tools for importing and working with bibliographic
17634 references. It greatly enhances the @code{bibentry} class by providing a
17635 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17636 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17637 by various formats for name lists (author by last names, translator by full
17638 names, etc.). Entries can be updated, combined, sorted, printed in a number
17639 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17640 into R and converted to @code{BibEntry} objects.")
17641 ;; Any of these licenses may be picked.
17642 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17644 (define-public r-citr
17651 (uri (cran-uri "citr" version))
17654 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17655 (build-system r-build-system)
17657 `(("r-assertthat" ,r-assertthat)
17660 ("r-miniui" ,r-miniui)
17661 ("r-refmanager" ,r-refmanager)
17662 ("r-rstudioapi" ,r-rstudioapi)
17663 ("r-shiny" ,r-shiny)
17664 ("r-shinyjs" ,r-shinyjs)
17665 ("r-yaml" ,r-yaml)))
17666 (home-page "https://github.com/crsh/citr")
17667 (synopsis "RStudio add-in to insert Markdown citations")
17669 "This package provides functions and an RStudio add-in that search a
17670 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17671 the current document.")
17672 (license license:expat)))
17674 (define-public r-xgboost
17677 (version "1.3.2.1")
17681 (uri (cran-uri "xgboost" version))
17684 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17685 (build-system r-build-system)
17687 `(("r-data-table" ,r-data-table)
17688 ("r-magrittr" ,r-magrittr)
17689 ("r-matrix" ,r-matrix)))
17691 `(("r-knitr" ,r-knitr)))
17692 (home-page "https://github.com/dmlc/xgboost")
17693 (synopsis "Extreme gradient boosting")
17695 "This package provides an R interface to Extreme Gradient Boosting, which
17696 is an efficient implementation of the gradient boosting framework from Chen
17697 and Guestrin (2016). The package includes efficient linear model solver and
17698 tree learning algorithms. The package can automatically do parallel
17699 computation on a single machine. It supports various objective functions,
17700 including regression, classification and ranking. The package is made to be
17701 extensible, so that users are also allowed to define their own objectives
17703 (license license:asl2.0)))
17705 (define-public r-umap
17708 (version "0.2.7.0")
17712 (uri (cran-uri "umap" version))
17715 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17716 (build-system r-build-system)
17718 `(("r-openssl" ,r-openssl)
17720 ("r-reticulate" ,r-reticulate)
17721 ("r-rspectra" ,r-rspectra)))
17723 `(("r-knitr" ,r-knitr)))
17724 (home-page "https://github.com/tkonopka/umap")
17725 (synopsis "Uniform manifold approximation and projection")
17727 "Uniform manifold approximation and projection is a technique for
17728 dimension reduction. This package provides an interface to the UMAP algorithm
17729 in R, including a translation of the original algorithm into R.")
17730 (license license:expat)))
17732 (define-public r-uwot
17739 (uri (cran-uri "uwot" version))
17742 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17743 (build-system r-build-system)
17745 `(("r-dqrng" ,r-dqrng)
17747 ("r-irlba" ,r-irlba)
17748 ("r-matrix" ,r-matrix)
17750 ("r-rcppannoy" ,r-rcppannoy)
17751 ("r-rcppprogress" ,r-rcppprogress)
17752 ("r-rspectra" ,r-rspectra)))
17753 (home-page "https://github.com/jlmelville/uwot")
17754 (synopsis "Uniform manifold approximation and projection")
17756 "This package provides an implementation of the Uniform Manifold
17757 Approximation and Projection dimensionality reduction by McInnes et
17758 al. (2018). It also provides means to transform new data and to carry out
17759 supervised dimensionality reduction. An implementation of the related
17760 LargeVis method of Tang et al. (2016) is also provided.")
17761 (license license:gpl3)))
17763 (define-public r-kableextra
17765 (name "r-kableextra")
17770 (uri (cran-uri "kableExtra" version))
17773 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
17774 (properties `((upstream-name . "kableExtra")))
17775 (build-system r-build-system)
17777 `(("r-digest" ,r-digest)
17779 ("r-htmltools" ,r-htmltools)
17780 ("r-knitr" ,r-knitr)
17781 ("r-magrittr" ,r-magrittr)
17782 ("r-rmarkdown" ,r-rmarkdown)
17783 ("r-rstudioapi" ,r-rstudioapi)
17784 ("r-rvest" ,r-rvest)
17785 ("r-scales" ,r-scales)
17786 ("r-stringr" ,r-stringr)
17787 ("r-svglite" ,r-svglite)
17788 ("r-viridislite" ,r-viridislite)
17789 ("r-webshot" ,r-webshot)
17790 ("r-xml2" ,r-xml2)))
17792 `(("r-knitr" ,r-knitr)))
17793 (home-page "https://haozhu233.github.io/kableExtra/")
17794 (synopsis "Construct complex tables with pipe syntax")
17796 "Build complex HTML or LaTeX tables using @code{kable()} from
17797 @code{knitr} and the piping syntax from @code{magrittr}. The function
17798 @code{kable()} is a light weight table generator coming from @code{knitr}.
17799 This package simplifies the way to manipulate the HTML or LaTeX codes
17800 generated by @code{kable()} and allows users to construct complex tables and
17801 customize styles using a readable syntax.")
17802 (license license:expat)))
17804 (define-public r-glasso
17811 (uri (cran-uri "glasso" version))
17813 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17814 (build-system r-build-system)
17815 (native-inputs `(("gfortran" ,gfortran)))
17816 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17817 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17819 "This is a package for estimation of a sparse inverse covariance matrix
17820 using a lasso (L1) penalty. Facilities are provided for estimates along a
17821 path of values for the regularization parameter.")
17822 (license license:gpl2)))
17824 (define-public r-rhpcblasctl
17826 (name "r-rhpcblasctl")
17827 (version "0.20-137")
17831 (uri (cran-uri "RhpcBLASctl" version))
17834 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17835 (properties `((upstream-name . "RhpcBLASctl")))
17836 (build-system r-build-system)
17837 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17838 (synopsis "Control the number of threads on BLAS")
17840 "This package allows you to control the number of threads the BLAS
17841 library uses. It is also possible to control the number of threads in
17843 (license license:agpl3+)))
17845 (define-public r-lda
17852 (uri (cran-uri "lda" version))
17855 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17856 (build-system r-build-system)
17857 (home-page "https://cran.r-project.org/web/packages/lda/")
17858 (synopsis "Collapsed Gibbs sampling methods for topic models")
17860 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17861 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17862 mixed-membership stochastic blockmodel. Inference for all of these models is
17863 implemented via a fast collapsed Gibbs sampler written in C. Utility
17864 functions for reading/writing data typically used in topic models, as well as
17865 tools for examining posterior distributions are also included.")
17866 ;; Any version of the LGPL
17867 (license license:lgpl3+)))
17869 (define-public r-rann-l1
17876 (uri (cran-uri "RANN.L1" version))
17879 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17880 (properties `((upstream-name . "RANN.L1")))
17881 (build-system r-build-system)
17882 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17883 (synopsis "Fast nearest neighbour search using L1 metric")
17885 "This package provides tools to find the k nearest neighbours for every
17886 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17887 library. There is support for approximate as well as exact searches, fixed
17888 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17889 computed using the L1 (Manhattan, taxicab) metric.")
17890 (license license:gpl3+)))
17892 (define-public r-leiden
17899 (uri (cran-uri "leiden" version))
17902 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17903 (properties `((upstream-name . "leiden")))
17904 (build-system r-build-system)
17906 `(("r-igraph" ,r-igraph)
17907 ("r-matrix" ,r-matrix)
17908 ("r-reticulate" ,r-reticulate)))
17910 `(("r-knitr" ,r-knitr)))
17911 (home-page "https://github.com/TomKellyGenetics/leiden")
17912 (synopsis "R implementation of Leiden clustering algorithm")
17914 "This package implements the Python @code{leidenalg} module to be called
17915 in R. It enables clustering using the Leiden algorithm for partitioning a
17916 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17917 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17918 (license license:gpl3)))
17920 (define-public r-patchwork
17922 (name "r-patchwork")
17927 (uri (cran-uri "patchwork" version))
17930 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17931 (build-system r-build-system)
17933 `(("r-ggplot2" ,r-ggplot2)
17934 ("r-gtable" ,r-gtable)))
17936 `(("r-knitr" ,r-knitr)))
17937 (home-page "https://github.com/thomasp85/patchwork")
17938 (synopsis "Compose ggplot2 plots")
17940 "The @code{ggplot2} package provides a strong API for sequentially
17941 building up a plot, but does not concern itself with composition of multiple
17942 plots. Patchwork is a package that expands the API to allow for arbitrarily
17943 complex composition of plots by providing mathematical operators for combining
17945 (license license:expat)))
17947 (define-public r-liger
17954 (uri (git-reference
17955 (url "https://github.com/MacoskoLab/liger")
17956 (commit (string-append "v" version))))
17957 (file-name (git-file-name name version))
17960 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17961 (modules '((guix build utils)))
17964 (delete-file "inst/java/ModularityOptimizer.jar")
17966 (build-system r-build-system)
17969 (modify-phases %standard-phases
17970 (add-after 'unpack 'build-java-part
17971 (lambda* (#:key inputs #:allow-other-keys)
17972 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17973 (for-each (lambda (file) (invoke "javac" file))
17974 (find-files "." "\\.java$"))
17975 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17976 (find-files "." "\\.class$"))
17979 `(("r-cowplot" ,r-cowplot)
17980 ("r-dosnow" ,r-dosnow)
17981 ("r-dplyr" ,r-dplyr)
17983 ("r-foreach" ,r-foreach)
17984 ("r-ggplot2" ,r-ggplot2)
17985 ("r-ggrepel" ,r-ggrepel)
17986 ("r-hmisc" ,r-hmisc)
17988 ("r-irlba" ,r-irlba)
17989 ("r-matrix" ,r-matrix)
17990 ("r-mclust" ,r-mclust)
17991 ("r-patchwork" ,r-patchwork)
17993 ("r-rann-l1" ,r-rann-l1)
17995 ("r-rcpparmadillo" ,r-rcpparmadillo)
17996 ("r-riverplot" ,r-riverplot)
17997 ("r-rtsne" ,r-rtsne)
17998 ("r-snow" ,r-snow)))
18000 `(("jdk" ,icedtea "jdk")
18001 ;; See https://github.com/MacoskoLab/liger/issues/96
18002 ;; The optimizer is released under the Expat license.
18006 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
18009 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
18011 ("r-knitr" ,r-knitr))) ; for vignettes
18012 (home-page "https://github.com/MacoskoLab/liger")
18013 (synopsis "Integrate and analyze multiple single-cell datasets")
18015 "LIGER is a package for integrating and analyzing multiple single-cell
18016 datasets, developed and maintained by the Macosko lab. It relies on
18017 integrative non-negative matrix factorization to identify shared and
18018 dataset-specific factors.")
18019 (license license:gpl3)))
18021 (define-public r-harmony
18028 (uri (git-reference
18029 (url "https://github.com/immunogenomics/harmony")
18031 (file-name (git-file-name name version))
18034 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18035 (modules '((guix build utils)))
18038 (for-each delete-file '("config.status" "configure"))
18040 (build-system r-build-system)
18042 `(("r-cowplot" ,r-cowplot)
18043 ("r-dplyr" ,r-dplyr)
18044 ("r-ggplot2" ,r-ggplot2)
18045 ("r-irlba" ,r-irlba)
18046 ("r-matrix" ,r-matrix)
18048 ("r-rcpparmadillo" ,r-rcpparmadillo)
18049 ("r-rcppprogress" ,r-rcppprogress)
18050 ("r-rlang" ,r-rlang)
18051 ("r-tibble" ,r-tibble)
18052 ("r-tidyr" ,r-tidyr)))
18054 `(("autoconf" ,autoconf)))
18055 (home-page "https://github.com/immunogenomics/harmony")
18056 (synopsis "Integration of single cell sequencing data")
18058 "This package provides an implementation of the Harmony algorithm for
18059 single cell integration, described in Korsunsky et al
18060 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18061 function and interfaces to external frameworks.")
18062 (license license:gpl3)))
18064 (define-public r-covr
18071 (uri (cran-uri "covr" version))
18073 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18074 (properties `((upstream-name . "covr")))
18075 (build-system r-build-system)
18077 `(("r-crayon" ,r-crayon)
18078 ("r-digest" ,r-digest)
18080 ("r-jsonlite" ,r-jsonlite)
18082 ("r-withr" ,r-withr)
18083 ("r-yaml" ,r-yaml)))
18085 `(("r-knitr" ,r-knitr))) ; for vignettes
18086 (home-page "https://github.com/r-lib/covr")
18087 (synopsis "Test coverage for R packages")
18089 "Thisp package enables you to track and report code coverage for your
18090 package and (optionally) upload the results to a coverage service. Code
18091 coverage is a measure of the amount of code being exercised by a set of tests.
18092 It is an indirect measure of test quality and completeness. This package is
18093 compatible with any testing methodology or framework and tracks coverage of
18094 both R code and compiled C/C++/FORTRAN code.")
18095 (license license:gpl3)))
18097 (define-public r-systemfonts
18099 (name "r-systemfonts")
18104 (uri (cran-uri "systemfonts" version))
18107 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18108 (properties `((upstream-name . "systemfonts")))
18109 (build-system r-build-system)
18111 `(("r-cpp11" ,r-cpp11)))
18113 `(("fontconfig" ,fontconfig)
18116 `(("pkg-config" ,pkg-config)
18117 ("r-knitr" ,r-knitr)))
18118 (home-page "https://github.com/r-lib/systemfonts")
18119 (synopsis "System native font finding")
18121 "This package provides system native access to the font catalogue. As
18122 font handling varies between systems it is difficult to correctly locate
18123 installed fonts across different operating systems. The 'systemfonts' package
18124 provides bindings to the native libraries for finding font files that can then
18125 be used further by e.g. graphic devices.")
18126 (license license:expat)))
18128 (define-public r-graphlayouts
18130 (name "r-graphlayouts")
18135 (uri (cran-uri "graphlayouts" version))
18138 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18139 (properties `((upstream-name . "graphlayouts")))
18140 (build-system r-build-system)
18142 `(("r-igraph" ,r-igraph)
18144 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18145 (home-page "https://github.com/schochastics/graphlayouts")
18146 (synopsis "Additional layout algorithms for network visualizations")
18148 "This package provides several layout algorithms to visualize networks
18149 which are not part of the igraph library. Most are based on the concept of
18150 stress majorization by Gansner et al. (2004)
18151 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18152 emphasize hidden group structures in networks or focus on specific nodes.")
18153 (license license:expat)))
18155 (define-public r-terra
18162 (uri (cran-uri "terra" version))
18165 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18166 (properties `((upstream-name . "terra")))
18167 (build-system r-build-system)
18172 ("sqlite" ,sqlite) ; needed for proj
18175 `(("r-raster" ,r-raster)
18176 ("r-rcpp" ,r-rcpp)))
18178 `(("pkg-config" ,pkg-config)))
18179 (home-page "https://rspatial.org/terra")
18180 (synopsis "Spatial data analysis")
18182 "This package provides methods for spatial data analysis, especially
18183 raster data. The included methods allow for low-level data manipulation as
18184 well as high-level global, local, zonal, and focal computation. The predict
18185 and interpolate methods facilitate the use of regression type (interpolation,
18186 machine learning) models for spatial prediction. Processing of very large
18187 files is supported.")
18188 (license license:gpl3+)))
18190 (define-public r-tidygraph
18192 (name "r-tidygraph")
18197 (uri (cran-uri "tidygraph" version))
18200 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18201 (properties `((upstream-name . "tidygraph")))
18202 (build-system r-build-system)
18204 `(("r-dplyr" ,r-dplyr)
18205 ("r-igraph" ,r-igraph)
18206 ("r-magrittr" ,r-magrittr)
18207 ("r-pillar" ,r-pillar)
18210 ("r-rlang" ,r-rlang)
18211 ("r-tibble" ,r-tibble)
18212 ("r-tidyr" ,r-tidyr)))
18213 (home-page "https://github.com/thomasp85/tidygraph")
18214 (synopsis "Tidy API for graph manipulation")
18216 "This package provides a graph implementation that can be thought of as
18217 two tidy data frames describing node and edge data respectively. It provides
18218 an approach to manipulate these two virtual data frames using the API defined
18219 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18220 common graph algorithms.")
18221 (license license:expat)))
18223 (define-public r-soupx
18224 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18228 (version (git-version "0.3.1" revision commit))
18232 (uri (git-reference
18233 (url "https://github.com/constantAmateur/SoupX")
18235 (file-name (git-file-name name version))
18238 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18239 (properties `((upstream-name . "SoupX")))
18240 (build-system r-build-system)
18242 `(("r-ggplot2" ,r-ggplot2)
18243 ("r-matrix" ,r-matrix)
18244 ("r-seurat" ,r-seurat)))
18245 (home-page "https://github.com/constantAmateur/SoupX")
18246 (synopsis "Single cell mRNA Soup eXterminator")
18248 "This package provides a package for quantifying, profiling and
18249 removing cell free mRNA contamination (the \"soup\") from droplet based single
18250 cell RNA-seq experiments.")
18251 (license license:gpl2))))
18253 (define-public r-assertr
18260 (uri (cran-uri "assertr" version))
18263 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18264 (build-system r-build-system)
18266 `(("r-dplyr" ,r-dplyr)
18268 ("r-rlang" ,r-rlang)))
18270 `(("r-knitr" ,r-knitr))) ; needed for vignette
18271 (home-page "https://github.com/ropensci/assertr")
18272 (synopsis "Assertive programming for R analysis pipelines")
18274 "This package provides functionality to assert conditions that have to be
18275 met so that errors in data used in analysis pipelines can fail quickly. It is
18276 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18278 (license license:expat)))
18280 (define-public r-parameters
18282 (name "r-parameters")
18287 (uri (cran-uri "parameters" version))
18290 "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm"))))
18291 (properties `((upstream-name . "parameters")))
18292 (build-system r-build-system)
18294 `(("r-bayestestr" ,r-bayestestr)
18295 ("r-insight" ,r-insight)))
18297 `(("r-knitr" ,r-knitr)))
18298 (home-page "https://cran.r-project.org/web/packages/parameters")
18299 (synopsis "Processing of model parameters")
18301 "This package provides utilities for processing the parameters of various
18302 statistical models. Beyond computing p values, CIs, and other indices for a
18303 wide variety of models, this package implements features like standardization
18304 or bootstrapping of parameters and models, feature reduction (feature
18305 extraction and variable selection) as well as conversion between indices of
18307 (license license:gpl3)))
18309 (define-public r-rgdal
18316 (uri (cran-uri "rgdal" version))
18318 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18319 (properties `((upstream-name . "rgdal")))
18320 (build-system r-build-system)
18328 `(("pkg-config" ,pkg-config)
18329 ("r-knitr" ,r-knitr)))
18330 (home-page "http://rgdal.r-forge.r-project.org")
18331 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18333 "This package provides bindings to the Geospatial Data Abstraction
18334 Library (GDAL) and access to projection/transformation operations from the
18336 (license license:gpl2+)))
18338 (define-public r-insol
18345 (uri (cran-uri "insol" version))
18348 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18349 (properties `((upstream-name . "insol")))
18350 (build-system r-build-system)
18352 `(("r-raster" ,r-raster)))
18354 `(("gfortran" ,gfortran)))
18355 (home-page "https://meteoexploration.com/R/insol/index.html")
18356 (synopsis "Tools for calculating solar radiation")
18358 "This package provides functions to compute insolation on tilted
18359 surfaces, computes atmospheric transmittance and related parameters such as:
18360 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18361 time, vector in the direction of the sun, vector normal to surface, and some
18362 atmospheric physics.")
18363 (license license:gpl2+)))
18365 (define-public r-lifecycle
18367 (name "r-lifecycle")
18372 (uri (cran-uri "lifecycle" version))
18375 "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3"))))
18376 (properties `((upstream-name . "lifecycle")))
18377 (build-system r-build-system)
18379 `(("r-glue" ,r-glue)
18380 ("r-rlang" ,r-rlang)))
18382 `(("r-knitr" ,r-knitr))) ; for vignettes
18383 (home-page "https://github.com/r-lib/lifecycle")
18384 (synopsis "Manage the life cycle of your package functions")
18386 "Manage the life cycle of your exported functions with shared
18387 conventions, documentation badges, and non-invasive deprecation warnings. The
18388 lifecycle package defines four development stages (experimental, maturing,
18389 stable, and questioning) and three deprecation stages (soft-deprecated,
18390 deprecated, and defunct). It makes it easy to insert badges corresponding to
18391 these stages in your documentation. Usage of deprecated functions are
18392 signalled with increasing levels of non-invasive verbosity.")
18393 (license license:gpl3)))
18395 (define-public r-assertable
18397 (name "r-assertable")
18402 (uri (cran-uri "assertable" version))
18405 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18406 (build-system r-build-system)
18408 `(("r-data-table" ,r-data-table)))
18410 `(("r-knitr" ,r-knitr)))
18411 (home-page "https://cran.r-project.org/web/packages/assertable/")
18412 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18413 (description "This package provides simple, flexible assertions on
18414 data.frame or data.table objects with verbose output for vetting. While other
18415 assertion packages apply towards more general use-cases, @code{assertable} is
18416 tailored towards tabular data. It includes functions to check variable names
18417 and values, whether the dataset contains all combinations of a given set of
18418 unique identifiers, and whether it is a certain length. In addition,
18419 @code{assertable} includes utility functions to check the existence of target
18420 files and to efficiently import multiple tabular data files into one
18422 (license license:gpl3)))
18424 (define-public r-quadprog
18426 (name "r-quadprog")
18431 (uri (cran-uri "quadprog" version))
18433 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18434 (build-system r-build-system)
18436 `(("gfortran" ,gfortran)))
18437 (home-page "https://cran.r-project.org/web/packages/quadprog")
18438 (synopsis "Functions to solve quadratic programming problems")
18440 "This package contains routines and documentation for solving quadratic
18441 programming problems.")
18442 (license license:gpl3+)))
18444 (define-public r-desolve
18451 (uri (cran-uri "deSolve" version))
18453 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18454 (properties `((upstream-name . "deSolve")))
18455 (build-system r-build-system)
18457 `(("gfortran" ,gfortran)))
18458 (home-page "https://desolve.r-forge.r-project.org/")
18459 (synopsis "Solvers for initial value problems of differential equations")
18460 (description "This package provides functions that solve initial value
18461 problems of a system of first-order @dfn{ordinary differential
18462 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18463 @dfn{differential algebraic equations} (DAE), and of delay differential
18464 equations. The functions provide an interface to the FORTRAN functions
18465 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18466 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18467 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18468 time steps. The package contains routines designed for solving ODEs resulting
18469 from 1-D, 2-D and 3-D partial differential equations that have been converted
18470 to ODEs by numerical differencing.")
18471 (license license:gpl2+)))
18473 (define-public r-pracma
18479 (uri (cran-uri "pracma" version))
18481 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18482 (build-system r-build-system)
18483 (home-page "https://cran.r-project.org/web/packages/pracma/")
18484 (synopsis "Practical numerical math functions")
18485 (description "This package provides functions for numerical analysis and
18486 linear algebra, numerical optimization, differential equations, plus some
18487 special functions. It uses Matlab function names where appropriate to simplify
18489 (license license:gpl3+)))
18491 (define-public r-subplex
18498 (uri (cran-uri "subplex" version))
18501 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18502 (build-system r-build-system)
18504 `(("gfortran" ,gfortran)))
18505 (home-page "https://cran.r-project.org/web/packages/subplex")
18506 (synopsis "Unconstrained optimization using the subplex algorithm")
18508 "This package implements the Subplex optimization algorithm.
18509 It solves unconstrained optimization problems using a simplex method on
18510 subspaces. The method is well suited for optimizing objective functions that
18511 are noisy or are discontinuous at the solution.")
18512 (license license:gpl3+)))
18514 (define-public r-txtplot
18521 (uri (cran-uri "txtplot" version))
18524 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18525 (build-system r-build-system)
18526 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18527 (synopsis "Text-based plotting")
18528 (description "This package provides functions to produce rudimentary ASCII
18529 graphics directly in the terminal window. This package provides a basic
18530 plotting function (and equivalents of curve, density, acf and barplot) as well
18531 as a boxplot function.")
18532 (license license:lgpl3+)))
18534 (define-public r-bio3d
18541 (uri (cran-uri "bio3d" version))
18544 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18545 (properties `((upstream-name . "bio3d")))
18546 (build-system r-build-system)
18547 (inputs `(("zlib" ,zlib)))
18548 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18549 (home-page "http://thegrantlab.org/bio3d/")
18550 (synopsis "Biological structure analysis")
18552 "This package provides utilities to process, organize and explore protein
18553 structure, sequence and dynamics data. Features include the ability to read
18554 and write structure, sequence and dynamic trajectory data, perform sequence
18555 and structure database searches, data summaries, atom selection, alignment,
18556 superposition, rigid core identification, clustering, torsion analysis,
18557 distance matrix analysis, structure and sequence conservation analysis, normal
18558 mode analysis, principal component analysis of heterogeneous structure data,
18559 and correlation network analysis from normal mode and molecular dynamics data.
18560 In addition, various utility functions are provided to enable the statistical
18561 and graphical power of the R environment to work with biological sequence and
18563 (license license:gpl2+)))
18565 (define-public r-bios2cor
18567 (name "r-bios2cor")
18572 (uri (cran-uri "Bios2cor" version))
18575 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18576 (properties `((upstream-name . "Bios2cor")))
18577 (build-system r-build-system)
18579 `(("r-bigmemory" ,r-bigmemory)
18580 ("r-bio3d" ,r-bio3d)
18581 ("r-circular" ,r-circular)
18582 ("r-igraph" ,r-igraph)))
18583 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18584 (synopsis "From biological sequences and simulations to correlation analysis")
18586 "This package provides utilities for computation and analysis of
18587 correlation/covariation in multiple sequence alignments and in side chain
18588 motions during molecular dynamics simulations. Features include the
18589 computation of correlation/covariation scores using a variety of scoring
18590 functions between either sequence positions in alignments or side chain
18591 dihedral angles in molecular dynamics simulations and utilities to analyze the
18592 correlation/covariation matrix through a variety of tools including network
18593 representation and principal components analysis. In addition, several
18594 utility functions are based on the R graphical environment to provide friendly
18595 tools for help in data interpretation.")
18596 (license license:gpl2+)))
18598 ;; This package includes minified JavaScript files. When upgrading please
18599 ;; check that there are no new minified JavaScript files.
18600 (define-public r-networkd3
18602 (name "r-networkd3")
18607 (uri (cran-uri "networkD3" version))
18610 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18613 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18615 (properties `((upstream-name . "networkD3")))
18616 (build-system r-build-system)
18618 `(#:modules ((guix build utils)
18619 (guix build r-build-system)
18623 (modify-phases %standard-phases
18624 (add-after 'unpack 'process-javascript
18625 (lambda* (#:key inputs #:allow-other-keys)
18626 (with-directory-excursion "inst/htmlwidgets/lib/"
18630 `((,(assoc-ref inputs "d3.v4.js")
18631 "d3-4.5.0/d3.min.js"))))
18632 (lambda (sources targets)
18633 (for-each (lambda (source target)
18634 (format #t "Processing ~a --> ~a~%"
18636 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18637 (call-with-output-file target
18639 (dump-port minified port)))))
18640 sources targets))))
18643 `(("uglify-js" ,uglify-js)
18644 ;; NOTE: Make sure that this version of d3 is still valid when
18645 ;; upgrading the package.
18649 (uri "https://d3js.org/d3.v4.js")
18652 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18654 `(("r-htmlwidgets" ,r-htmlwidgets)
18655 ("r-igraph" ,r-igraph)
18656 ("r-magrittr" ,r-magrittr)))
18657 (home-page "https://cran.r-project.org/package=networkD3")
18658 (synopsis "D3 JavaScript network graphs from R")
18660 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18662 (license license:gpl3+)))
18664 (define-public r-aasea
18671 (uri (cran-uri "aaSEA" version))
18674 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18675 (properties `((upstream-name . "aaSEA")))
18676 (build-system r-build-system)
18678 `(("r-bios2cor" ,r-bios2cor)
18680 ("r-hmisc" ,r-hmisc)
18681 ("r-magrittr" ,r-magrittr)
18682 ("r-networkd3" ,r-networkd3)
18683 ("r-plotly" ,r-plotly)
18684 ("r-seqinr" ,r-seqinr)
18685 ("r-shiny" ,r-shiny)
18686 ("r-shinydashboard" ,r-shinydashboard)))
18687 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18688 (synopsis "Amino acid substitution effect analyzer")
18690 "Given a protein multiple sequence alignment, it is a daunting task to
18691 assess the effects of substitutions along sequence length. The aaSEA package
18692 is intended to help researchers to rapidly analyze property changes caused by
18693 single, multiple and correlated amino acid substitutions in proteins.")
18694 (license license:gpl3)))
18696 (define-public r-abacus
18703 (uri (cran-uri "ABACUS" version))
18706 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18707 (properties `((upstream-name . "ABACUS")))
18708 (build-system r-build-system)
18710 `(("r-ggplot2" ,r-ggplot2)
18711 ("r-shiny" ,r-shiny)))
18712 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18713 (synopsis "Apps-based activities for communicating and understanding statistics")
18715 "This package provides a set of Shiny apps for effective communication
18716 and understanding in statistics. The current version includes properties of
18717 normal distribution, properties of sampling distribution, one-sample z and t
18718 tests, two samples independent (unpaired) t test and analysis of variance.")
18719 (license license:gpl3)))
18721 (define-public r-abc-rap
18728 (uri (cran-uri "ABC.RAP" version))
18731 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18732 (properties `((upstream-name . "ABC.RAP")))
18733 (build-system r-build-system)
18734 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18735 (synopsis "Array-based CpG region analysis pipeline")
18737 "This package aims to identify candidate genes that are differentially
18738 methylated between cases and controls. It applies Student's t-test and delta
18739 beta analysis to identify candidate genes containing multiple CpG sites.")
18740 (license license:gpl3)))
18742 (define-public r-abcadm
18749 (uri (cran-uri "abcADM" version))
18752 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18753 (properties `((upstream-name . "abcADM")))
18754 (build-system r-build-system)
18757 ("r-rcpp" ,r-rcpp)))
18758 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18759 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18761 "This package provides tools to estimate parameters of accumulated
18762 damage (load duration) models based on failure time data under a Bayesian
18763 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18764 long-term reliability under stochastic load profiles.")
18765 (license license:gpl3)))
18767 (define-public r-rglpk
18774 (uri (cran-uri "Rglpk" version))
18777 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18778 (properties `((upstream-name . "Rglpk")))
18779 (build-system r-build-system)
18781 `(("r-slam" ,r-slam)))
18784 (home-page "https://r-forge.r-project.org/projects/rglp/")
18785 (synopsis "R interface to the GNU Linear Programming Kit")
18787 "This package provides an R interface to the GNU Linear Programming Kit,
18788 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18789 integer linear programming} (MILP) and other related problems.")
18791 (license (list license:gpl2 license:gpl3))))
18793 (define-public r-abcdefba
18795 (name "r-abcdefba")
18800 (uri (cran-uri "abcdeFBA" version))
18803 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18804 (properties `((upstream-name . "abcdeFBA")))
18805 (build-system r-build-system)
18807 `(("r-corrplot" ,r-corrplot)
18808 ("r-lattice" ,r-lattice)
18810 ("r-rglpk" ,r-rglpk)))
18811 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18812 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18814 "This package provides functions for Constraint Based Simulation using
18815 Flux Balance Analysis and informative analysis of the data generated during
18817 (license license:gpl2)))
18819 (define-public r-abcrlda
18826 (uri (cran-uri "abcrlda" version))
18829 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18830 (properties `((upstream-name . "abcrlda")))
18831 (build-system r-build-system)
18832 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18833 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18835 "This package offers methods to perform @dfn{asymptotically
18836 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18837 cost-sensitive binary classification. The bias-correction is an estimate of
18838 the bias term added to regularized discriminant analysis that minimizes the
18840 (license license:gpl3)))
18842 (define-public r-abemus
18849 (uri (cran-uri "abemus" version))
18852 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18853 (properties `((upstream-name . "abemus")))
18854 (build-system r-build-system)
18856 `(("r-data-table" ,r-data-table)))
18857 (home-page "https://cran.r-project.org/web/packages/abemus/")
18858 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18860 "This package provides an implementation of @dfn{Adaptive Base Error
18861 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18862 platform-specific genetic knowledge and empirical signal to readily detect and
18863 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18864 cell free DNA} (cfDNA).")
18865 (license license:gpl3)))
18867 ;; This package includes minified JavaScript files. When upgrading please
18868 ;; check that there are no new minified JavaScript files.
18869 (define-public r-rintrojs
18871 (name "r-rintrojs")
18876 (uri (cran-uri "rintrojs" version))
18879 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18880 (properties `((upstream-name . "rintrojs")))
18881 (build-system r-build-system)
18883 `(#:modules ((guix build utils)
18884 (guix build r-build-system)
18888 (modify-phases %standard-phases
18889 (add-after 'unpack 'process-javascript
18890 (lambda* (#:key inputs #:allow-other-keys)
18891 (with-directory-excursion "inst/javascript/introjs/"
18895 `((,(assoc-ref inputs "intro.js")
18897 (lambda (sources targets)
18898 (for-each (lambda (source target)
18899 (format #t "Processing ~a --> ~a~%"
18901 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18902 (call-with-output-file target
18904 (dump-port minified port)))))
18905 sources targets))))
18908 `(("uglify-js" ,uglify-js)
18912 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18915 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18917 `(("r-jsonlite" ,r-jsonlite)
18918 ("r-shiny" ,r-shiny)))
18919 (home-page "https://github.com/carlganz/rintrojs")
18920 (synopsis "Wrapper for the Intro.js library")
18922 "This package provides a wrapper for the @url{http://www.introjs.com,
18923 Intro.js} library. This package makes it easy to include step-by-step
18924 introductions, and clickable hints in a Shiny application. It supports both
18925 static introductions in the UI, and programmatic introductions from the
18927 (license license:agpl3+)))
18929 (define-public r-sysfonts
18931 (name "r-sysfonts")
18936 (uri (cran-uri "sysfonts" version))
18939 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18940 (properties `((upstream-name . "sysfonts")))
18941 (build-system r-build-system)
18943 `(("freetype" ,freetype)
18947 `(("pkg-config" ,pkg-config)))
18948 (home-page "https://github.com/yixuan/sysfonts")
18949 (synopsis "Loading fonts into R")
18951 "This is a package to simplify loading of system fonts and Google Fonts
18952 into R, in order to support other packages.")
18953 (license license:gpl2)))
18955 (define-public r-showtextdb
18957 (name "r-showtextdb")
18962 (uri (cran-uri "showtextdb" version))
18965 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18966 (properties `((upstream-name . "showtextdb")))
18967 (build-system r-build-system)
18969 `(("r-sysfonts" ,r-sysfonts)))
18970 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18971 (synopsis "Font files for the 'showtext' package")
18973 "This package provides font files that can be used by the @code{showtext}
18975 (license license:asl2.0)))
18977 (define-public r-showtext
18979 (name "r-showtext")
18984 (uri (cran-uri "showtext" version))
18987 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
18988 (properties `((upstream-name . "showtext")))
18989 (build-system r-build-system)
18991 `(("freetype" ,freetype)
18995 `(("r-showtextdb" ,r-showtextdb)
18996 ("r-sysfonts" ,r-sysfonts)))
18998 `(("pkg-config" ,pkg-config)
18999 ("r-knitr" ,r-knitr)))
19000 (home-page "https://github.com/yixuan/showtext")
19001 (synopsis "Using fonts more easily in R graphs")
19003 "This package aims to make it easy to use various types of
19004 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
19005 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
19006 will be converted into polygons or raster images, hence after the plot has
19007 been created, it no longer relies on the font files. No external software
19008 such as Ghostscript is needed to use this package.")
19009 (license license:asl2.0)))
19011 (define-public r-emojifont
19013 (name "r-emojifont")
19018 (uri (cran-uri "emojifont" version))
19021 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
19022 (properties `((upstream-name . "emojifont")))
19023 (build-system r-build-system)
19025 `(("r-ggplot2" ,r-ggplot2)
19026 ("r-proto" ,r-proto)
19027 ("r-showtext" ,r-showtext)
19028 ("r-sysfonts" ,r-sysfonts)))
19029 (home-page "https://guangchuangyu.github.io/emojifont")
19030 (synopsis "Emoji and Font Awesome in R graphics")
19032 "This package enables the use of emoji and the Font Awesome glyphs in
19033 both base and ggplot2 graphics.")
19034 (license license:artistic2.0)))
19036 (define-public r-abstractr
19038 (name "r-abstractr")
19043 (uri (cran-uri "abstractr" version))
19046 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19047 (properties `((upstream-name . "abstractr")))
19048 (build-system r-build-system)
19050 `(("r-colourpicker" ,r-colourpicker)
19051 ("r-emojifont" ,r-emojifont)
19052 ("r-ggplot2" ,r-ggplot2)
19053 ("r-gridextra" ,r-gridextra)
19054 ("r-rintrojs" ,r-rintrojs)
19055 ("r-shiny" ,r-shiny)
19056 ("r-shinythemes" ,r-shinythemes)))
19057 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19058 (synopsis "R-Shiny application for creating visual abstracts")
19060 "This package provides an R Shiny application to create visual abstracts
19061 for original research. A variety of user defined options and formatting are
19063 (license license:gpl3)))
19065 (define-public r-qgam
19072 (uri (cran-uri "qgam" version))
19075 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19076 (properties `((upstream-name . "qgam")))
19077 (build-system r-build-system)
19079 `(("r-doparallel" ,r-doparallel)
19082 ("r-shiny" ,r-shiny)))
19083 (native-inputs `(("r-knitr" ,r-knitr)))
19084 (home-page "https://cran.r-project.org/web/packages/qgam/")
19085 (synopsis "Smooth additive quantile regression models")
19087 "This package provides smooth additive quantile regression models, fitted
19088 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19089 the smoothing parameters are estimated automatically by marginal loss
19090 minimization, while the regression coefficients are estimated using either
19091 PIRLS or Newton algorithm. The learning rate is determined so that the
19092 Bayesian credible intervals of the estimated effects have approximately the
19093 correct coverage. The main function is @code{qgam()} which is similar to
19094 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19095 regression models.")
19096 (license license:gpl2+)))
19098 (define-public r-abtest
19105 (uri (cran-uri "abtest" version))
19108 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19109 (properties `((upstream-name . "abtest")))
19110 (build-system r-build-system)
19112 `(("r-matrix" ,r-matrix)
19113 ("r-mvtnorm" ,r-mvtnorm)
19114 ("r-plotrix" ,r-plotrix)
19116 ("r-rcolorbrewer" ,r-rcolorbrewer)
19119 ("r-truncnorm" ,r-truncnorm)))
19120 (home-page "https://cran.r-project.org/web/packages/abtest/")
19121 (synopsis "Bayesian A/B testing")
19123 "This package provides functions for Bayesian A/B testing including prior
19124 elicitation options based on Kass and Vaidyanathan (1992)
19125 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19126 (license license:gpl2+)))
19128 (define-public r-accept
19135 (uri (cran-uri "accept" version))
19138 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19139 (properties `((upstream-name . "accept")))
19140 (build-system r-build-system)
19142 `(("r-dplyr" ,r-dplyr)
19143 ("r-extrafont" ,r-extrafont)
19145 ("r-plotly" ,r-plotly)
19146 ("r-stringr" ,r-stringr)
19147 ("r-viridis" ,r-viridis)))
19148 (home-page "https://cran.r-project.org/web/packages/accept/")
19149 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19151 "This package allows clinicians to predict the rate and severity of
19152 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19153 Disease} (COPD) patients, based on the clinical prediction model published in
19154 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19155 (license license:gpl3)))
19157 (define-public r-smpracticals
19159 (name "r-smpracticals")
19164 (uri (cran-uri "SMPracticals" version))
19167 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19168 (properties `((upstream-name . "SMPracticals")))
19169 (build-system r-build-system)
19171 `(("r-ellipse" ,r-ellipse)
19174 ("r-survival" ,r-survival)))
19175 (home-page "http://statwww.epfl.ch/davison/SM/")
19176 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19178 "This package contains the datasets and a few functions for use with the
19179 practicals outlined in Appendix A of the book Statistical Models (Davison,
19180 2003, Cambridge University Press). The practicals themselves can be found at
19181 @url{http://statwww.epfl.ch/davison/SM/}.")
19182 (license license:gpl2+)))
19184 (define-public r-fgui
19191 (uri (cran-uri "fgui" version))
19194 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19195 (properties `((upstream-name . "fgui")))
19196 (build-system r-build-system)
19198 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19199 (synopsis "Create GUI for R functions")
19201 "Rapidly create a GUI for a function you created by automatically
19202 creating widgets for arguments of the function. This package automatically
19203 parses help routines for context-sensitive help to these arguments. The
19204 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19205 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19206 incorporated into the interface for greater customization for the more
19208 ;; Any version of the GPL.
19209 (license (list license:gpl2+ license:gpl3+))))
19211 (define-public r-tcltk2
19218 (uri (cran-uri "tcltk2" version))
19221 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19222 (properties `((upstream-name . "tcltk2")))
19223 (build-system r-build-system)
19227 (home-page "https://www.sciviews.org/SciViews-R")
19228 (synopsis "Tcl/Tk additions")
19230 "This package provides a series of additional Tcl commands and Tk widgets
19231 with style and various functions to supplement the tcltk package")
19232 (license license:lgpl3)))
19234 (define-public r-accrual
19241 (uri (cran-uri "accrual" version))
19244 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19245 (properties `((upstream-name . "accrual")))
19246 (build-system r-build-system)
19248 `(("r-fgui" ,r-fgui)
19249 ("r-smpracticals" ,r-smpracticals)
19250 ("r-tcltk2" ,r-tcltk2)))
19251 (home-page "https://cran.r-project.org/web/packages/accrual/")
19252 (synopsis "Bayesian accrual prediction")
19254 "Subject recruitment for medical research is challenging. Slow patient
19255 accrual leads to delay in research. Accrual monitoring during the process of
19256 recruitment is critical. Researchers need reliable tools to manage the
19257 accrual rate. This package provides an implementation of a Bayesian method
19258 that integrates researcher's experience on previous trials and data from the
19259 current study, providing reliable prediction on accrual rate for clinical
19260 studies. It provides functions for Bayesian accrual prediction which can be
19261 easily used by statisticians and clinical researchers.")
19262 (license license:gpl2)))
19264 (define-public r-accrued
19271 (uri (cran-uri "accrued" version))
19274 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19275 (properties `((upstream-name . "accrued")))
19276 (build-system r-build-system)
19277 (home-page "https://cran.r-project.org/web/packages/accrued/")
19278 (synopsis "Data quality visualization tools for partially accruing data")
19280 "This is a package for visualizing data quality of partially accruing
19282 (license license:gpl3)))
19284 (define-public r-mda
19291 (uri (cran-uri "mda" version))
19294 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19295 (properties `((upstream-name . "mda")))
19296 (build-system r-build-system)
19297 (propagated-inputs `(("r-class" ,r-class)))
19298 (native-inputs `(("gfortran" ,gfortran)))
19299 (home-page "https://cran.r-project.org/web/packages/mda/")
19300 (synopsis "Mixture and flexible discriminant analysis")
19302 "This is a package for mixture and flexible discriminant analysis,
19303 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19304 (license license:gpl2)))
19306 (define-public r-elasticnet
19308 (name "r-elasticnet")
19313 (uri (cran-uri "elasticnet" version))
19316 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19317 (properties `((upstream-name . "elasticnet")))
19318 (build-system r-build-system)
19320 `(("r-lars" ,r-lars)))
19321 (home-page "http://users.stat.umn.edu/~zouxx019/")
19322 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19324 "This package provides functions for fitting the entire solution path of
19325 the Elastic-Net and also provides functions for estimating sparse Principal
19326 Components. The Lasso solution paths can be computed by the same function.")
19327 (license license:gpl2+)))
19329 (define-public r-sparselda
19331 (name "r-sparselda")
19336 (uri (cran-uri "sparseLDA" version))
19339 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19340 (properties `((upstream-name . "sparseLDA")))
19341 (build-system r-build-system)
19343 `(("r-elasticnet" ,r-elasticnet)
19346 (home-page "https://www.imm.dtu.dk/~lkhc/")
19347 (synopsis "Sparse discriminant analysis")
19349 "This package performs sparse linear discriminant analysis for Gaussians
19350 and mixture of Gaussian models.")
19351 (license license:gpl2+)))
19353 (define-public r-accsda
19360 (uri (cran-uri "accSDA" version))
19363 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19364 (properties `((upstream-name . "accSDA")))
19365 (build-system r-build-system)
19367 `(("r-ggplot2" ,r-ggplot2)
19368 ("r-ggthemes" ,r-ggthemes)
19369 ("r-gridextra" ,r-gridextra)
19371 ("r-rarpack" ,r-rarpack)
19372 ("r-sparselda" ,r-sparselda)))
19373 (home-page "https://github.com/gumeo/accSDA/wiki")
19374 (synopsis "Accelerated sparse discriminant analysis")
19376 "This package provides an implementation of sparse linear discriminant
19377 analysis, which is a supervised classification method for multiple classes.
19378 Various novel optimization approaches to this problem are implemented
19379 including @dfn{alternating direction method of multipliers} (ADMM),
19380 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19381 Functions for performing cross validation are also supplied along with basic
19382 prediction and plotting functions. @dfn{Sparse zero variance
19383 discriminant} (SZVD) analysis is also included in the package.")
19384 (license license:gpl2+)))
19386 (define-public r-ace2fastq
19388 (name "r-ace2fastq")
19393 (uri (cran-uri "ace2fastq" version))
19396 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19397 (properties `((upstream-name . "ace2fastq")))
19398 (build-system r-build-system)
19400 `(("r-stringr" ,r-stringr)))
19401 (home-page "https://github.com/c5sire/ace2fastq")
19402 (synopsis "ACE file to FASTQ converter")
19404 "The ACE file format is used in genomics to store contigs from sequencing
19405 machines. This tools converts it into FASTQ format. Both formats contain the
19406 sequence characters and their corresponding quality information. Unlike the
19407 FASTQ file, the ACE file stores the quality values numerically. The
19408 conversion algorithm uses the standard Sanger formula. The package
19409 facilitates insertion into pipelines, and content inspection.")
19410 (license license:gpl3)))
19412 (define-public r-rngwell
19419 (uri (cran-uri "rngWELL" version))
19422 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19423 (properties `((upstream-name . "rngWELL")))
19424 (build-system r-build-system)
19425 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19426 (synopsis "Toolbox for WELL random number generators")
19428 "This is a dedicated package to WELL pseudo random generators, which were
19429 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19430 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19431 (license license:bsd-3)))
19433 (define-public r-randtoolbox
19435 (name "r-randtoolbox")
19440 (uri (cran-uri "randtoolbox" version))
19443 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19444 (properties `((upstream-name . "randtoolbox")))
19445 (build-system r-build-system)
19447 `(("r-rngwell" ,r-rngwell)))
19449 `(("gfortran" ,gfortran)))
19450 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19451 (synopsis "Toolbox for pseudo and quasi random number generation")
19453 "This package provides
19456 @item pseudo random generators, such as general linear
19457 congruential generators, multiple recursive generators and generalized
19458 feedback shift register (SF-Mersenne Twister algorithm and WELL
19461 @item quasi random generators, such as the Torus algorithm, the Sobol
19462 sequence, the Halton sequence (including the Van der Corput sequence), and
19464 @item some generator tests: the gap test, the serial test, the poker test.
19467 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19468 (license license:bsd-3)))
19470 (define-public r-lhs
19477 (uri (cran-uri "lhs" version))
19480 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19481 (properties `((upstream-name . "lhs")))
19482 (build-system r-build-system)
19483 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19485 `(("r-knitr" ,r-knitr)))
19486 (home-page "https://github.com/bertcarnell/lhs")
19487 (synopsis "Latin Hypercube Samples")
19489 "This package provides a number of methods for creating and augmenting
19490 Latin Hypercube Samples.")
19491 (license license:gpl3)))
19493 (define-public r-acebayes
19495 (name "r-acebayes")
19500 (uri (cran-uri "acebayes" version))
19503 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19504 (properties `((upstream-name . "acebayes")))
19505 (build-system r-build-system)
19507 `(("r-compare" ,r-compare)
19509 ("r-randtoolbox" ,r-randtoolbox)
19511 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19512 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19513 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19515 "Finding an optimal Bayesian experimental design involves maximizing an
19516 objective function given by the expectation of some appropriately chosen
19517 utility function with respect to the joint distribution of unknown
19518 quantities (including responses). This objective function is usually not
19519 available in closed form and the design space can be continuous and of high
19520 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19521 to maximise an approximation to the expectation of the utility function.")
19522 (license license:gpl2)))
19524 (define-public r-acet
19531 (uri (cran-uri "ACEt" version))
19534 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19535 (properties `((upstream-name . "ACEt")))
19536 (build-system r-build-system)
19541 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19542 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19543 (synopsis "Estimating dynamic heritability and twin model comparison")
19545 "This package supports twin models that are able to estimate the dynamic
19546 behaviour of the variance components in the classical twin models with respect
19547 to age using B-splines and P-splines.")
19548 (license license:gpl2+)))
19550 (define-public r-acfmperiod
19552 (name "r-acfmperiod")
19557 (uri (cran-uri "acfMPeriod" version))
19560 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19561 (properties `((upstream-name . "acfMPeriod")))
19562 (build-system r-build-system)
19564 `(("r-mass" ,r-mass)))
19565 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19566 (synopsis "Estimation of the ACF from the M-periodogram")
19568 "This package support non-robust and robust computations of the sample
19569 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19570 univariate and multivariate processes. The methodology consists in reversing
19571 the diagonalization procedure involving the periodogram or the
19572 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19573 ACOVF or the ACF as discussed in Fuller (1995)
19574 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19575 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19576 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19577 (license license:gpl2+)))
19579 (define-public r-gamlss-data
19581 (name "r-gamlss-data")
19586 (uri (cran-uri "gamlss.data" version))
19589 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19590 (properties `((upstream-name . "gamlss.data")))
19591 (build-system r-build-system)
19592 (home-page "http://www.gamlss.org/")
19593 (synopsis "GAMLSS data")
19595 "This package provides data used as examples to demonstrate GAMLSS
19597 ;; Either version of the license
19598 (license (list license:gpl2 license:gpl3))))
19600 (define-public r-gamlss
19607 (uri (cran-uri "gamlss" version))
19610 "1ngf6g4zixwm6ni5r0fs0f6132xd2f2a6mlski9hlqnvvwb46iwr"))))
19611 (properties `((upstream-name . "gamlss")))
19612 (build-system r-build-system)
19614 `(("r-gamlss-data" ,r-gamlss-data)
19615 ("r-gamlss-dist" ,r-gamlss-dist)
19618 ("r-survival" ,r-survival)))
19619 (home-page "http://www.gamlss.org/")
19620 (synopsis "Generalized additive models for location scale and shape")
19622 "This package provides functions for fitting the generalized additive
19623 models for location scale and shape introduced by Rigby and
19624 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19625 use a distributional regression approach where all the parameters of the
19626 conditional distribution of the response variable are modelled using
19627 explanatory variables.")
19628 ;; Either version of the license
19629 (license (list license:gpl2 license:gpl3))))
19631 (define-public r-acid
19638 (uri (cran-uri "acid" version))
19641 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19642 (properties `((upstream-name . "acid")))
19643 (build-system r-build-system)
19645 `(("r-gamlss" ,r-gamlss)
19646 ("r-gamlss-dist" ,r-gamlss-dist)
19647 ("r-hmisc" ,r-hmisc)))
19648 (home-page "https://cran.r-project.org/web/packages/acid/")
19649 (synopsis "Analysing conditional income distributions")
19651 "This package provides functions for the analysis of income distributions
19652 for subgroups of the population as defined by a set of variables like age,
19653 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19654 distribution as well as functions for moments, inequality measures, entropy
19655 measures and polarisation measures of income distributions. This package thus
19656 aides the analysis of income inequality by offering tools for the exploratory
19657 analysis of income distributions at the disaggregated level.")
19658 (license license:gpl3)))
19660 (define-public r-acm4r
19667 (uri (cran-uri "acm4r" version))
19670 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19671 (properties `((upstream-name . "acm4r")))
19672 (build-system r-build-system)
19673 (propagated-inputs `(("r-mass" ,r-mass)))
19674 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19675 (synopsis "Align-and-count method comparisons of RFLP data")
19677 "This is a package to compare sequence fragment lengths or molecular
19678 weights from pairs of lanes. The number of matching bands in the
19679 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19680 the align-and-count method.")
19681 ;; Any version of the GPL
19682 (license (list license:gpl2+ license:gpl3+))))
19684 (define-public r-filelock
19686 (name "r-filelock")
19691 (uri (cran-uri "filelock" version))
19694 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19695 (properties `((upstream-name . "filelock")))
19696 (build-system r-build-system)
19697 (home-page "https://github.com/r-lib/filelock")
19698 (synopsis "Portable file locking")
19700 "This library lets you place an exclusive or shared lock on a file using
19701 the appropriate system call provided by the underlying operating system.")
19702 (license license:expat)))
19704 (define-public r-filematrix
19706 (name "r-filematrix")
19711 (uri (cran-uri "filematrix" version))
19714 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19715 (properties `((upstream-name . "filematrix")))
19716 (build-system r-build-system)
19717 ;; These inputs are needed for vignettes
19719 `(("r-knitr" ,r-knitr)
19720 ("r-rmarkdown" ,r-rmarkdown)
19721 ("pandoc-citeproc" ,pandoc-citeproc)))
19722 (home-page "https://github.com/andreyshabalin/filematrix")
19723 (synopsis "File-backed matrix class with convenient read and write access")
19725 "This package provides an interface for working with large matrices
19726 stored in files, not in computer memory. It supports multiple non-character
19727 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19728 byte real values). Access to parts of the matrix is done by indexing, exactly
19729 as with usual R matrices. It supports very large matrices; the package has
19730 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19731 columns, ad allows for quick addition of extra columns to a filematrix.")
19732 (license license:lgpl3)))
19734 (define-public r-acmeeqtl
19736 (name "r-acmeeqtl")
19741 (uri (cran-uri "ACMEeqtl" version))
19744 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19745 (properties `((upstream-name . "ACMEeqtl")))
19746 (build-system r-build-system)
19748 `(("r-filematrix" ,r-filematrix)))
19749 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19750 (synopsis "Estimation of interpretable eQTL effect sizes")
19752 "This package provides a non-linear model, termed ACME, that reflects a
19753 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19754 With non-linear least-squares algorithm the maximum likelihood parameters can
19755 be estimated. The ACME model provides interpretable effect size estimates and
19756 p-values with well controlled Type-I error.")
19757 (license license:lgpl3)))
19759 (define-public r-acmer
19766 (uri (cran-uri "acmeR" version))
19769 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19770 (properties `((upstream-name . "acmeR")))
19771 (build-system r-build-system)
19772 (propagated-inputs `(("r-foreign" ,r-foreign)))
19773 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19774 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19776 "This package provides an implementation of the ACME estimator, described
19777 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19778 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19779 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19780 as carcasses age; variable bleed-through at successive searches; and interval
19781 mortality estimates. The package provides, based on search data, functions
19782 for estimating the mortality inflation factor in Frequentist and Bayesian
19784 (license license:expat)))
19786 (define-public r-r-huge
19793 (uri (cran-uri "R.huge" version))
19796 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19797 (properties `((upstream-name . "R.huge")))
19798 (build-system r-build-system)
19800 `(("r-r-methodss3" ,r-r-methodss3)
19802 ("r-r-utils" ,r-r-utils)))
19803 (home-page "https://github.com/HenrikBengtsson/R.huge")
19804 (synopsis "Methods for accessing huge amounts of data")
19806 "This is a deprecated package for accessing huge amounts of data.
19807 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19808 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19809 the @code{aroma.affymetrix} package.")
19810 (license license:lgpl2.1+)))
19812 (define-public r-r-filesets
19814 (name "r-r-filesets")
19819 (uri (cran-uri "R.filesets" version))
19822 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19823 (properties `((upstream-name . "R.filesets")))
19824 (build-system r-build-system)
19826 `(("r-digest" ,r-digest)
19827 ("r-r-cache" ,r-r-cache)
19828 ("r-r-methodss3" ,r-r-methodss3)
19830 ("r-r-utils" ,r-r-utils)))
19831 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19832 (synopsis "Easy handling of and access to files")
19834 "This package provides classes and methods to locate, setup, subset,
19835 navigate and iterate file sets, i.e. sets of files located in one or more
19836 directories on the file system. The API is designed such that these classes
19837 can be extended via inheritance to provide a richer API for special file
19838 formats. Moreover, a specific name format is defined such that filenames and
19839 directories can be considered to have full names which consists of a name
19840 followed by comma-separated tags. This adds additional flexibility to
19841 identify file sets and individual files.")
19842 (license license:lgpl2.1+)))
19844 (define-public r-r-devices
19846 (name "r-r-devices")
19851 (uri (cran-uri "R.devices" version))
19854 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19855 (properties `((upstream-name . "R.devices")))
19856 (build-system r-build-system)
19858 `(("r-base64enc" ,r-base64enc)
19859 ("r-r-methodss3" ,r-r-methodss3)
19861 ("r-r-utils" ,r-r-utils)))
19862 (home-page "https://github.com/HenrikBengtsson/R.devices")
19863 (synopsis "Unified handling of graphics devices")
19865 "This package provides functions for creating plots and image files in a
19866 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19867 Default device options as well as scales and aspect ratios are controlled in a
19868 uniform way across all device types. Switching output format requires minimal
19869 changes in code. This package is ideal for large-scale batch processing,
19870 because it will never leave open graphics devices or incomplete image files
19871 behind, even on errors or user interrupts.")
19872 (license license:lgpl2.1+)))
19874 (define-public r-acnr
19881 (uri (cran-uri "acnr" version))
19884 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19885 (properties `((upstream-name . "acnr")))
19886 (build-system r-build-system)
19887 (home-page "https://github.com/mpierrejean/acnr")
19888 (synopsis "Annotated copy-number regions")
19890 "This package provides SNP array data from different types of copy-number
19891 regions. These regions were identified manually by the authors of the package
19892 and may be used to generate realistic data sets with known truth.")
19893 (license license:lgpl2.1+)))
19895 (define-public r-acopula
19902 (uri (cran-uri "acopula" version))
19905 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19906 (properties `((upstream-name . "acopula")))
19907 (build-system r-build-system)
19908 (home-page "https://cran.r-project.org/web/packages/acopula/")
19909 (synopsis "Modelling dependence with multivariate Archimax copulas")
19911 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19912 package provides definitions of several parametric families of generator and
19913 dependence function, computes CDF and PDF, estimates parameters, tests for
19914 goodness of fit, generates random sample and checks copula properties for
19915 custom constructs. In the 2-dimensional case explicit formulas for density
19916 are used, contrary to higher dimensions when all derivatives are linearly
19917 approximated. Several non-archimax families (normal, FGM, Plackett) are
19918 provided as well.")
19919 (license license:gpl2)))
19921 (define-public r-tuner
19928 (uri (cran-uri "tuneR" version))
19931 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19932 (properties `((upstream-name . "tuneR")))
19933 (build-system r-build-system)
19934 (propagated-inputs `(("r-signal" ,r-signal)))
19935 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19936 (synopsis "Analysis of music and speech")
19938 "This is a package for the analysis of music and speech. Analyze music
19939 and speech, extract features like MFCCs, handle wave files and their
19940 representation in various ways, read MP3, read MIDI, perform steps of a
19941 transcription, ...")
19942 ;; Either of these versions.
19943 (license (list license:gpl2 license:gpl3))))
19945 (define-public r-seewave
19952 (uri (cran-uri "seewave" version))
19955 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19956 (properties `((upstream-name . "seewave")))
19957 (build-system r-build-system)
19959 `(("libsndfile" ,libsndfile)))
19961 `(("r-tuner" ,r-tuner)))
19962 (home-page "http://rug.mnhn.fr/seewave")
19963 (synopsis "Sound analysis and synthesis")
19965 "This package provides functions for analysing, manipulating, displaying,
19966 editing and synthesizing time waves (particularly sound). This package
19967 processes time analysis (oscillograms and envelopes), spectral content,
19968 resonance quality factor, entropy, cross correlation and autocorrelation,
19969 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19970 and 3D spectrograms and many other analyses.")
19971 (license license:gpl2+)))
19973 (define-public r-acousticndlcoder
19975 (name "r-acousticndlcoder")
19980 (uri (cran-uri "AcousticNDLCodeR" version))
19983 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
19985 `((upstream-name . "AcousticNDLCodeR")))
19986 (build-system r-build-system)
19988 `(("r-seewave" ,r-seewave)
19989 ("r-tuner" ,r-tuner)
19991 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
19992 (synopsis "Coding sound files for use with NDL")
19994 "Make acoustic cues to use with the R package @code{ndl}.
19995 The package implements functions used in the PLoS ONE paper \"Words from
19996 spontaneous conversational speech can be recognized with human-like accuracy
19997 by an error-driven learning algorithm that discriminates between meanings
19998 straight from smart acoustic features, bypassing the phoneme as recognition
19999 unit.\" @url{doi:10.1371/journal.pone.0174623}")
20000 (license license:gpl2+)))
20002 (define-public r-acp
20009 (uri (cran-uri "acp" version))
20012 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
20013 (properties `((upstream-name . "acp")))
20014 (build-system r-build-system)
20016 `(("r-quantmod" ,r-quantmod)
20017 ("r-tseries" ,r-tseries)))
20018 (home-page "https://cran.r-project.org/web/packages/acp/")
20019 (synopsis "Autoregressive conditional Poisson")
20021 "This package supports the analysis of count data exhibiting
20022 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
20023 model (ACP(p,q)) proposed by Heinen (2003).")
20024 (license license:gpl2)))
20026 (define-public r-ada
20033 (uri (cran-uri "ada" version))
20036 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20037 (properties `((upstream-name . "ada")))
20038 (build-system r-build-system)
20039 (propagated-inputs `(("r-rpart" ,r-rpart)))
20040 (home-page "https://cran.r-project.org/web/packages/ada/")
20041 (synopsis "Stochastic boosting")
20043 "This package provides a straightforward, well-documented, and broad
20044 boosting routine for classification, ideally suited for small to
20045 moderate-sized data sets. It performs discrete, real, and gentle boost under
20046 both exponential and logistic loss on a given data set.")
20047 ;; Any version of the GPL.
20048 (license (list license:gpl2+ license:gpl3+))))
20050 (define-public r-genalg
20057 (uri (cran-uri "genalg" version))
20060 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20061 (properties `((upstream-name . "genalg")))
20062 (build-system r-build-system)
20063 (home-page "https://github.com/egonw/genalg")
20064 (synopsis "R based genetic algorithm")
20066 "This package provides an R based genetic algorithm for binary and
20067 floating point chromosomes.")
20068 (license license:gpl2)))
20070 (define-public r-kernelfactory
20072 (name "r-kernelfactory")
20077 (uri (cran-uri "kernelFactory" version))
20080 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20081 (properties `((upstream-name . "kernelFactory")))
20082 (build-system r-build-system)
20085 ("r-genalg" ,r-genalg)
20086 ("r-kernlab" ,r-kernlab)
20087 ("r-randomforest" ,r-randomforest)))
20088 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20089 (synopsis "Ensemble of kernel machines")
20091 "Kernel factory is an ensemble method where each base classifier (random
20092 forest) is fit on the kernel matrix of a subset of the training data.")
20093 (license license:gpl2+)))
20095 (define-public r-dummies
20102 (uri (cran-uri "dummies" version))
20105 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20106 (properties `((upstream-name . "dummies")))
20107 (build-system r-build-system)
20108 (home-page "https://decisionpatterns.com")
20109 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20111 "This package lets you expand factors, characters and other eligible
20112 classes into dummy/indicator variables.")
20113 (license license:gpl2+)))
20115 (define-public r-acrm
20122 (uri (cran-uri "aCRM" version))
20125 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20126 (properties `((upstream-name . "aCRM")))
20127 (build-system r-build-system)
20130 ("r-dummies" ,r-dummies)
20131 ("r-kernelfactory" ,r-kernelfactory)
20132 ("r-randomforest" ,r-randomforest)))
20133 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20134 (synopsis "Convenience functions for analytical customer relationship management")
20136 "This package provides convenience functions for data preparation and
20137 modeling often used in @dfn{analytical customer relationship
20138 management} (aCRM).")
20139 (license license:gpl2+)))
20141 (define-public r-treeclust
20143 (name "r-treeclust")
20148 (uri (cran-uri "treeClust" version))
20151 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20152 (properties `((upstream-name . "treeClust")))
20153 (build-system r-build-system)
20155 `(("r-cluster" ,r-cluster)
20156 ("r-rpart" ,r-rpart)))
20157 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20158 (synopsis "Cluster distances through trees")
20160 "This package provides tools to create a measure of inter-point
20161 dissimilarity useful for clustering mixed data, and, optionally, perform the
20163 (license license:gpl2+)))
20165 (define-public r-acrosstic
20167 (name "r-acrosstic")
20172 (uri (cran-uri "AcrossTic" version))
20175 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20176 (properties `((upstream-name . "AcrossTic")))
20177 (build-system r-build-system)
20179 `(("r-lpsolve" ,r-lpsolve)
20180 ("r-treeclust" ,r-treeclust)))
20181 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20182 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20184 "This is a package for constructing minimum-cost regular spanning
20185 subgraph as part of a non-parametric two-sample test for equality of
20187 (license license:gpl2+)))
20189 (define-public r-acrt
20196 (uri (cran-uri "acrt" version))
20199 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20200 (properties `((upstream-name . "acrt")))
20201 (build-system r-build-system)
20203 `(("r-rcpp" ,r-rcpp)
20204 ("r-rcppeigen" ,r-rcppeigen)
20205 ("r-sandwich" ,r-sandwich)))
20206 (home-page "https://cran.r-project.org/web/packages/acrt/")
20207 (synopsis "Autocorrelation robust testing")
20209 "This package provides functions for testing affine hypotheses on the
20210 regression coefficient vector in regression models with autocorrelated
20212 (license license:gpl2)))
20214 (define-public r-acs
20221 (uri (cran-uri "acs" version))
20224 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20225 (properties `((upstream-name . "acs")))
20226 (build-system r-build-system)
20228 `(("r-httr" ,r-httr)
20231 ("r-stringr" ,r-stringr)
20233 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20234 (synopsis "Work with data from the US Census")
20236 "This package provides a general toolkit for downloading, managing,
20237 analyzing, and presenting data from the
20238 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20239 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20240 American Community Survey (ACS). Confidence intervals provided with ACS data
20241 are converted to standard errors to be bundled with estimates in complex
20242 @code{acs} objects. The package provides new methods to conduct standard
20243 operations on @code{acs} objects and present/plot data in statistically
20244 appropriate ways.")
20245 (license license:gpl3)))
20247 (define-public r-acss-data
20249 (name "r-acss-data")
20254 (uri (cran-uri "acss.data" version))
20257 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20258 (properties `((upstream-name . "acss.data")))
20259 (build-system r-build-system)
20260 (home-page "http://complexitycalculator.com/methodology.html")
20261 (synopsis "Data for algorithmic complexity of short strings")
20263 "This is a data only package providing the algorithmic complexity of
20264 short strings, computed using the coding theorem method. For a given set of
20265 symbols in a string, all possible or a large number of random samples of
20266 Turing machines with a given number of states (e.g., 5) and number of symbols
20267 corresponding to the number of symbols in the strings were simulated until
20268 they reached a halting state or failed to end. This package contains data on
20269 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20270 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20271 distribution of the halting states.")
20272 (license license:gpl2+)))
20274 (define-public r-acss
20281 (uri (cran-uri "acss" version))
20284 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20285 (properties `((upstream-name . "acss")))
20286 (build-system r-build-system)
20288 `(("r-acss-data" ,r-acss-data)
20290 (home-page "http://complexitycalculator.com/methodology.html")
20291 (synopsis "Algorithmic complexity for short strings")
20293 "The main purpose of this package is to provide the algorithmic
20294 complexity for short strings, an approximation of the Kolmogorov Complexity of
20295 a short string using the coding theorem method. While the database containing
20296 the complexity is provided in the data only package @code{acss.data}, this
20297 package provides functions accessing the data such as @code{prob_random}
20298 returning the posterior probability that a given string was produced by a
20299 random process. In addition, two traditional (but problematic) measures of
20300 complexity are also provided: entropy and change complexity.")
20301 (license license:gpl2+)))
20303 (define-public r-acswr
20310 (uri (cran-uri "ACSWR" version))
20313 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20314 (properties `((upstream-name . "ACSWR")))
20315 (build-system r-build-system)
20317 `(("r-mass" ,r-mass)))
20318 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20319 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20321 "This is a companion package for the book \"A Course in Statistics with
20322 R\" (ISBN 978-1-119-15272-9.)")
20323 (license license:gpl2)))
20325 (define-public r-alabama
20328 (version "2015.3-1")
20332 (uri (cran-uri "alabama" version))
20335 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20336 (properties `((upstream-name . "alabama")))
20337 (build-system r-build-system)
20338 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20339 (home-page "https://cran.r-project.org/web/packages/alabama/")
20340 (synopsis "Constrained nonlinear optimization")
20342 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20343 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20344 constraints. Linear or nonlinear equality and inequality constraints are
20346 (license license:gpl2+)))
20348 (define-public r-gdina
20355 (uri (cran-uri "GDINA" version))
20358 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20359 (properties `((upstream-name . "GDINA")))
20360 (build-system r-build-system)
20362 `(("r-alabama" ,r-alabama)
20363 ("r-ggplot2" ,r-ggplot2)
20365 ("r-nloptr" ,r-nloptr)
20366 ("r-numderiv" ,r-numderiv)
20368 ("r-rcpparmadillo" ,r-rcpparmadillo)
20369 ("r-rsolnp" ,r-rsolnp)
20370 ("r-shiny" ,r-shiny)
20371 ("r-shinydashboard" ,r-shinydashboard)))
20373 `(("r-knitr" ,r-knitr)))
20374 (home-page "https://github.com/Wenchao-Ma/GDINA")
20375 (synopsis "Generalized DINA model framework")
20377 "This package provides a set of psychometric tools for cognitive
20378 diagnosis modeling based on the generalized deterministic inputs, noisy and
20379 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20380 and its extensions, including the sequential G-DINA model by Ma and de la
20381 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20382 polytomous G-DINA model by Chen and de la Torre
20383 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20384 distribution can be independent, saturated, higher-order, loglinear smoothed
20385 or structured. Q-matrix validation, item and model fit statistics, model
20386 comparison at test and item level and differential item functioning can also
20387 be conducted. A graphical user interface is also provided.")
20388 (license license:gpl3)))
20390 (define-public r-actcd
20397 (uri (cran-uri "ACTCD" version))
20400 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20401 (properties `((upstream-name . "ACTCD")))
20402 (build-system r-build-system)
20404 `(("r-gdina" ,r-gdina)
20405 ("r-r-methodss3" ,r-r-methodss3)))
20407 `(("gfortran" ,gfortran)))
20408 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20409 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20411 "This is a package supporting cluster analysis for cognitive diagnosis
20412 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20413 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20414 sum-scores, cluster analysis techniques can be used to classify examinees into
20415 latent classes based on their attribute patterns. In addition to the
20416 algorithms used to classify data, three labeling approaches are proposed to
20417 label clusters so that examinees' attribute profiles can be obtained.")
20418 (license license:gpl2+)))
20420 (define-public r-ineq
20427 (uri (cran-uri "ineq" version))
20430 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20431 (properties `((upstream-name . "ineq")))
20432 (build-system r-build-system)
20433 (home-page "https://cran.r-project.org/web/packages/ineq/")
20434 (synopsis "Measuring inequality, concentration, and poverty")
20436 "This package provides tools for measuring inequality, concentration, and
20437 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20438 ;; Either of these two versions.
20439 (license (list license:gpl2 license:gpl3))))
20441 (define-public r-actfrag
20448 (uri (cran-uri "ActFrag" version))
20451 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20452 (properties `((upstream-name . "ActFrag")))
20453 (build-system r-build-system)
20455 `(("r-accelerometry" ,r-accelerometry)
20456 ("r-dplyr" ,r-dplyr)
20458 ("r-survival" ,r-survival)
20459 ("r-tidyr" ,r-tidyr)))
20460 (home-page "https://github.com/junruidi/ActFrag")
20461 (synopsis "Activity fragmentation metrics extraction")
20463 "This package provides functions to extract commonly used fragmentation
20464 metrics to quantify time accumulation strategies based on minute level
20465 actigraphy-measured activity counts data.")
20466 (license license:gpl3)))
20468 (define-public r-ash
20475 (uri (cran-uri "ash" version))
20478 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20479 (properties `((upstream-name . "ash")))
20480 (build-system r-build-system)
20481 (native-inputs `(("gfortran" ,gfortran)))
20482 (home-page "https://cran.r-project.org/web/packages/ash/")
20483 (synopsis "David Scott's ASH routines")
20485 "This package provides David Scott's ASH routines ported from S-PLUS to
20487 (license license:gpl2+)))
20489 (define-public r-hdrcde
20496 (uri (cran-uri "hdrcde" version))
20499 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20500 (properties `((upstream-name . "hdrcde")))
20501 (build-system r-build-system)
20504 ("r-ggplot2" ,r-ggplot2)
20505 ("r-kernsmooth" ,r-kernsmooth)
20507 ("r-locfit" ,r-locfit)
20508 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20509 (native-inputs `(("gfortran" ,gfortran)))
20510 (home-page "http://pkg.robjhyndman.com/hdrcde")
20511 (synopsis "Highest density regions and conditional density estimation")
20513 "This is a package for the computation of highest density regions in one
20514 and two dimensions, kernel estimation of univariate density functions
20515 conditional on one covariate, and multimodal regression.")
20516 (license license:gpl3)))
20518 (define-public r-rainbow
20525 (uri (cran-uri "rainbow" version))
20528 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20529 (properties `((upstream-name . "rainbow")))
20530 (build-system r-build-system)
20532 `(("r-cluster" ,r-cluster)
20533 ("r-colorspace" ,r-colorspace)
20534 ("r-hdrcde" ,r-hdrcde)
20537 ("r-pcapp" ,r-pcapp)))
20538 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20539 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20541 "This is a package for visualizing functional data and identifying
20542 functional outliers with bagplots, boxplots and rainbow plots.")
20543 (license license:gpl3)))
20545 (define-public r-fds
20552 (uri (cran-uri "fds" version))
20555 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20556 (properties `((upstream-name . "fds")))
20557 (build-system r-build-system)
20559 `(("r-rainbow" ,r-rainbow)
20560 ("r-rcurl" ,r-rcurl)))
20561 (home-page "https://cran.r-project.org/web/packages/fds/")
20562 (synopsis "Functional data sets")
20563 (description "This package contains a list of functional time series,
20564 sliced functional time series, and functional data sets. Functional time
20565 series is a special type of functional data observed over time. Sliced
20566 functional time series is a special type of functional time series with a time
20567 variable observed over time.")
20568 (license license:gpl2+)))
20570 (define-public r-fda
20577 (uri (cran-uri "fda" version))
20580 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20581 (properties `((upstream-name . "fda")))
20582 (build-system r-build-system)
20585 ("r-matrix" ,r-matrix)))
20586 (home-page "https://www.functionaldata.org")
20587 (synopsis "Functional data analysis")
20589 "These functions were developed to support functional data analysis as
20590 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20591 Analysis. The package includes data sets and script files working many
20593 (license license:gpl2+)))
20595 (define-public r-actigraphy
20597 (name "r-actigraphy")
20602 (uri (cran-uri "Actigraphy" version))
20605 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20606 (properties `((upstream-name . "Actigraphy")))
20607 (build-system r-build-system)
20609 `(("r-fda" ,r-fda)))
20610 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20611 (synopsis "Actigraphy data analysis")
20613 "This package provides tools for functional linear modeling and analysis
20614 of actigraphy data.")
20615 (license license:asl2.0)))
20617 (define-public r-activedriver
20619 (name "r-activedriver")
20624 (uri (cran-uri "ActiveDriver" version))
20627 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20628 (properties `((upstream-name . "ActiveDriver")))
20629 (build-system r-build-system)
20631 `(("r-mass" ,r-mass)))
20632 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20633 (synopsis "Tools for finding cancer driver proteins")
20635 "This package provides a mutation analysis tool that discovers cancer
20636 driver genes with frequent mutations in protein signalling sites such as
20637 post-translational modifications (phosphorylation, ubiquitination, etc). The
20638 Poisson generalized linear regression model identifies genes where cancer
20639 mutations in signalling sites are more frequent than expected from the
20640 sequence of the entire gene. Integration of mutations with signalling
20641 information helps find new driver genes and propose candidate mechanisms to
20643 (license license:gpl2+)))
20645 (define-public r-activitycounts
20647 (name "r-activitycounts")
20652 (uri (cran-uri "activityCounts" version))
20655 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20657 `((upstream-name . "activityCounts")))
20658 (build-system r-build-system)
20660 `(("r-lubridate" ,r-lubridate)
20661 ("r-magrittr" ,r-magrittr)
20662 ("r-seewave" ,r-seewave)
20663 ("r-signal" ,r-signal)
20664 ("r-tibble" ,r-tibble)))
20665 (home-page "https://github.com/walkabillylab/activityCounts")
20666 (synopsis "Generate ActiLife counts")
20668 "ActiLife generates activity counts from data collected by Actigraph
20669 accelerometers. Actigraph is one of the most common research-grade
20670 accelerometers. There is considerable research validating and developing
20671 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20672 counts are proprietary and difficult to implement if researchers use different
20673 accelerometer brands. The code creates ActiLife counts from raw acceleration
20674 data for different accelerometer brands.")
20675 (license license:gpl3)))
20677 (define-public r-activityindex
20679 (name "r-activityindex")
20684 (uri (cran-uri "ActivityIndex" version))
20687 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20688 (properties `((upstream-name . "ActivityIndex")))
20689 (build-system r-build-system)
20691 `(("r-data-table" ,r-data-table)
20692 ("r-matrixstats" ,r-matrixstats)
20693 ("r-r-utils" ,r-r-utils)))
20695 `(("r-knitr" ,r-knitr)))
20696 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20697 (synopsis "Activity Index calculation using raw accelerometry data")
20699 "This is a package to read raw accelerometry from GT3X+ accelerometry
20700 data and plain table data to calculate the Activity Index from Bai et
20701 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20702 (license license:gpl3)))
20704 (define-public r-activpal
20706 (name "r-activpal")
20711 (uri (cran-uri "activPAL" version))
20714 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20715 (properties `((upstream-name . "activPAL")))
20716 (build-system r-build-system)
20718 `(("r-devtools" ,r-devtools)
20719 ("r-dplyr" ,r-dplyr)
20720 ("r-ggplot2" ,r-ggplot2)
20721 ("r-lubridate" ,r-lubridate)
20722 ("r-magrittr" ,r-magrittr)
20723 ("r-tidyr" ,r-tidyr)))
20724 (home-page "https://cran.r-project.org/web/packages/activPAL")
20725 (synopsis "Processing and chart generation from activPAL events files")
20727 "This package contains functions to generate pre-defined summary
20728 statistics from activPAL events files. The package also contains functions to
20729 produce informative graphics that visualize physical activity behaviour and
20730 trends. This includes generating graphs that align physical activity
20731 behaviour with additional time based observations described by other data
20732 sets, such as sleep diaries and continuous glucose monitoring data.")
20733 (license license:gpl3)))
20735 (define-public r-activpalprocessing
20737 (name "r-activpalprocessing")
20742 (uri (cran-uri "activpalProcessing" version))
20745 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20747 `((upstream-name . "activpalProcessing")))
20748 (build-system r-build-system)
20750 `(("r-chron" ,r-chron)))
20751 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20752 (synopsis "Process activPAL events files")
20754 "This package performs estimation of physical activity and sedentary
20755 behavior variables from activPAL events files.")
20756 ;; Either version of the GPL.
20757 (license (list license:gpl2 license:gpl3))))
20759 (define-public r-actogrammr
20761 (name "r-actogrammr")
20766 (uri (cran-uri "actogrammr" version))
20769 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20770 (properties `((upstream-name . "actogrammr")))
20771 (build-system r-build-system)
20773 `(("r-dplyr" ,r-dplyr)
20774 ("r-ggplot2" ,r-ggplot2)
20775 ("r-lubridate" ,r-lubridate)
20776 ("r-readr" ,r-readr)
20777 ("r-tidyr" ,r-tidyr)))
20778 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20779 (synopsis "Read in activity data and plot actograms")
20781 "Read in activity measurements from standard file formats used by
20782 circadian rhythm researchers, currently only ClockLab format, and process and
20783 plot the data. The central type of plot is the actogram, as first described
20784 in \"Activity and distribution of certain wild mice in relation to biotic
20785 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20786 (license license:gpl3)))
20788 (define-public r-expint
20795 (uri (cran-uri "expint" version))
20798 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20799 (properties `((upstream-name . "expint")))
20800 (build-system r-build-system)
20801 (home-page "https://gitlab.com/vigou3/expint")
20802 (synopsis "Exponential integral and incomplete Gamma function")
20804 "This package provides the exponential integrals @code{E_1(x)},
20805 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20806 function @code{G(a, x)} defined for negative values of its first argument.
20807 The package also gives easy access to the underlying C routines through an
20808 API; see the package vignette for details.")
20809 (license license:gpl2+)))
20811 (define-public r-actuar
20818 (uri (cran-uri "actuar" version))
20821 "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
20822 (properties `((upstream-name . "actuar")))
20823 (build-system r-build-system)
20824 (propagated-inputs `(("r-expint" ,r-expint)))
20825 (home-page "https://gitlab.com/vigou3/actuar")
20826 (synopsis "Actuarial functions and heavy tailed distributions")
20828 "This package provides functions and data sets for actuarial science:
20829 modeling of loss distributions; risk theory and ruin theory; simulation of
20830 compound models, discrete mixtures and compound hierarchical models;
20831 credibility theory. It boasts support for many additional probability
20832 distributions to model insurance loss amounts and loss frequency: 19
20833 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20834 distribution; zero-truncated and zero-modified extensions of the standard
20835 discrete distributions. It also supports phase-type distributions commonly
20836 used to compute ruin probabilities.")
20837 (license license:gpl2+)))
20839 (define-public r-bmp
20846 (uri (cran-uri "bmp" version))
20849 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20850 (properties `((upstream-name . "bmp")))
20851 (build-system r-build-system)
20852 (home-page "https://cran.r-project.org/web/packages/bmp/")
20853 (synopsis "Read Bitmap (BMP) images")
20855 "This package provides pure R tools to read BMP format images. It is
20856 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20857 (license license:gpl2+)))
20859 (define-public r-readbitmap
20861 (name "r-readbitmap")
20866 (uri (cran-uri "readbitmap" version))
20869 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20870 (properties `((upstream-name . "readbitmap")))
20871 (build-system r-build-system)
20873 `(("libjpeg" ,libjpeg-turbo)
20874 ("libpng" ,libpng)))
20879 ("r-tiff" ,r-tiff)))
20880 (home-page "https://github.com/jefferis/readbitmap")
20881 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20883 "This package provides tools to identify and read BMP, JPEG, PNG, and
20884 TIFF format bitmap images. Identification defaults to the use of the magic
20885 number embedded in the file rather than the file extension.")
20886 (license license:gpl2+)))
20888 (define-public r-imager
20895 (uri (cran-uri "imager" version))
20898 "1dq0rblnrmnk689bcdmml179gk9lff8x92s2npkjllgjq5q2vfpd"))))
20899 (properties `((upstream-name . "imager")))
20900 (build-system r-build-system)
20903 ("libtiff" ,libtiff)
20907 `(("r-downloader" ,r-downloader)
20908 ("r-igraph" ,r-igraph)
20910 ("r-magrittr" ,r-magrittr)
20912 ("r-purrr" ,r-purrr)
20914 ("r-readbitmap" ,r-readbitmap)
20915 ("r-stringr" ,r-stringr)))
20917 `(("pkg-config" ,pkg-config)
20918 ("r-knitr" ,r-knitr)))
20919 (home-page "https://dahtah.github.io/imager/")
20920 (synopsis "Image processing library")
20922 "This is a package for fast image processing for images in up to 4
20923 dimensions (two spatial dimensions, one time/depth dimension, one color
20924 dimension). It provides most traditional image processing tools (filtering,
20925 morphology, transformations, etc.) as well as various functions for easily
20926 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20927 simple, modern C++ library for image processing.")
20928 (license license:lgpl3)))
20930 (define-public r-acuityview
20932 (name "r-acuityview")
20937 (uri (cran-uri "AcuityView" version))
20940 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20941 (properties `((upstream-name . "AcuityView")))
20942 (build-system r-build-system)
20944 `(("r-fftwtools" ,r-fftwtools)
20945 ("r-imager" ,r-imager)
20946 ("r-plotrix" ,r-plotrix)))
20947 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20948 (synopsis "Display scenes as seen by an animal with less acute vision")
20950 "This package provides a simple method for representing a visual scene as
20951 it may be seen by an animal with less acute vision.")
20952 (license license:gpl2+)))
20954 (define-public r-caret
20961 (uri (cran-uri "caret" version))
20964 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20965 (build-system r-build-system)
20967 `(("r-foreach" ,r-foreach)
20968 ("r-ggplot2" ,r-ggplot2)
20969 ("r-lattice" ,r-lattice)
20970 ("r-modelmetrics" ,r-modelmetrics)
20974 ("r-recipes" ,r-recipes)
20975 ("r-reshape2" ,r-reshape2)
20976 ("r-withr" ,r-withr)))
20978 `(("r-knitr" ,r-knitr)))
20979 (home-page "https://github.com/topepo/caret")
20980 (synopsis "Classification and regression training")
20982 "This package provides miscellaneous functions for training and plotting
20983 classification and regression models.")
20984 (license license:gpl2+)))
20986 (define-public r-adabag
20993 (uri (cran-uri "adabag" version))
20996 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
20997 (properties `((upstream-name . "adabag")))
20998 (build-system r-build-system)
21000 `(("r-caret" ,r-caret)
21001 ("r-doparallel" ,r-doparallel)
21002 ("r-foreach" ,r-foreach)
21003 ("r-rpart" ,r-rpart)))
21004 (home-page "https://cran.r-project.org/web/packages/adabag/")
21005 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
21007 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
21008 Breiman's Bagging algorithm using classification trees as individual
21009 classifiers. Once these classifiers have been trained, they can be used to
21010 predict on new data. Also, cross validation estimation of the error can be
21012 (license license:gpl2+)))
21014 (define-public r-adagio
21021 (uri (cran-uri "adagio" version))
21024 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21025 (properties `((upstream-name . "adagio")))
21026 (build-system r-build-system)
21027 (native-inputs `(("gfortran" ,gfortran)))
21028 (home-page "https://cran.r-project.org/web/packages/adagio/")
21029 (synopsis "Discrete and global optimization routines")
21031 "This package provides methods and algorithms for discrete optimization,
21032 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21033 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21035 (license license:gpl3+)))
21037 (define-public r-univoutl
21039 (name "r-univoutl")
21044 (uri (cran-uri "univOutl" version))
21047 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
21048 (properties `((upstream-name . "univOutl")))
21049 (build-system r-build-system)
21051 `(("r-hmisc" ,r-hmisc)
21052 ("r-robustbase" ,r-robustbase)))
21053 (home-page "https://github.com/marcellodo/univOutl")
21054 (synopsis "Detection of univariate outliers")
21056 "This package provides well-known outlier detection techniques in the
21057 univariate case. Methods to deal with skewed distribution are included too.
21058 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21059 historical data is implemented as well. When available, survey weights can be
21060 used in outliers detection.")
21061 (license license:gpl2+)))
21063 (define-public r-tolerance
21065 (name "r-tolerance")
21070 (uri (cran-uri "tolerance" version))
21073 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21074 (properties `((upstream-name . "tolerance")))
21075 (build-system r-build-system)
21077 `(("r-mass" ,r-mass)
21079 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21080 (synopsis "Statistical tolerance intervals and regions")
21082 "This package provides functions for estimating tolerance
21083 limits (intervals) for various univariate distributions (binomial, Cauchy,
21084 discrete Pareto, exponential, two-parameter exponential, extreme value,
21085 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21086 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21087 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21088 nonparametric tolerance intervals, tolerance bands for regression
21089 settings (linear regression, nonlinear regression, nonparametric regression,
21090 and multivariate regression), and analysis of variance tolerance intervals.
21091 Visualizations are also available for most of these settings.")
21092 (license license:gpl2+)))
21094 (define-public r-additivitytests
21096 (name "r-additivitytests")
21101 (uri (cran-uri "additivityTests" version))
21104 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21106 `((upstream-name . "additivityTests")))
21107 (build-system r-build-system)
21108 (home-page "https://github.com/simecek/additivityTests")
21109 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21111 "This package provides an implementation of the Tukey, Mandel,
21112 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21113 (license license:gpl3)))
21115 (define-public r-flexclust
21117 (name "r-flexclust")
21122 (uri (cran-uri "flexclust" version))
21125 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21126 (properties `((upstream-name . "flexclust")))
21127 (build-system r-build-system)
21129 `(("r-class" ,r-class)
21130 ("r-lattice" ,r-lattice)
21131 ("r-modeltools" ,r-modeltools)))
21132 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21133 (synopsis "Flexible cluster algorithms")
21135 "The main function @code{kcca} implements a general framework for
21136 k-centroids cluster analysis supporting arbitrary distance measures and
21137 centroid computation. Further cluster methods include hard competitive
21138 learning, neural gas, and QT clustering. There are numerous visualization
21139 methods for cluster results (neighborhood graphs, convex cluster hulls,
21140 barcharts of centroids, ...), and bootstrap methods for the analysis of
21141 cluster stability.")
21142 (license license:gpl2)))
21144 (define-public r-biclust
21151 (uri (cran-uri "biclust" version))
21154 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21155 (properties `((upstream-name . "biclust")))
21156 (build-system r-build-system)
21158 `(("r-additivitytests" ,r-additivitytests)
21159 ("r-colorspace" ,r-colorspace)
21160 ("r-flexclust" ,r-flexclust)
21161 ("r-ggplot2" ,r-ggplot2)
21162 ("r-lattice" ,r-lattice)
21164 ("r-tidyr" ,r-tidyr)))
21165 (home-page "https://cran.r-project.org/web/packages/biclust/")
21166 (synopsis "BiCluster algorithms")
21168 "The main function @code{biclust()} provides several algorithms to find
21169 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21170 In addition, the package provides methods for data
21171 preprocessing (normalization and discretization), visualization, and
21172 validation of bicluster solutions.")
21173 (license license:gpl3)))
21175 (define-public r-icge
21182 (uri (cran-uri "ICGE" version))
21185 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21186 (properties `((upstream-name . "ICGE")))
21187 (build-system r-build-system)
21189 `(("r-cluster" ,r-cluster)
21190 ("r-mass" ,r-mass)))
21191 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21192 (synopsis "Cluster estimation and identification of atypical units")
21194 "ICGE is a package that helps to estimate the number of real clusters in
21195 data as well as to identify atypical units. The underlying methods are based
21196 on distances rather than on unit x variables.")
21197 (license license:gpl2+)))
21199 (define-public r-depth
21202 (version "2.1-1.1")
21206 (uri (cran-uri "depth" version))
21209 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21210 (properties `((upstream-name . "depth")))
21211 (build-system r-build-system)
21213 `(("r-abind" ,r-abind)
21214 ("r-circular" ,r-circular)
21217 `(("gfortran" ,gfortran)))
21218 (home-page "https://cran.r-project.org/web/packages/depth/")
21219 (synopsis "Nonparametric depth functions for multivariate analysis")
21221 "This package provides tools for depth functions methodology applied to
21222 multivariate analysis. Besides allowing calculation of depth values and
21223 depth-based location estimators, the package includes functions or drawing
21224 contour plots and perspective plots of depth functions. Euclidean and
21225 spherical depths are supported.")
21226 (license license:gpl2)))
21228 (define-public r-archetypes
21230 (name "r-archetypes")
21231 (version "2.2-0.1")
21235 (uri (cran-uri "archetypes" version))
21238 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21239 (properties `((upstream-name . "archetypes")))
21240 (build-system r-build-system)
21242 `(("r-modeltools" ,r-modeltools)
21243 ("r-nnls" ,r-nnls)))
21244 (home-page "https://cran.r-project.org/web/packages/archetypes")
21245 (synopsis "Archetypal analysis")
21247 "The main function @code{archetypes} implements a framework for
21248 archetypal analysis supporting arbitrary problem solving mechanisms for the
21249 different conceptual parts of the algorithm.")
21250 (license license:gpl2+)))
21252 (define-public r-shapes
21259 (uri (cran-uri "shapes" version))
21262 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
21263 (properties `((upstream-name . "shapes")))
21264 (build-system r-build-system)
21266 `(("r-mass" ,r-mass)
21267 ("r-minpack-lm" ,r-minpack-lm)
21269 ("r-scatterplot3d" ,r-scatterplot3d)))
21270 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21271 (synopsis "Statistical shape analysis")
21273 "This package provides routines for the statistical analysis of landmark
21274 shapes, including Procrustes analysis, graphical displays, principal
21275 components analysis, permutation and bootstrap tests, thin-plate spline
21276 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21277 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21278 Edition), John Wiley and Sons.")
21279 (license license:gpl2)))
21281 (define-public r-anthropometry
21283 (name "r-anthropometry")
21288 (uri (cran-uri "Anthropometry" version))
21291 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21292 (properties `((upstream-name . "Anthropometry")))
21293 (build-system r-build-system)
21295 `(("r-archetypes" ,r-archetypes)
21296 ("r-biclust" ,r-biclust)
21297 ("r-cluster" ,r-cluster)
21298 ("r-depth" ,r-depth)
21303 ("r-shapes" ,r-shapes)))
21305 `(("r-knitr" ,r-knitr)))
21306 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21307 (synopsis "Statistical methods for anthropometric data")
21309 "This package provides statistical methods especially developed to
21310 analyze anthropometric data. These methods are aimed at providing effective
21311 solutions to some commons problems related to Ergonomics and Anthropometry.
21312 They are based on clustering, the statistical concept of data depth,
21313 statistical shape analysis and archetypal analysis.")
21314 (license license:gpl2+)))
21316 (define-public r-adamethods
21318 (name "r-adamethods")
21323 (uri (cran-uri "adamethods" version))
21326 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21327 (properties `((upstream-name . "adamethods")))
21328 (build-system r-build-system)
21330 `(("r-anthropometry" ,r-anthropometry)
21331 ("r-archetypes" ,r-archetypes)
21333 ("r-foreach" ,r-foreach)
21335 ("r-tolerance" ,r-tolerance)
21336 ("r-univoutl" ,r-univoutl)))
21337 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21338 (synopsis "Archetypoid algorithms and anomaly detection")
21340 "This package is a collection of several algorithms to obtain
21341 archetypoids with small and large databases and with both classical
21342 multivariate data and functional data (univariate and multivariate). Some of
21343 these algorithms also detect anomalies (outliers).")
21344 (license license:gpl2+)))
21346 (define-public r-idpmisc
21353 (uri (cran-uri "IDPmisc" version))
21356 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21357 (properties `((upstream-name . "IDPmisc")))
21358 (build-system r-build-system)
21360 `(("r-lattice" ,r-lattice)))
21361 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21362 (synopsis "Functions for data analyses and visualization")
21364 "This package provides different high-level graphics functions for
21365 displaying large datasets, displaying circular data in a very flexible way,
21366 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21367 2D-plots, creating figures with differently colored margin and plot region.
21368 In addition, the package contains auxiliary functions for data manipulation
21369 like omitting observations with irregular values or selecting data by logical
21370 vectors, which include NAs. Other functions are especially useful in
21371 spectroscopy and analyses of environmental data: robust baseline fitting,
21372 finding peaks in spectra, converting humidity measures.")
21373 (license license:gpl3+)))
21375 (define-public r-qqman
21382 (uri (cran-uri "qqman" version))
21385 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21386 (properties `((upstream-name . "qqman")))
21387 (build-system r-build-system)
21389 `(("r-calibrate" ,r-calibrate)))
21390 (home-page "https://cran.r-project.org/web/packages/qqman/")
21391 (synopsis "Q-Q and Manhattan plots for GWAS data")
21393 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21394 from PLINK results.")
21395 (license license:gpl3)))
21397 (define-public r-ggplot-multistats
21399 (name "r-ggplot-multistats")
21404 (uri (cran-uri "ggplot.multistats" version))
21407 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21409 `((upstream-name . "ggplot.multistats")))
21410 (build-system r-build-system)
21412 `(("r-ggplot2" ,r-ggplot2)
21413 ("r-hexbin" ,r-hexbin)
21414 ("r-rlang" ,r-rlang)
21415 ("r-scales" ,r-scales)))
21416 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21417 (synopsis "Multiple summary statistics for binned stats/geometries")
21419 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21420 which functions similar to its singular form, but allows the use of multiple
21421 statistics per bin. Those statistics can be mapped to multiple bin
21423 (license license:gpl3)))
21425 (define-public r-knn-covertree
21427 (name "r-knn-covertree")
21432 (uri (cran-uri "knn.covertree" version))
21435 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21436 (properties `((upstream-name . "knn.covertree")))
21437 (build-system r-build-system)
21439 `(("r-matrix" ,r-matrix)
21441 ("r-rcppeigen" ,r-rcppeigen)))
21442 (home-page "https://github.com/flying-sheep/knn.covertree")
21443 (synopsis "Accurate kNN Implementation with multiple distance measures")
21445 "Similarly to the FNN package, this package allows calculation of the k
21446 nearest neighbors (kNN) of a data matrix. The implementation is based on
21447 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21448 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21449 (license license:agpl3+)))
21451 (define-public r-poibin
21458 (uri (cran-uri "poibin" version))
21461 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21462 (properties `((upstream-name . "poibin")))
21463 (build-system r-build-system)
21464 (home-page "https://cran.r-project.org/web/packages/poibin/")
21465 (synopsis "Poisson binomial distribution")
21467 "This package provides an implementation of both the exact and
21468 approximation methods for computing the @dfn{cumulative distribution
21469 function} (CDF) of the Poisson binomial distribution. It also provides the
21470 @dfn{probability mass function} (PMF), quantile function, and random number
21471 generation for the Poisson binomial distribution.")
21472 (license license:gpl2)))
21474 (define-public r-diagram
21481 (uri (cran-uri "diagram" version))
21484 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21485 (properties `((upstream-name . "diagram")))
21486 (build-system r-build-system)
21488 `(("r-shape" ,r-shape)))
21489 (home-page "https://cran.r-project.org/web/packages/diagram/")
21490 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21492 "This package provides tools to visualize simple graphs (networks) based
21493 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21494 electrical networks, etc. It also includes supporting material for the book
21495 \"A practical guide to ecological modelling - using R as a simulation
21496 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21497 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21498 Francesca Mazzia (2012).")
21499 (license license:gpl2+)))
21501 (define-public r-lim
21508 (uri (cran-uri "LIM" version))
21511 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21512 (properties `((upstream-name . "LIM")))
21513 (build-system r-build-system)
21515 `(("r-diagram" ,r-diagram)
21516 ("r-limsolve" ,r-limsolve)))
21517 (home-page "https://cran.r-project.org/web/packages/LIM/")
21518 (synopsis "Linear inverse model examples and solution methods")
21520 "This package provides functions that read and solve linear inverse
21521 problems (food web problems, linear programming problems).")
21522 (license license:gpl2+)))
21524 (define-public r-shinycssloaders
21526 (name "r-shinycssloaders")
21531 (uri (cran-uri "shinycssloaders" version))
21534 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21536 `((upstream-name . "shinycssloaders")))
21537 (build-system r-build-system)
21539 `(("r-digest" ,r-digest)
21541 ("r-shiny" ,r-shiny)))
21542 (home-page "https://github.com/andrewsali/shinycssloaders")
21543 (synopsis "Add CSS loading animations to Shiny outputs")
21545 "This package provides tools to create a lightweight Shiny wrapper for
21546 the css-loaders created by Luke Hass
21547 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21548 automatically show a loader when the output is (re)calculating.")
21549 (license license:gpl3)))
21551 (define-public r-rsvg
21558 (uri (cran-uri "rsvg" version))
21561 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21562 (properties `((upstream-name . "rsvg")))
21563 (build-system r-build-system)
21565 `(("librsvg" ,librsvg)
21568 `(("pkg-config" ,pkg-config)
21569 ("r-knitr" ,r-knitr)))
21570 (home-page "https://github.com/jeroen/rsvg#readme")
21571 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21573 "This package allows you to render vector-based SVG images into
21574 high-quality custom-size bitmap arrays using the librsvg2 library. The
21575 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21576 addition, the package can convert images directly to various formats such as
21577 PDF or PostScript.")
21578 (license license:expat)))
21580 (define-public r-influencer
21582 (name "r-influencer")
21587 (uri (cran-uri "influenceR" version))
21590 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21591 (properties `((upstream-name . "influenceR")))
21592 (build-system r-build-system)
21594 `(("r-igraph" ,r-igraph)
21595 ("r-matrix" ,r-matrix)))
21596 (home-page "https://github.com/rcc-uchicago/influenceR")
21597 (synopsis "Tools to quantify structural importance of nodes in a network")
21599 "This package provides functionality to compute various node centrality
21600 measures on networks. Included are functions to compute betweenness
21601 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21602 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21603 algorithm to identify key players, and Valente's bridging metric. The
21604 betweenness, Key Players, and bridging implementations are parallelized with
21606 (license license:gpl2)))
21608 (define-public r-emplik
21615 (uri (cran-uri "emplik" version))
21618 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21619 (properties `((upstream-name . "emplik")))
21620 (build-system r-build-system)
21622 `(("r-quantreg" ,r-quantreg)))
21623 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21624 (synopsis "Empirical likelihood ratio for censored/truncated data")
21626 "This package provides empirical likelihood ratio tests for
21627 means/quantiles/hazards from possibly censored and/or truncated data. It also
21629 (license license:gpl2+)))
21631 (define-public r-imputeyn
21633 (name "r-imputeyn")
21638 (uri (cran-uri "imputeYn" version))
21641 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21642 (properties `((upstream-name . "imputeYn")))
21643 (build-system r-build-system)
21645 `(("r-boot" ,r-boot)
21646 ("r-emplik" ,r-emplik)
21647 ("r-mvtnorm" ,r-mvtnorm)
21648 ("r-quadprog" ,r-quadprog)
21649 ("r-survival" ,r-survival)))
21650 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21651 (synopsis "Impute last largest censored observation under weighted least squares")
21653 "This package allows for the imputation of the last largest censored
21654 observantions. This method brings less bias and more efficient estimates for
21656 (license license:gpl2)))
21658 (define-public r-adapenetclass
21660 (name "r-adapenetclass")
21665 (uri (cran-uri "AdapEnetClass" version))
21668 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21669 (properties `((upstream-name . "AdapEnetClass")))
21670 (build-system r-build-system)
21672 `(("r-glmnet" ,r-glmnet)
21673 ("r-imputeyn" ,r-imputeyn)
21675 ("r-quadprog" ,r-quadprog)))
21676 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21677 (synopsis "Class of adaptive elastic net methods for censored data")
21679 "This package provides methods for variable selection for AFT models.")
21680 (license license:gpl2)))
21682 (define-public r-flock
21689 (uri (cran-uri "flock" version))
21692 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21693 (properties `((upstream-name . "flock")))
21694 (build-system r-build-system)
21695 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21696 (home-page "https://cran.r-project.org/web/packages/flock/")
21697 (synopsis "Process synchronization using file locks")
21699 "This package implements synchronization between R processes (spawned by
21700 using the @code{parallel} package for instance) using file locks. It supports
21701 both exclusive and shared locking.")
21702 (license license:asl2.0)))
21704 (define-public r-archivist
21706 (name "r-archivist")
21711 (uri (cran-uri "archivist" version))
21714 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21715 (properties `((upstream-name . "archivist")))
21716 (build-system r-build-system)
21719 ("r-digest" ,r-digest)
21720 ("r-flock" ,r-flock)
21722 ("r-lubridate" ,r-lubridate)
21723 ("r-magrittr" ,r-magrittr)
21724 ("r-rcurl" ,r-rcurl)
21725 ("r-rsqlite" ,r-rsqlite)))
21727 `(("r-knitr" ,r-knitr)))
21728 (home-page "https://pbiecek.github.io/archivist/")
21729 (synopsis "Tools for storing, restoring and searching for R objects")
21731 "Data exploration and modelling is a process in which a lot of data
21732 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21733 statistical models, different versions of data sets and different versions of
21734 results. Archivist helps to store and manage artifacts created in R. It
21735 allows you to store selected artifacts as binary files together with their
21736 metadata and relations. Archivist allows sharing artifacts with others. It
21737 can look for already created artifacts by using its class, name, date of the
21738 creation or other properties. It also makes it easy to restore such
21740 (license license:gpl2)))
21742 (define-public r-versions
21744 (name "r-versions")
21749 (uri (cran-uri "versions" version))
21752 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21753 (properties `((upstream-name . "versions")))
21754 (build-system r-build-system)
21755 (home-page "https://cran.r-project.org/web/packages/versions/")
21756 (synopsis "Query and install specific versions of CRAN packages")
21758 "This package allows you to install specified versions of R packages
21759 hosted on CRAN and provides functions to list available versions and the
21760 versions of currently installed packages.")
21761 (license license:bsd-3)))
21763 (define-public r-adapr
21770 (uri (cran-uri "adapr" version))
21773 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21774 (properties `((upstream-name . "adapr")))
21775 (build-system r-build-system)
21777 `(("r-archivist" ,r-archivist)
21778 ("r-devtools" ,r-devtools)
21779 ("r-digest" ,r-digest)
21780 ("r-doparallel" ,r-doparallel)
21781 ("r-gdata" ,r-gdata)
21782 ("r-ggplot2" ,r-ggplot2)
21783 ("r-git2r" ,r-git2r)
21784 ("r-igraph" ,r-igraph)
21785 ("r-knitr" ,r-knitr)
21786 ("r-plotly" ,r-plotly)
21788 ("r-rmarkdown" ,r-rmarkdown)
21789 ("r-shiny" ,r-shiny)
21790 ("r-shinydashboard" ,r-shinydashboard)
21791 ("r-versions" ,r-versions)))
21792 (home-page "https://cran.r-project.org/web/packages/adapr/")
21793 (synopsis "Implementation of an accountable data analysis process")
21795 "This package tracks reading and writing within R scripts that are
21796 organized into a directed acyclic graph. It contains an interactive Shiny
21797 application @code{adaprApp()}. It uses Git and file hashes to track version
21798 histories of inputs and outputs.")
21799 (license license:lgpl2.0)))
21801 (define-public r-adapsamp
21803 (name "r-adapsamp")
21808 (uri (cran-uri "AdapSamp" version))
21811 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21812 (properties `((upstream-name . "AdapSamp")))
21813 (build-system r-build-system)
21814 (propagated-inputs `(("r-pracma" ,r-pracma)))
21815 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21816 (synopsis "Adaptive sampling algorithms")
21818 "For distributions whose probability density functions are log-concave,
21819 the adaptive rejection sampling algorithm can be used to build envelope
21820 functions for sampling. For others, the modified adaptive rejection sampling
21821 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21822 adaptive slice sampling algorithm can be used. This R package mainly includes
21823 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21824 @code{rASS()}. These functions can realize sampling based on the algorithms
21826 (license license:gpl2)))
21828 (define-public r-adaptalint
21830 (name "r-adaptalint")
21835 (uri (cran-uri "adaptalint" version))
21838 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21839 (properties `((upstream-name . "adaptalint")))
21840 (build-system r-build-system)
21842 `(("r-dplyr" ,r-dplyr)
21843 ("r-lintr" ,r-lintr)
21844 ("r-purrr" ,r-purrr)))
21845 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21846 (synopsis "Check R code style")
21848 "This package provides tools to infer the code style (which style rules
21849 are followed and which ones are not) from one package and use it to check
21850 another. This makes it easier to find and correct the most important problems
21852 (license license:gpl3)))
21854 (define-public r-fracdiff
21856 (name "r-fracdiff")
21861 (uri (cran-uri "fracdiff" version))
21864 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21865 (properties `((upstream-name . "fracdiff")))
21866 (build-system r-build-system)
21867 (home-page "https://github.com/mmaechler/fracdiff")
21869 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21871 "This package provides tools for the maximum likelihood estimation of the
21872 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21873 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21874 (license license:gpl2+)))
21876 (define-public r-forecast
21878 (name "r-forecast")
21883 (uri (cran-uri "forecast" version))
21886 "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
21887 (properties `((upstream-name . "forecast")))
21888 (build-system r-build-system)
21890 `(("r-colorspace" ,r-colorspace)
21891 ("r-fracdiff" ,r-fracdiff)
21892 ("r-ggplot2" ,r-ggplot2)
21893 ("r-lmtest" ,r-lmtest)
21894 ("r-magrittr" ,r-magrittr)
21897 ("r-rcpparmadillo" ,r-rcpparmadillo)
21898 ("r-timedate" ,r-timedate)
21899 ("r-tseries" ,r-tseries)
21903 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21904 (home-page "https://pkg.robjhyndman.com/forecast/")
21905 (synopsis "Forecasting functions for time series and linear models")
21907 "This package provides methods and tools for displaying and analysing
21908 univariate time series forecasts including exponential smoothing via state
21909 space models and automatic ARIMA modelling.")
21910 (license license:gpl3)))
21912 (define-public r-xmisc
21919 (uri (cran-uri "Xmisc" version))
21922 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21923 (properties `((upstream-name . "Xmisc")))
21924 (build-system r-build-system)
21925 (home-page "https://cran.r-project.org/package=Xmisc")
21927 "Xiaobei's miscellaneous classes and functions")
21929 "This package provides Xiaobei's miscellaneous classes and functions,
21930 which are useful when developing R packages for @dfn{object oriented
21931 programming} (OOP) using R Reference Class.")
21932 (license license:gpl2+)))
21934 (define-public r-proxyc
21941 (uri (cran-uri "proxyC" version))
21944 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21945 (properties `((upstream-name . "proxyC")))
21946 (build-system r-build-system)
21948 `(("r-matrix" ,r-matrix)
21950 ("r-rcpparmadillo" ,r-rcpparmadillo)
21951 ("r-rcppparallel" ,r-rcppparallel)))
21952 (home-page "https://cran.r-project.org/package=proxyC")
21953 (synopsis "Compute proximity in large sparse matrices")
21955 "This package provides efficient tools to compute the proximity between
21956 rows or columns of large matrices. Functions are optimised for large sparse
21957 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21958 similarity/distance measures, computation of correlation, cosine similarity
21959 and Euclidean distance is particularly fast.")
21960 (license license:gpl3)))
21962 (define-public r-isocodes
21964 (name "r-isocodes")
21965 (version "2021.02.24")
21969 (uri (cran-uri "ISOcodes" version))
21972 "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm"))))
21973 (properties `((upstream-name . "ISOcodes")))
21974 (build-system r-build-system)
21975 (home-page "https://cran.r-project.org/package=ISOcodes")
21976 (synopsis "Selected ISO codes")
21978 "This package provides ISO language, territory, currency, script and
21979 character codes. It provides ISO 639 language codes, ISO 3166 territory
21980 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21981 character codes as well as the UN M.49 area codes.")
21982 (license license:gpl2)))
21984 (define-public r-stopwords
21986 (name "r-stopwords")
21991 (uri (cran-uri "stopwords" version))
21994 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
21995 (properties `((upstream-name . "stopwords")))
21996 (build-system r-build-system)
21998 `(("r-isocodes" ,r-isocodes)))
21999 (home-page "https://github.com/quanteda/stopwords")
22000 (synopsis "Multilingual stopword lists")
22002 "This package provides multiple sources of stopwords, for use in text
22003 analysis and natural language processing.")
22004 (license license:expat)))
22006 (define-public r-spacyr
22013 (uri (cran-uri "spacyr" version))
22016 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
22017 (properties `((upstream-name . "spacyr")))
22018 (build-system r-build-system)
22020 `(("r-data-table" ,r-data-table)
22021 ("r-reticulate" ,r-reticulate)))
22022 (home-page "https://spacyr.quanteda.io")
22023 (synopsis "R wrapper for the spaCy NLP library")
22025 "This package provides an R wrapper to the Python @dfn{natural language
22026 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22027 (license license:gpl3)))
22029 (define-public r-snowballc
22031 (name "r-snowballc")
22036 (uri (cran-uri "SnowballC" version))
22039 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22040 (properties `((upstream-name . "SnowballC")))
22041 (build-system r-build-system)
22042 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22043 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22045 "This package provides an R interface to the C @code{libstemmer} library
22046 that implements Porter's word stemming algorithm for collapsing words to a
22047 common root to aid comparison of vocabulary. Currently supported languages
22048 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22049 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22050 (license license:bsd-3)))
22052 (define-public r-quanteda
22054 (name "r-quanteda")
22059 (uri (cran-uri "quanteda" version))
22062 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
22063 (properties `((upstream-name . "quanteda")))
22064 (build-system r-build-system)
22066 `(("r-data-table" ,r-data-table)
22067 ("r-digest" ,r-digest)
22068 ("r-extrafont" ,r-extrafont)
22069 ("r-fastmatch" ,r-fastmatch)
22070 ("r-ggplot2" ,r-ggplot2)
22071 ("r-ggrepel" ,r-ggrepel)
22072 ("r-jsonlite" ,r-jsonlite)
22073 ("r-magrittr" ,r-magrittr)
22074 ("r-matrix" ,r-matrix)
22075 ("r-network" ,r-network)
22076 ("r-proxyc" ,r-proxyc)
22078 ("r-rcpparmadillo" ,r-rcpparmadillo)
22079 ("r-rcppparallel" ,r-rcppparallel)
22081 ("r-snowballc" ,r-snowballc)
22082 ("r-stopwords" ,r-stopwords)
22083 ("r-stringi" ,r-stringi)
22085 ("r-yaml" ,r-yaml)))
22087 `(("r-knitr" ,r-knitr)))
22088 (home-page "https://quanteda.io")
22089 (synopsis "Quantitative analysis of textual data")
22091 "This package provides a fast, flexible, and comprehensive framework for
22092 quantitative text analysis in R. It provides functionality for corpus
22093 management, creating and manipulating tokens and ngrams, exploring keywords in
22094 context, forming and manipulating sparse matrices of documents by features and
22095 feature co-occurrences, analyzing keywords, computing feature similarities and
22096 distances, applying content dictionaries, applying supervised and unsupervised
22097 machine learning, visually representing text and text analyses, and more.")
22098 (license license:gpl3)))
22100 (define-public r-topicmodels
22102 (name "r-topicmodels")
22107 (uri (cran-uri "topicmodels" version))
22110 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22111 (properties `((upstream-name . "topicmodels")))
22112 (build-system r-build-system)
22116 `(("r-modeltools" ,r-modeltools)
22119 (home-page "https://cran.r-project.org/package=topicmodels")
22120 (synopsis "Topic models")
22122 "This package provides an interface to the C code for @dfn{Latent
22123 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22124 David M. Blei and co-authors and the C++ code for fitting LDA models using
22125 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22126 (license license:gpl2)))
22128 (define-public r-stm
22135 (uri (cran-uri "stm" version))
22138 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22139 (properties `((upstream-name . "stm")))
22140 (build-system r-build-system)
22142 `(("r-data-table" ,r-data-table)
22143 ("r-glmnet" ,r-glmnet)
22145 ("r-matrix" ,r-matrix)
22146 ("r-matrixstats" ,r-matrixstats)
22147 ("r-quadprog" ,r-quadprog)
22148 ("r-quanteda" ,r-quanteda)
22150 ("r-rcpparmadillo" ,r-rcpparmadillo)
22152 ("r-stringr" ,r-stringr)))
22153 (home-page "http://www.structuraltopicmodel.com/")
22154 (synopsis "Estimation of the Structural Topic Model")
22156 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22157 topic models with document-level covariates. The package also includes tools
22158 for model selection, visualization, and estimation of topic-covariate
22160 (license license:expat)))
22162 (define-public r-polycor
22169 (uri (cran-uri "polycor" version))
22172 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22173 (properties `((upstream-name . "polycor")))
22174 (build-system r-build-system)
22176 `(("r-matrix" ,r-matrix)
22177 ("r-mvtnorm" ,r-mvtnorm)))
22178 (home-page "https://r-forge.r-project.org/projects/polycor/")
22179 (synopsis "Polychoric and polyserial correlations")
22181 "This package provides tools to compute polychoric and polyserial
22182 correlations by quick \"two-step\" methods or ML, optionally with standard
22183 errors; tetrachoric and biserial correlations are special cases.")
22184 (license license:gpl2+)))
22186 (define-public r-msm
22193 (uri (cran-uri "msm" version))
22196 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22197 (properties `((upstream-name . "msm")))
22198 (build-system r-build-system)
22200 `(("r-expm" ,r-expm)
22201 ("r-mvtnorm" ,r-mvtnorm)
22202 ("r-survival" ,r-survival)))
22203 (home-page "https://github.com/chjackson/msm")
22204 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22206 "This package provides functions for fitting continuous-time Markov and
22207 hidden Markov multi-state models to longitudinal data. It was designed for
22208 processes observed at arbitrary times in continuous time (panel data) but some
22209 other observation schemes are supported. Both Markov transition rates and the
22210 hidden Markov output process can be modelled in terms of covariates, which may
22211 be constant or piecewise-constant in time.")
22212 (license license:gpl2+)))
22214 (define-public r-ltm
22221 (uri (cran-uri "ltm" version))
22224 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22225 (properties `((upstream-name . "ltm")))
22226 (build-system r-build-system)
22228 `(("r-mass" ,r-mass)
22230 ("r-polycor" ,r-polycor)))
22231 (home-page "https://github.com/drizopoulos/ltm")
22232 (synopsis "Latent trait models under IRT")
22234 "This is a package supporting the analysis of multivariate dichotomous
22235 and polytomous data using latent trait models under the Item Response Theory
22236 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22237 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22239 (license license:gpl2+)))
22241 (define-public r-mi
22248 (uri (cran-uri "mi" version))
22251 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22252 (properties `((upstream-name . "mi")))
22253 (build-system r-build-system)
22256 ("r-matrix" ,r-matrix)))
22257 (home-page "http://www.stat.columbia.edu/~gelman/")
22258 (synopsis "Missing data imputation and model checking")
22260 "This package provides functions for data manipulation, imputing missing
22261 values in an approximate Bayesian framework, diagnostics of the models used to
22262 generate the imputations, confidence-building mechanisms to validate some of
22263 the assumptions of the imputation algorithm, and functions to analyze multiply
22264 imputed data sets with the appropriate degree of sampling uncertainty.")
22265 (license license:gpl2+)))
22267 (define-public r-matrixcalc
22269 (name "r-matrixcalc")
22274 (uri (cran-uri "matrixcalc" version))
22277 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22278 (properties `((upstream-name . "matrixcalc")))
22279 (build-system r-build-system)
22280 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22281 (synopsis "Collection of functions for matrix calculations")
22283 "This package provides a collection of functions to support matrix
22284 calculations for probability, econometric and numerical analysis. There are
22285 additional functions that are comparable to APL functions which are useful for
22286 actuarial models such as pension mathematics.")
22287 (license license:gpl2+)))
22289 (define-public r-sem
22296 (uri (cran-uri "sem" version))
22299 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22300 (properties `((upstream-name . "sem")))
22301 (build-system r-build-system)
22303 `(("r-boot" ,r-boot)
22305 ("r-matrixcalc" ,r-matrixcalc)
22307 (home-page "https://cran.r-project.org/package=sem")
22308 (synopsis "Structural equation models")
22310 "This package provides functions for fitting general linear structural
22311 equation models (with observed and latent variables) using the RAM approach,
22312 and for fitting structural equations in observed-variable models by two-stage
22314 (license license:gpl2+)))
22316 (define-public r-semtools
22318 (name "r-semtools")
22323 (uri (cran-uri "semTools" version))
22326 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22327 (properties `((upstream-name . "semTools")))
22328 (build-system r-build-system)
22330 `(("r-lavaan" ,r-lavaan)))
22331 (home-page "https://github.com/simsem/semTools/wiki")
22332 (synopsis "Useful tools for structural equation modeling")
22334 "This package provides useful tools for structural equation modeling.")
22335 (license license:gpl2+)))
22337 (define-public r-regsem
22344 (uri (cran-uri "regsem" version))
22347 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22348 (properties `((upstream-name . "regsem")))
22349 (build-system r-build-system)
22351 `(("r-lavaan" ,r-lavaan)
22353 ("r-rcpparmadillo" ,r-rcpparmadillo)
22354 ("r-rsolnp" ,r-rsolnp)))
22356 `(("r-knitr" ,r-knitr)))
22357 (home-page "https://cran.r-project.org/package=regsem")
22358 (synopsis "Regularized structural equation modeling")
22360 "This package uses both ridge and lasso penalties (and extensions) to
22361 penalize specific parameters in structural equation models. The package
22362 offers additional cost functions, cross validation, and other extensions
22363 beyond traditional structural equation models. It also contains a function to
22364 perform @dfn{exploratory mediation} (XMed).")
22365 (license license:gpl2+)))
22367 (define-public r-stanheaders
22369 (name "r-stanheaders")
22370 (version "2.21.0-7")
22374 (uri (cran-uri "StanHeaders" version))
22377 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22378 (properties `((upstream-name . "StanHeaders")))
22379 (build-system r-build-system)
22380 (inputs `(("pandoc" ,pandoc)))
22382 `(("r-rcppeigen" ,r-rcppeigen)
22383 ("r-rcppparallel" ,r-rcppparallel)))
22385 `(("gfortran" ,gfortran)
22386 ("r-knitr" ,r-knitr))) ; for vignettes
22387 (home-page "https://mc-stan.org/")
22388 (synopsis "C++ header files for Stan")
22390 "The C++ header files of the Stan project are provided by this package.
22391 There is a shared object containing part of the @code{CVODES} library, but it
22392 is not accessible from R. @code{r-stanheaders} is only useful for developers
22393 who want to utilize the @code{LinkingTo} directive of their package's
22394 DESCRIPTION file to build on the Stan library without incurring unnecessary
22397 The Stan project develops a probabilistic programming language that implements
22398 full or approximate Bayesian statistical inference via Markov Chain Monte
22399 Carlo or variational methods and implements (optionally penalized) maximum
22400 likelihood estimation via optimization. The Stan library includes an advanced
22401 automatic differentiation scheme, templated statistical and linear algebra
22402 functions that can handle the automatically differentiable scalar types (and
22403 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22404 package provides user-facing R functions to parse, compile, test, estimate,
22405 and analyze Stan models.")
22406 (license license:bsd-3)))
22408 (define-public r-rpf
22415 (uri (cran-uri "rpf" version))
22418 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22419 (properties `((upstream-name . "rpf")))
22420 (build-system r-build-system)
22422 `(("r-lifecycle" ,r-lifecycle)
22423 ("r-mvtnorm" ,r-mvtnorm)
22425 ("r-rcppeigen" ,r-rcppeigen)))
22427 `(("r-knitr" ,r-knitr)))
22428 (home-page "https://github.com/jpritikin/rpf")
22429 (synopsis "Response probability functions")
22431 "The purpose of this package is to factor out logic and math common to
22432 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22433 core support code suitable for more specialized IRT packages to build upon.
22434 Complete access to optimized C functions is made available with
22435 @code{R_RegisterCCallable()}.")
22436 (license license:gpl3+)))
22438 (define-public r-openmx
22445 (uri (cran-uri "OpenMx" version))
22448 "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj"))))
22449 (properties `((upstream-name . "OpenMx")))
22450 (build-system r-build-system)
22453 ("r-digest" ,r-digest)
22454 ("r-lifecycle" ,r-lifecycle)
22456 ("r-matrix" ,r-matrix)
22458 ("r-rcppeigen" ,r-rcppeigen)
22460 ("r-stanheaders" ,r-stanheaders)))
22461 (native-inputs `(("gfortran" ,gfortran)))
22462 (home-page "http://openmx.ssri.psu.edu")
22463 (synopsis "Extended structural equation modelling")
22465 "This package allows for the estimation of a wide variety of advanced
22466 multivariate statistical models. It consists of a library of functions and
22467 optimizers that allow you to quickly and flexibly define an SEM model and
22468 estimate parameters given observed data.")
22469 (license license:asl2.0)))
22471 (define-public r-kutils
22478 (uri (cran-uri "kutils" version))
22481 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22482 (properties `((upstream-name . "kutils")))
22483 (build-system r-build-system)
22485 `(("r-foreign" ,r-foreign)
22486 ("r-openxlsx" ,r-openxlsx)
22488 ("r-runit" ,r-runit)
22489 ("r-xtable" ,r-xtable)))
22490 (home-page "https://cran.r-project.org/package=kutils")
22491 (synopsis "Project management tools")
22493 "This package provides tools for data importation, recoding, and
22494 inspection. There are functions to create new project folders, R code
22495 templates, create uniquely named output directories, and to quickly obtain a
22496 visual summary for each variable in a data frame. The main feature here is
22497 the systematic implementation of the \"variable key\" framework for data
22498 importation and recoding.")
22499 (license license:gpl2)))
22501 (define-public r-rockchalk
22503 (name "r-rockchalk")
22504 (version "1.8.144")
22508 (uri (cran-uri "rockchalk" version))
22511 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22512 (properties `((upstream-name . "rockchalk")))
22513 (build-system r-build-system)
22515 `(("r-cardata" ,r-cardata)
22516 ("r-kutils" ,r-kutils)
22518 ("r-mass" ,r-mass)))
22519 (home-page "https://cran.r-project.org/package=rockchalk")
22520 (synopsis "Regression estimation and presentation")
22522 "This package provides a collection of functions for interpretation and
22523 presentation of regression analysis. These functions are used to produce the
22524 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22525 includes regression diagnostics, regression tables, and plots of interactions
22526 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22527 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22528 fairly comprehensive overview.")
22529 (license license:gpl3+)))
22531 (define-public r-lisreltor
22533 (name "r-lisreltor")
22538 (uri (cran-uri "lisrelToR" version))
22541 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22542 (properties `((upstream-name . "lisrelToR")))
22543 (build-system r-build-system)
22544 (home-page "https://cran.r-project.org/package=lisrelToR")
22545 (synopsis "Import output from LISREL into R")
22547 "This is an unofficial package aimed at automating the import of LISREL
22549 (license license:gpl2)))
22551 (define-public r-bdgraph
22558 (uri (cran-uri "BDgraph" version))
22561 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22562 (properties `((upstream-name . "BDgraph")))
22563 (build-system r-build-system)
22565 `(("r-igraph" ,r-igraph)))
22566 (home-page "https://www.uva.nl/profile/a.mohammadi")
22567 (synopsis "Bayesian structure learning in graphical models")
22569 "This package provides statistical tools for Bayesian structure learning
22570 in undirected graphical models for continuous, discrete, and mixed data. It
22571 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22572 on a continuous-time birth-death process.")
22573 (license license:gpl2+)))
22575 (define-public r-d3network
22577 (name "r-d3network")
22578 (version "0.5.2.1")
22582 (uri (cran-uri "d3Network" version))
22585 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22586 (properties `((upstream-name . "d3Network")))
22587 (build-system r-build-system)
22589 `(("r-plyr" ,r-plyr)
22590 ("r-rjson" ,r-rjson)
22591 ("r-whisker" ,r-whisker)))
22592 (home-page "http://christophergandrud.github.io/d3Network/")
22593 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22595 "This package is intended to make it easy to create D3 JavaScript
22596 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22597 (license license:gpl3+)))
22599 (define-public r-qgraph
22606 (uri (cran-uri "qgraph" version))
22609 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22610 (properties `((upstream-name . "qgraph")))
22611 (build-system r-build-system)
22613 `(("r-abind" ,r-abind)
22614 ("r-colorspace" ,r-colorspace)
22615 ("r-corpcor" ,r-corpcor)
22616 ("r-dplyr" ,r-dplyr)
22617 ("r-fdrtool" ,r-fdrtool)
22618 ("r-ggplot2" ,r-ggplot2)
22619 ("r-glasso" ,r-glasso)
22620 ("r-gtools" ,r-gtools)
22621 ("r-hmisc" ,r-hmisc)
22622 ("r-igraph" ,r-igraph)
22624 ("r-lavaan" ,r-lavaan)
22625 ("r-matrix" ,r-matrix)
22626 ("r-pbapply" ,r-pbapply)
22629 ("r-psych" ,r-psych)
22631 ("r-reshape2" ,r-reshape2)))
22632 (home-page "http://sachaepskamp.com/qgraph/")
22633 (synopsis "Weighted network visualization and analysis")
22635 "This package implements tools for weighted network visualization and
22636 analysis, as well as Gaussian graphical model computation. It contains graph
22637 plotting methods, and tools for psychometric data visualization and graphical
22638 model estimation. See Epskamp et al. (2012)
22639 @url{doi:10.18637/jss.v048.i04}.")
22640 (license license:gpl2)))
22642 (define-public r-semplot
22649 (uri (cran-uri "semPlot" version))
22652 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22653 (properties `((upstream-name . "semPlot")))
22654 (build-system r-build-system)
22656 `(("r-colorspace" ,r-colorspace)
22657 ("r-corpcor" ,r-corpcor)
22658 ("r-igraph" ,r-igraph)
22659 ("r-lavaan" ,r-lavaan)
22660 ("r-lisreltor" ,r-lisreltor)
22661 ("r-openmx" ,r-openmx)
22663 ("r-qgraph" ,r-qgraph)
22664 ("r-regsem" ,r-regsem)
22665 ("r-rockchalk" ,r-rockchalk)
22668 (home-page "https://github.com/SachaEpskamp/semPlot")
22669 (synopsis "Unified visualizations of structural equation models")
22671 "Structural equation modeling (SEM) has a long history of representing
22672 models graphically as path diagrams. The semPlot package for R fills the gap
22673 between advanced, but time-consuming, graphical software and the limited
22674 graphics produced automatically by SEM software. In addition, semPlot offers
22675 more functionality than drawing path diagrams: it can act as a common ground
22676 for importing SEM results into R. Any result usable as input to semPlot can
22677 also be represented in any of the three popular SEM frame-works, as well as
22678 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22679 (license license:gpl2)))
22681 (define-public r-cdm
22688 (uri (cran-uri "CDM" version))
22691 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22692 (properties `((upstream-name . "CDM")))
22693 (build-system r-build-system)
22695 `(("r-mvtnorm" ,r-mvtnorm)
22696 ("r-polycor" ,r-polycor)
22698 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22700 "https://github.com/alexanderrobitzsch/CDM")
22701 (synopsis "Cognitive diagnosis modeling")
22703 "This package provides functions for cognitive diagnosis modeling and
22704 multidimensional item response modeling for dichotomous and polytomous item
22705 responses. It enables the estimation of the DINA and DINO model, the multiple
22706 group (polytomous) GDINA model, the multiple choice DINA model, the general
22707 diagnostic model (GDM), the structured latent class model (SLCA), and
22708 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22709 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22710 estimation and the package structure. For tutorials on how to use the CDM
22711 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22712 well as Ravand and Robitzsch (2015).")
22713 (license license:gpl2+)))
22715 (define-public r-tam
22722 (uri (cran-uri "TAM" version))
22725 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22726 (properties `((upstream-name . "TAM")))
22727 (build-system r-build-system)
22731 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22732 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22733 (synopsis "Test analysis modules")
22735 "This package includes tools for marginal maximum likelihood estimation
22736 and joint maximum likelihood estimation for unidimensional and
22737 multidimensional item response models. The package functionality covers the
22738 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22739 multi-faceted Rasch model, nominal item response model, structured latent
22740 class model, mixture distribution IRT models, and located latent class models.
22741 Latent regression models and plausible value imputation are also supported.")
22742 (license license:gpl2+)))
22744 (define-public r-erm
22751 (uri (cran-uri "eRm" version))
22754 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
22755 (properties `((upstream-name . "eRm")))
22756 (build-system r-build-system)
22758 `(("r-colorspace" ,r-colorspace)
22759 ("r-lattice" ,r-lattice)
22761 ("r-matrix" ,r-matrix)
22762 ("r-psych" ,r-psych)))
22763 (native-inputs `(("gfortran" ,gfortran)))
22764 (home-page "https://cran.r-project.org/package=eRm")
22765 (synopsis "Extended Rasch modeling")
22767 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22768 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22769 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22770 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22771 data matrix. Additional features are the ML estimation of the person
22772 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22773 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22774 infit and outfit measures, ICC and other plots, automated stepwise item
22775 elimination, and a simulation module for various binary data matrices.")
22776 (license license:gpl3)))
22778 (define-public r-irtoys
22785 (uri (cran-uri "irtoys" version))
22788 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22789 (properties `((upstream-name . "irtoys")))
22790 (build-system r-build-system)
22794 (home-page "https://cran.r-project.org/package=irtoys")
22795 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22797 "This package provides a collection of functions useful in learning and
22798 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22799 programs. It provides basic CTT analysis, a simple common interface to the
22800 estimation of item parameters in IRT models for binary responses with three
22801 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22802 EAP, WLE, plausible values), item and person fit statistics, scaling
22803 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22804 array of parametric and non-parametric (kernel) plots. It estimates and plots
22805 Haberman's interaction model when all items are dichotomously scored.")
22806 (license license:gpl2+)))
22808 (define-public r-iheatmapr
22810 (name "r-iheatmapr")
22815 (uri (cran-uri "iheatmapr" version))
22818 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22819 (properties `((upstream-name . "iheatmapr")))
22820 (build-system r-build-system)
22822 `(("r-fastcluster" ,r-fastcluster)
22823 ("r-ggdendro" ,r-ggdendro)
22824 ("r-htmlwidgets" ,r-htmlwidgets)
22825 ("r-jsonlite" ,r-jsonlite)
22826 ("r-knitr" ,r-knitr)
22827 ("r-magrittr" ,r-magrittr)
22828 ("r-rcolorbrewer" ,r-rcolorbrewer)
22829 ("r-scales" ,r-scales)))
22831 `(("r-knitr" ,r-knitr)))
22832 (home-page "https://docs.ropensci.org/iheatmapr")
22833 (synopsis "Interactive, Complex Heatmaps")
22835 "iheatmapr is an R package for building complex, interactive heatmaps
22836 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22837 subplots along the rows or columns of the main heatmap add more information
22838 about each row or column. For example, a one column additional heatmap may
22839 indicate what group a particular row or column belongs to. Complex heatmaps
22840 may also include multiple side by side heatmaps which show different types of
22841 data for the same conditions. Interactivity can improve complex heatmaps by
22842 providing tooltips with information about each cell and enabling zooming into
22843 interesting features. iheatmapr uses the plotly library for interactivity.")
22844 (license license:expat)))
22846 (define-public r-packrat
22853 (uri (cran-uri "packrat" version))
22856 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22857 (properties `((upstream-name . "packrat")))
22858 (build-system r-build-system)
22859 (home-page "https://github.com/rstudio/packrat/")
22860 (synopsis "Dependency management R projects")
22862 "This package provides a dependency manager for R projects that allows
22863 you to manage the R packages your project depends on in an isolated, portable,
22864 and reproducible way.")
22865 (license license:gpl2)))
22867 (define-public r-rsconnect
22869 (name "r-rsconnect")
22874 (uri (cran-uri "rsconnect" version))
22877 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22878 (properties `((upstream-name . "rsconnect")))
22879 (build-system r-build-system)
22881 `(("r-curl" ,r-curl)
22882 ("r-digest" ,r-digest)
22883 ("r-jsonlite" ,r-jsonlite)
22884 ("r-openssl" ,r-openssl)
22885 ("r-packrat" ,r-packrat)
22886 ("r-rstudioapi" ,r-rstudioapi)
22887 ("r-yaml" ,r-yaml)))
22888 (home-page "https://github.com/rstudio/rsconnect")
22889 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22891 "This package provides a programmatic deployment interface for RPubs,
22892 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22893 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22894 (license license:gpl2)))
22896 ;; This package includes minified JavaScript files. When upgrading please
22897 ;; check that there are no new minified JavaScript files.
22898 (define-public r-dygraphs
22900 (name "r-dygraphs")
22901 (version "1.1.1.6")
22905 (uri (cran-uri "dygraphs" version))
22908 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22909 (properties `((upstream-name . "dygraphs")))
22910 (build-system r-build-system)
22912 `(#:modules ((guix build utils)
22913 (guix build r-build-system)
22917 (modify-phases %standard-phases
22918 (add-after 'unpack 'process-javascript
22919 (lambda* (#:key inputs #:allow-other-keys)
22920 (with-directory-excursion "inst/htmlwidgets/lib/"
22924 `(("dygraphs/dygraph-combined-dev.js"
22925 "dygraph-combined.js")
22926 (,(assoc-ref inputs "js-jquery")
22927 "jquery/jquery.min.js")
22928 (,(assoc-ref inputs "js-fquarter")
22929 "fquarter/moment-fquarter.min.js"))))
22930 (lambda (sources targets)
22931 (for-each (lambda (source target)
22932 (format #t "Processing ~a --> ~a~%"
22934 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22935 (call-with-output-file target
22937 (dump-port minified port)))))
22938 sources targets))))
22941 `(("uglify-js" ,uglify-js)
22942 ;; They actually use version 1.11.1, but this more recent version
22943 ;; should be just fine.
22947 (uri "https://code.jquery.com/jquery-1.12.4.js")
22950 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22954 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22955 "moment-fquarter/1.0.1/moment-fquarter.js"))
22958 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22960 `(("r-htmltools" ,r-htmltools)
22961 ("r-htmlwidgets" ,r-htmlwidgets)
22962 ("r-magrittr" ,r-magrittr)
22965 (home-page "https://github.com/rstudio/dygraphs")
22966 (synopsis "Interface to Dygraphs interactive time series charting library")
22968 "This package provides an R interface to the dygraphs JavaScript charting
22969 library (a copy of which is included in the package). It provides rich
22970 facilities for charting time-series data in R, including highly configurable
22971 series- and axis-display and interactive features like zoom/pan and
22972 series/point highlighting.")
22973 (license license:expat)))
22975 (define-public r-shinystan
22977 (name "r-shinystan")
22982 (uri (cran-uri "shinystan" version))
22985 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22986 (properties `((upstream-name . "shinystan")))
22987 (build-system r-build-system)
22989 `(("r-bayesplot" ,r-bayesplot)
22990 ("r-colourpicker" ,r-colourpicker)
22992 ("r-dygraphs" ,r-dygraphs)
22993 ("r-ggplot2" ,r-ggplot2)
22994 ("r-gridextra" ,r-gridextra)
22995 ("r-gtools" ,r-gtools)
22996 ("r-markdown" ,r-markdown)
22997 ("r-reshape2" ,r-reshape2)
22998 ("r-rsconnect" ,r-rsconnect)
22999 ("r-rstan" ,r-rstan)
23000 ("r-shiny" ,r-shiny)
23001 ("r-shinyjs" ,r-shinyjs)
23002 ("r-shinythemes" ,r-shinythemes)
23003 ("r-threejs" ,r-threejs)
23004 ("r-xtable" ,r-xtable)
23006 (home-page "https://mc-stan.org/")
23007 (synopsis "Interactive visual and numerical analysis for Bayesian models")
23009 "This package provides a graphical user interface for interactive
23010 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
23011 for analyzing a posterior sample. The interface is powered by the Shiny web
23012 application framework and works with the output of MCMC programs written in
23013 any programming language (and has extended functionality for Stan models fit
23014 using the @code{rstan} and @code{rstanarm} packages).")
23015 (license license:gpl3+)))
23017 (define-public r-rstantools
23019 (name "r-rstantools")
23024 (uri (cran-uri "rstantools" version))
23027 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23028 (properties `((upstream-name . "rstantools")))
23029 (build-system r-build-system)
23030 (inputs `(("pandoc" ,pandoc)))
23032 `(("r-desc" ,r-desc)
23034 ("r-rcppparallel" ,r-rcppparallel)))
23036 `(("r-knitr" ,r-knitr)))
23037 (home-page "https://mc-stan.org/rstantools/")
23038 (synopsis "Tools for developing R packages interfacing with Stan")
23040 "This package provides various tools for developers of R packages
23041 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23042 up the required package structure, S3 generics and default methods to unify
23043 function naming across Stan-based R packages, and vignettes with
23044 recommendations for developers.")
23045 (license license:gpl3+)))
23047 (define-public r-loo
23054 (uri (cran-uri "loo" version))
23056 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23057 (properties `((upstream-name . "loo")))
23058 (build-system r-build-system)
23060 `(("pandoc" ,pandoc)
23061 ("pandoc-citeproc" ,pandoc-citeproc)))
23063 `(("r-checkmate" ,r-checkmate)
23064 ("r-matrixstats" ,r-matrixstats)))
23066 `(("r-knitr" ,r-knitr)))
23067 (home-page "https://mc-stan.org/loo/")
23068 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23070 "This package provides an implementation of efficient approximate
23071 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23072 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23073 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23074 procedure for regularizing importance weights. As a byproduct of the
23075 calculations, we also obtain approximate standard errors for estimated
23076 predictive errors and for the comparison of predictive errors between models.
23077 The package also provides methods for using stacking and other model weighting
23078 techniques to average Bayesian predictive distributions.")
23079 (license license:gpl3+)))
23081 (define-public r-rstan
23088 (uri (cran-uri "rstan" version))
23091 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23092 (properties `((upstream-name . "rstan")))
23093 (build-system r-build-system)
23096 (modify-phases %standard-phases
23097 (add-before 'install 'set-timezone
23098 ;; This package is picky about timezones.
23099 (lambda* (#:key inputs #:allow-other-keys)
23100 (setenv "TZ" "UTC+1")
23102 (string-append (assoc-ref inputs "tzdata")
23103 "/share/zoneinfo"))
23106 `(("tzdata" ,tzdata-for-tests)
23108 ("r-knitr" ,r-knitr)))
23111 ("r-ggplot2" ,r-ggplot2)
23112 ("r-gridextra" ,r-gridextra)
23113 ("r-inline" ,r-inline)
23115 ("r-pkgbuild" ,r-pkgbuild)
23117 ("r-rcppeigen" ,r-rcppeigen)
23118 ("r-rcppparallel" ,r-rcppparallel)
23119 ("r-stanheaders" ,r-stanheaders)
23121 ("r-withr" ,r-withr)))
23122 (home-page "https://discourse.mc-stan.org/")
23123 (synopsis "R interface to Stan")
23125 "User-facing R functions are provided to parse, compile, test, estimate,
23126 and analyze Stan models by accessing the header-only Stan library provided by
23127 the StanHeaders package. The Stan project develops a probabilistic
23128 programming language that implements full Bayesian statistical inference via
23129 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23130 approximation, and (optionally penalized) maximum likelihood estimation via
23131 optimization. In all three cases, automatic differentiation is used to
23132 quickly and accurately evaluate gradients without burdening the user with the
23133 need to derive the partial derivatives.")
23134 (license license:gpl3+)))
23136 (define-public r-rstanarm
23138 (name "r-rstanarm")
23143 (uri (cran-uri "rstanarm" version))
23146 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23147 (properties `((upstream-name . "rstanarm")))
23148 (build-system r-build-system)
23150 `(("pandoc" ,pandoc)
23151 ("pandoc-citeproc" ,pandoc-citeproc)))
23153 `(("r-bayesplot" ,r-bayesplot)
23155 ("r-ggplot2" ,r-ggplot2)
23158 ("r-matrix" ,r-matrix)
23161 ("r-rcppeigen" ,r-rcppeigen)
23162 ("r-rcppparallel" ,r-rcppparallel)
23163 ("r-rstan" ,r-rstan)
23164 ("r-rstantools" ,r-rstantools)
23165 ("r-shinystan" ,r-shinystan)
23166 ("r-stanheaders" ,r-stanheaders)
23167 ("r-survival" ,r-survival)))
23169 `(("r-knitr" ,r-knitr)))
23170 (home-page "https://mc-stan.org/rstanarm/")
23171 (synopsis "Bayesian applied regression modeling via Stan")
23173 "This package estimates previously compiled regression models using the
23174 @code{rstan} package, which provides the R interface to the Stan C++ library
23175 for Bayesian estimation. Users specify models via the customary R syntax with
23176 a formula and @code{data.frame} plus some additional arguments for priors.")
23177 (license license:gpl3+)))
23179 (define-public r-kendall
23186 (uri (cran-uri "Kendall" version))
23189 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23190 (properties `((upstream-name . "Kendall")))
23191 (build-system r-build-system)
23193 `(("r-boot" ,r-boot)))
23195 `(("gfortran" ,gfortran)))
23196 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23197 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23199 "This package computes the Kendall rank correlation and Mann-Kendall
23201 (license license:gpl2+)))
23203 (define-public r-keyring
23210 (uri (cran-uri "keyring" version))
23213 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23214 (properties `((upstream-name . "keyring")))
23215 (build-system r-build-system)
23217 `(("r-assertthat" ,r-assertthat)
23218 ("r-filelock" ,r-filelock)
23219 ("r-getpass" ,r-getpass)
23220 ("r-openssl" ,r-openssl)
23222 ("r-rappdirs" ,r-rappdirs)
23223 ("r-sodium" ,r-sodium)
23224 ("r-yaml" ,r-yaml)))
23225 (native-inputs `(("pkg-config" ,pkg-config)))
23226 (home-page "https://github.com/r-lib/keyring")
23227 (synopsis "Access the system credential store from R")
23229 "This package provides a platform-independent API to access the operating
23230 system's credential store. It currently supports Keychain on macOS,
23231 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23232 simple, platform independent store implemented with environment variables.
23233 Additional storage back-ends can be added easily.")
23234 (license license:expat)))
23236 (define-public r-zyp
23239 (version "0.10-1.1")
23243 (uri (cran-uri "zyp" version))
23246 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23247 (properties `((upstream-name . "zyp")))
23248 (build-system r-build-system)
23250 `(("r-kendall" ,r-kendall)))
23251 (home-page "https://cran.r-project.org/web/packages/zyp/")
23252 (synopsis "Zhang + Yue-Pilon Trends Package")
23254 "This package contains an efficient implementation of Sen's slope
23255 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23256 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23258 (license license:lgpl2.1)))
23260 (define-public r-rlinsolve
23262 (name "r-rlinsolve")
23267 (uri (cran-uri "Rlinsolve" version))
23270 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23271 (properties `((upstream-name . "Rlinsolve")))
23272 (build-system r-build-system)
23274 `(("r-matrix" ,r-matrix)
23276 ("r-rcpparmadillo" ,r-rcpparmadillo)
23277 ("r-rdpack" ,r-rdpack)))
23278 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23279 (synopsis "Iterative solvers for (sparse) linear system of equations")
23281 "Solving a system of linear equations is one of the most fundamental
23282 computational problems for many fields of mathematical studies, such as
23283 regression problems from statistics or numerical partial differential
23284 equations. This package provides basic stationary iterative solvers such as
23285 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23286 Nonstationary, also known as Krylov subspace methods are also provided.
23287 Sparse matrix computation is also supported in that solving large and sparse
23288 linear systems can be manageable using the @code{Matrix} package along with
23289 @code{RcppArmadillo}.")
23290 (license license:gpl3+)))
23292 (define-public r-zvcv
23299 (uri (cran-uri "ZVCV" version))
23302 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23303 (properties `((upstream-name . "ZVCV")))
23304 (build-system r-build-system)
23306 `(("r-abind" ,r-abind)
23308 ("r-dplyr" ,r-dplyr)
23309 ("r-glmnet" ,r-glmnet)
23310 ("r-magrittr" ,r-magrittr)
23311 ("r-mvtnorm" ,r-mvtnorm)
23313 ("r-rcpparmadillo" ,r-rcpparmadillo)
23314 ("r-rlinsolve" ,r-rlinsolve)))
23315 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23316 (synopsis "Zero-Variance Control Variates")
23318 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23319 to reduce the variance of Monte Carlo estimators of expectations using the
23320 derivatives of the log target. Once the derivatives are available, the only
23321 additional computational effort is in solving a linear regression problem.
23322 This method has been extended to higher dimensions using regularisation. This
23323 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23324 samples, derivatives and function evaluations are available. Additional
23325 functions for applying ZV-CV to two estimators for the normalising constant of
23326 the posterior distribution in Bayesian statistics are also supplied.")
23327 (license license:gpl2+)))
23329 (define-public r-ztype
23336 (uri (cran-uri "ztype" version))
23339 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23340 (properties `((upstream-name . "ztype")))
23341 (build-system r-build-system)
23343 `(("r-assertthat" ,r-assertthat)
23344 ("r-dplyr" ,r-dplyr)
23345 ("r-ggplot2" ,r-ggplot2)
23346 ("r-lubridate" ,r-lubridate)
23347 ("r-magrittr" ,r-magrittr)
23348 ("r-rvest" ,r-rvest)
23349 ("r-stringr" ,r-stringr)))
23350 (home-page "https://cran.r-project.org/web/packages/ztype/")
23351 (synopsis "Run a Ztype game loaded with R functions")
23353 "How fast can you type R functions on your keyboard? Find out by running
23354 a @code{zty.pe} game: export R functions as instructions to type to destroy
23355 opponents' vessels.")
23356 (license license:gpl3)))
23358 (define-public r-zseq
23365 (uri (cran-uri "Zseq" version))
23368 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23369 (properties `((upstream-name . "Zseq")))
23370 (build-system r-build-system)
23372 `(("r-gmp" ,r-gmp)))
23373 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23374 (synopsis "Integer sequence generator")
23376 "This package generates well-known integer sequences. The @code{gmp}
23377 package is adopted for computing with arbitrarily large numbers. Every
23378 function has a hyperlink to its corresponding item in the @dfn{On-Line
23379 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23380 (license license:gpl3+)))
23382 (define-public r-isoband
23389 (uri (cran-uri "isoband" version))
23392 "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn"))))
23393 (properties `((upstream-name . "isoband")))
23394 (build-system r-build-system)
23396 `(("r-knitr" ,r-knitr)))
23397 (home-page "https://github.com/wilkelab/isoband")
23398 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23400 "This package provides a fast C++ implementation to generate contour
23401 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23402 containing elevation data.")
23403 (license license:expat)))
23405 (define-public r-ppcor
23412 (uri (cran-uri "ppcor" version))
23415 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23416 (properties `((upstream-name . "ppcor")))
23417 (build-system r-build-system)
23419 `(("r-mass" ,r-mass)))
23420 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23421 (synopsis "Partial and semi-partial correlation")
23423 "This package provides users not only with a function to readily
23424 calculate the higher-order partial and semi-partial correlations but also with
23425 statistics and p-values of the correlation coefficients.")
23426 (license license:gpl2)))
23428 (define-public r-hrbrthemes
23430 (name "r-hrbrthemes")
23435 (uri (cran-uri "hrbrthemes" version))
23437 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23438 (properties `((upstream-name . "hrbrthemes")))
23439 (build-system r-build-system)
23441 `(("r-extrafont" ,r-extrafont)
23442 ("r-gdtools" ,r-gdtools)
23443 ("r-ggplot2" ,r-ggplot2)
23444 ("r-htmltools" ,r-htmltools)
23445 ("r-knitr" ,r-knitr)
23446 ("r-magrittr" ,r-magrittr)
23447 ("r-rmarkdown" ,r-rmarkdown)
23448 ("r-scales" ,r-scales)))
23450 `(("r-knitr" ,r-knitr)))
23451 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23452 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23454 "This package provides a compilation of extra @code{ggplot2} themes,
23455 scales and utilities, including a spell check function for plot label fields
23456 and an overall emphasis on typography.")
23457 (license license:expat)))
23459 (define-public r-crochet
23466 (uri (cran-uri "crochet" version))
23469 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23470 (build-system r-build-system)
23472 `(("r-knitr" ,r-knitr)))
23473 (home-page "https://github.com/agrueneberg/crochet")
23474 (synopsis "Implementation Helper for Matrix-Like Types")
23476 "Functions to help implement the extraction / subsetting / indexing
23477 function @code{[} and replacement function @code{[<-} of custom matrix-like
23478 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23479 as possible (with tests to prove it).")
23480 (license license:expat)))
23482 (define-public r-boa
23485 (version "1.1.8-2")
23489 (uri (cran-uri "boa" version))
23492 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23493 (properties `((upstream-name . "boa")))
23494 (build-system r-build-system)
23495 (home-page "https://www.jstatsoft.org/v21/i11")
23496 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23498 "This package provides a menu-driven program and library of functions for
23499 carrying out convergence diagnostics and statistical and graphical analysis of
23500 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23501 (license license:gpl2+)))
23503 (define-public r-httpcode
23505 (name "r-httpcode")
23509 (uri (cran-uri "httpcode" version))
23512 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23513 (build-system r-build-system)
23514 (home-page "https://github.com/sckott/httpcode")
23515 (synopsis "HTTP status code helper")
23516 (description "@code{httpcode} provides functionality for finding and
23517 explaining the meaning of @code{HTTP} status codes. Functions are included for
23518 searching for codes by full or partial number, by message, and to get
23519 appropriate dog and cat images for many status codes.")
23520 (license license:expat)))
23522 (define-public r-latex2exp
23524 (name "r-latex2exp")
23528 (uri (cran-uri "latex2exp" version))
23531 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23532 (build-system r-build-system)
23534 `(("r-stringr" ,r-stringr)
23535 ("r-magrittr" ,r-magrittr)))
23536 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23537 (synopsis "Use LaTeX expressions in plots")
23538 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23539 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23540 rendered as text, axis labels, etc. throughout R's plotting system.")
23541 (license license:expat)))
23543 (define-public r-oai
23549 (uri (cran-uri "oai" version))
23552 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23553 (build-system r-build-system)
23555 `(("r-xml2" ,r-xml2)
23558 ("r-stringr" ,r-stringr)
23559 ("r-tibble" ,r-tibble)))
23560 (home-page "https://github.com/ropensci/oai/")
23561 (synopsis "General purpose OAI-PMH services client")
23562 (description "@code{oai} provides a general purpose client to work with
23563 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23564 service. Functions are provided to work with the OAI-PMH verbs:
23565 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23566 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23567 (license license:expat)))
23569 (define-public r-argon2
23576 (uri (cran-uri "argon2" version))
23579 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23580 (properties `((upstream-name . "argon2")))
23581 (build-system r-build-system)
23582 (home-page "https://github.com/wrathematics/argon2")
23583 (synopsis "Secure password hashing based on the argon2 algorithm")
23585 "This package provides utilities for secure password hashing via the
23586 argon2 algorithm.")
23587 (license license:bsd-2)))
23589 (define-public r-getpass
23596 (uri (cran-uri "getPass" version))
23599 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23600 (properties `((upstream-name . "getPass")))
23601 (build-system r-build-system)
23603 `(("r-rstudioapi" ,r-rstudioapi)))
23604 (home-page "https://github.com/wrathematics/getPass")
23605 (synopsis "Masked user input")
23607 "This package provides a micro-package for reading \"passwords\", i.e.
23608 reading user input with masking, so that the input is not displayed as it is
23609 typed. Currently, RStudio, the command line (every OS), and any platform
23610 where tcltk is present are supported.")
23611 (license license:bsd-2)))
23613 (define-public r-remoter
23620 (uri (cran-uri "remoter" version))
23623 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23624 (properties `((upstream-name . "remoter")))
23625 (build-system r-build-system)
23627 `(("r-argon2" ,r-argon2)
23628 ("r-getpass" ,r-getpass)
23629 ("r-pbdzmq" ,r-pbdzmq)
23631 (home-page "https://github.com/RBigData/remoter")
23632 (synopsis "Control a remote R session from a local one")
23634 "This package provides a set of utilities for client/server computing
23635 with R, controlling a remote R session (the server) from a local one (the
23637 (license license:bsd-2)))
23639 (define-public r-asd
23646 (uri (cran-uri "asd" version))
23649 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23650 (properties `((upstream-name . "asd")))
23651 (build-system r-build-system)
23653 `(("r-mvtnorm" ,r-mvtnorm)))
23654 (home-page "https://cran.r-project.org/web/packages/asd")
23655 (synopsis "Simulations for Adaptive Seamless Designs")
23657 "This package provdes means to run simulations for adaptive seamless
23658 designs with and without early outcomes for treatment selection and
23659 subpopulation type designs.")
23660 (license license:gpl3)))
23662 (define-public r-nbconvertr
23664 (name "r-nbconvertr")
23669 (uri (cran-uri "nbconvertR" version))
23672 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23673 (properties `((upstream-name . "nbconvertR")))
23674 (build-system r-build-system)
23676 `(("jupyter" ,python-nbconvert)
23677 ("pandoc" ,pandoc)))
23678 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23679 (synopsis "Vignette engine wrapping Jupyter notebooks")
23681 "This package calls the Jupyter script @code{nbconvert} to create
23682 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23683 containing rich text, code, and its output. Code cells can be edited and
23684 evaluated interactively.")
23685 (license license:gpl3)))
23687 (define-public r-bridgesampling
23689 (name "r-bridgesampling")
23694 (uri (cran-uri "bridgesampling" version))
23697 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23699 `((upstream-name . "bridgesampling")))
23700 (build-system r-build-system)
23702 `(("r-brobdingnag" ,r-brobdingnag)
23704 ("r-matrix" ,r-matrix)
23705 ("r-mvtnorm" ,r-mvtnorm)
23706 ("r-scales" ,r-scales)
23707 ("r-stringr" ,r-stringr)))
23709 `(("r-knitr" ,r-knitr)))
23710 (home-page "https://github.com/quentingronau/bridgesampling")
23711 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23713 "This package provides functions for estimating marginal likelihoods,
23714 Bayes factors, posterior model probabilities, and normalizing constants in
23715 general, via different versions of bridge sampling.")
23716 (license license:gpl2+)))
23718 (define-public r-tea
23725 (uri (cran-uri "tea" version))
23728 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23730 `((upstream-name . "tea")))
23731 (build-system r-build-system)
23733 `(("r-matrix" ,r-matrix)))
23734 (home-page "https://cran.r-project.org/web/packages/tea/")
23735 (synopsis "Threshold estimation approaches")
23737 "This package provides different approaches for selecting the threshold
23738 in generalized Pareto distributions. Most of them are based on minimizing the
23739 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23740 Others are heuristically motivated by searching for stable sample paths, i.e.
23741 a nearly constant region of the tail index estimator with respect to k, which
23742 is the number of data in the tail. The third class is motivated by graphical
23743 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23744 is also implemented here.")
23745 (license license:gpl3)))
23747 (define-public r-awsmethods
23749 (name "r-awsmethods")
23754 (uri (cran-uri "awsMethods" version))
23757 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23759 `((upstream-name . "awsMethods")))
23760 (build-system r-build-system)
23761 (home-page "http://www.wias-berlin.de/software/imaging/")
23762 (synopsis "Class and methods definitions")
23764 "This package defines the generic method @code{extract} and provides
23765 @code{openMP} support as needed in several packages like
23766 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23767 (license license:gpl2+)))
23769 (define-public r-aws
23776 (uri (cran-uri "aws" version))
23779 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23781 `((upstream-name . "aws")))
23782 (build-system r-build-system)
23784 `(("r-awsmethods" ,r-awsmethods)
23787 `(("gfortran" ,gfortran)))
23788 (home-page "https://cran.r-project.org/web/packages/aws/")
23789 (synopsis "Adaptive weights smoothing")
23791 "This package provides a collection of R-functions implementing adaptive
23792 smoothing procedures in 1D, 2D and 3D. This includes the
23793 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23794 Confidence Intervals} (ICI), variational approaches, and a non-local means
23796 (license license:gpl2+)))
23798 (define-public r-sgloptim
23800 (name "r-sgloptim")
23805 (uri (cran-uri "sglOptim" version))
23808 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23810 `((upstream-name . "sglOptim")))
23811 (build-system r-build-system)
23814 ("r-doparallel" ,r-doparallel)
23815 ("r-foreach" ,r-foreach)
23816 ("r-matrix" ,r-matrix)
23818 ("r-rcpparmadillo" ,r-rcpparmadillo)
23819 ("r-rcppprogress" ,r-rcppprogress)))
23821 `(("r-knitr" ,r-knitr)))
23822 (home-page "https://github.com/nielsrhansen/sglOptim")
23823 (synopsis "Generic sparse group Lasso solver")
23825 "This package provides a fast generic solver for sparse group lasso
23826 optimization problems. The loss (objective) function must be defined in a C++
23827 module. The optimization problem is solved using a coordinate gradient
23828 descent algorithm. Convergence of the algorithm is established and the
23829 algorithm is applicable to a broad class of loss functions. Use of parallel
23830 computing for cross validation and subsampling is supported through the
23831 @code{foreach} and @code{doParallel} packages.")
23832 (license license:gpl2+)))
23834 (define-public r-grouped
23841 (uri (cran-uri "grouped" version))
23844 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23846 `((upstream-name . "grouped")))
23847 (build-system r-build-system)
23849 `(("r-mass" ,r-mass)))
23850 (home-page "https://cran.r-project.org/web/packages/grouped/")
23851 (synopsis "Regression analysis of grouped and coarse data")
23853 "This package provides regression models for grouped and coarse data,
23854 under the coarsened at random assumption.")
23855 (license license:gpl2+)))
23857 (define-public r-stam
23864 (uri (cran-uri "stam" version))
23867 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23869 `((upstream-name . "stam")))
23870 (build-system r-build-system)
23874 (home-page "https://cran.r-project.org/web/packages/stam")
23875 (synopsis "Spatio-temporal analysis and modelling")
23877 "This package provides various methods to conduct Spatio-Temporal
23878 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23879 Inferred Spatio-Temporal Modelling.")
23880 (license license:gpl2+)))
23882 (define-public r-dcv
23889 (uri (cran-uri "dcv" version))
23892 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23894 `((upstream-name . "dcv")))
23895 (build-system r-build-system)
23897 `(("r-lmtest" ,r-lmtest)))
23898 (home-page "https://cran.r-project.org/web/packages/dcv/")
23899 (synopsis "Conventional cross-validation statistics for climate-growth model")
23901 "This package performs several conventional cross-validation statistical
23902 methods for climate-growth model in the climate reconstruction from tree
23903 rings, including Sign Test statistic, Reduction of Error statistic, Product
23904 Mean Test, Durbin-Watson statistic etc.")
23905 (license license:gpl2)))
23907 (define-public r-rcdd
23914 (uri (cran-uri "rcdd" version))
23917 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23919 `((upstream-name . "rcdd")))
23920 (build-system r-build-system)
23923 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23924 (synopsis "Computational geometry")
23926 "This package converts back and forth between two representations of a
23927 convex polytope: as solution of a set of linear equalities and inequalities
23928 and as convex hull of set of points and rays. Also does linear programming
23929 and redundant generator elimination. All functions can use exact
23930 infinite-precision rational arithmetic.")
23931 (license license:gpl2)))
23933 (define-public r-rxnat
23940 (uri (cran-uri "Rxnat" version))
23943 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23945 `((upstream-name . "Rxnat")))
23946 (build-system r-build-system)
23948 `(("r-dplyr" ,r-dplyr)
23950 ("r-rcurl" ,r-rcurl)
23951 ("r-tibble" ,r-tibble)))
23953 `(("r-knitr" ,r-knitr)))
23954 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23955 (synopsis "Queries and extracts images from neuroimaging datasets")
23957 "This package allows communication with the Extensible Neuroimaging
23958 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23960 (license license:gpl2)))
23962 (define-public r-rserve
23969 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23970 version ".tar.gz"))
23973 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23974 (build-system r-build-system)
23977 (modify-phases %standard-phases
23978 (add-before 'install 'install-server-binary
23979 ;; Makevars tries to install to R's store directory.
23980 (lambda* (#:key outputs #:allow-other-keys)
23981 (let* ((out (assoc-ref outputs "out"))
23982 (bin (string-append out "/bin")))
23983 (substitute* "src/Makevars.in"
23984 (("\\$\\(R_HOME\\)") out))
23985 (mkdir-p bin)))))))
23987 `(("r-checkmate" ,r-checkmate)
23989 ("r-jsonlite" ,r-jsonlite)
23990 ("r-knitr" ,r-knitr)
23993 ("r-uuid" ,r-uuid)))
23995 `(("openssl" ,openssl)
23997 (home-page "https://github.com/s-u/Rserve")
23999 "Server providing access to R from many languages and systems")
24001 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
24002 binary requests to be sent to R. Every connection has a separate workspace
24003 and working directory. Client-side implementations are available for popular
24004 languages such as C/C++ and Java, allowing any application to use facilities
24005 of R without the need of linking to R code. Rserve supports remote
24006 connection, user authentication and file transfer. A simple R client is
24007 included in this package as well.")
24008 (license license:gpl2)))
24010 (define-public r-gamm4
24017 (uri (cran-uri "gamm4" version))
24020 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
24021 (properties `((upstream-name . "gamm4")))
24022 (build-system r-build-system)
24024 `(("r-lme4" ,r-lme4)
24025 ("r-matrix" ,r-matrix)
24026 ("r-mgcv" ,r-mgcv)))
24027 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24028 (synopsis "Generalized additive mixed models using mgcv and lme4")
24030 "Estimate generalized additive mixed models via a version of function
24031 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24033 (license license:gpl2+)))
24035 (define-public r-optimx
24038 (version "2020-4.2")
24042 (uri (cran-uri "optimx" version))
24045 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24046 (properties `((upstream-name . "optimx")))
24047 (build-system r-build-system)
24048 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24049 (native-inputs `(("r-knitr" ,r-knitr)))
24050 (home-page "https://cran.r-project.org/web/packages/optimx/")
24051 (synopsis "Expanded replacement and extension of the optim function")
24053 "This package provides a replacement and extension of the @code{optim}
24054 function to call to several function minimization codes in R in a single
24055 statement. These methods handle smooth, possibly box constrained functions of
24056 several or many parameters. Note that the function @code{optimr} was prepared
24057 to simplify the incorporation of minimization codes going forward. This
24058 package also implements some utility codes and some extra solvers, including
24059 safeguarded Newton methods. Many methods previously separate are now included
24061 (license license:gpl2)))
24063 (define-public r-projpred
24065 (name "r-projpred")
24070 (uri (cran-uri "projpred" version))
24073 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24074 (properties `((upstream-name . "projpred")))
24075 (build-system r-build-system)
24077 `(("r-dplyr" ,r-dplyr)
24078 ("r-gamm4" ,r-gamm4)
24079 ("r-ggplot2" ,r-ggplot2)
24082 ("r-magrittr" ,r-magrittr)
24085 ("r-optimx" ,r-optimx)
24087 ("r-rcpparmadillo" ,r-rcpparmadillo)
24088 ("r-rngtools" ,r-rngtools)
24089 ("r-rstantools" ,r-rstantools)
24090 ("r-tidyverse" ,r-tidyverse)))
24091 (native-inputs `(("r-knitr" ,r-knitr)))
24092 (home-page "https://mc-stan.org/projpred/")
24093 (synopsis "Projection predictive feature selection")
24095 "This package performs projection predictive feature selection for
24096 generalized linear models and generalized linear and additive multilevel
24097 models. The package is compatible with the @code{rstanarm} and @code{brms}
24098 packages, but other reference models can also be used. See the package
24099 vignette for more information and examples.")
24100 (license license:gpl3)))
24102 (define-public r-brms
24109 (uri (cran-uri "brms" version))
24112 "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1"))))
24113 (properties `((upstream-name . "brms")))
24114 (build-system r-build-system)
24116 `(("r-abind" ,r-abind)
24117 ("r-backports" ,r-backports)
24118 ("r-bayesplot" ,r-bayesplot)
24119 ("r-bridgesampling" ,r-bridgesampling)
24121 ("r-future" ,r-future)
24122 ("r-ggplot2" ,r-ggplot2)
24125 ("r-matrix" ,r-matrix)
24126 ("r-matrixstats" ,r-matrixstats)
24128 ("r-nleqslv" ,r-nleqslv)
24130 ("r-projpred" ,r-projpred)
24132 ("r-rstan" ,r-rstan)
24133 ("r-rstantools" ,r-rstantools)
24134 ("r-shinystan" ,r-shinystan)))
24135 (native-inputs `(("r-knitr" ,r-knitr)))
24137 "https://github.com/paul-buerkner/brms")
24139 "Bayesian Regression Models using 'Stan'")
24141 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24142 using 'Stan' for full Bayesian inference. A wide range of distributions and
24143 link functions are supported, allowing users to fit -- among others -- linear,
24144 robust linear, count data, survival, response times, ordinal, zero-inflated,
24145 hurdle, and even self-defined mixture models all in a multilevel context.
24146 Further modeling options include non-linear and smooth terms, auto-correlation
24147 structures, censored data, meta-analytic standard errors, and quite a few
24148 more. In addition, all parameters of the response distribution can be
24149 predicted in order to perform distributional regression. Prior specifications
24150 are flexible and explicitly encourage users to apply prior distributions that
24151 actually reflect their beliefs. Model fit can easily be assessed and compared
24152 with posterior predictive checks and leave-one-out cross-validation.")
24153 (license license:gpl2)))
24155 (define-public r-mstate
24162 (uri (cran-uri "mstate" version))
24165 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24166 (properties `((upstream-name . "mstate")))
24167 (build-system r-build-system)
24169 `(("r-data-table" ,r-data-table)
24170 ("r-lattice" ,r-lattice)
24171 ("r-magrittr" ,r-magrittr)
24172 ("r-rcolorbrewer" ,r-rcolorbrewer)
24173 ("r-rlang" ,r-rlang)
24174 ("r-survival" ,r-survival)
24175 ("r-viridis" ,r-viridis)))
24177 `(("r-knitr" ,r-knitr)))
24179 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24181 "Data Preparation, Estimation and Prediction in Multi-State Models")
24183 "Contains functions for data preparation, descriptives, hazard estimation
24184 and prediction with Aalen-Johansen or simulation in competing risks and
24185 multi-state models.")
24186 (license license:gpl2+)))
24188 (define-public r-scatterpie
24190 (name "r-scatterpie")
24195 (uri (cran-uri "scatterpie" version))
24198 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24199 (properties `((upstream-name . "scatterpie")))
24200 (build-system r-build-system)
24202 `(("r-ggforce" ,r-ggforce)
24203 ("r-ggplot2" ,r-ggplot2)
24204 ("r-rlang" ,r-rlang)
24205 ("r-rvcheck" ,r-rvcheck)
24206 ("r-tidyr" ,r-tidyr)))
24208 `(("r-knitr" ,r-knitr)))
24209 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24210 (synopsis "Scatter pie plot")
24212 "This package creates scatterpie plots, especially useful for plotting
24214 (license license:artistic2.0)))
24216 (define-public r-scrypt
24223 (uri (cran-uri "scrypt" version))
24226 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24227 (properties `((upstream-name . "scrypt")))
24228 (build-system r-build-system)
24230 `(("r-rcpp" ,r-rcpp)))
24231 (home-page "https://github.com/rstudio/rscrypt")
24232 (synopsis "Key derivation functions for R based on Scrypt")
24234 "This package provides functions for working with the scrypt key
24235 derivation functions. Scrypt is a password-based key derivation function
24236 created by Colin Percival. The algorithm was specifically designed to make it
24237 costly to perform large-scale custom hardware attacks by requiring large
24238 amounts of memory.")
24239 (license license:bsd-2)))
24241 (define-public r-boruta
24248 (uri (cran-uri "Boruta" version))
24251 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24252 (properties `((upstream-name . "Boruta")))
24253 (build-system r-build-system)
24254 (propagated-inputs `(("r-ranger" ,r-ranger)))
24255 (home-page "https://gitlab.com/mbq/Boruta/")
24256 (synopsis "Wrapper algorithm for all relevant feature selection")
24258 "This package provides an all relevant feature selection wrapper
24259 algorithm. It finds relevant features by comparing original attributes'
24260 importance with importance achievable at random, estimated using their
24261 permuted copies (shadows).")
24262 (license license:gpl2+)))
24264 (define-public r-directlabels
24266 (name "r-directlabels")
24267 (version "2021.1.13")
24271 (uri (cran-uri "directlabels" version))
24274 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24275 (build-system r-build-system)
24277 `(("r-quadprog" ,r-quadprog)))
24279 `(("r-knitr" ,r-knitr)))
24280 (home-page "http://directlabels.r-forge.r-project.org/")
24281 (synopsis "Direct labels for multicolor plots")
24283 "This package provides an extensible framework for automatically placing
24284 direct labels onto multicolor plots. Label positions are described using
24285 positioning methods that can be re-used across several different plots. There
24286 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24287 inferring an appropriate positioning method.")
24288 (license license:gpl3)))
24290 (define-public r-lsd
24297 (uri (cran-uri "LSD" version))
24299 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24300 (properties `((upstream-name . "LSD")))
24301 (build-system r-build-system)
24302 (home-page "https://cran.r-project.org/web/packages/LSD/")
24303 (synopsis "Lots of superior depictions tool creates colorful plots")
24305 "This package creates lots of colorful plots in a multitude of variations.
24306 Try a demo of the LSD by running @code{demotour()}.")
24308 (license (list license:gpl2 license:gpl3))))
24310 (define-public r-phylogram
24312 (name "r-phylogram")
24317 (uri (cran-uri "phylogram" version))
24319 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24320 (properties `((upstream-name . "phylogram")))
24321 (build-system r-build-system)
24322 (propagated-inputs `(("r-ape" ,r-ape)))
24323 (home-page "https://github.com/ropensci/phylogram/")
24324 (synopsis "Dendrograms for evolutionary analysis")
24326 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24327 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24328 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24329 as well as several tools for command-line tree manipulation and import/export
24330 via Newick parenthetic text. This improves accessibility to the comprehensive
24331 range of object-specific analytical and tree-visualization functions found
24332 across a wide array of bioinformatic R packages.")
24333 (license license:gpl3)))
24335 (define-public r-kmer
24342 (uri (cran-uri "kmer" version))
24344 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24345 (properties `((upstream-name . "kmer")))
24346 (build-system r-build-system)
24348 `(("r-openssl" ,r-openssl)
24349 ("r-phylogram" ,r-phylogram)
24350 ("r-rcpp" ,r-rcpp)))
24351 (home-page "https://github.com/shaunpwilkinson/kmer/")
24352 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24354 "@code{r-kmer} is an R package for rapidly computing distance matrices
24355 and clustering large sequence datasets using fast alignment-free k-mer
24356 counting and recursive k-means partitioning.")
24357 (license license:gpl3)))
24359 (define-public r-hardhat
24366 (uri (cran-uri "hardhat" version))
24369 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24370 (properties `((upstream-name . "hardhat")))
24371 (build-system r-build-system)
24373 `(("r-glue" ,r-glue)
24374 ("r-rlang" ,r-rlang)
24375 ("r-tibble" ,r-tibble)
24376 ("r-vctrs" ,r-vctrs)))
24378 `(("r-knitr" ,r-knitr)))
24379 (home-page "https://github.com/tidymodels/hardhat")
24380 (synopsis "Construct modeling packages")
24382 "Building modeling packages is hard. A large amount of effort generally
24383 goes into providing an implementation for a new method that is efficient,
24384 fast, and correct, but often less emphasis is put on the user interface. A
24385 good interface requires specialized knowledge about S3 methods and formulas,
24386 which the average package developer might not have. The goal of
24387 @code{hardhat} is to reduce the burden around building new modeling packages
24388 by providing functionality for preprocessing, predicting, and validating
24390 (license license:expat)))
24392 (define-public r-lightgbm
24394 (name "r-lightgbm")
24399 (uri (cran-uri "lightgbm" version))
24402 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
24403 (properties `((upstream-name . "lightgbm")))
24404 (build-system r-build-system)
24406 `(("r-data-table" ,r-data-table)
24407 ("r-jsonlite" ,r-jsonlite)
24408 ("r-matrix" ,r-matrix)
24410 (home-page "https://github.com/Microsoft/LightGBM")
24411 (synopsis "Light gradient boosting machine")
24413 "Tree based algorithms can be improved by introducing boosting
24414 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24415 al. (2017). This package offers an R interface to work with it. It is
24416 designed to be distributed and efficient with the following goals:
24419 @item Faster training speed and higher efficiency;
24420 @item lower memory usage;
24421 @item better accuracy;
24422 @item parallel learning supported; and
24423 @item capable of handling large-scale data.
24426 (license license:expat)))
24428 (define-public r-shapforxgboost
24430 (name "r-shapforxgboost")
24435 (uri (cran-uri "SHAPforxgboost" version))
24438 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
24440 `((upstream-name . "SHAPforxgboost")))
24441 (build-system r-build-system)
24443 `(("r-bbmisc" ,r-bbmisc)
24444 ("r-data-table" ,r-data-table)
24445 ("r-ggextra" ,r-ggextra)
24446 ("r-ggforce" ,r-ggforce)
24447 ("r-ggplot2" ,r-ggplot2)
24448 ("r-ggpubr" ,r-ggpubr)
24449 ("r-lightgbm" ,r-lightgbm)
24450 ("r-rcolorbrewer" ,r-rcolorbrewer)
24451 ("r-xgboost" ,r-xgboost)))
24452 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24453 (synopsis "SHAP Plots for XGBoost")
24455 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24456 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24457 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24458 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24460 (license license:expat)))
24462 (define-public r-rismed
24469 (uri (cran-uri "RISmed" version))
24472 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24473 (properties `((upstream-name . "RISmed")))
24474 (build-system r-build-system)
24475 (home-page "https://cran.r-project.org/web/packages/RISmed")
24476 (synopsis "Download content from NCBI databases")
24478 "This package provides a set of tools to extract bibliographic
24479 content from the National Center for Biotechnology Information (NCBI)
24480 databases, including PubMed. The name RISmed is a portmanteau of
24481 RIS (for Research Information Systems, a common tag format for
24482 bibliographic data) and PubMed.")
24483 (license license:gpl2+)))
24485 (define-public r-semver
24492 (uri (cran-uri "semver" version))
24495 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24496 (properties `((upstream-name . "semver")))
24497 (build-system r-build-system)
24499 `(("r-assertthat" ,r-assertthat)
24500 ("r-rcpp" ,r-rcpp)))
24501 (native-inputs `(("r-knitr" ,r-knitr)))
24502 (home-page "https://github.com/johndharrison/semver")
24503 (synopsis "Parser for Semantic Versioning 2.0.0")
24505 "This package provides tools and functions for parsing, rendering and
24506 operating on semantic version strings. Semantic versioning is a simple set of
24507 rules and requirements that dictate how version numbers are assigned and
24508 incremented as outlined at @url{http://semver.org}.")
24509 (license license:expat)))
24511 (define-public r-binman
24518 (uri (cran-uri "binman" version))
24521 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24522 (properties `((upstream-name . "binman")))
24523 (build-system r-build-system)
24525 `(("r-assertthat" ,r-assertthat)
24527 ("r-jsonlite" ,r-jsonlite)
24528 ("r-rappdirs" ,r-rappdirs)
24529 ("r-semver" ,r-semver)
24531 ("r-yaml" ,r-yaml)))
24532 (native-inputs `(("r-knitr" ,r-knitr)))
24533 (home-page "https://github.com/ropensci/binman")
24534 (synopsis "Binary download manager")
24536 "This package provides tools and functions for managing the download of
24537 binary files. Binary repositories are defined in the YAML format. Defining
24538 new pre-download, download and post-download templates allow additional
24539 repositories to be added.")
24540 (license license:expat)))
24542 (define-public r-wdman
24549 (uri (cran-uri "wdman" version))
24552 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24553 (properties `((upstream-name . "wdman")))
24554 (build-system r-build-system)
24556 `(("r-assertthat" ,r-assertthat)
24557 ("r-binman" ,r-binman)
24558 ("r-processx" ,r-processx)
24559 ("r-semver" ,r-semver)
24560 ("r-yaml" ,r-yaml)))
24561 (native-inputs `(("r-knitr" ,r-knitr)))
24562 (home-page "https://docs.ropensci.org/wdman/")
24563 (synopsis "Webdriver/Selenium binary manager")
24565 "There are a number of binary files associated with the
24566 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24567 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24568 @url{https://github.com/mozilla/geckodriver},
24569 @url{http://phantomjs.org/download.html}, and
24570 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24571 more information). This package provides functions to download these binaries
24572 and to manage processes involving them.")
24573 (license license:expat)))
24575 (define-public r-rselenium
24577 (name "r-rselenium")
24582 (uri (cran-uri "RSelenium" version))
24585 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24586 (properties `((upstream-name . "RSelenium")))
24587 (build-system r-build-system)
24589 `(("r-binman" ,r-binman)
24590 ("r-catools" ,r-catools)
24592 ("r-openssl" ,r-openssl)
24593 ("r-wdman" ,r-wdman)
24595 (native-inputs `(("r-knitr" ,r-knitr)))
24596 (home-page "https://docs.ropensci.org/RSelenium/")
24597 (synopsis "R bindings for Selenium WebDriver")
24599 "This package provides a set of R bindings for the Selenium 2.0
24600 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24601 information) using the @code{JsonWireProtocol} (see
24602 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24603 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24604 a user would either locally or on a remote machine using the Selenium server
24605 it marks a leap forward in terms of web browser automation. Selenium
24606 automates web browsers (commonly referred to as browsers). Using RSelenium
24607 you can automate browsers locally or remotely.")
24608 (license license:agpl3+)))
24610 (define-public r-conquer
24617 (uri (cran-uri "conquer" version))
24620 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24621 (properties `((upstream-name . "conquer")))
24622 (build-system r-build-system)
24624 `(("r-matrix" ,r-matrix)
24625 ("r-matrixstats" ,r-matrixstats)
24627 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24628 (home-page "https://github.com/XiaoouPan/conquer")
24629 (synopsis "Convolution-type smoothed quantile regression")
24631 "This package provides fast and accurate convolution-type smoothed
24632 quantile regression, implemented using Barzilai-Borwein gradient descent with
24633 a Huber regression warm start. Confidence intervals for regression
24634 coefficients are constructed using multiplier bootstrap.")
24635 (license license:gpl3)))
24637 (define-public r-fastshap
24639 (name "r-fastshap")
24644 (uri (cran-uri "fastshap" version))
24647 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24648 (properties `((upstream-name . "fastshap")))
24649 (build-system r-build-system)
24651 `(("r-abind" ,r-abind)
24652 ("r-ggplot2" ,r-ggplot2)
24653 ("r-gridextra" ,r-gridextra)
24654 ("r-matrixstats" ,r-matrixstats)
24657 ("r-rcpparmadillo" ,r-rcpparmadillo)
24658 ("r-tibble" ,r-tibble)))
24659 (home-page "https://github.com/bgreenwell/fastshap")
24660 (synopsis "Fast approximate Shapley values")
24662 "This package computes fast (relative to other implementations)
24663 approximate Shapley values for any supervised learning model. Shapley values
24664 help to explain the predictions from any black box model using ideas from game
24665 theory; see @url{Strumbel and Kononenko (2014),
24666 doi.org/10.1007/s10115-013-0679-x} for details.")
24667 (license license:gpl2+)))
24669 (define-public r-metrics
24676 (uri (cran-uri "Metrics" version))
24679 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24680 (properties `((upstream-name . "Metrics")))
24681 (build-system r-build-system)
24682 (home-page "https://github.com/mfrasco/Metrics")
24683 (synopsis "Evaluation metrics for machine learning")
24685 "This package provides an implementation of evaluation metrics in R that
24686 are commonly used in supervised machine learning. It implements metrics for
24687 regression, time series, binary classification, classification, and
24688 information retrieval problems. It has zero dependencies and a consistent,
24689 simple interface for all functions.")
24690 (license license:bsd-3)))
24692 (define-public r-iml
24699 (uri (cran-uri "iml" version))
24702 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24703 (properties `((upstream-name . "iml")))
24704 (build-system r-build-system)
24706 `(("r-checkmate" ,r-checkmate)
24707 ("r-data-table" ,r-data-table)
24708 ("r-formula" ,r-formula)
24709 ("r-future" ,r-future)
24710 ("r-future-apply" ,r-future-apply)
24711 ("r-ggplot2" ,r-ggplot2)
24712 ("r-gridextra" ,r-gridextra)
24713 ("r-metrics" ,r-metrics)
24714 ("r-prediction" ,r-prediction)
24716 (native-inputs `(("r-knitr" ,r-knitr)))
24717 (home-page "https://github.com/christophM/iml")
24718 (synopsis "Interpretable machine learning")
24720 "This package provides interpretability methods to analyze the behavior
24721 and predictions of any machine learning model. Implemented methods are:
24724 @item Feature importance described by Fisher et al. (2018),
24725 @item accumulated local effects plots described by Apley (2018),
24726 @item partial dependence plots described by Friedman (2001),
24727 @item individual conditional expectation ('ice') plots described by Goldstein
24728 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24729 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24730 @item the Shapley Value described by Strumbelj et. al (2014)
24731 @url{https://doi.org/10.1007/s10115-013-0679-x},
24732 @item feature interactions described by Friedman et. al
24733 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24736 (license license:expat)))
24738 (define-public r-goftest
24745 (uri (cran-uri "goftest" version))
24748 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24749 (properties `((upstream-name . "goftest")))
24750 (build-system r-build-system)
24751 (home-page "https://github.com/baddstats/goftest")
24752 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24754 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24755 goodness-of-fit for continuous univariate distributions, using efficient
24757 (license license:gpl2+)))
24759 (define-public r-tensor
24766 (uri (cran-uri "tensor" version))
24769 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24770 (properties `((upstream-name . "tensor")))
24771 (build-system r-build-system)
24772 (home-page "https://cran.r-project.org/web/packages/tensor/")
24773 (synopsis "Tensor product of arrays")
24775 "The tensor product of two arrays is notionally an outer product of the
24776 arrays collapsed in specific extents by summing along the appropriate
24777 diagonals. This package allows you to compute the tensor product of arrays.")
24778 (license license:gpl2+)))
24780 (define-public r-spatstat-utils
24782 (name "r-spatstat-utils")
24787 (uri (cran-uri "spatstat.utils" version))
24790 "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
24792 `((upstream-name . "spatstat.utils")))
24793 (build-system r-build-system)
24794 (home-page "http://www.spatstat.org")
24795 (synopsis "Utility functions for spatstat")
24797 "This package contains utility functions for the @code{spatstat} package
24798 which may also be useful for other purposes.")
24799 (license license:gpl2+)))
24801 (define-public r-spatstat-sparse
24803 (name "r-spatstat-sparse")
24808 (uri (cran-uri "spatstat.sparse" version))
24811 "1w312q7gxzchigxxzk9akscdsz66j5085lgjryamschjgp4f8yk2"))))
24813 `((upstream-name . "spatstat.sparse")))
24814 (build-system r-build-system)
24816 `(("r-abind" ,r-abind)
24817 ("r-matrix" ,r-matrix)
24818 ("r-spatstat-utils" ,r-spatstat-utils)
24819 ("r-tensor" ,r-tensor)))
24820 (home-page "http://spatstat.org/")
24821 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
24823 "This package defines sparse three-dimensional arrays and supports
24824 standard operations on them. The package also includes utility functions for
24825 matrix calculations that are common in statistics, such as quadratic forms.")
24826 (license license:gpl2+)))
24828 (define-public r-spatstat-data
24830 (name "r-spatstat-data")
24835 (uri (cran-uri "spatstat.data" version))
24838 "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
24839 (properties `((upstream-name . "spatstat.data")))
24840 (build-system r-build-system)
24842 `(("r-matrix" ,r-matrix)
24843 ("r-spatstat-utils" ,r-spatstat-utils)))
24844 (home-page "http://www.spatstat.org")
24845 (synopsis "Datasets for spatstat")
24847 "This package contains all the datasets for the @code{spatstat}
24849 (license license:gpl2+)))
24851 (define-public r-spatstat-geom
24853 (name "r-spatstat-geom")
24858 (uri (cran-uri "spatstat.geom" version))
24861 "0g0m5b3nbzpyblbp77n56k6aiw3fn23jkk72h9fhqlg1ydn2fzpk"))))
24862 (properties `((upstream-name . "spatstat.geom")))
24863 (build-system r-build-system)
24865 `(("r-deldir" ,r-deldir)
24866 ("r-polyclip" ,r-polyclip)
24867 ("r-spatstat-data" ,r-spatstat-data)
24868 ("r-spatstat-sparse" ,r-spatstat-sparse)
24869 ("r-spatstat-utils" ,r-spatstat-utils)))
24870 (home-page "http://spatstat.org/")
24871 (synopsis "Geometrical functionality of the spatstat package")
24873 "This is a subset of the original spatstat package, containing the
24874 user-level code from spatstat which performs geometrical operations, except
24875 for the geometry of linear networks.")
24876 (license license:gpl2+)))
24878 (define-public r-spatstat-core
24880 (name "r-spatstat-core")
24885 (uri (cran-uri "spatstat.core" version))
24888 "0wq61sd53hwyk3fzjdc2prrr66n67zbwb5i3ii7kvyhfwx0xikm3"))))
24889 (properties `((upstream-name . "spatstat.core")))
24890 (build-system r-build-system)
24892 `(("r-abind" ,r-abind)
24893 ("r-goftest" ,r-goftest)
24894 ("r-matrix" ,r-matrix)
24897 ("r-rpart" ,r-rpart)
24898 ("r-spatstat-data" ,r-spatstat-data)
24899 ("r-spatstat-geom" ,r-spatstat-geom)
24900 ("r-spatstat-sparse" ,r-spatstat-sparse)
24901 ("r-spatstat-utils" ,r-spatstat-utils)
24902 ("r-tensor" ,r-tensor)))
24903 (home-page "http://spatstat.org/")
24904 (synopsis "Core functionality of the spatstat package")
24906 "This is a subset of the original spatstat package, containing all of the
24907 user-level code from spatstat, except for the code for linear networks.")
24908 (license license:gpl2+)))
24910 (define-public r-spatstat-linnet
24912 (name "r-spatstat-linnet")
24917 (uri (cran-uri "spatstat.linnet" version))
24920 "1y088r26h5yv006ydgcb4iwpvnc7ql857gky0hbi7xqqciqr8wdv"))))
24922 `((upstream-name . "spatstat.linnet")))
24923 (build-system r-build-system)
24925 `(("r-matrix" ,r-matrix)
24926 ("r-spatstat-core" ,r-spatstat-core)
24927 ("r-spatstat-data" ,r-spatstat-data)
24928 ("r-spatstat-geom" ,r-spatstat-geom)
24929 ("r-spatstat-utils" ,r-spatstat-utils)))
24930 (home-page "http://spatstat.org/")
24931 (synopsis "Linear networks functionality of the spatstat package")
24933 "This is a subset of the spatstat package, containing its functionality
24934 for spatial data on a linear network.")
24935 (license license:gpl2+)))
24937 (define-public r-spatstat
24939 (name "r-spatstat")
24944 (uri (cran-uri "spatstat" version))
24947 "1xq11ijc0d0lbixxb3wnvyr4gplfj2d2i64ynsa089xd525zzzbw"))))
24948 (properties `((upstream-name . "spatstat")))
24949 (build-system r-build-system)
24951 `(("r-spatstat-core" ,r-spatstat-core)
24952 ("r-spatstat-data" ,r-spatstat-data)
24953 ("r-spatstat-geom" ,r-spatstat-geom)
24954 ("r-spatstat-linnet" ,r-spatstat-linnet)
24955 ("r-spatstat-utils" ,r-spatstat-utils)))
24956 (home-page "http://www.spatstat.org")
24957 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24959 "This package provides a comprehensive toolbox for analysing Spatial
24960 Point Patterns. It is focused mainly on two-dimensional point patterns,
24961 including multitype/marked points, in any spatial region. It also supports
24962 three-dimensional point patterns, space-time point patterns in any number of
24963 dimensions, point patterns on a linear network, and patterns of other
24964 geometrical objects. It supports spatial covariate data such as pixel images
24965 and contains over 2000 functions for plotting spatial data, exploratory data
24966 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24967 formal inference.")
24968 (license license:gpl2+)))
24970 (define-public r-gaston
24977 (uri (cran-uri "gaston" version))
24980 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24981 (properties `((upstream-name . "gaston")))
24982 (build-system r-build-system)
24983 (inputs `(("zlib" ,zlib)))
24985 `(("r-rcpp" ,r-rcpp)
24986 ("r-rcppeigen" ,r-rcppeigen)
24987 ("r-rcppparallel" ,r-rcppparallel)))
24988 (native-inputs `(("r-knitr" ,r-knitr)))
24989 (home-page "https://cran.r-project.org/web/packages/gaston/")
24990 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
24992 "This is a package for the manipulation of genetic data (SNPs).
24993 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
24994 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
24995 for linear mixed models (AIREML).")
24996 (license license:gpl3)))
24998 (define-public r-cpp11
25005 (uri (cran-uri "cpp11" version))
25008 "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
25009 (properties `((upstream-name . "cpp11")))
25010 (build-system r-build-system)
25011 (native-inputs `(("r-knitr" ,r-knitr)))
25012 (home-page "https://github.com/r-lib/cpp11")
25013 (synopsis "C++11 Interface for R's C Interface")
25015 "This package provides a header only, C++11 interface to R's C interface.
25016 Compared to other approaches @code{cpp11} strives to be safe against long
25017 jumps from the C API as well as C++ exceptions, conform to normal R function
25018 semantics and supports interaction with @code{ALTREP} vectors.")
25019 (license license:expat)))
25021 (define-public r-rcppziggurat
25023 (name "r-rcppziggurat")
25028 (uri (cran-uri "RcppZiggurat" version))
25031 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
25032 (properties `((upstream-name . "RcppZiggurat")))
25033 (build-system r-build-system)
25035 `(("r-rcpp" ,r-rcpp)
25036 ("r-rcppgsl" ,r-rcppgsl)))
25037 (native-inputs `(("r-knitr" ,r-knitr)))
25038 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
25039 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
25041 "The Ziggurat generator for normally distributed random numbers,
25042 originally proposed by Marsaglia and Tsang (2000,
25043 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
25044 times starting with Leong et al (2005,
25045 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
25046 aggregation for comparing different implementations in order to provide a
25047 'faster but good enough' alternative for use with R and C++ code.")
25048 (license license:gpl2+)))
25050 (define-public r-rfast
25057 (uri (cran-uri "Rfast" version))
25060 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
25061 (properties `((upstream-name . "Rfast")))
25062 (build-system r-build-system)
25064 `(("r-rcpp" ,r-rcpp)
25065 ("r-rcpparmadillo" ,r-rcpparmadillo)
25066 ("r-rcppziggurat" ,r-rcppziggurat)))
25067 (home-page "https://github.com/RfastOfficial/Rfast")
25068 (synopsis "Collection of efficient and fast R functions")
25070 "This package provides a collection of fast (utility) functions for data
25071 analysis. Column- and row- wise means, medians, variances, minimums,
25072 maximums, many t, F and G-square tests, many regressions (normal, logistic,
25073 Poisson), are some of the many fast functions.")
25074 (license license:gpl2+)))
25076 (define-public r-clusterr
25078 (name "r-clusterr")
25083 (uri (cran-uri "ClusterR" version))
25086 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
25087 (properties `((upstream-name . "ClusterR")))
25088 (build-system r-build-system)
25090 `(("r-ggplot2" ,r-ggplot2)
25092 ("r-gtools" ,r-gtools)
25094 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25095 (native-inputs `(("r-knitr" ,r-knitr)))
25096 (home-page "https://github.com/mlampros/ClusterR")
25097 (synopsis "Clustering")
25099 "This package provides Gaussian mixture models, k-means,
25100 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
25101 option to plot, validate, predict (new data) and estimate the optimal number
25102 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
25103 the computationally intensive parts of the functions. For more information,
25107 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
25108 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
25109 @url{https://doi.org/10.18637/jss.v001.i04};
25110 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
25111 Library, @url{https://doi.org/10.1145/1772690.1772862};
25112 @item \"Armadillo: a template-based C++ library
25113 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
25114 Software, @url{https://doi.org/10.21105/joss.00026};
25115 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
25116 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
25117 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
25120 (license license:gpl3)))
25122 (define-public r-spectrum
25124 (name "r-spectrum")
25129 (uri (cran-uri "Spectrum" version))
25132 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25133 (properties `((upstream-name . "Spectrum")))
25134 (build-system r-build-system)
25136 `(("r-clusterr" ,r-clusterr)
25137 ("r-diptest" ,r-diptest)
25138 ("r-ggplot2" ,r-ggplot2)
25139 ("r-rfast" ,r-rfast)))
25140 (native-inputs `(("r-knitr" ,r-knitr)))
25141 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25142 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25144 "This package provides a self-tuning spectral clustering method for
25145 single or multi-view data. Spectrum uses a new type of adaptive density aware
25146 kernel that strengthens connections in the graph based on common nearest
25147 neighbours. It uses a tensor product graph data integration and diffusion
25148 procedure to integrate different data sources and reduce noise. Spectrum uses
25149 either the eigengap or multimodality gap heuristics to determine the number of
25150 clusters. The method is sufficiently flexible so that a wide range of
25151 Gaussian and non-Gaussian structures can be clustered with automatic selection
25153 (license license:agpl3+)))
25155 (define-public r-nabor
25162 (uri (cran-uri "nabor" version))
25165 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25166 (properties `((upstream-name . "nabor")))
25167 (build-system r-build-system)
25171 ("r-rcppeigen" ,r-rcppeigen)))
25172 (home-page "https://cran.r-project.org/web/packages/nabor/")
25173 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25175 "This package provides an R wrapper for libnabo, an exact or approximate
25176 k nearest neighbour library which is optimised for low dimensional
25177 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25178 designed as a drop-in replacement for the RANN function @code{nn2}. In
25179 addition, objects which include the k-d tree search structure can be returned
25180 to speed up repeated queries of the same set of target points.")
25181 (license license:bsd-3)))
25183 (define-public r-muhaz
25186 (version "1.2.6.1")
25190 (uri (cran-uri "muhaz" version))
25193 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
25194 (properties `((upstream-name . "muhaz")))
25195 (build-system r-build-system)
25197 `(("r-survival" ,r-survival)))
25199 `(("gfortran" ,gfortran)))
25200 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25201 (synopsis "Hazard function estimation in survival analysis")
25203 "This package produces a smooth estimate of the hazard function for
25205 ;; Any version of the GPL.
25206 (license license:gpl3+)))
25208 (define-public r-flexsurv
25210 (name "r-flexsurv")
25215 (uri (cran-uri "flexsurv" version))
25218 "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9"))))
25219 (properties `((upstream-name . "flexsurv")))
25220 (build-system r-build-system)
25222 `(("r-assertthat" ,r-assertthat)
25223 ("r-desolve" ,r-desolve)
25224 ("r-dplyr" ,r-dplyr)
25225 ("r-generics" ,r-generics)
25226 ("r-magrittr" ,r-magrittr)
25227 ("r-matrix" ,r-matrix)
25228 ("r-mstate" ,r-mstate)
25229 ("r-muhaz" ,r-muhaz)
25230 ("r-mvtnorm" ,r-mvtnorm)
25231 ("r-numderiv" ,r-numderiv)
25232 ("r-purrr" ,r-purrr)
25233 ("r-quadprog" ,r-quadprog)
25235 ("r-rlang" ,r-rlang)
25236 ("r-rstpm2" ,r-rstpm2)
25237 ("r-survival" ,r-survival)
25238 ("r-tibble" ,r-tibble)
25239 ("r-tidyr" ,r-tidyr)
25240 ("r-tidyselect" ,r-tidyselect)))
25242 `(("r-knitr" ,r-knitr)))
25243 (home-page "https://github.com/chjackson/flexsurv-dev")
25244 (synopsis "Flexible parametric survival and multi-state models")
25246 "This package provides flexible parametric models for time-to-event data,
25247 including the Royston-Parmar spline model, generalized gamma and generalized F
25248 distributions. Any user-defined parametric distribution can be fitted, given
25249 at least an R function defining the probability density or hazard. There are
25250 also tools for fitting and predicting from fully parametric multi-state
25252 (license license:gpl2+)))
25254 (define-public r-transphylo
25256 (name "r-transphylo")
25261 (uri (cran-uri "TransPhylo" version))
25264 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25265 (properties `((upstream-name . "TransPhylo")))
25266 (build-system r-build-system)
25269 ("r-rcpp" ,r-rcpp)))
25271 `(("r-knitr" ,r-knitr)))
25272 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25273 (synopsis "Inference of transmission tree from a dated phylogeny")
25275 "This is a package to infer transmission trees from a dated phylogeny.
25276 It includes methods to simulate and analyze outbreaks. The methodology is
25277 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25278 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25279 (license license:gpl2+)))
25281 (define-public r-km-ci
25288 (uri (cran-uri "km.ci" version))
25291 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25292 (properties `((upstream-name . "km.ci")))
25293 (build-system r-build-system)
25295 `(("r-survival" ,r-survival)))
25296 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25297 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25299 "This package computes various @dfn{confidence intervals} (CI) for the
25300 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25301 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25302 Nair and Hall and Wellner.")
25303 (license license:gpl2+)))
25305 (define-public r-kmsurv
25312 (uri (cran-uri "KMsurv" version))
25315 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25316 (properties `((upstream-name . "KMsurv")))
25317 (build-system r-build-system)
25318 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25319 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25321 "This package provides data sets and functions for Klein and Moeschberger
25322 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25324 (license license:gpl3+)))
25326 (define-public r-survmisc
25328 (name "r-survmisc")
25333 (uri (cran-uri "survMisc" version))
25336 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25337 (properties `((upstream-name . "survMisc")))
25338 (build-system r-build-system)
25340 `(("r-data-table" ,r-data-table)
25341 ("r-ggplot2" ,r-ggplot2)
25342 ("r-gridextra" ,r-gridextra)
25343 ("r-km-ci" ,r-km-ci)
25344 ("r-kmsurv" ,r-kmsurv)
25345 ("r-knitr" ,r-knitr)
25346 ("r-survival" ,r-survival)
25347 ("r-xtable" ,r-xtable)
25350 `(("r-knitr" ,r-knitr)))
25351 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25352 (synopsis "Miscellaneous functions for survival data")
25354 "This package provides a collection of functions to help in the analysis
25355 of right-censored survival data. These extend the methods available in
25356 the @code{survival} package.")
25357 (license license:gpl2)))
25359 (define-public r-exactranktests
25361 (name "r-exactranktests")
25366 (uri (cran-uri "exactRankTests" version))
25369 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25371 `((upstream-name . "exactRankTests")))
25372 (build-system r-build-system)
25373 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25374 (synopsis "Exact distributions for rank and permutation tests")
25376 "This package computes exact conditional p-values and quantiles using an
25377 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25378 (license license:gpl2+)))
25380 (define-public r-maxstat
25387 (uri (cran-uri "maxstat" version))
25390 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25391 (properties `((upstream-name . "maxstat")))
25392 (build-system r-build-system)
25394 `(("r-exactranktests" ,r-exactranktests)
25395 ("r-mvtnorm" ,r-mvtnorm)))
25396 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25397 (synopsis "Maximally selected rank statistics")
25399 "This package provides maximally selected rank statistics with several
25400 p-value approximations.")
25401 (license license:gpl2+)))
25403 (define-public r-survminer
25405 (name "r-survminer")
25410 (uri (cran-uri "survminer" version))
25413 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
25414 (properties `((upstream-name . "survminer")))
25415 (build-system r-build-system)
25417 `(("r-broom" ,r-broom)
25418 ("r-dplyr" ,r-dplyr)
25419 ("r-ggplot2" ,r-ggplot2)
25420 ("r-ggpubr" ,r-ggpubr)
25421 ("r-ggtext" ,r-ggtext)
25422 ("r-gridextra" ,r-gridextra)
25423 ("r-magrittr" ,r-magrittr)
25424 ("r-maxstat" ,r-maxstat)
25425 ("r-purrr" ,r-purrr)
25426 ("r-rlang" ,r-rlang)
25427 ("r-scales" ,r-scales)
25428 ("r-survival" ,r-survival)
25429 ("r-survmisc" ,r-survmisc)
25430 ("r-tibble" ,r-tibble)
25431 ("r-tidyr" ,r-tidyr)))
25433 `(("r-knitr" ,r-knitr)))
25434 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25435 (synopsis "Drawing survival curves using ggplot2")
25437 "This package contains the function @code{ggsurvplot()} for easily
25438 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25439 risk' table and 'censoring count plot'. Other functions are also available to
25440 plot adjusted curves for Cox model and to visually examine Cox model
25442 (license license:gpl2)))
25444 (define-public r-forge
25451 (uri (cran-uri "forge" version))
25454 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25455 (properties `((upstream-name . "forge")))
25456 (build-system r-build-system)
25458 `(("r-magrittr" ,r-magrittr)
25459 ("r-rlang" ,r-rlang)))
25460 (home-page "https://cran.r-project.org/web/packages/forge/")
25461 (synopsis "Cast values into shape")
25463 "This package provides helper functions with a consistent interface to
25464 coerce and verify the types and shapes of values for input checking.")
25465 (license license:asl2.0)))
25467 (define-public r-config
25474 (uri (cran-uri "config" version))
25477 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25478 (properties `((upstream-name . "config")))
25479 (build-system r-build-system)
25481 `(("r-yaml" ,r-yaml)))
25483 `(("r-knitr" ,r-knitr)))
25484 (home-page "https://github.com/rstudio/config")
25485 (synopsis "Manage environment specific configuration values")
25487 "This package lets you manage configuration values across multiple
25488 environments (e.g. development, test, production). It reads values using a
25489 function that determines the current environment and returns the appropriate
25491 (license license:gpl3)))
25493 (define-public r-adaptivesparsity
25495 (name "r-adaptivesparsity")
25499 (uri (cran-uri "AdaptiveSparsity" version))
25502 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25504 `((upstream-name . "AdaptiveSparsity")))
25505 (build-system r-build-system)
25508 (modify-phases %standard-phases
25509 (add-after 'unpack 'link-against-armadillo
25511 (substitute* "src/Makevars"
25512 (("PKG_LIBS=" prefix)
25513 (string-append prefix "-larmadillo")))
25516 `(("r-mass" ,r-mass)
25517 ("r-matrix" ,r-matrix)
25519 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25521 `(("armadillo" ,armadillo)))
25522 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25523 (synopsis "Adaptive sparsity models")
25525 "This package implements the Figueiredo machine learning algorithm for
25526 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25527 geometric models.")
25528 (license license:lgpl3+)))
25530 (define-public r-diffusionmap
25532 (name "r-diffusionmap")
25537 (uri (cran-uri "diffusionMap" version))
25540 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25541 (properties `((upstream-name . "diffusionMap")))
25542 (build-system r-build-system)
25544 `(("r-igraph" ,r-igraph)
25545 ("r-matrix" ,r-matrix)
25546 ("r-scatterplot3d" ,r-scatterplot3d)))
25547 (home-page "https://www.r-project.org")
25548 (synopsis "Diffusion map")
25549 (description "This package implements the diffusion map method of data
25550 parametrization, including creation and visualization of diffusion maps,
25551 clustering with diffusion K-means and regression using the adaptive regression
25553 (license license:gpl2)))
25555 (define-public r-igraph
25562 (uri (cran-uri "igraph" version))
25565 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25566 (build-system r-build-system)
25568 `(("gfortran" ,gfortran)))
25572 ("libxml2" ,libxml2)
25575 `(("r-magrittr" ,r-magrittr)
25576 ("r-matrix" ,r-matrix)
25577 ("r-pkgconfig" ,r-pkgconfig)))
25578 (home-page "https://igraph.org")
25579 (synopsis "Network analysis and visualization")
25581 "This package provides routines for simple graphs and network analysis.
25582 It can handle large graphs very well and provides functions for generating
25583 random and regular graphs, graph visualization, centrality methods and much
25585 (license license:gpl2+)))
25587 (define-public r-workflows
25589 (name "r-workflows")
25594 (uri (cran-uri "workflows" version))
25597 "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz"))))
25598 (properties `((upstream-name . "workflows")))
25599 (build-system r-build-system)
25602 ("r-ellipsis" ,r-ellipsis)
25603 ("r-generics" ,r-generics)
25605 ("r-hardhat" ,r-hardhat)
25606 ("r-parsnip" ,r-parsnip)
25607 ("r-rlang" ,r-rlang)
25608 ("r-tidyselect" ,r-tidyselect)
25609 ("r-vctrs" ,r-vctrs)))
25611 `(("r-knitr" ,r-knitr)))
25612 (home-page "https://github.com/tidymodels/workflows")
25613 (synopsis "Modeling workflows")
25615 "A workflow is an object that can bundle together your pre-processing,
25616 modeling, and post-processing requests. For example, if you have a
25617 @code{recipe} and @code{parsnip} model, these can be combined into a
25618 workflow. The advantages are:
25621 @item You don’t have to keep track of separate objects in your workspace.
25622 @item The recipe prepping and model fitting can be executed using a single
25623 call to @code{fit()}.
25624 @item If you have custom tuning parameter settings, these can be defined using
25625 a simpler interface when combined with @code{tune}.
25626 @item In the future, workflows will be able to add post-processing operations,
25627 such as modifying the probability cutoff for two-class models.
25630 (license license:expat)))
25632 (define-public r-gpfit
25639 (uri (cran-uri "GPfit" version))
25642 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25643 (properties `((upstream-name . "GPfit")))
25644 (build-system r-build-system)
25646 `(("r-lattice" ,r-lattice)
25648 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25649 (synopsis "Gaussian Processes modeling")
25651 "This package provides a computationally stable approach of fitting a
25652 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25653 (license license:gpl2)))
25655 (define-public r-yardstick
25657 (name "r-yardstick")
25662 (uri (cran-uri "yardstick" version))
25665 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25666 (properties `((upstream-name . "yardstick")))
25667 (build-system r-build-system)
25669 `(("r-dplyr" ,r-dplyr)
25670 ("r-generics" ,r-generics)
25672 ("r-rlang" ,r-rlang)
25673 ("r-tidyselect" ,r-tidyselect)))
25675 `(("r-knitr" ,r-knitr)))
25676 (home-page "https://github.com/tidymodels/yardstick")
25677 (synopsis "Tidy characterizations of model performance")
25679 "This package provides tidy tools for quantifying how well a model fits
25680 to a data set such as confusion matrices, class probability curve summaries,
25681 and regression metrics (e.g., RMSE).")
25682 (license license:gpl2)))
25684 (define-public r-warp
25691 (uri (cran-uri "warp" version))
25694 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25695 (properties `((upstream-name . "warp")))
25696 (build-system r-build-system)
25697 (native-inputs `(("r-knitr" ,r-knitr)))
25698 (home-page "https://github.com/DavisVaughan/warp")
25699 (synopsis "Group dates")
25701 "This package provides tooling to group dates by a variety of periods
25702 including: yearly, monthly, by second, by week of the month, and more. The
25703 groups are defined in such a way that they also represent the distance between
25704 dates in terms of the period. This extracts valuable information that can be
25705 used in further calculations that rely on a specific temporal spacing between
25707 (license license:expat)))
25709 (define-public r-slider
25716 (uri (cran-uri "slider" version))
25719 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25720 (properties `((upstream-name . "slider")))
25721 (build-system r-build-system)
25723 `(("r-glue" ,r-glue)
25724 ("r-rlang" ,r-rlang)
25725 ("r-vctrs" ,r-vctrs)
25726 ("r-warp" ,r-warp)))
25727 (native-inputs `(("r-knitr" ,r-knitr)))
25728 (home-page "https://github.com/DavisVaughan/slider")
25729 (synopsis "Sliding window functions")
25731 "This package provides type-stable rolling window functions over any R
25732 data type. Cumulative and expanding windows are also supported. For more
25733 advanced usage, an index can be used as a secondary vector that defines how
25734 sliding windows are to be created.")
25735 (license license:expat)))
25737 (define-public r-rsample
25744 (uri (cran-uri "rsample" version))
25747 "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c"))))
25748 (properties `((upstream-name . "rsample")))
25749 (build-system r-build-system)
25751 `(("r-dplyr" ,r-dplyr)
25752 ("r-ellipsis" ,r-ellipsis)
25753 ("r-furrr" ,r-furrr)
25754 ("r-generics" ,r-generics)
25755 ("r-purrr" ,r-purrr)
25756 ("r-rlang" ,r-rlang)
25757 ("r-slider" ,r-slider)
25758 ("r-tibble" ,r-tibble)
25759 ("r-tidyr" ,r-tidyr)
25760 ("r-tidyselect" ,r-tidyselect)
25761 ("r-vctrs" ,r-vctrs)))
25763 `(("r-knitr" ,r-knitr)))
25764 (home-page "https://rsample.tidymodels.org")
25765 (synopsis "General resampling infrastructure")
25767 "This package provides classes and functions to create and summarize
25768 different types of resampling objects (e.g. bootstrap, cross-validation).")
25769 (license license:gpl2)))
25771 (define-public r-dicedesign
25773 (name "r-dicedesign")
25778 (uri (cran-uri "DiceDesign" version))
25781 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
25782 (properties `((upstream-name . "DiceDesign")))
25783 (build-system r-build-system)
25784 (home-page "http://dice.emse.fr/")
25785 (synopsis "Designs of computer experiments")
25787 "This package provides tools to create some specific @code{Space-Filling
25788 Design} (SFD) and to test their quality.")
25789 (license license:gpl3)))
25791 (define-public r-dials
25798 (uri (cran-uri "dials" version))
25801 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25802 (properties `((upstream-name . "dials")))
25803 (build-system r-build-system)
25805 `(("r-dicedesign" ,r-dicedesign)
25806 ("r-dplyr" ,r-dplyr)
25808 ("r-purrr" ,r-purrr)
25809 ("r-rlang" ,r-rlang)
25810 ("r-scales" ,r-scales)
25811 ("r-tibble" ,r-tibble)
25812 ("r-vctrs" ,r-vctrs)
25813 ("r-withr" ,r-withr)))
25814 (native-inputs `(("r-knitr" ,r-knitr)))
25815 (home-page "https://dials.tidymodels.org/")
25816 (synopsis "Tools for creating tuning parameter values")
25818 "Many models contain tuning parameters (i.e. parameters that cannot be
25819 directly estimated from the data). These tools can be used to define objects
25820 for creating, simulating, or validating values for such parameters.")
25821 (license license:gpl2)))
25823 (define-public r-tune
25830 (uri (cran-uri "tune" version))
25833 "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293"))))
25834 (properties `((upstream-name . "tune")))
25835 (build-system r-build-system)
25838 ("r-dials" ,r-dials)
25839 ("r-dplyr" ,r-dplyr)
25840 ("r-foreach" ,r-foreach)
25841 ("r-generics" ,r-generics)
25842 ("r-ggplot2" ,r-ggplot2)
25844 ("r-gpfit" ,r-gpfit)
25845 ("r-parsnip" ,r-parsnip)
25846 ("r-purrr" ,r-purrr)
25847 ("r-recipes" ,r-recipes)
25848 ("r-rlang" ,r-rlang)
25849 ("r-rsample" ,r-rsample)
25850 ("r-tibble" ,r-tibble)
25851 ("r-tidyr" ,r-tidyr)
25852 ("r-vctrs" ,r-vctrs)
25853 ("r-workflows" ,r-workflows)
25854 ("r-yardstick" ,r-yardstick)))
25855 (home-page "https://github.com/tidymodels/tune")
25856 (synopsis "Tidy tuning tools")
25858 "The ability to tune models is important. @code{tune} contains functions
25859 and classes to be used in conjunction with other @code{tidymodels} packages
25860 for finding reasonable values of hyper-parameters in models, pre-processing
25861 methods, and post-processing steps.")
25862 (license license:expat)))
25864 (define-public r-workflowsets
25866 (name "r-workflowsets")
25871 (uri (cran-uri "workflowsets" version))
25874 "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p"))))
25875 (properties `((upstream-name . "workflowsets")))
25876 (build-system r-build-system)
25879 ("r-dplyr" ,r-dplyr)
25880 ("r-ggplot2" ,r-ggplot2)
25881 ("r-prettyunits" ,r-prettyunits)
25882 ("r-purrr" ,r-purrr)
25883 ("r-rlang" ,r-rlang)
25884 ("r-rsample" ,r-rsample)
25885 ("r-tibble" ,r-tibble)
25886 ("r-tidyr" ,r-tidyr)
25888 ("r-vctrs" ,r-vctrs)
25889 ("r-withr" ,r-withr)
25890 ("r-workflows" ,r-workflows)))
25892 `(("r-knitr" ,r-knitr)))
25893 (home-page "https://github.com/tidymodels/workflowsets")
25894 (synopsis "Create a collection of tidymodels workflows")
25896 "A workflow is a combination of a model and preprocessors (e.g, a
25897 formula, recipe, etc.). In order to try different combinations of these, an
25898 object can be created that contains many workflows. There are functions to
25899 create workflows en masse as well as training them and visualizing the
25901 (license license:expat)))
25903 (define-public r-tidyposterior
25905 (name "r-tidyposterior")
25910 (uri (cran-uri "tidyposterior" version))
25913 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25914 (properties `((upstream-name . "tidyposterior")))
25915 (build-system r-build-system)
25917 `(("r-dplyr" ,r-dplyr)
25918 ("r-generics" ,r-generics)
25919 ("r-ggplot2" ,r-ggplot2)
25920 ("r-lifecycle" ,r-lifecycle)
25921 ("r-purrr" ,r-purrr)
25922 ("r-rlang" ,r-rlang)
25923 ("r-rsample" ,r-rsample)
25924 ("r-rstanarm" ,r-rstanarm)
25925 ("r-tibble" ,r-tibble)
25926 ("r-tidyr" ,r-tidyr)
25927 ("r-vctrs" ,r-vctrs)))
25929 `(("r-knitr" ,r-knitr)))
25930 (home-page "https://tidyposterior.tidymodels.org")
25931 (synopsis "Bayesian analysis to compare models using resampling statistics")
25933 "This package can be used to conduct post hoc analyses of resampling
25934 results generated by models. For example, if two models are evaluated with
25935 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25936 are 10 paired statistics. These can be used to make comparisons between
25937 models without involving a test set.")
25938 (license license:gpl2)))
25940 (define-public r-tidypredict
25942 (name "r-tidypredict")
25947 (uri (cran-uri "tidypredict" version))
25950 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25951 (properties `((upstream-name . "tidypredict")))
25952 (build-system r-build-system)
25954 `(("r-dplyr" ,r-dplyr)
25955 ("r-generics" ,r-generics)
25956 ("r-knitr" ,r-knitr)
25957 ("r-purrr" ,r-purrr)
25958 ("r-rlang" ,r-rlang)
25959 ("r-stringr" ,r-stringr)
25960 ("r-tibble" ,r-tibble)
25961 ("r-tidyr" ,r-tidyr)))
25963 `(("r-knitr" ,r-knitr)))
25964 (home-page "https://tidypredict.tidymodels.org")
25965 (synopsis "Run predictions inside the database")
25967 "This package parses a fitted R model object, and returns a formula in
25968 Tidy Eval code that calculates the predictions. It works with several
25969 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25970 final SQL translation of the algorithm. It currently supports @code{lm()},
25971 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25972 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25973 (license license:gpl3)))
25975 (define-public r-janeaustenr
25977 (name "r-janeaustenr")
25982 (uri (cran-uri "janeaustenr" version))
25985 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25986 (properties `((upstream-name . "janeaustenr")))
25987 (build-system r-build-system)
25988 (home-page "https://github.com/juliasilge/janeaustenr")
25989 (synopsis "Jane Austen's complete novels")
25991 "This package provides the full texts for Jane Austen's six completed
25992 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25993 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25994 and \"Persuasion\".")
25995 (license license:expat)))
25997 (define-public r-tokenizers
25999 (name "r-tokenizers")
26004 (uri (cran-uri "tokenizers" version))
26007 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
26008 (properties `((upstream-name . "tokenizers")))
26009 (build-system r-build-system)
26011 `(("r-rcpp" ,r-rcpp)
26012 ("r-snowballc" ,r-snowballc)
26013 ("r-stringi" ,r-stringi)))
26015 `(("r-knitr" ,r-knitr)))
26016 (home-page "https://lincolnmullen.com/software/tokenizers/")
26017 (synopsis "Fast, consistent tokenization of natural language text")
26019 "This is a package for converting natural language text into tokens.
26020 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
26021 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
26022 Treebank, regular expressions, as well as functions for counting characters,
26023 words, and sentences, and a function for splitting longer texts into separate
26024 documents, each with the same number of words. The tokenizers have a
26025 consistent interface, and the package is built on the @code{stringi} and
26026 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
26027 (license license:expat)))
26029 (define-public r-hunspell
26031 (name "r-hunspell")
26036 (uri (cran-uri "hunspell" version))
26039 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
26040 (properties `((upstream-name . "hunspell")))
26041 (build-system r-build-system)
26043 `(("r-digest" ,r-digest)
26044 ("r-rcpp" ,r-rcpp)))
26046 `(("r-knitr" ,r-knitr)))
26047 (home-page "https://github.com/ropensci/hunspell#readme")
26048 (synopsis "High-performance stemmer, tokenizer, and spell checker")
26050 "This package provides a low-level spell checker and morphological
26051 analyzer based on the famous @code{hunspell} library. The package can analyze
26052 or check individual words as well as parse text, LaTeX, HTML or XML documents.
26053 For a more user-friendly interface use the @code{spelling} package which
26054 builds on this package to automate checking of files, documentation and
26055 vignettes in all common formats.")
26056 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
26057 ;; MPL; in addition to these licenses the rest of the R wrapper is also
26058 ;; available under the Expat license.
26059 (license (list license:gpl2
26064 (define-public r-tidytext
26066 (name "r-tidytext")
26071 (uri (cran-uri "tidytext" version))
26074 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
26075 (properties `((upstream-name . "tidytext")))
26076 (build-system r-build-system)
26078 `(("r-dplyr" ,r-dplyr)
26079 ("r-generics" ,r-generics)
26080 ("r-hunspell" ,r-hunspell)
26081 ("r-janeaustenr" ,r-janeaustenr)
26082 ("r-lifecycle" ,r-lifecycle)
26083 ("r-matrix" ,r-matrix)
26084 ("r-purrr" ,r-purrr)
26085 ("r-rlang" ,r-rlang)
26086 ("r-stringr" ,r-stringr)
26087 ("r-tibble" ,r-tibble)
26088 ("r-tokenizers" ,r-tokenizers)
26089 ("r-vctrs" ,r-vctrs)))
26091 `(("r-knitr" ,r-knitr)))
26092 (home-page "https://github.com/juliasilge/tidytext")
26093 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
26095 "This is a package for text mining for word processing and sentiment
26096 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
26097 (license license:expat)))
26099 (define-public r-parsnip
26106 (uri (cran-uri "parsnip" version))
26109 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
26110 (properties `((upstream-name . "parsnip")))
26111 (build-system r-build-system)
26113 `(("r-dplyr" ,r-dplyr)
26114 ("r-generics" ,r-generics)
26115 ("r-globals" ,r-globals)
26117 ("r-magrittr" ,r-magrittr)
26118 ("r-prettyunits" ,r-prettyunits)
26119 ("r-purrr" ,r-purrr)
26120 ("r-rlang" ,r-rlang)
26121 ("r-tibble" ,r-tibble)
26122 ("r-tidyr" ,r-tidyr)
26123 ("r-vctrs" ,r-vctrs)))
26125 `(("r-knitr" ,r-knitr)))
26126 (home-page "https://parsnip.tidymodels.org")
26127 (synopsis "Common API to modeling and analysis functions")
26129 "This package provides a common interface to allow users to specify a
26130 model without having to remember the different argument names across different
26131 functions or computational engines (e.g. R, Spark, Stan, etc).")
26132 (license license:gpl2)))
26134 (define-public r-infer
26141 (uri (cran-uri "infer" version))
26144 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
26145 (properties `((upstream-name . "infer")))
26146 (build-system r-build-system)
26148 `(("r-dplyr" ,r-dplyr)
26149 ("r-ggplot2" ,r-ggplot2)
26151 ("r-magrittr" ,r-magrittr)
26152 ("r-purrr" ,r-purrr)
26153 ("r-rlang" ,r-rlang)
26154 ("r-tibble" ,r-tibble)))
26156 `(("r-knitr" ,r-knitr)))
26157 (home-page "https://github.com/tidymodels/infer")
26158 (synopsis "Tidy statistical inference")
26160 "The objective of this package is to perform inference using an
26161 expressive statistical grammar that coheres with the Tidy design framework.")
26162 (license license:cc0)))
26164 (define-public r-modeldata
26166 (name "r-modeldata")
26171 (uri (cran-uri "modeldata" version))
26174 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
26175 (properties `((upstream-name . "modeldata")))
26176 (build-system r-build-system)
26177 (home-page "https://modeldata.tidymodels.org")
26178 (synopsis "Data sets useful for modeling packages")
26180 "This package provides data sets used for demonstrating or testing
26181 model-related packages.")
26182 (license license:expat)))
26184 (define-public r-tidymodels
26186 (name "r-tidymodels")
26191 (uri (cran-uri "tidymodels" version))
26194 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26195 (properties `((upstream-name . "tidymodels")))
26196 (build-system r-build-system)
26198 `(("r-broom" ,r-broom)
26200 ("r-dials" ,r-dials)
26201 ("r-dplyr" ,r-dplyr)
26202 ("r-ggplot2" ,r-ggplot2)
26203 ("r-infer" ,r-infer)
26204 ("r-magrittr" ,r-magrittr)
26205 ("r-modeldata" ,r-modeldata)
26206 ("r-parsnip" ,r-parsnip)
26207 ("r-purrr" ,r-purrr)
26208 ("r-recipes" ,r-recipes)
26209 ("r-rlang" ,r-rlang)
26210 ("r-rsample" ,r-rsample)
26211 ("r-rstudioapi" ,r-rstudioapi)
26212 ("r-tibble" ,r-tibble)
26213 ("r-tidyr" ,r-tidyr)
26215 ("r-workflows" ,r-workflows)
26216 ("r-yardstick" ,r-yardstick)))
26218 `(("r-knitr" ,r-knitr)
26219 ("r-rmarkdown" ,r-rmarkdown)
26221 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26222 (home-page "https://github.com/tidymodels/tidymodels")
26223 (synopsis "Tidy collection for modeling and statistical analysis")
26225 "The tidy modeling \"verse\" is a collection of packages for modeling and
26226 statistical analysis that share the underlying design philosophy, grammar, and
26227 data structures of the tidyverse.")
26228 (license license:gpl3)))
26230 (define-public r-lsa
26237 (uri (cran-uri "lsa" version))
26240 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
26241 (properties `((upstream-name . "lsa")))
26242 (build-system r-build-system)
26244 `(("r-snowballc" ,r-snowballc)))
26245 (home-page "https://cran.r-project.org/package=lsa")
26246 (synopsis "Latent semantic analysis")
26248 "The basic idea of latent semantic analysis (LSA) is, that text do have a
26249 higher order (=latent semantic) structure which, however, is obscured by word
26250 usage (e.g. through the use of synonyms or polysemy). By using conceptual
26251 indices that are derived statistically via a truncated singular value
26252 decomposition (a two-mode factor analysis) over a given document-term matrix,
26253 this variability problem can be overcome.")
26254 (license license:gpl2+)))
26256 (define-public r-mlecens
26263 (uri (cran-uri "MLEcens" version))
26266 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26267 (properties `((upstream-name . "MLEcens")))
26268 (build-system r-build-system)
26269 (home-page "http://stat.ethz.ch/~maathuis/")
26270 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26272 "This package contains functions to compute the nonparametric
26273 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26274 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26275 To be more precise, we consider the situation where we observe a set of
26276 rectangles that are known to contain the unobservable realizations of (X,Y).
26277 We compute the MLE based on such a set of rectangles. The methods can also be
26278 used for univariate censored data (see data set @code{cosmesis}), and for
26279 censored data with competing risks (see data set @code{menopause}). The
26280 package also provides functions to visualize the observed data and the MLE.")
26281 (license license:gpl2+)))
26283 (define-public r-metafor
26290 (uri (cran-uri "metafor" version))
26293 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26294 (properties `((upstream-name . "metafor")))
26295 (build-system r-build-system)
26297 `(("r-matrix" ,r-matrix)
26298 ("r-nlme" ,r-nlme)))
26299 (home-page "https://cran.r-project.org/web/packages/metafor/")
26300 (synopsis "Meta-analysis package for R")
26302 "This package provides a comprehensive collection of functions for
26303 conducting meta-analyses in R. The package includes functions to calculate
26304 various effect sizes or outcome measures, fit fixed-, random-, and
26305 mixed-effects models to such data, carry out moderator and meta-regression
26306 analyses, and create various types of meta-analytical plots (e.g., forest,
26307 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26308 and person-time data, the package also provides functions that implement
26309 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26310 a variety of suitable generalized linear (mixed-effects) models (i.e.
26311 mixed-effects logistic and Poisson regression models). Finally, the package
26312 provides functionality for fitting meta-analytic multivariate/multilevel
26313 models that account for non-independent sampling errors and/or true
26314 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26315 endpoints, or other forms of clustering). Network meta-analyses and
26316 meta-analyses accounting for known correlation structures (e.g. due to
26317 phylogenetic relatedness) can also be conducted.")
26318 (license license:gpl2+)))
26320 (define-public r-altmeta
26327 (uri (cran-uri "altmeta" version))
26330 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
26331 (properties `((upstream-name . "altmeta")))
26332 (build-system r-build-system)
26334 `(("r-coda" ,r-coda)
26336 ("r-matrix" ,r-matrix)
26337 ("r-metafor" ,r-metafor)
26338 ("r-rjags" ,r-rjags)))
26339 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26340 (synopsis "Alternative meta-analysis methods")
26342 "This package provides alternative statistical methods for meta-analysis,
26346 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26347 relative risks, and risk differences
26348 @item heterogeneity tests and measures that are robust to outliers;
26349 @item measures, tests, and visualization tools for publication bias or
26350 small-study effects;
26351 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26352 specificities, etc.;
26353 @item meta-analysis methods for synthesizing proportions;
26354 @item models for multivariate meta-analysis.
26357 (license license:gpl2+)))
26359 (define-public r-perm
26362 (version "1.0-0.0")
26366 (uri (cran-uri "perm" version))
26369 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26370 (properties `((upstream-name . "perm")))
26371 (build-system r-build-system)
26372 (home-page "https://cran.r-project.org/web/packages/perm/")
26373 (synopsis "Exact or asymptotic permutation tests")
26375 "This package provides several methods for performing permutation tests.
26376 It has three main functions, to perform linear permutation tests. These tests
26377 are tests where the test statistic is the sum of the product of a
26378 covariate (usually group indicator) and the scores.")
26379 ;; Any version of the GPL
26380 (license license:gpl2+)))
26382 (define-public r-qtl
26389 (uri (cran-uri "qtl" version))
26392 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
26393 (build-system r-build-system)
26394 (home-page "https://rqtl.org/")
26395 (synopsis "R package for analyzing QTL experiments in genetics")
26396 (description "R/qtl is an extension library for the R statistics system.
26397 It is used to analyze experimental crosses for identifying genes contributing
26398 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26400 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26401 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26403 (license license:gpl3)))
26405 (define-public r-qtl2
26411 (uri (cran-uri "qtl2" version))
26413 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26414 (build-system r-build-system)
26416 `(("r-data-table" ,r-data-table)
26417 ("r-jsonlite" ,r-jsonlite)
26419 ("r-rcppeigen" ,r-rcppeigen)
26420 ("r-rsqlite" ,r-rsqlite)
26421 ("r-yaml" ,r-yaml)))
26422 (home-page "https://kbroman.org/qtl2/")
26423 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26425 "This package provides a set of tools to perform @dfn{Quantitative Trait
26426 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26427 @code{R/qtl} package to better handle high-dimensional data and complex cross
26428 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26429 (license license:gpl3)))
26431 (define-public r-seqminer
26433 (name "r-seqminer")
26438 (uri (cran-uri "seqminer" version))
26441 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26442 (build-system r-build-system)
26445 (home-page "http://seqminer.genomic.codes")
26446 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26448 "This package provides tools to integrate nucleotide sequencing
26449 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26450 ;; Any version of the GPL is acceptable
26451 (license (list license:gpl2+ license:gpl3+))))
26453 (define-public r-maldiquant
26455 (name "r-maldiquant")
26460 (uri (cran-uri "MALDIquant" version))
26463 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26464 (properties `((upstream-name . "MALDIquant")))
26465 (build-system r-build-system)
26466 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26467 (synopsis "Quantitative analysis of mass spectrometry data")
26469 "This package provides a complete analysis pipeline for matrix-assisted
26470 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26471 two-dimensional mass spectrometry data. In addition to commonly used plotting
26472 and processing methods it includes distinctive features, namely baseline
26473 subtraction methods such as morphological filters (TopHat) or the
26474 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26475 alignment using warping functions, handling of replicated measurements as well
26476 as allowing spectra with different resolutions.")
26477 (license license:gpl3+)))
26479 (define-public r-scattermore
26481 (name "r-scattermore")
26486 (uri (cran-uri "scattermore" version))
26489 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26490 (properties `((upstream-name . "scattermore")))
26491 (build-system r-build-system)
26493 `(("r-ggplot2" ,r-ggplot2)
26494 ("r-scales" ,r-scales)))
26495 (home-page "https://github.com/exaexa/scattermore")
26496 (synopsis "Scatterplots with more points")
26498 "This package provides C-based tools for converting large scatterplot
26499 data to rasters. It speeds up plotting of data with millions of points.")
26500 (license license:gpl3+)))
26502 (define-public r-seuratobject
26504 (name "r-seuratobject")
26509 (uri (cran-uri "SeuratObject" version))
26512 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26513 (properties `((upstream-name . "SeuratObject")))
26514 (build-system r-build-system)
26516 `(("r-matrix" ,r-matrix)
26518 ("r-rcppeigen" ,r-rcppeigen)
26519 ("r-rlang" ,r-rlang)
26520 ("r-sctransform" ,r-sctransform)))
26521 (home-page "https://satijalab.org/seurat")
26522 (synopsis "Data structures for single cell data")
26524 "This package defines S4 classes for single-cell genomic data and
26525 associated information, such as dimensionality reduction embeddings,
26526 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26527 access methods and R-native hooks to ensure the Seurat object is familiar to
26529 (license license:gpl3)))
26531 (define-public r-seurat
26537 (uri (cran-uri "Seurat" version))
26540 "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p"))))
26541 (properties `((upstream-name . "Seurat")))
26542 (build-system r-build-system)
26544 `(("r-cluster" ,r-cluster)
26545 ("r-cowplot" ,r-cowplot)
26546 ("r-fitdistrplus" ,r-fitdistrplus)
26547 ("r-future" ,r-future)
26548 ("r-future-apply" ,r-future-apply)
26549 ("r-ggplot2" ,r-ggplot2)
26550 ("r-ggrepel" ,r-ggrepel)
26551 ("r-ggridges" ,r-ggridges)
26554 ("r-igraph" ,r-igraph)
26555 ("r-irlba" ,r-irlba)
26556 ("r-jsonlite" ,r-jsonlite)
26557 ("r-kernsmooth" ,r-kernsmooth)
26558 ("r-leiden" ,r-leiden)
26559 ("r-lmtest" ,r-lmtest)
26561 ("r-matrix" ,r-matrix)
26562 ("r-matrixstats" ,r-matrixstats)
26563 ("r-miniui" ,r-miniui)
26564 ("r-patchwork" ,r-patchwork)
26565 ("r-pbapply" ,r-pbapply)
26566 ("r-plotly" ,r-plotly)
26569 ("r-rcolorbrewer" ,r-rcolorbrewer)
26571 ("r-rcppannoy" ,r-rcppannoy)
26572 ("r-rcppeigen" ,r-rcppeigen)
26573 ("r-rcppprogress" ,r-rcppprogress)
26574 ("r-reticulate" ,r-reticulate)
26575 ("r-rlang" ,r-rlang)
26577 ("r-rtsne" ,r-rtsne)
26578 ("r-scales" ,r-scales)
26579 ("r-scattermore" ,r-scattermore)
26580 ("r-sctransform" ,r-sctransform)
26581 ("r-seuratobject" ,r-seuratobject)
26582 ("r-shiny" ,r-shiny)
26583 ("r-spatstat-core" ,r-spatstat-core)
26584 ("r-spatstat-geom" ,r-spatstat-geom)
26585 ("r-tibble" ,r-tibble)
26586 ("r-uwot" ,r-uwot)))
26587 (home-page "http://www.satijalab.org/seurat")
26588 (synopsis "Seurat is an R toolkit for single cell genomics")
26590 "This package is an R package designed for QC, analysis, and
26591 exploration of single cell RNA-seq data. It easily enables widely-used
26592 analytical techniques, including the identification of highly variable genes,
26593 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26594 algorithms; density clustering, hierarchical clustering, k-means, and the
26595 discovery of differentially expressed genes and markers.")
26596 (license license:gpl3)))
26598 (define-public r-phangorn
26600 (name "r-phangorn")
26605 (uri (cran-uri "phangorn" version))
26608 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
26609 (build-system r-build-system)
26612 ("r-fastmatch" ,r-fastmatch)
26613 ("r-igraph" ,r-igraph)
26614 ("r-magrittr" ,r-magrittr)
26615 ("r-matrix" ,r-matrix)
26616 ("r-quadprog" ,r-quadprog)
26617 ("r-rcpp" ,r-rcpp)))
26618 (home-page "https://github.com/KlausVigo/phangorn")
26619 (synopsis "Phylogenetic analysis in R")
26621 "Phangorn is a package for phylogenetic analysis in R. It supports
26622 estimation of phylogenetic trees and networks using Maximum Likelihood,
26623 Maximum Parsimony, distance methods and Hadamard conjugation.")
26624 (license license:gpl2+)))
26626 (define-public r-diversitree
26628 (name "r-diversitree")
26633 (uri (cran-uri "diversitree" version))
26636 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26637 (build-system r-build-system)
26639 `(("gfortran" ,gfortran)))
26640 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26643 ("r-desolve" ,r-desolve)
26645 ("r-subplex" ,r-subplex)))
26646 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26647 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26648 (description "This package contains a number of comparative \"phylogenetic\"
26649 methods, mostly focusing on analysing diversification and character evolution.
26650 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26651 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26652 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26653 include Markov models of discrete and continuous trait evolution and constant
26654 rate speciation and extinction.")
26655 (license license:gpl2+)))
26657 (define-public r-calculus
26659 (name "r-calculus")
26664 (uri (cran-uri "calculus" version))
26667 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26668 (properties `((upstream-name . "calculus")))
26669 (build-system r-build-system)
26671 `(("r-rcpp" ,r-rcpp)))
26673 `(("r-knitr" ,r-knitr)))
26674 (home-page "https://github.com/eguidotti/calculus")
26675 (synopsis "High dimensional numerical and symbolic calculus")
26677 "Efficient C++ optimized functions for numerical and symbolic calculus.
26678 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26679 convention, fast computation of the Levi-Civita symbol and generalized
26680 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26681 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26682 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26683 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26684 parabolic or user defined by custom scale factors.")
26685 (license license:gpl3)))
26687 (define-public r-decon
26694 (uri (cran-uri "decon" version))
26697 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26698 (properties `((upstream-name . "decon")))
26699 (build-system r-build-system)
26701 `(("gfortran" ,gfortran)))
26703 "https://cran.r-project.org/web/packages/decon/")
26704 (synopsis "Deconvolution Estimation in Measurement Error Models")
26706 "This package contains a collection of functions to deal with
26707 nonparametric measurement error problems using deconvolution
26708 kernel methods. We focus two measurement error models in the
26709 package: (1) an additive measurement error model, where the
26710 goal is to estimate the density or distribution function from
26711 contaminated data; (2) nonparametric regression model with
26712 errors-in-variables. The R functions allow the measurement errors
26713 to be either homoscedastic or heteroscedastic. To make the
26714 deconvolution estimators computationally more efficient in R,
26715 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26716 density estimation with error-free data to the deconvolution
26717 kernel estimation. Several methods for the selection of the
26718 data-driven smoothing parameter are also provided in the package.
26719 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26720 estimation in measurement error models: The R package decon.
26721 Journal of Statistical Software, 39(10), 1-24.")
26722 (license license:gpl3+)))
26724 (define-public r-locpol
26731 (uri (cran-uri "locpol" version))
26734 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26735 (properties `((upstream-name . "locpol")))
26736 (build-system r-build-system)
26738 "https://cran.r-project.org/web/packages/locpol/")
26739 (synopsis "Kernel Local Polynomial Regression")
26741 "Computes local polynomial estimators for the regression and
26742 also density. It comprises several different utilities to handle
26743 kernel estimators.")
26744 (license license:gpl2+)))
26746 (define-public r-lpme
26753 (uri (cran-uri "lpme" version))
26756 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26757 (properties `((upstream-name . "lpme")))
26758 (build-system r-build-system)
26760 `(("r-decon" ,r-decon)
26761 ("r-flexmix" ,r-flexmix)
26762 ("r-locpol" ,r-locpol)
26764 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26766 "https://cran.r-project.org/web/packages/lpme/")
26767 (synopsis "Nonparametric Estimation of Measurement Error Models")
26769 "Provide nonparametric methods for mean regression model,
26770 modal regression and conditional density estimation in the
26771 presence/absence of measurement error. Bandwidth selection is
26772 also provided for each method.")
26773 (license license:gpl2+)))
26775 (define-public r-aws-signature
26777 (name "r-aws-signature")
26782 (uri (cran-uri "aws.signature" version))
26785 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26786 (properties `((upstream-name . "aws.signature")))
26787 (build-system r-build-system)
26789 `(("r-base64enc" ,r-base64enc)
26790 ("r-digest" ,r-digest)))
26791 (home-page "https://github.com/cloudyr/aws.signature")
26792 (synopsis "Amazon Web Services Request Signatures")
26794 "This package generates version 2 and 4 request signatures for Amazon Web
26795 Services (AWS) and provides a mechanism for retrieving credentials from
26796 environment variables, AWS credentials files, and EC2 instance metadata. For
26797 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26798 (license license:gpl2+)))
26800 (define-public r-aws-s3
26807 (uri (cran-uri "aws.s3" version))
26810 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26811 (properties `((upstream-name . "aws.s3")))
26812 (build-system r-build-system)
26814 `(("r-aws-signature" ,r-aws-signature)
26815 ("r-base64enc" ,r-base64enc)
26817 ("r-digest" ,r-digest)
26819 ("r-xml2" ,r-xml2)))
26820 (home-page "https://github.com/cloudyr/aws.s3")
26821 (synopsis "AWS S3 Client Package")
26823 "This package provides a simple client package for the Amazon Web
26824 Services (AWS) Simple Storage Service (S3) REST API.")
26825 (license license:gpl2+)))
26827 (define-public r-lgr
26833 (uri (cran-uri "lgr" version))
26836 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26837 (build-system r-build-system)
26841 `(("r-knitr" ,r-knitr)))
26842 (home-page "https://s-fleck.github.io/lgr/")
26843 (synopsis "Fully featured logging framework")
26844 (description "This package offers a flexible, feature-rich yet
26845 light-weight logging framework based on @code{R6} classes. It supports
26846 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26847 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26848 well as email and push notifications.")
26849 (license license:expat)))
26851 (define-public r-mlr3measures
26853 (name "r-mlr3measures")
26857 (uri (cran-uri "mlr3measures" version))
26860 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26861 (build-system r-build-system)
26863 `(("r-checkmate" ,r-checkmate)
26864 ("r-prroc" ,r-prroc)))
26865 (home-page "https://mlr3measures.mlr-org.com/")
26866 (synopsis "Performance measures for mlr3")
26867 (description "This package implements multiple performance measures for
26868 supervised learning. It includes over 40 measures for regression and
26869 classification. Additionally, meta information about the performance measures
26870 can be queried, e.g. what the best and worst possible performances scores
26872 (license license:lgpl3)))
26874 (define-public r-mlr3misc
26876 (name "r-mlr3misc")
26880 (uri (cran-uri "mlr3misc" version))
26883 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26884 (build-system r-build-system)
26886 `(("r-backports" ,r-backports)
26887 ("r-checkmate" ,r-checkmate)
26888 ("r-data-table" ,r-data-table)
26890 (home-page "https://mlr3misc.mlr-org.com/")
26891 (synopsis "Helper functions for mlr3")
26892 (description "@code{mlr3misc} provides frequently used helper functions
26893 and assertions used in @code{mlr3} and its companion packages. It comes with
26894 helper functions for functional programming, for printing, to work with
26895 @code{data.table}, as well as some generally useful @code{R6} classes. This
26896 package also supersedes the package @code{BBmisc}.")
26897 (license license:lgpl3)))
26899 (define-public r-paradox
26905 (uri (cran-uri "paradox" version))
26908 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
26909 (build-system r-build-system)
26911 `(("r-backports" ,r-backports)
26912 ("r-checkmate" ,r-checkmate)
26913 ("r-data-table" ,r-data-table)
26914 ("r-mlr3misc" ,r-mlr3misc)
26916 (home-page "https://paradox.mlr-org.com/")
26917 (synopsis "Define and work with parameter spaces for complex algorithms")
26918 (description "With this package it is possible to define parameter spaces,
26919 constraints and dependencies for arbitrary algorithms, and to program on such
26920 spaces. It also includes statistical designs and random samplers. Objects are
26921 implemented as @code{R6} classes.")
26922 (license license:lgpl3)))
26924 (define-public r-mlr3
26930 (uri (cran-uri "mlr3" version))
26933 "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl"))))
26934 (build-system r-build-system)
26937 ("r-backports" ,r-backports)
26938 ("r-checkmate" ,r-checkmate)
26939 ("r-data-table" ,r-data-table)
26940 ("r-digest" ,r-digest)
26941 ("r-future-apply" ,r-future-apply)
26943 ("r-mlbench" ,r-mlbench)
26944 ("r-mlr3measures" ,r-mlr3measures)
26945 ("r-mlr3misc" ,r-mlr3misc)
26946 ("r-palmerpenguins" ,r-palmerpenguins)
26947 ("r-paradox" ,r-paradox)
26948 ("r-parallelly" ,r-parallelly)
26949 ("r-uuid" ,r-uuid)))
26950 (home-page "https://mlr3.mlr-org.com/")
26951 (synopsis "Machine Learning in R - Next Generation")
26952 (description "@code{mlr3} enables efficient, object-oriented programming
26953 on the building blocks of machine learning. It provides @code{R6} objects for
26954 tasks, learners, resamplings, and measures. The package is geared towards
26955 scalability and larger datasets by supporting parallelization and out-of-memory
26956 data-backends like databases. While @code{mlr3} focuses on the core
26957 computational operations, add-on packages provide additional functionality.")
26958 (license license:lgpl3)))
26960 (define-public r-mlr3learners
26962 (name "r-mlr3learners")
26966 (uri (cran-uri "mlr3learners" version))
26969 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26970 (build-system r-build-system)
26972 `(("r-data-table" ,r-data-table)
26974 ("r-mlr3misc" ,r-mlr3misc)
26975 ("r-paradox" ,r-paradox)
26977 (home-page "https://mlr3learners.mlr-org.com/")
26978 (synopsis "Recommended Learners for @code{mlr3}")
26979 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26980 with interfaces to essential machine learning packages on CRAN. This includes,
26981 but is not limited to: (penalized) linear and logistic regression, linear and
26982 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26983 vector machines, and gradient boosting.")
26984 (license license:lgpl3)))
26986 (define-public r-bbotk
26993 (uri (cran-uri "bbotk" version))
26996 "1f29wxnxr73c4yp5afk05jqggpm7k1z8wiak8xsyw68h7xflq550"))))
26997 (properties `((upstream-name . "bbotk")))
26998 (build-system r-build-system)
27000 `(("r-checkmate" ,r-checkmate)
27001 ("r-data-table" ,r-data-table)
27003 ("r-mlr3misc" ,r-mlr3misc)
27004 ("r-paradox" ,r-paradox)
27007 `(("r-knitr" ,r-knitr)))
27008 (home-page "https://bbotk.mlr-org.com")
27009 (synopsis "Black-Box Optimization Toolkit")
27010 (description "This package provides a common framework for optimization of
27011 black-box functions for other packages, e.g. @code{mlr3}. It offers various
27012 optimization methods e.g. grid search, random search and generalized simulated
27014 (license license:lgpl3)))
27016 (define-public r-mlr3tuning
27018 (name "r-mlr3tuning")
27022 (uri (cran-uri "mlr3tuning" version))
27025 "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv"))))
27026 (build-system r-build-system)
27028 `(("r-bbotk" ,r-bbotk)
27029 ("r-checkmate" ,r-checkmate)
27030 ("r-data-table" ,r-data-table)
27033 ("r-mlr3misc" ,r-mlr3misc)
27034 ("r-paradox" ,r-paradox)
27036 (home-page "https://mlr3tuning.mlr-org.com/")
27037 (synopsis "Tuning for @code{mlr3}")
27038 (description "@code{mlr3tuning} implements methods for hyperparameter
27039 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
27040 termination criteria can be set and combined. The class @code{AutoTuner} provides a
27041 convenient way to perform nested resampling in combination with @code{mlr3}.")
27042 (license license:lgpl3)))
27044 (define-public r-fontliberation
27046 (name "r-fontliberation")
27051 (uri (cran-uri "fontLiberation" version))
27054 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
27056 `((upstream-name . "fontLiberation")))
27057 (build-system r-build-system)
27058 (home-page "https://cran.r-project.org/package=fontLiberation")
27059 (synopsis "Liberation fonts")
27061 "This package provides a placeholder for the Liberation fontset intended
27062 for the fontquiver package. This fontset covers the 12 combinations of
27063 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
27064 supported in R graphics devices.")
27065 (license license:silofl1.1)))
27067 (define-public r-fontbitstreamvera
27069 (name "r-fontbitstreamvera")
27074 (uri (cran-uri "fontBitstreamVera" version))
27077 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
27079 `((upstream-name . "fontBitstreamVera")))
27080 (build-system r-build-system)
27081 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
27082 (synopsis "Fonts for fontquiver")
27084 "This package is a placeholder for the Bitstream Vera font. It is
27085 intended for the fontquiver package.")
27087 (license:fsdg-compatible
27088 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
27089 "The Font Software may be sold as part of a larger software package but
27090 no copy of one or more of the Font Software typefaces may be sold by
27093 (define-public r-fontquiver
27095 (name "r-fontquiver")
27100 (uri (cran-uri "fontquiver" version))
27103 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
27104 (properties `((upstream-name . "fontquiver")))
27105 (build-system r-build-system)
27107 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
27108 ("r-fontliberation" ,r-fontliberation)))
27109 (home-page "https://cran.r-project.org/package=fontquiver")
27110 (synopsis "Set of installed fonts")
27112 "This package provides a set of fonts. This is useful when you want to
27113 avoid system fonts to make sure your outputs are reproducible.")
27114 (license license:gpl3)))
27116 (define-public r-freetypeharfbuzz
27118 (name "r-freetypeharfbuzz")
27123 (uri (cran-uri "freetypeharfbuzz" version))
27126 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
27128 `((upstream-name . "freetypeharfbuzz")))
27129 (build-system r-build-system)
27132 (modify-phases %standard-phases
27133 (add-after 'unpack 'prepare-static-libraries
27134 (lambda* (#:key inputs #:allow-other-keys)
27135 (mkdir-p "src/target/include")
27136 (let ((freetype (assoc-ref inputs "static-freetype"))
27137 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
27138 (substitute* "src/Makevars.in"
27139 (("include @MK_FILE@") "") ; do not build static libs
27140 (("^HB_STATIC_LIB =.*")
27141 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
27142 (("^FT_STATIC_LIB =.*")
27143 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
27144 (copy-recursively (string-append freetype "/include")
27145 "src/target/include")
27146 (copy-recursively (string-append harfbuzz "/include")
27147 "src/target/include")))))))
27149 `(("r-fontquiver" ,r-fontquiver)))
27150 ;; This may defeat the purpose of this package as our versions of freetype
27151 ;; and harfbuzz obviously differ from the tarballs offered by this
27152 ;; project. On the other hand, Guix arguably does a better job at
27153 ;; "ensur[ing] deterministic computation".
27155 `(("static-freetype"
27157 (inherit (static-package freetype))
27159 `(#:configure-flags
27160 (list "--enable-static=yes"
27165 "--without-harfbuzz")))))
27168 (inherit (static-package harfbuzz))
27170 `(#:tests? #false ; fail because shared library is disabled
27172 (list "--enable-static=yes"
27173 "--enable-shared=no"
27175 "--with-freetype=yes"
27178 "--without-fontconfig"
27179 "--without-glib")))))))
27182 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27183 (synopsis "Deterministic computation of text box metrics")
27185 "Unlike other tools that dynamically link to the Cairo stack,
27186 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27187 harfbuzz libraries. This ensures deterministic computation of text box
27188 extents for situations where reproducible results are crucial (for instance
27189 unit tests of graphics).")
27190 (license license:gpl3)))
27192 (define-public r-vdiffr
27199 (uri (cran-uri "vdiffr" version))
27202 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27205 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27206 (properties `((upstream-name . "vdiffr")))
27207 (build-system r-build-system)
27210 (modify-phases %standard-phases
27211 (add-after 'unpack 'process-javascript
27212 (lambda* (#:key inputs #:allow-other-keys)
27213 (with-directory-excursion "inst/htmlwidgets/lib/"
27214 (let ((source (assoc-ref inputs "js-jquery"))
27215 (target "jquery.min.js"))
27216 (format #true "Processing ~a --> ~a~%"
27218 (invoke "esbuild" source "--minify"
27219 (string-append "--outfile=" target)))))))))
27221 `(("freetype" ,freetype)
27222 ("harfbuzz" ,harfbuzz)))
27225 ("r-devtools" ,r-devtools)
27226 ("r-diffobj" ,r-diffobj)
27227 ("r-fontquiver" ,r-fontquiver)
27228 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27229 ("r-gdtools" ,r-gdtools)
27231 ("r-htmltools" ,r-htmltools)
27232 ("r-htmlwidgets" ,r-htmlwidgets)
27233 ("r-purrr" ,r-purrr)
27236 ("r-rlang" ,r-rlang)
27237 ("r-shiny" ,r-shiny)
27238 ("r-testthat" ,r-testthat)
27239 ("r-usethis" ,r-usethis)
27240 ("r-xml2" ,r-xml2)))
27242 `(("esbuild" ,esbuild)
27246 (uri "https://code.jquery.com/jquery-1.12.4.js")
27249 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27250 (home-page "https://github.com/r-lib/vdiffr")
27251 (synopsis "Visual regression testing and graphical diffing")
27253 "This package is an extension to the testthat package that makes it easy
27254 to add graphical unit tests. It provides a Shiny application to manage the
27256 (license license:gpl3)))
27258 (define-public r-highlight
27260 (name "r-highlight")
27265 (uri (cran-uri "highlight" version))
27268 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27269 (properties `((upstream-name . "highlight")))
27270 (build-system r-build-system)
27271 (home-page "https://github.com/hadley/highlight")
27272 (synopsis "Syntax highlighter for R code")
27274 "This package provides a syntax highlighter for R code based on the
27275 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27276 includes a custom Sweave driver performing syntax highlighting of R code
27278 (license license:gpl3+)))
27280 (define-public r-clustree
27282 (name "r-clustree")
27287 (uri (cran-uri "clustree" version))
27290 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27291 (properties `((upstream-name . "clustree")))
27292 (build-system r-build-system)
27294 `(("r-checkmate" ,r-checkmate)
27295 ("r-dplyr" ,r-dplyr)
27296 ("r-ggplot2" ,r-ggplot2)
27297 ("r-ggraph" ,r-ggraph)
27298 ("r-ggrepel" ,r-ggrepel)
27299 ("r-igraph" ,r-igraph)
27300 ("r-rlang" ,r-rlang)
27301 ("r-tidygraph" ,r-tidygraph)
27302 ("r-viridis" ,r-viridis)))
27304 `(("r-knitr" ,r-knitr)))
27305 (home-page "https://github.com/lazappi/clustree")
27306 (synopsis "Visualize clusterings at different resolutions")
27308 "Deciding what resolution to use can be a difficult question when
27309 approaching a clustering analysis. One way to approach this problem is to
27310 look at how samples move as the number of clusters increases. This package
27311 allows you to produce clustering trees, a visualization for interrogating
27312 clusterings as resolution increases.")
27313 (license license:gpl3)))
27315 (define-public r-textshaping
27317 (name "r-textshaping")
27322 (uri (cran-uri "textshaping" version))
27325 "0fqh4z505b2qriqcj70g2hhdgiawd3w2rs9rqxdwizz5vk8jjygx"))))
27326 (properties `((upstream-name . "textshaping")))
27327 (build-system r-build-system)
27329 `(("freetype" ,freetype)
27330 ("fribidi" ,fribidi)
27331 ("harfbuzz" ,harfbuzz)
27334 `(("r-cpp11" ,r-cpp11)
27335 ("r-systemfonts" ,r-systemfonts)))
27337 `(("pkg-config" ,pkg-config)
27338 ("r-knitr" ,r-knitr)))
27339 (home-page "https://github.com/r-lib/textshaping")
27340 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27342 "This package provides access to the text shaping functionality in the
27343 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27344 is a low-level utility package mainly for graphic devices that expands upon
27345 the font tool-set provided by the @code{systemfonts} package.")
27346 (license license:expat)))
27348 (define-public r-ragg
27355 (uri (cran-uri "ragg" version))
27358 "0nh1xxrxgdbq9anzkc6k3n519czp9hqyiizakm3m2gl4l4w0vp0q"))))
27359 (properties `((upstream-name . "ragg")))
27360 (build-system r-build-system)
27362 `(("freetype" ,freetype)
27363 ("libjpeg" ,libjpeg-turbo)
27365 ("libtiff" ,libtiff)
27368 `(("r-systemfonts" ,r-systemfonts)
27369 ("r-textshaping" ,r-textshaping)))
27371 `(("pkg-config" ,pkg-config)))
27372 (home-page "https://ragg.r-lib.org")
27373 (synopsis "Graphic devices based on AGG")
27375 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27376 drawing library. The ragg package provides a set of graphic devices based on
27377 AGG to use as alternative to the raster devices provided through the
27378 @code{grDevices} package.")
27379 (license license:expat)))
27381 (define-public r-downlit
27388 (uri (cran-uri "downlit" version))
27391 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27392 (properties `((upstream-name . "downlit")))
27393 (build-system r-build-system)
27395 `(("r-brio" ,r-brio)
27396 ("r-digest" ,r-digest)
27397 ("r-evaluate" ,r-evaluate)
27398 ("r-fansi" ,r-fansi)
27399 ("r-rlang" ,r-rlang)
27400 ("r-vctrs" ,r-vctrs)
27401 ("r-yaml" ,r-yaml)))
27402 (home-page "https://downlit.r-lib.org/")
27403 (synopsis "Syntax highlighting and automatic linking")
27405 "This package provides syntax highlighting of R code, specifically
27406 designed for the needs of RMarkdown packages like @code{pkgdown},
27407 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27408 to their documentation on the web, and automatic translation of ANSI escapes
27409 in output to the equivalent HTML.")
27410 (license license:expat)))
27412 (define-public r-pkgdown
27419 (uri (cran-uri "pkgdown" version))
27422 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27423 (properties `((upstream-name . "pkgdown")))
27424 (build-system r-build-system)
27425 (inputs `(("pandoc" ,pandoc)))
27427 `(("r-callr" ,r-callr)
27428 ("r-crayon" ,r-crayon)
27430 ("r-digest" ,r-digest)
27431 ("r-downlit" ,r-downlit)
27434 ("r-magrittr" ,r-magrittr)
27435 ("r-memoise" ,r-memoise)
27436 ("r-openssl" ,r-openssl)
27437 ("r-purrr" ,r-purrr)
27439 ("r-rematch2" ,r-rematch2)
27440 ("r-rlang" ,r-rlang)
27441 ("r-rmarkdown" ,r-rmarkdown)
27442 ("r-tibble" ,r-tibble)
27443 ("r-whisker" ,r-whisker)
27444 ("r-withr" ,r-withr)
27446 ("r-yaml" ,r-yaml)))
27448 `(("r-knitr" ,r-knitr)))
27449 (home-page "https://pkgdown.r-lib.org")
27450 (synopsis "Make static HTML documentation for an R package")
27452 "The goal of this package is to generate an attractive and useful website
27453 from a source package. @code{pkgdown} converts your documentation, vignettes,
27454 README file, and more to HTML making it easy to share information about your
27456 (license license:expat)))
27458 (define-public r-prereg
27465 (uri (cran-uri "prereg" version))
27468 "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi"))))
27469 (properties `((upstream-name . "prereg")))
27470 (build-system r-build-system)
27472 `(("r-rmarkdown" ,r-rmarkdown)))
27473 (home-page "https://github.com/crsh/prereg")
27475 "R Markdown Templates to preregister Scientific Studies")
27477 "This package provides a collection of templates to author
27478 preregistration documents for scientific studies in PDF format.")
27479 (license license:gpl3)))
27481 (define-public r-ez
27488 (uri (cran-uri "ez" version))
27491 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
27492 (properties `((upstream-name . "ez")))
27493 (build-system r-build-system)
27496 ("r-ggplot2" ,r-ggplot2)
27499 ("r-matrix" ,r-matrix)
27502 ("r-reshape2" ,r-reshape2)
27503 ("r-scales" ,r-scales)
27504 ("r-stringr" ,r-stringr)))
27505 (home-page "https://github.com/mike-lawrence/ez")
27506 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
27508 "Facilitates easy analysis of factorial experiments, including purely
27509 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
27510 and mixed within-and-between-Ss designs. The functions in this package aim to
27511 provide simple, intuitive and consistent specification of data analysis and
27512 visualization. Visualization functions also include design visualization for
27513 pre-analysis data auditing, and correlation matrix visualization. Finally,
27514 this package includes functions for non-parametric analysis, including
27515 permutation tests and bootstrap resampling. The bootstrap function obtains
27516 predictions either by cell means or by more advanced/powerful mixed effects
27517 models, yielding predictions and confidence intervals that may be easily
27518 visualized at any level of the experiment's design.")
27519 (license license:gpl2+)))
27521 (define-public r-qdapregex
27523 (name "r-qdapregex")
27528 (uri (cran-uri "qdapRegex" version))
27531 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
27532 (properties `((upstream-name . "qdapRegex")))
27533 (build-system r-build-system)
27534 (propagated-inputs `(("r-stringi" ,r-stringi)))
27536 "https://trinker.github.com/qdapRegex/")
27538 "Regular Expression Removal, Extraction, and Replacement Tools")
27540 "This package provides a collection of regular expression tools
27541 associated with the @code{qdap} package that may be useful outside of the
27542 context of discourse analysis. Tools include removal/extraction/replacement of
27543 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
27544 percentages, citations, person tags, phone numbers, times, and zip codes.")
27545 (license license:gpl2)))
27547 (define-public r-mgsub
27554 (uri (cran-uri "mgsub" version))
27557 "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr"))))
27558 (properties `((upstream-name . "mgsub")))
27559 (build-system r-build-system)
27560 (native-inputs `(("r-knitr" ,r-knitr)))
27562 "https://cran.r-project.org/package=mgsub")
27564 "Safe, Multiple, Simultaneous String Substitution")
27566 "Designed to enable simultaneous substitution in strings in a safe
27567 fashion. Safe means it does not rely on placeholders (which can cause errors
27568 in same length matches).")
27569 (license license:expat)))
27571 (define-public r-textshape
27573 (name "r-textshape")
27578 (uri (cran-uri "textshape" version))
27581 "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
27582 (properties `((upstream-name . "textshape")))
27583 (build-system r-build-system)
27585 `(("r-data-table" ,r-data-table)
27587 ("r-stringi" ,r-stringi)))
27588 (home-page "https://github.com/trinker/textshape")
27589 (synopsis "Tools for Reshaping Text")
27591 "Tools that can be used to reshape and restructure text data.")
27592 (license license:gpl2)))
27594 (define-public r-syuzhet
27601 (uri (cran-uri "syuzhet" version))
27604 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
27605 (properties `((upstream-name . "syuzhet")))
27606 (build-system r-build-system)
27608 `(("r-dplyr" ,r-dplyr)
27611 ("r-rlang" ,r-rlang)
27612 ("r-textshape" ,r-textshape)
27613 ("r-tidyr" ,r-tidyr)
27615 (native-inputs `(("r-knitr" ,r-knitr)))
27616 (home-page "https://github.com/mjockers/syuzhet")
27618 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
27620 "Extracts sentiment and sentiment-derived plot arcs from text using a
27621 variety of sentiment dictionaries conveniently packaged for consumption by R
27622 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
27623 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
27624 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
27625 M. and Turney, Peter D. Applicable references are available in
27626 @file{README.md} and in the documentation for the @code{get_sentiment}
27627 function. The package also provides a hack for implementing Stanford's coreNLP
27628 sentiment parser. The package provides several methods for plot arc
27630 (license license:gpl3)))
27632 (define-public r-lexicon
27639 (uri (cran-uri "lexicon" version))
27642 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
27643 (properties `((upstream-name . "lexicon")))
27644 (build-system r-build-system)
27646 `(("r-data-table" ,r-data-table)
27647 ("r-syuzhet" ,r-syuzhet)))
27648 (home-page "https://github.com/trinker/lexicon")
27649 (synopsis "Lexicons for Text Analysis")
27651 "This package provides a collection of lexical hash tables, dictionaries,
27653 (license license:gpl3)))
27655 (define-public r-english
27662 (uri (cran-uri "english" version))
27665 "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1"))))
27666 (properties `((upstream-name . "english")))
27667 (build-system r-build-system)
27668 (native-inputs `(("r-knitr" ,r-knitr)))
27670 "https://cran.r-project.org/package=english")
27671 (synopsis "Translate Integers into English")
27673 "Allow numbers to be presented in an English language version, one, two,
27674 three, ... Ordinals are also available, first, second, third, ... and
27675 indefinite article choice, \"a\" or \"an\".")
27676 (license license:gpl2)))
27678 (define-public r-textclean
27680 (name "r-textclean")
27685 (uri (cran-uri "textclean" version))
27688 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
27689 (properties `((upstream-name . "textclean")))
27690 (build-system r-build-system)
27692 `(("r-data-table" ,r-data-table)
27693 ("r-english" ,r-english)
27695 ("r-lexicon" ,r-lexicon)
27696 ("r-mgsub" ,r-mgsub)
27697 ("r-qdapregex" ,r-qdapregex)
27698 ("r-stringi" ,r-stringi)
27699 ("r-textshape" ,r-textshape)))
27701 "https://github.com/trinker/textclean")
27702 (synopsis "Text Cleaning Tools")
27704 "Tools to clean and process text. Tools are geared at checking for
27705 substrings that are not optimal for analysis and replacing or removing them
27706 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
27707 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
27708 extracting them into new variables. For example, emoticons are often used in
27709 text but not always easily handled by analysis algorithms. The
27710 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
27711 (license license:gpl2)))
27713 (define-public r-striprtf
27715 (name "r-striprtf")
27720 (uri (cran-uri "striprtf" version))
27723 "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd"))))
27724 (properties `((upstream-name . "striprtf")))
27725 (build-system r-build-system)
27727 `(("r-magrittr" ,r-magrittr)
27729 ("r-stringr" ,r-stringr)))
27730 (home-page "https://github.com/kota7/striprtf")
27731 (synopsis "Extract Text from RTF File")
27733 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
27734 (license license:expat)))
27736 (define-public r-ndjson
27743 (uri (cran-uri "ndjson" version))
27746 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
27747 (modules '((guix build utils)))
27750 ;; unvendor gzstream
27751 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
27753 (properties `((upstream-name . "ndjson")))
27754 (build-system r-build-system)
27757 (modify-phases %standard-phases
27758 (add-after 'unpack 'use-system-gzstream
27759 (lambda* (#:key inputs #:allow-other-keys)
27760 (substitute* "src/Makevars"
27761 (("PKG_LIBS = " all)
27762 (string-append all "-lgzstream ")))
27764 (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream)))
27766 `(("r-data-table" ,r-data-table)
27768 ("r-tibble" ,r-tibble)))
27769 (home-page "https://gitlab.com/hrbrmstr/ndjson")
27771 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
27773 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
27774 modern ndjson files contain large numbers of records. These constructs may not
27775 be columnar in nature, but it is often useful to read in these files and
27776 \"flatten\" the structure out to enable working with the data in an R
27777 @code{data.frame}-like context. Functions are provided that make it possible
27778 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
27779 validate the format of the records or create \"flat\" @code{data.table}
27780 structures from them.")
27781 (license license:expat)))
27783 (define-public r-streamr
27790 (uri (cran-uri "streamR" version))
27793 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
27794 (properties `((upstream-name . "streamR")))
27795 (build-system r-build-system)
27797 `(("r-ndjson" ,r-ndjson)
27798 ("r-rcurl" ,r-rcurl)
27799 ("r-rjson" ,r-rjson)))
27801 "https://cran.r-project.org/package=streamR")
27803 "Access to Twitter Streaming API via R")
27805 "This package provides functions to access Twitter's filter, sample, and
27806 user streams, and to parse the output into data frames.")
27807 (license license:gpl2)))
27809 (define-public r-readods
27816 (uri (cran-uri "readODS" version))
27819 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
27820 (properties `((upstream-name . "readODS")))
27821 (build-system r-build-system)
27823 `(("r-cellranger" ,r-cellranger)
27824 ("r-readr" ,r-readr)
27825 ("r-stringi" ,r-stringi)
27826 ("r-xml2" ,r-xml2)))
27827 (native-inputs `(("r-knitr" ,r-knitr)))
27829 "https://cran.r-project.org/package=readODS")
27830 (synopsis "Read and Write ODS Files")
27832 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
27833 Also support writing data frame into ODS file.")
27834 (license license:gpl3)))
27836 (define-public r-qpdf
27843 (uri (cran-uri "qpdf" version))
27846 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
27847 (modules '((guix build utils)))
27850 ;; unvendor libqpdf
27851 (delete-file-recursively "src/libqpdf")
27852 (delete-file-recursively "src/include/qpdf")
27854 (properties `((upstream-name . "qpdf")))
27855 (build-system r-build-system)
27858 (modify-phases %standard-phases
27859 (add-after 'unpack 'configure
27861 (setenv "EXTERNAL_QPDF" "1")
27867 `(("r-askpass" ,r-askpass)
27869 ("r-rcpp" ,r-rcpp)))
27870 (native-inputs `(("pkg-config" ,pkg-config)))
27871 (home-page "https://github.com/ropensci/qpdf")
27873 "Split, Combine and Compress PDF Files")
27875 "Content-preserving transformations transformations of PDF files such as
27876 split, combine, and compress. This package interfaces directly to the
27877 @code{qpdf} C++ API and does not require any command line utilities. Note that
27878 @code{qpdf} does not read actual content from PDF files: to extract text and
27879 data you need the @code{pdftools} package.")
27880 (license license:asl2.0)))
27882 (define-public r-pdftools
27884 (name "r-pdftools")
27889 (uri (cran-uri "pdftools" version))
27892 "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx"))))
27893 (properties `((upstream-name . "pdftools")))
27894 (build-system r-build-system)
27897 ("poppler" ,poppler)))
27899 `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp)))
27900 (native-inputs `(("pkg-config" ,pkg-config)))
27902 "https://docs.ropensci.org/pdftools/")
27904 "Text Extraction, Rendering and Converting of PDF Documents")
27906 "Utilities based on @code{libpoppler} for extracting text, fonts,
27907 attachments and metadata from a PDF file. Also supports high quality rendering
27908 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
27909 further processing in R.")
27910 (license license:expat)))
27912 (define-public r-antiword
27914 (name "r-antiword")
27919 (uri (cran-uri "antiword" version))
27922 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
27923 (modules '((guix build utils)))
27926 ;; unvendor libantiword
27927 (delete-file-recursively "src")
27929 (properties `((upstream-name . "antiword")))
27930 (build-system r-build-system)
27933 (modify-phases %standard-phases
27934 (add-after 'unpack 'use-system-antiword
27935 (lambda* (#:key inputs #:allow-other-keys)
27936 (substitute* "R/antiword.R"
27937 (("system.file\\(\"bin\", package = \"antiword\"\\)")
27938 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
27940 (inputs `(("antiword" ,antiword)))
27941 (propagated-inputs `(("r-sys" ,r-sys)))
27943 "https://github.com/ropensci/antiword#readme")
27945 "Extract Text from Microsoft Word Documents")
27947 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
27948 documents. The utility only supports the old @code{doc} format, not the new
27949 xml based @code{docx} format. Use the @code{xml2} package to read the
27951 (license license:gpl2)))
27953 (define-public r-readtext
27955 (name "r-readtext")
27960 (uri (cran-uri "readtext" version))
27963 "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y"))))
27964 (properties `((upstream-name . "readtext")))
27965 (build-system r-build-system)
27967 `(("r-antiword" ,r-antiword)
27968 ("r-data-table" ,r-data-table)
27969 ("r-digest" ,r-digest)
27971 ("r-jsonlite" ,r-jsonlite)
27972 ("r-pdftools" ,r-pdftools)
27973 ("r-readods" ,r-readods)
27974 ("r-readxl" ,r-readxl)
27975 ("r-streamr" ,r-streamr)
27976 ("r-stringi" ,r-stringi)
27977 ("r-striprtf" ,r-striprtf)
27978 ("r-tibble" ,r-tibble)
27979 ("r-xml2" ,r-xml2)))
27980 (native-inputs `(("r-knitr" ,r-knitr)))
27982 "https://github.com/quanteda/readtext")
27984 "Import and Handling for Plain and Formatted Text Files")
27986 "This package provides functions for importing and handling text files
27987 and formatted text files with additional meta-data, such including @code{.csv},
27988 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
27989 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
27990 (license license:gpl3)))
27992 (define-public r-packcircles
27994 (name "r-packcircles")
27999 (uri (cran-uri "packcircles" version))
28002 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
28003 (properties `((upstream-name . "packcircles")))
28004 (build-system r-build-system)
28005 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28006 (native-inputs `(("r-knitr" ,r-knitr)))
28008 "https://github.com/mbedward/packcircles")
28009 (synopsis "Circle Packing")
28011 "Algorithms to find arrangements of non-overlapping circles.")
28012 (license license:expat)))
28014 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
28016 (define-public r-lwgeom
28023 (uri (cran-uri "lwgeom" version))
28026 "0byhjqa2acns8mznl1ngnfygxxxyszvnq66qfg0smhhhdkwr67aa"))))
28027 (properties `((upstream-name . "lwgeom")))
28028 (build-system r-build-system)
28029 (inputs `(("geos" ,geos) ("proj" ,proj) ("sqlite" ,sqlite)))
28031 `(("r-rcpp" ,r-rcpp)
28033 ("r-units" ,r-units)))
28034 (native-inputs `(("pkg-config" ,pkg-config)))
28036 "https://github.com/r-spatial/lwgeom/")
28038 "Bindings to Selected 'liblwgeom' Functions for Simple Features")
28040 "Access to selected functions found in
28041 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
28042 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
28043 (license license:gpl2)))
28045 (define-public r-stars
28052 (uri (cran-uri "stars" version))
28055 "0ybk899rc0rpf2cv5kwk78fvis5xnr255hfcy5khdxsxdqgl0m9j"))))
28056 (properties `((upstream-name . "stars")))
28057 (build-system r-build-system)
28059 `(("r-abind" ,r-abind)
28060 ("r-classint" ,r-classint)
28061 ("r-lwgeom" ,r-lwgeom)
28062 ("r-rlang" ,r-rlang)
28064 ("r-units" ,r-units)))
28065 (native-inputs `(("r-knitr" ,r-knitr)))
28066 (home-page "https://r-spatial.github.io/stars/")
28068 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
28070 "Reading, manipulating, writing and plotting spatiotemporal arrays
28071 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
28072 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
28073 (license license:asl2.0)))
28075 (define-public r-tmaptools
28077 (name "r-tmaptools")
28082 (uri (cran-uri "tmaptools" version))
28085 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
28086 (properties `((upstream-name . "tmaptools")))
28087 (build-system r-build-system)
28089 `(("r-dichromat" ,r-dichromat)
28090 ("r-lwgeom" ,r-lwgeom)
28091 ("r-magrittr" ,r-magrittr)
28092 ("r-rcolorbrewer" ,r-rcolorbrewer)
28094 ("r-stars" ,r-stars)
28095 ("r-units" ,r-units)
28096 ("r-viridislite" ,r-viridislite)
28099 "https://github.com/mtennekes/tmaptools")
28100 (synopsis "Thematic Map Tools")
28102 "Set of tools for reading and processing spatial data. The aim is to
28103 supply the workflow to create thematic maps. This package also facilitates
28104 @code{tmap}, the package for visualizing thematic maps.")
28105 (license license:gpl3)))
28107 (define-public r-rworldmap
28109 (name "r-rworldmap")
28114 (uri (cran-uri "rworldmap" version))
28117 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
28118 (properties `((upstream-name . "rworldmap")))
28119 (build-system r-build-system)
28121 `(("r-fields" ,r-fields)
28122 ("r-maptools" ,r-maptools)
28125 "https://github.com/AndySouth/rworldmap/")
28126 (synopsis "Mapping Global Data")
28128 "Enables mapping of country level and gridded user datasets.")
28129 (license license:gpl2+)))
28131 (define-public r-rtweet
28138 (uri (cran-uri "rtweet" version))
28141 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
28142 (properties `((upstream-name . "rtweet")))
28143 (build-system r-build-system)
28145 `(("r-httpuv" ,r-httpuv)
28147 ("r-jsonlite" ,r-jsonlite)
28148 ("r-magrittr" ,r-magrittr)
28149 ("r-progress" ,r-progress)
28151 ("r-tibble" ,r-tibble)))
28152 (native-inputs `(("r-knitr" ,r-knitr)))
28154 "https://docs.ropensci.org/rtweet/")
28155 (synopsis "Collecting Twitter Data")
28157 "An implementation of calls designed to collect and organize Twitter data
28158 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
28159 Application Program Interfaces (API)}.")
28160 (license license:expat)))
28162 (define-public r-intervals
28164 (name "r-intervals")
28169 (uri (cran-uri "intervals" version))
28172 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
28173 (properties `((upstream-name . "intervals")))
28174 (build-system r-build-system)
28175 (home-page "https://github.com/edzer/intervals")
28177 "Tools for Working with Points and Intervals")
28179 "Tools for working with and comparing sets of points and intervals.")
28180 (license license:artistic2.0)))
28182 (define-public r-eyelinker
28184 (name "r-eyelinker")
28189 (uri (cran-uri "eyelinker" version))
28192 "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2"))))
28193 (properties `((upstream-name . "eyelinker")))
28194 (build-system r-build-system)
28196 `(("r-intervals" ,r-intervals)
28197 ("r-readr" ,r-readr)
28198 ("r-stringi" ,r-stringi)
28199 ("r-stringr" ,r-stringr)
28200 ("r-tibble" ,r-tibble)))
28201 (native-inputs `(("r-knitr" ,r-knitr)))
28203 "https://github.com/a-hurst/eyelinker")
28205 "Import ASC Files from EyeLink Eye Trackers")
28207 "Imports plain-text ASC data files from EyeLink eye trackers into
28208 (relatively) tidy data frames for analysis and visualization.")
28209 (license license:gpl3)))
28211 (define-public r-btm
28218 (uri (cran-uri "BTM" version))
28221 "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb"))))
28222 (properties `((upstream-name . "BTM")))
28223 (build-system r-build-system)
28224 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28225 (home-page "https://github.com/bnosac/BTM")
28226 (synopsis "Biterm Topic Models for Short Text")
28228 "Biterm Topic Models find topics in collections of short texts. It is a
28229 word co-occurrence based topic model that learns topics by modeling word-word
28230 co-occurrences patterns which are called biterms. This in contrast to
28231 traditional topic models like Latent Dirichlet Allocation and Probabilistic
28232 Latent Semantic Analysis which are word-document co-occurrence topic models. A
28233 biterm consists of two words co-occurring in the same short text window. This
28234 context window can for example be a twitter message, a short answer on a
28235 survey, a sentence of a text or a document identifier. The techniques are
28236 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
28237 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
28238 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
28240 (license license:asl2.0)))
28242 (define-public r-textplot
28244 (name "r-textplot")
28249 (uri (cran-uri "textplot" version))
28252 "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy"))))
28253 (properties `((upstream-name . "textplot")))
28254 (build-system r-build-system)
28256 `(("r-data-table" ,r-data-table)
28257 ("r-lattice" ,r-lattice)
28258 ("r-matrix" ,r-matrix)))
28259 (native-inputs `(("r-knitr" ,r-knitr)))
28260 (home-page "https://github.com/bnosac/textplot")
28261 (synopsis "Text Plots")
28263 "Visualise complex relations in texts. This is done by providing
28264 functionalities for displaying text co-occurrence networks, text correlation
28265 networks, dependency relationships as well as text clustering. Feel free to
28266 join the effort of providing interesting text visualisations.")
28267 (license license:gpl2)))
28269 (define-public r-gsa
28276 (uri (cran-uri "GSA" version))
28279 "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
28280 (properties `((upstream-name . "GSA")))
28281 (build-system r-build-system)
28282 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
28283 (synopsis "Gene set analysis")
28284 (description "This package lets you determine the significance of
28285 pre-defined sets of genes with respect to an outcome variable, such as a group
28286 indicator, a quantitative variable or a survival time.")
28287 ;; Any version of the LGPL
28288 (license license:lgpl3+)))
28290 (define-public r-samr
28297 (uri (cran-uri "samr" version))
28300 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
28301 (properties `((upstream-name . "samr")))
28302 (build-system r-build-system)
28305 ("r-impute" ,r-impute)
28306 ("r-matrixstats" ,r-matrixstats)
28307 ("r-openxlsx" ,r-openxlsx)
28308 ("r-shiny" ,r-shiny)
28309 ("r-shinyfiles" ,r-shinyfiles)))
28310 (native-inputs `(("gfortran" ,gfortran)))
28311 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
28312 (synopsis "Significance analysis of Microarrays")
28314 "This is a package for significance analysis of Microarrays for
28315 differential expression analysis, RNAseq data and related problems.")
28316 ;; Any version of the LGPL
28317 (license license:lgpl3+)))