1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
35 ;;; This file is part of GNU Guix.
37 ;;; GNU Guix is free software; you can redistribute it and/or modify it
38 ;;; under the terms of the GNU General Public License as published by
39 ;;; the Free Software Foundation; either version 3 of the License, or (at
40 ;;; your option) any later version.
42 ;;; GNU Guix is distributed in the hope that it will be useful, but
43 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
44 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
45 ;;; GNU General Public License for more details.
47 ;;; You should have received a copy of the GNU General Public License
48 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
50 (define-module (gnu packages cran)
51 #:use-module ((guix licenses) #:prefix license:)
52 #:use-module (guix packages)
53 #:use-module (guix download)
54 #:use-module (guix git-download)
55 #:use-module (guix utils)
56 #:use-module (guix build-system r)
57 #:use-module (gnu packages)
58 #:use-module (gnu packages algebra)
59 #:use-module (gnu packages autotools)
60 #:use-module (gnu packages base)
61 #:use-module (gnu packages bioinformatics)
62 #:use-module (gnu packages c)
63 #:use-module (gnu packages compression)
64 #:use-module (gnu packages curl)
65 #:use-module (gnu packages databases)
66 #:use-module (gnu packages fontutils)
67 #:use-module (gnu packages gcc)
68 #:use-module (gnu packages geo)
69 #:use-module (gnu packages ghostscript)
70 #:use-module (gnu packages gl)
71 #:use-module (gnu packages gnome)
72 #:use-module (gnu packages graph)
73 #:use-module (gnu packages gtk)
74 #:use-module (gnu packages haskell-xyz)
75 #:use-module (gnu packages icu4c)
76 #:use-module (gnu packages image)
77 #:use-module (gnu packages imagemagick)
78 #:use-module (gnu packages java)
79 #:use-module (gnu packages javascript)
80 #:use-module (gnu packages libevent)
81 #:use-module (gnu packages lisp-xyz)
82 #:use-module (gnu packages machine-learning)
83 #:use-module (gnu packages maths)
84 #:use-module (gnu packages mpi)
85 #:use-module (gnu packages multiprecision)
86 #:use-module (gnu packages networking)
87 #:use-module (gnu packages node)
88 #:use-module (gnu packages pcre)
89 #:use-module (gnu packages perl)
90 #:use-module (gnu packages pkg-config)
91 #:use-module (gnu packages pulseaudio) ;libsndfile
92 #:use-module (gnu packages python)
93 #:use-module (gnu packages python-xyz)
94 #:use-module (gnu packages sqlite)
95 #:use-module (gnu packages statistics)
96 #:use-module (gnu packages tcl)
97 #:use-module (gnu packages tls)
98 #:use-module (gnu packages web)
99 #:use-module (gnu packages xml)
100 #:use-module (gnu packages xorg))
102 (define-public r-rticles
109 (uri (cran-uri "rticles" version))
112 "1ca3k5sdy9mnm6frcimqwf5k18j14wn69x5iagjnjwhq711l8dv0"))))
113 (properties `((upstream-name . "rticles")))
114 (build-system r-build-system)
116 `(("r-knitr" ,r-knitr)
117 ("r-rmarkdown" ,r-rmarkdown)
118 ("r-tinytex" ,r-tinytex)
121 (home-page "https://github.com/rstudio/rticles")
122 (synopsis "Article formats for R Markdown")
124 "This package provides a suite of custom R Markdown formats and templates
125 for authoring journal articles and conference submissions.")
126 (license license:gpl3)))
128 (define-public r-bezier
134 (uri (cran-uri "bezier" version))
137 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
138 (build-system r-build-system)
139 (home-page "https://cran.r-project.org/web/packages/bezier/")
140 (synopsis "Bezier curve and spline toolkit")
142 "This package is a toolkit for working with Bezier curves and splines.
143 The package provides functions for point generation, arc length estimation,
144 degree elevation and curve fitting.")
145 (license license:gpl2+)))
154 (uri (cran-uri "V8" version))
157 "1d2j9p1fsz9hp8n8lrywyrkwivhfa3qx5ha5f24vin8b6l04xy67"))))
158 (properties `((upstream-name . "V8")))
159 (build-system r-build-system)
162 (modify-phases %standard-phases
163 (add-after 'unpack 'find-v8
164 (lambda* (#:key inputs #:allow-other-keys)
165 (substitute* "configure"
167 (string-append "PKG_LIBS="
168 (assoc-ref inputs "node")
169 "/lib/libnode.so.64\n")))
170 (setenv "INCLUDE_DIR"
172 (assoc-ref inputs "node")
176 (assoc-ref inputs "node") "/lib"))
179 `(("node" ,libnode)))
182 ("r-jsonlite" ,r-jsonlite)
185 `(("r-knitr" ,r-knitr)))
186 (home-page "https://jeroen.cran.dev/V8")
187 (synopsis "Embedded JavaScript and WebAssembly engine for R")
189 "This package provides an R interface to V8: Google's JavaScript and
190 WebAssembly engine.")
191 (license license:expat)))
200 (uri (cran-uri "DOT" version))
203 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
204 (properties `((upstream-name . "DOT")))
205 (build-system r-build-system)
208 (home-page "http://haghish.com/dot")
209 (synopsis "Render and Export DOT Graphs in R")
211 "This package provides tools to render DOT diagram markup language in R
212 and also provides the possibility to export the graphs in PostScript and
213 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
214 programming packages such as @code{knitr} and @code{rmarkdown}.")
215 (license license:expat)))
217 (define-public r-clipr
224 (uri (cran-uri "clipr" version))
227 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
228 (build-system r-build-system)
230 `(("r-knitr" ,r-knitr)))
231 (home-page "https://github.com/mdlincoln/clipr")
232 (synopsis "Read and write from the system clipboard")
234 "This package provides simple utility functions to read from and write to
235 the system clipboards.")
236 (license license:gpl3)))
244 (uri (cran-uri "zoo" version))
247 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
248 (build-system r-build-system)
250 `(("r-lattice" ,r-lattice)))
251 (home-page "http://zoo.R-Forge.R-project.org/")
252 (synopsis "S3 infrastructure for regular and irregular time series")
253 (description "This package contains an S3 class with methods for totally
254 ordered indexed observations. It is particularly aimed at irregular time
255 series of numeric vectors/matrices and factors.")
256 (license license:gpl2+)))
258 (define-public r-ggpmisc
264 (uri (cran-uri "ggpmisc" version))
267 "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
268 (build-system r-build-system)
270 `(("r-broom" ,r-broom)
273 ("r-ggplot2" ,r-ggplot2)
274 ("r-gridextra" ,r-gridextra)
275 ("r-lubridate" ,r-lubridate)
276 ("r-magrittr" ,r-magrittr)
279 ("r-polynom" ,r-polynom)
281 ("r-scales" ,r-scales)
282 ("r-splus2r" ,r-splus2r)
283 ("r-stringr" ,r-stringr)
284 ("r-tibble" ,r-tibble)
288 `(("r-knitr" ,r-knitr)))
289 (home-page "https://www.r4photobiology.info/")
290 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
291 (description "This package provides extensions to @code{ggplot2},
292 respecting the grammar of its graphics paradigm.")
293 (license license:gpl2+)))
295 (define-public r-gprofiler
302 (uri (cran-uri "gProfileR" version))
305 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
306 (properties `((upstream-name . "gProfileR")))
307 (build-system r-build-system)
310 ("r-rcurl" ,r-rcurl)))
311 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
312 (synopsis "Interface to the g:Profiler toolkit")
314 "This package provides tools for functional enrichment analysis,
315 gene identifier conversion and mapping homologous genes across related
316 organisms via the @code{g:Profiler} toolkit.")
317 (license license:gpl2+)))
319 (define-public r-gprofiler2
321 (name "r-gprofiler2")
326 (uri (cran-uri "gprofiler2" version))
329 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
330 (properties `((upstream-name . "gprofiler2")))
331 (build-system r-build-system)
333 `(("r-crosstalk" ,r-crosstalk)
335 ("r-ggplot2" ,r-ggplot2)
336 ("r-gridextra" ,r-gridextra)
337 ("r-jsonlite" ,r-jsonlite)
338 ("r-plotly" ,r-plotly)
341 ("r-viridislite" ,r-viridislite)))
342 (native-inputs `(("r-knitr" ,r-knitr)))
343 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
344 (synopsis "Interface to the g:Profiler toolset")
346 "This package provides a toolset for functional enrichment analysis and
347 visualization, gene/protein/SNP identifier conversion and mapping orthologous
348 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
352 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
354 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
356 @item @code{g:Orth}, orthology search across species;
357 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
358 genes and variant effects.
361 This package is an R interface corresponding to the 2019 update of
362 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
364 (license license:gpl2+)))
366 (define-public r-oenb
373 (uri (cran-uri "oenb" version))
376 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
377 (properties `((upstream-name . "oenb")))
378 (build-system r-build-system)
380 `(("r-dplyr" ,r-dplyr)
382 (native-inputs `(("r-knitr" ,r-knitr)))
383 (home-page "https://github.com/franzmohr/oenb")
384 (synopsis "Tools for the OeNB Data Web Service")
386 "Tools to access data from the data web service of the
387 @acronym{OeNB, Oesterreichische Nationalbank},
388 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
389 (license license:gpl2+)))
391 (define-public r-scales
398 (uri (cran-uri "scales" version))
400 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
401 (build-system r-build-system)
403 `(("r-farver" ,r-farver)
404 ("r-labeling" ,r-labeling)
405 ("r-lifecycle" ,r-lifecycle)
406 ("r-munsell" ,r-munsell)
407 ("r-rcolorbrewer" ,r-rcolorbrewer)
409 ("r-viridislite" ,r-viridislite)))
410 (home-page "https://github.com/hadley/scales")
411 (synopsis "Scale functions for visualization")
413 "This package provides graphical scales that map data to aesthetics, and
414 provides methods for automatically determining breaks and labels for axes and
416 (license license:expat)))
418 (define-public r-pheatmap
425 (uri (cran-uri "pheatmap" version))
428 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
429 (build-system r-build-system)
431 `(("r-gtable" ,r-gtable)
432 ("r-rcolorbrewer" ,r-rcolorbrewer)
433 ("r-scales" ,r-scales)))
434 (home-page "https://cran.r-project.org/web/packages/pheatmap")
435 (synopsis "Pretty heatmaps")
437 "This package provides an implementation of heatmaps that offers more
438 control over dimensions and appearance.")
439 (license license:gpl2+)))
447 (uri (cran-uri "ecp" version))
450 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
451 (build-system r-build-system)
453 `(("r-rcpp" ,r-rcpp)))
454 (home-page "https://cran.r-project.org/web/packages/ecp/")
455 (synopsis "Multiple change-point analysis of multivariate data")
457 "This package implements various procedures for finding multiple
458 change-points. Two methods make use of dynamic programming and pruning, with
459 no distributional assumptions other than the existence of certain absolute
460 moments in one method. Hierarchical and exact search methods are included.
461 All methods return the set of estimated change-points as well as other summary
463 (license license:gpl2+)))
465 (define-public r-ellipsis
472 (uri (cran-uri "ellipsis" version))
475 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
476 (build-system r-build-system)
478 `(("r-rlang" ,r-rlang)))
479 (home-page "https://github.com/hadley/ellipsis")
480 (synopsis "Tools for working with additional arguments")
482 "In S3 generics, it's useful to take @code{...} so that methods can have
483 additional arguments. But this flexibility comes at a cost: misspelled
484 arguments will be silently ignored. The @code{ellipsis} package is an
485 experiment that allows a generic to warn if any arguments passed in @code{...}
487 (license license:gpl3)))
496 (uri (cran-uri "grr" version))
499 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
500 (build-system r-build-system)
501 (home-page "https://cran.r-project.org/web/packages/grr")
502 (synopsis "Alternative implementations of base R functions")
504 "This package provides alternative implementations of some base R
505 functions, including @code{sort}, @code{order}, and @code{match}. The
506 functions are simplified but can be faster or have other advantages.")
507 (license license:gpl3)))
509 (define-public r-matrix-utils
511 (name "r-matrix-utils")
516 (uri (cran-uri "Matrix.utils" version))
519 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
520 (properties `((upstream-name . "Matrix.utils")))
521 (build-system r-build-system)
524 ("r-matrix" ,r-matrix)))
525 (home-page "https://github.com/cvarrichio/Matrix.utils")
527 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
529 "This package implements data manipulation methods such as @code{cast},
530 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
532 (license license:gpl3)))
534 (define-public r-mboost
540 (uri (cran-uri "mboost" version))
543 "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf"))))
544 (build-system r-build-system)
546 `(("r-lattice" ,r-lattice)
547 ("r-matrix" ,r-matrix)
549 ("r-partykit" ,r-partykit)
550 ("r-quadprog" ,r-quadprog)
552 ("r-survival" ,r-survival)))
553 (home-page "https://github.com/boost-R/mboost")
554 (synopsis "Model-based boosting")
556 "This package provides a functional gradient descent algorithm (boosting)
557 for optimizing general risk functions utilizing component-wise (penalised)
558 least squares estimates or regression trees as base-learners for fitting
559 generalized linear, additive and interaction models to potentially
560 high-dimensional data.")
561 (license license:gpl2)))
570 (uri (cran-uri "sys" version))
573 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
574 (build-system r-build-system)
575 (home-page "https://github.com/jeroen/sys")
576 (synopsis "Powerful and reliable tools for running system commands in R")
578 "This package provides drop-in replacements for the base @code{system2()}
579 function with fine control and consistent behavior across platforms. It
580 supports clean interruption, timeout, background tasks, and streaming STDIN /
581 STDOUT / STDERR over binary or text connections. The package also provides
582 functions for evaluating expressions inside a temporary fork. Such
583 evaluations have no side effects on the main R process, and support reliable
584 interrupts and timeouts. This provides the basis for a sandboxing
586 (license license:expat)))
588 (define-public r-askpass
595 (uri (cran-uri "askpass" version))
598 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
599 (build-system r-build-system)
600 (propagated-inputs `(("r-sys" ,r-sys)))
601 (home-page "https://github.com/jeroen/askpass")
602 (synopsis "Safe password entry for R")
604 "This package provides cross-platform utilities for prompting the user
605 for credentials or a passphrase, for example to authenticate with a server or
606 read a protected key.")
607 (license license:expat)))
609 (define-public r-vegan
616 (uri (cran-uri "vegan" version))
619 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
620 (build-system r-build-system)
622 `(("gfortran" ,gfortran)))
624 `(("r-cluster" ,r-cluster)
625 ("r-knitr" ,r-knitr) ; needed for vignettes
626 ("r-lattice" ,r-lattice)
629 ("r-permute" ,r-permute)))
630 (home-page "https://cran.r-project.org/web/packages/vegan")
631 (synopsis "Functions for community ecology")
633 "The vegan package provides tools for descriptive community ecology. It
634 has most basic functions of diversity analysis, community ordination and
635 dissimilarity analysis. Most of its multivariate tools can be used for other
636 data types as well.")
637 (license license:gpl2+)))
639 (define-public r-tidyverse
646 (uri (cran-uri "tidyverse" version))
649 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
650 (build-system r-build-system)
652 `(("r-broom" ,r-broom)
654 ("r-crayon" ,r-crayon)
655 ("r-dbplyr" ,r-dbplyr)
657 ("r-forcats" ,r-forcats)
658 ("r-ggplot2" ,r-ggplot2)
662 ("r-jsonlite" ,r-jsonlite)
663 ("r-lubridate" ,r-lubridate)
664 ("r-magrittr" ,r-magrittr)
665 ("r-modelr" ,r-modelr)
666 ("r-pillar" ,r-pillar)
669 ("r-readxl" ,r-readxl)
670 ("r-reprex" ,r-reprex)
672 ("r-rstudioapi" ,r-rstudioapi)
674 ("r-stringr" ,r-stringr)
675 ("r-tibble" ,r-tibble)
678 (home-page "https://tidyverse.tidyverse.org")
679 (synopsis "Install and load packages from the \"Tidyverse\"")
681 "The @code{tidyverse} is a set of packages that work in harmony because
682 they share common data representations and API design. This package is
683 designed to make it easy to install and load multiple tidyverse packages in a
685 (license license:gpl3)))
687 (define-public r-rvest
694 (uri (cran-uri "rvest" version))
696 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
697 (build-system r-build-system)
700 ("r-magrittr" ,r-magrittr)
701 ("r-selectr" ,r-selectr)
704 `(("r-knitr" ,r-knitr)))
705 (home-page "https://github.com/hadley/rvest")
706 (synopsis "Simple web scraping for R")
708 "@code{r-rvest} helps you scrape information from web pages. It is
709 designed to work with @code{magrittr} to make it easy to express common web
710 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
711 (license license:gpl3)))
713 (define-public r-selectr
720 (uri (cran-uri "selectr" version))
722 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
723 (build-system r-build-system)
725 `(("r-stringr" ,r-stringr)
727 (home-page "https://sjp.co.nz/projects/selectr/")
728 (synopsis "Translate CSS selectors to XPath expressions")
730 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
731 expression. This allows you to use CSS selectors when working with the XML
732 package as it can only evaluate XPath expressions. Also provided are
733 convenience functions useful for using CSS selectors on XML nodes. This
734 package is a port of the Python package @code{cssselect}.")
735 (license license:bsd-3)))
737 (define-public r-reprex
744 (uri (cran-uri "reprex" version))
747 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
748 (build-system r-build-system)
750 `(("r-callr" ,r-callr)
754 ("r-rmarkdown" ,r-rmarkdown)
755 ("r-whisker" ,r-whisker)
756 ("r-withr" ,r-withr)))
757 (home-page "https://github.com/tidyverse/reprex")
758 (synopsis "Prepare reproducible R code examples for sharing")
760 "This package provides a convenience wrapper that uses the
761 @code{rmarkdown} package to render small snippets of code to target formats
762 that include both code and output. The goal is to encourage the sharing of
763 small, reproducible, and runnable examples on code-oriented websites or email.
764 @code{reprex} also extracts clean, runnable R code from various common formats,
765 such as copy/paste from an R session.")
766 (license license:expat)))
768 (define-public r-reordercluster
770 (name "r-reordercluster")
774 (uri (cran-uri "ReorderCluster" version))
777 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
778 (build-system r-build-system)
780 `(("r-gplots" ,r-gplots)
782 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
783 (synopsis "Reordering the dendrogram according to the class labels")
784 (description "This package provides tools for performing the leaf reordering
785 for the dendrogram that preserves the hierarchical clustering result and at the
786 same time tries to group instances from the same class together.")
787 (license license:gpl3+)))
789 (define-public r-callr
796 (uri (cran-uri "callr" version))
799 "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf"))))
800 (build-system r-build-system)
803 ("r-processx" ,r-processx)))
804 (home-page "https://github.com/r-lib/callr#readme")
805 (synopsis "Call R from R")
807 "It is sometimes useful to perform a computation in a separate R process,
808 without affecting the current R process at all. This package does exactly
810 (license license:expat)))
812 (define-public r-readxl
819 (uri (cran-uri "readxl" version))
822 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
823 (build-system r-build-system)
825 `(("r-cellranger" ,r-cellranger)
826 ("r-progress" ,r-progress)
828 ("r-tibble" ,r-tibble)))
829 (home-page "https://readxl.tidyverse.org")
830 (synopsis "Read Excel files")
832 "This package lets you import Excel files into R. It supports
833 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
834 the embedded @code{RapidXML} C++ library.")
835 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
836 ;; 'rapidxml' which is Boost.
837 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
839 (define-public r-modelr
846 (uri (cran-uri "modelr" version))
849 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
850 (build-system r-build-system)
852 `(("r-broom" ,r-broom)
853 ("r-magrittr" ,r-magrittr)
856 ("r-tibble" ,r-tibble)
858 ("r-tidyselect" ,r-tidyselect)
859 ("r-vctrs" ,r-vctrs)))
860 (home-page "https://github.com/tidyverse/modelr")
861 (synopsis "Helper functions for modelling in pipelines")
863 "Functions for modelling that help you seamlessly integrate modelling
864 into a pipeline of data manipulation and visualisation.")
865 (license license:gpl3)))
867 (define-public r-httpuv
873 (uri (cran-uri "httpuv" version))
876 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))
877 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
878 ;; only contains fixes for building on Solaris.
879 (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch"))
880 (modules '((guix build utils)
885 (delete-file-recursively "src/libuv")
886 ;; Cannot unbundle http-parser, because it contains local
889 (build-system r-build-system)
892 (modify-phases %standard-phases
893 (add-after 'unpack 'unbundle-libuv
894 (lambda* (#:key outputs #:allow-other-keys)
895 (substitute* (find-files "src" "\\.cpp$|\\.h$")
896 (("\"libuv/include/uv\\.h\"")
898 ;; Fix https://github.com/rstudio/httpuv/issues/282
899 (substitute* "src/http.cpp"
900 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
901 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
908 ("r-promises" ,r-promises)
911 (home-page "https://github.com/rstudio/httpuv")
912 (synopsis "HTTP and WebSocket server library for R")
914 "The httpuv package provides low-level socket and protocol support for
915 handling HTTP and WebSocket requests directly from within R. It is primarily
916 intended as a building block for other packages, rather than making it
917 particularly easy to create complete web applications using httpuv alone.")
918 ;; This package includes third-party code that was originally released
919 ;; under various non-copyleft licenses. Full licensing information can be
920 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
921 (license license:gpl3+)))
923 (define-public r-jsonlite
929 (uri (cran-uri "jsonlite" version))
932 "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
933 (build-system r-build-system)
935 `(("r-knitr" ,r-knitr)))
936 (home-page "https://arxiv.org/abs/1403.2805")
937 (synopsis "Robust, high performance JSON parser and generator for R")
939 "The jsonlite package provides a fast JSON parser and generator optimized
940 for statistical data and the web. It offers flexible, robust, high
941 performance tools for working with JSON in R and is particularly powerful for
942 building pipelines and interacting with a web API. In addition to converting
943 JSON data from/to R objects, jsonlite contains functions to stream, validate,
944 and prettify JSON data. The unit tests included with the package verify that
945 all edge cases are encoded and decoded consistently for use with dynamic data
946 in systems and applications.")
947 (license license:expat)))
949 (define-public r-servr
955 (uri (cran-uri "servr" version))
958 "0px75vkc6q4iwbirr27bbrbpv0v9ial7zijnbd6dhjccwxl3x1l3"))))
959 (build-system r-build-system)
961 `(("r-httpuv" ,r-httpuv)
962 ("r-jsonlite" ,r-jsonlite)
965 (home-page "https://github.com/yihui/servr")
966 (synopsis "Simple HTTP server to serve static files or dynamic documents")
968 "Servr provides an HTTP server in R to serve static files, or dynamic
969 documents that can be converted to HTML files (e.g., R Markdown) under a given
971 (license license:expat)))
973 (define-public r-htmltools
979 (uri (cran-uri "htmltools" version))
982 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
983 (build-system r-build-system)
985 `(("r-base64enc" ,r-base64enc)
986 ("r-digest" ,r-digest)
987 ("r-rlang" ,r-rlang)))
988 (home-page "https://cran.r-project.org/web/packages/htmltools")
989 (synopsis "R tools for HTML")
991 "This package provides tools for HTML generation and output in R.")
992 (license license:expat)))
994 (define-public r-htmlwidgets
996 (name "r-htmlwidgets")
1000 (uri (cran-uri "htmlwidgets" version))
1003 "0072wlkl58lav3qszzqw6pmx8qra4784r0yb6rx4lg7rbrik6335"))))
1004 (build-system r-build-system)
1006 `(("r-htmltools" ,r-htmltools)
1007 ("r-jsonlite" ,r-jsonlite)
1008 ("r-yaml" ,r-yaml)))
1010 `(("r-knitr" ,r-knitr)))
1011 (home-page "https://github.com/ramnathv/htmlwidgets")
1012 (synopsis "HTML Widgets for R")
1014 "HTML widgets is a framework for creating HTML widgets that render in
1015 various contexts including the R console, R Markdown documents, and Shiny web
1017 (license license:expat)))
1019 (define-public r-htmltable
1021 (name "r-htmltable")
1026 (uri (cran-uri "htmlTable" version))
1028 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1029 (properties `((upstream-name . "htmlTable")))
1030 (build-system r-build-system)
1032 `(("r-checkmate" ,r-checkmate)
1033 ("r-htmltools" ,r-htmltools)
1034 ("r-htmlwidgets" ,r-htmlwidgets)
1035 ("r-knitr" ,r-knitr)
1036 ("r-magrittr" ,r-magrittr)
1037 ("r-rstudioapi" ,r-rstudioapi)
1038 ("r-stringr" ,r-stringr)))
1040 `(("r-knitr" ,r-knitr)))
1041 (home-page "http://gforge.se/packages/")
1042 (synopsis "Advanced tables for Markdown/HTML")
1044 "This package provides functions to build tables with advanced layout
1045 elements such as row spanners, column spanners, table spanners, zebra
1046 striping, and more. While allowing advanced layout, the underlying
1047 CSS-structure is simple in order to maximize compatibility with word
1048 processors such as LibreOffice. The package also contains a few text
1049 formatting functions that help outputting text compatible with HTML or
1051 (license license:gpl3+)))
1053 (define-public r-curl
1059 (uri (cran-uri "curl" version))
1062 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1063 (build-system r-build-system)
1066 (modify-phases %standard-phases
1067 ;; The environment variable CURL_CA_BUNDLE is only respected when
1068 ;; running Windows, so we disable the platform checks.
1069 ;; This can be removed once the libcurl has been patched.
1070 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1072 (substitute* "R/onload.R"
1073 (("if \\(!grepl\\(\"mingw\".*")
1075 (substitute* "src/handle.c"
1076 (("/\\* Only set" m)
1078 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1079 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1086 `(("pkg-config" ,pkg-config)))
1087 (home-page "https://github.com/jeroenooms/curl")
1088 (synopsis "HTTP client for R")
1090 "The @code{curl()} and @code{curl_download()} functions provide highly
1091 configurable drop-in replacements for base @code{url()} and
1092 @code{download.file()} with better performance, support for encryption, gzip
1093 compression, authentication, and other @code{libcurl} goodies. The core of
1094 the package implements a framework for performing fully customized requests
1095 where data can be processed either in memory, on disk, or streaming via the
1096 callback or connection interfaces.")
1097 (license license:expat)))
1099 (define-public r-hwriter
1106 (uri (cran-uri "hwriter" version))
1109 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1110 (build-system r-build-system)
1111 (home-page "https://cran.r-project.org/web/packages/hwriter")
1112 (synopsis "Output R objects in HTML format")
1114 "This package provides easy-to-use and versatile functions to output R
1115 objects in HTML format.")
1116 (license license:lgpl2.1+)))
1118 (define-public r-rjson
1125 (uri (cran-uri "rjson" version))
1128 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1129 (build-system r-build-system)
1130 (home-page "https://cran.r-project.org/web/packages/rjson")
1131 (synopsis "JSON library for R")
1133 "This package provides functions to convert R objects into JSON objects
1135 (license license:gpl2+)))
1137 (define-public r-fastmap
1144 (uri (cran-uri "fastmap" version))
1147 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1148 (properties `((upstream-name . "fastmap")))
1149 (build-system r-build-system)
1150 (home-page "https://r-lib.github.io/fastmap/")
1151 (synopsis "Fast implementation of a key-value store")
1153 "This package provides a fast implementation of a key-value store.
1154 Environments are commonly used as key-value stores, but every time a new key
1155 is used, it is added to R's global symbol table, causing a small amount of
1156 memory leakage. This can be problematic in cases where many different keys
1157 are used. Fastmap avoids this memory leak issue by implementing the map using
1158 data structures in C++.")
1159 (license license:expat)))
1161 (define-public r-shiny
1169 (url "https://github.com/rstudio/shiny")
1170 (commit (string-append "v" version))))
1171 (file-name (git-file-name name version))
1174 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1175 (build-system r-build-system)
1177 `(#:modules ((guix build r-build-system)
1178 (guix build minify-build-system)
1181 #:imported-modules (,@%r-build-system-modules
1182 (guix build minify-build-system))
1184 (modify-phases (@ (guix build r-build-system) %standard-phases)
1185 (add-after 'unpack 'replace-bundled-minified-JavaScript
1186 (lambda* (#:key inputs #:allow-other-keys)
1187 (let ((replace-file (lambda (old new)
1188 (format #t "replacing ~a with ~a\n" old new)
1190 (symlink new old))))
1191 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1192 ;; contain just data. They are not minified code, so we don't
1194 (with-directory-excursion "inst/www/shared"
1195 (replace-file "bootstrap/shim/respond.min.js"
1196 (string-append (assoc-ref inputs "js-respond")
1197 "/share/javascript/respond.min.js"))
1198 (replace-file "bootstrap/shim/html5shiv.min.js"
1199 (string-append (assoc-ref inputs "js-html5shiv")
1200 "/share/javascript/html5shiv.min.js"))
1201 (replace-file "json2-min.js"
1202 (string-append (assoc-ref inputs "js-json2")
1203 "/share/javascript/json2-min.js"))
1204 (replace-file "strftime/strftime-min.js"
1205 (string-append (assoc-ref inputs "js-strftime")
1206 "/share/javascript/strftime.min.js"))
1207 (replace-file "highlight/highlight.pack.js"
1208 (string-append (assoc-ref inputs "js-highlight")
1209 "/share/javascript/highlight.min.js"))
1210 (replace-file "datatables/js/jquery.dataTables.min.js"
1211 (string-append (assoc-ref inputs "js-datatables")
1212 "/share/javascript/jquery.dataTables.min.js"))
1213 (replace-file "selectize/js/selectize.min.js"
1214 (string-append (assoc-ref inputs "js-selectize")
1215 "/share/javascript/selectize.min.js"))
1216 (replace-file "selectize/js/es5-shim.min.js"
1217 (string-append (assoc-ref inputs "js-es5-shim")
1218 "/share/javascript/es5-shim.min.js"))
1219 (for-each (match-lambda
1221 (delete-file target)
1222 (minify source #:target target)))
1223 '(("jqueryui/jquery-ui.js" .
1224 "jqueryui/jquery-ui.min.js")
1225 ("datepicker/js/bootstrap-datepicker.js" .
1226 "datepicker/js/bootstrap-datepicker.min.js")
1227 ("ionrangeslider/js/ion.rangeSlider.js" .
1228 "ionrangeslider/js/ion.rangeSlider.min.js")
1229 ("bootstrap/js/bootstrap.js" .
1230 "bootstrap/js/bootstrap.min.js")
1235 ("legacy/jquery.js" .
1236 "legacy/jquery.min.js")
1237 ("showdown/src/showdown.js" .
1238 "showdown/compressed/showdown.js")))))
1241 `(("r-crayon" ,r-crayon)
1242 ("r-digest" ,r-digest)
1243 ("r-fastmap" ,r-fastmap)
1244 ("r-htmltools" ,r-htmltools)
1245 ("r-httpuv" ,r-httpuv)
1246 ("r-jsonlite" ,r-jsonlite)
1247 ("r-later" ,r-later)
1249 ("r-promises" ,r-promises)
1251 ("r-rlang" ,r-rlang)
1252 ("r-sourcetools" ,r-sourcetools)
1253 ("r-withr" ,r-withr)
1254 ("r-xtable" ,r-xtable)))
1256 `(("js-datatables" ,js-datatables)
1257 ("js-html5shiv" ,js-html5shiv)
1258 ("js-json2" ,js-json2)
1259 ("js-respond" ,js-respond)
1260 ("js-selectize" ,js-selectize)
1261 ("js-strftime" ,js-strftime)
1262 ("js-highlight" ,js-highlight)
1263 ("js-es5-shim" ,js-es5-shim)))
1265 `(("uglify-js" ,uglify-js)
1266 ("gfortran" ,gfortran)))
1267 (home-page "http://shiny.rstudio.com")
1268 (synopsis "Easy interactive web applications with R")
1270 "Makes it incredibly easy to build interactive web applications
1271 with R. Automatic \"reactive\" binding between inputs and outputs and
1272 extensive prebuilt widgets make it possible to build beautiful,
1273 responsive, and powerful applications with minimal effort.")
1274 (license license:artistic2.0)))
1276 ;; This package includes minified JavaScript files. When upgrading please
1277 ;; check that there are no new minified JavaScript files.
1278 (define-public r-shinytree
1280 (name "r-shinytree")
1285 (uri (cran-uri "shinyTree" version))
1288 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1289 (modules '((guix build utils)))
1292 ;; Delete minified JavaScript
1293 (for-each delete-file
1294 '("inst/www/jsTree-3.3.7/libs/require.js"
1295 "inst/www/jsTree-3.3.7/libs/jquery.js"
1296 "inst/www/jsTree-3.3.7/jstree.min.js"))
1298 (properties `((upstream-name . "shinyTree")))
1299 (build-system r-build-system)
1301 `(#:modules ((guix build utils)
1302 (guix build r-build-system)
1306 (modify-phases %standard-phases
1307 (add-after 'unpack 'replace-minified-javascript
1308 (lambda* (#:key inputs #:allow-other-keys)
1309 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1310 (symlink (string-append (assoc-ref inputs "js-requirejs")
1311 "/share/javascript/require.min.js")
1316 `((,(assoc-ref inputs "js-jquery")
1320 (lambda (sources targets)
1321 (for-each (lambda (source target)
1322 (format #t "Processing ~a --> ~a~%"
1324 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1325 (call-with-output-file target
1327 (dump-port minified port)))))
1331 `(("r-htmlwidgets" ,r-htmlwidgets)
1332 ("r-jsonlite" ,r-jsonlite)
1333 ("r-promises" ,r-promises)
1334 ("r-shiny" ,r-shiny)
1335 ("r-stringr" ,r-stringr)))
1337 `(("js-requirejs" ,js-requirejs)))
1339 `(("uglify-js" ,uglify-js)
1343 (uri "https://code.jquery.com/jquery-3.3.1.js")
1346 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1347 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1348 (synopsis "jsTree bindings for Shiny")
1350 "This package exposes R bindings to jsTree, a JavaScript library that
1351 supports interactive trees, to enable rich, editable trees in Shiny.")
1352 (license license:expat)))
1354 (define-public r-shinydashboard
1356 (name "r-shinydashboard")
1360 (uri (cran-uri "shinydashboard" version))
1363 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1364 (build-system r-build-system)
1365 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1366 ;; Regenerate it from the included sources.
1368 `(#:modules ((guix build utils)
1369 (guix build r-build-system)
1372 (modify-phases %standard-phases
1373 (add-after 'unpack 'generate-minified-javascript
1375 (with-directory-excursion "inst/AdminLTE"
1376 (delete-file "app.min.js")
1377 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1378 (call-with-output-file "app.min.js"
1380 (dump-port minified port))))))))))
1382 `(("r-htmltools" ,r-htmltools)
1383 ("r-promises" ,r-promises)
1384 ("r-shiny" ,r-shiny)))
1386 `(("uglify-js" ,uglify-js)))
1387 (home-page "https://rstudio.github.io/shinydashboard/")
1388 (synopsis "Create dashboards with shiny")
1389 (description "This package provides an extension to the Shiny web
1390 application framework for R, making it easy to create attractive dashboards.")
1391 ;; This package includes software that was released under the Expat
1392 ;; license, but the whole package is released under GPL version 2 or
1394 (license license:gpl2+)))
1396 (define-public r-shinyfiles
1398 (name "r-shinyfiles")
1403 (uri (cran-uri "shinyFiles" version))
1405 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1406 (properties `((upstream-name . "shinyFiles")))
1407 (build-system r-build-system)
1410 ("r-htmltools" ,r-htmltools)
1411 ("r-jsonlite" ,r-jsonlite)
1412 ("r-shiny" ,r-shiny)
1413 ("r-tibble" ,r-tibble)))
1414 (home-page "https://github.com/thomasp85/shinyFiles")
1415 (synopsis "Server-side file system viewer for Shiny")
1417 "This package provides functionality for client-side navigation of the
1418 server side file system in shiny apps. In case the app is running locally
1419 this gives the user direct access to the file system without the need to
1420 \"download\" files to a temporary location. Both file and folder selection as
1421 well as file saving is available.")
1422 (license license:gpl2+)))
1424 (define-public r-shinythemes
1426 (name "r-shinythemes")
1431 (uri (cran-uri "shinythemes" version))
1434 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1435 (properties `((upstream-name . "shinythemes")))
1436 (build-system r-build-system)
1437 (propagated-inputs `(("r-shiny" ,r-shiny)))
1438 (home-page "https://rstudio.github.io/shinythemes/")
1439 (synopsis "Themes for Shiny")
1441 "This package provides themes for use with Shiny. It includes several
1442 Bootstrap themes, which are packaged for use with Shiny applications.")
1443 ;; The package is released under version 3 of the GPL, but it includes
1444 ;; source files that are covered by the Expat license. It also includes
1445 ;; fonts under SIL or the ASL.
1446 (license (list license:gpl3 license:expat
1447 license:silofl1.1 license:asl2.0))))
1449 ;; The package sources include minified variants of d3.js and non-minified
1450 ;; source code of d3-jetpack.
1451 (define-public r-d3r
1458 (uri (cran-uri "d3r" version))
1461 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1462 (build-system r-build-system)
1464 `(#:modules ((guix build utils)
1465 (guix build r-build-system)
1469 (modify-phases %standard-phases
1470 (add-after 'unpack 'process-javascript
1471 (lambda* (#:key inputs #:allow-other-keys)
1472 (with-directory-excursion "inst/www/d3/"
1476 `((,(assoc-ref inputs "d3.v3.js")
1477 "v3/dist/d3.min.js")
1478 (,(assoc-ref inputs "d3.v4.js")
1479 "v4/dist/d3.min.js")
1480 (,(assoc-ref inputs "d3.v5.js")
1481 "v5/dist/d3.min.js"))))
1482 (lambda (sources targets)
1483 (for-each (lambda (source target)
1484 (format #t "Processing ~a --> ~a~%"
1486 (delete-file target)
1487 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1488 (call-with-output-file target
1490 (dump-port minified port)))))
1494 `(("r-dplyr" ,r-dplyr)
1495 ("r-htmltools" ,r-htmltools)
1496 ("r-rlang" ,r-rlang)
1497 ("r-tidyr" ,r-tidyr)))
1499 `(("uglify-js" ,uglify-js)
1503 (uri "https://d3js.org/d3.v3.js")
1506 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1510 (uri "https://d3js.org/d3.v4.js")
1513 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1517 (uri "https://d3js.org/d3.v5.js")
1520 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1521 (home-page "https://github.com/timelyportfolio/d3r")
1522 (synopsis "d3.js utilities for R")
1524 "This package provides a suite of functions to help ease the use of the
1525 d3.js visualization library in R. These helpers include
1526 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1527 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1528 R objects into the JSON format that the d3.js library expects.")
1529 (license license:bsd-3)))
1531 ;; We use the latest commit here because the last release was in 2016 while
1532 ;; the latest commit was in 2018.
1533 (define-public r-sankeyd3
1534 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1538 (version (git-version "0.3.2" revision commit))
1543 (url "https://github.com/fbreitwieser/sankeyD3")
1545 (file-name (git-file-name name version))
1548 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1549 (build-system r-build-system)
1552 ("r-htmlwidgets" ,r-htmlwidgets)
1553 ("r-shiny" ,r-shiny)
1554 ("r-magrittr" ,r-magrittr)))
1555 (home-page "https://github.com/fbreitwieser/sankeyD3")
1556 (synopsis "Sankey network graphs from R")
1558 "This package provides an R library to generate Sankey network graphs
1559 in R and Shiny via the D3 visualization library.")
1560 ;; The R code is licensed under GPLv3+. It includes the non-minified
1561 ;; JavaScript source code of d3-sankey, which is released under the
1562 ;; 3-clause BSD license.
1563 (license (list license:gpl3+ license:bsd-3)))))
1565 (define-public r-crosstalk
1567 (name "r-crosstalk")
1572 (uri (cran-uri "crosstalk" version))
1575 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1576 (build-system r-build-system)
1578 `(("r-htmltools" ,r-htmltools)
1579 ("r-jsonlite" ,r-jsonlite)
1580 ("r-lazyeval" ,r-lazyeval)
1582 (home-page "https://rstudio.github.io/crosstalk/")
1583 (synopsis "Inter-widget interactivity for HTML widgets")
1585 "This package provides building blocks for allowing HTML widgets to
1586 communicate with each other, with Shiny or without (i.e. static @code{.html}
1587 files). It currently supports linked brushing and filtering.")
1588 (license license:expat)))
1590 (define-public r-rook
1597 (uri (cran-uri "Rook" version))
1600 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1601 (properties `((upstream-name . "Rook")))
1602 (build-system r-build-system)
1603 (propagated-inputs `(("r-brew" ,r-brew)))
1604 (home-page "https://cran.r-project.org/web/packages/Rook")
1605 (synopsis "Web server interface for R")
1607 "This package contains the Rook specification and convenience software
1608 for building and running Rook applications. A Rook application is an R
1609 reference class object that implements a @code{call} method or an R closure
1610 that takes exactly one argument, an environment, and returns a list with three
1611 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1612 (license license:gpl2)))
1614 (define-public r-miniui
1621 (uri (cran-uri "miniUI" version))
1624 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1625 (properties `((upstream-name . "miniUI")))
1626 (build-system r-build-system)
1628 `(("r-htmltools" ,r-htmltools)
1629 ("r-shiny" ,r-shiny)))
1630 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1631 (synopsis "Shiny UI widgets for small screens")
1633 "This package provides UI widget and layout functions for writing Shiny apps that
1634 work well on small screens.")
1635 (license license:gpl3)))
1637 (define-public r-feather
1644 (uri (cran-uri "feather" version))
1647 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1648 (build-system r-build-system)
1652 ("r-tibble" ,r-tibble)))
1653 (home-page "https://github.com/wesm/feather")
1654 (synopsis "R Bindings to the Feather API")
1655 (description "Read and write feather files, a lightweight binary columnar
1656 data store designed for maximum speed.")
1657 (license license:asl2.0)))
1659 (define-public r-maps
1666 (uri (cran-uri "maps" version))
1669 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1670 (build-system r-build-system)
1671 (home-page "https://cran.r-project.org/web/packages/maps")
1672 (synopsis "Draw geographical maps")
1673 (description "This package provides an R module for display of maps.
1674 Projection code and larger maps are in separate packages (@code{mapproj} and
1676 (license license:gpl2)))
1678 (define-public r-mapproj
1685 (uri (cran-uri "mapproj" version))
1688 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1689 (build-system r-build-system)
1690 (propagated-inputs `(("r-maps" ,r-maps)))
1691 (home-page "https://cran.r-project.org/web/packages/mapproj")
1692 (synopsis "Map projection in R")
1693 (description "This package converts latitude/longitude into projected
1695 (license (list license:gpl2 ; The R interface
1696 (license:non-copyleft ; The C code
1697 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1698 "Lucent Public License Version 1.02")))))
1700 (define-public r-rgooglemaps
1702 (name "r-rgooglemaps")
1707 (uri (cran-uri "RgoogleMaps" version))
1710 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1711 (properties `((upstream-name . "RgoogleMaps")))
1712 (build-system r-build-system)
1716 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1717 (synopsis "Use Google Maps in R")
1718 (description "This package serves two purposes:
1720 @item Provide a comfortable R interface to query the Google server for static
1722 @item Use the map as a background image to overlay plots within R. This
1723 requires proper coordinate scaling.
1725 (license license:gpl2+)))
1727 (define-public r-geosphere
1729 (name "r-geosphere")
1734 (uri (cran-uri "geosphere" version))
1737 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1738 (build-system r-build-system)
1739 (propagated-inputs `(("r-sp" ,r-sp)))
1740 (home-page "https://cran.r-project.org/web/packages/geosphere")
1741 (synopsis "Spherical trigonometry")
1742 (description "This package computes spherical trigonometry for geographic
1743 applications. That is, compute distances and related measures for angular
1744 (longitude/latitude) locations.")
1745 (license license:gpl3+)))
1747 (define-public r-jpeg
1754 (uri (cran-uri "jpeg" version))
1757 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1758 (build-system r-build-system)
1759 (inputs `(("libjpeg" ,libjpeg-turbo)))
1760 (home-page "https://www.rforge.net/jpeg/")
1761 (synopsis "Read and write JPEG images with R")
1762 (description "This package provides a way to read, write and display
1763 bitmap images stored in the JPEG format with R. It can read and write both
1764 files and in-memory raw vectors.")
1765 (license license:gpl2+)))
1767 (define-public r-ggmap
1774 (uri (cran-uri "ggmap" version))
1777 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1778 (build-system r-build-system)
1780 `(("r-bitops" ,r-bitops)
1781 ("r-digest" ,r-digest)
1782 ("r-dplyr" ,r-dplyr)
1783 ("r-ggplot2" ,r-ggplot2)
1787 ("r-magrittr" ,r-magrittr)
1790 ("r-purrr" ,r-purrr)
1791 ("r-rgooglemaps" ,r-rgooglemaps)
1792 ("r-rjson" ,r-rjson)
1793 ("r-scales" ,r-scales)
1794 ("r-stringr" ,r-stringr)
1795 ("r-tibble" ,r-tibble)
1796 ("r-tidyr" ,r-tidyr)))
1797 (home-page "https://github.com/dkahle/ggmap")
1798 (synopsis "Spatial visualization with ggplot2")
1799 (description "This package provides a collection of functions to visualize
1800 spatial data and models on top of static maps from various online sources (e.g
1801 Google Maps and Stamen Maps). It includes tools common to those tasks,
1802 including functions for geolocation and routing.")
1803 (license license:gpl2)))
1805 (define-public r-haven
1812 (uri (cran-uri "haven" version))
1815 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1816 (build-system r-build-system)
1820 `(("r-knitr" ,r-knitr)))
1822 `(("r-forcats" ,r-forcats)
1825 ("r-rlang" ,r-rlang)
1826 ("r-readr" ,r-readr)
1827 ("r-tibble" ,r-tibble)
1828 ("r-tidyselect" ,r-tidyselect)
1829 ("r-vctrs" ,r-vctrs)))
1830 (home-page "https://haven.tidyverse.org")
1831 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1833 "This package lets you mport foreign statistical formats into R via the
1834 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1835 (license license:expat)))
1837 (define-public r-amap
1843 (uri (cran-uri "amap" version))
1846 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1847 (build-system r-build-system)
1849 `(("gfortran" ,gfortran)))
1850 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1851 (synopsis "Another multidimensional analysis package")
1852 (description "This package provides tools for clustering and principal
1853 component analysis (with robust methods, and parallelized functions).")
1854 (license license:gpl2+)))
1856 (define-public r-ape
1863 (uri (cran-uri "ape" version))
1866 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
1867 (build-system r-build-system)
1869 `(("r-lattice" ,r-lattice)
1871 ("r-rcpp" ,r-rcpp)))
1872 (home-page "http://ape-package.ird.fr/")
1873 (synopsis "Analyses of phylogenetics and evolution")
1875 "This package provides functions for reading, writing, plotting, and
1876 manipulating phylogenetic trees, analyses of comparative data in a
1877 phylogenetic framework, ancestral character analyses, analyses of
1878 diversification and macroevolution, computing distances from DNA sequences,
1879 and several other tools.")
1880 (license license:gpl2+)))
1882 (define-public r-abbyyr
1889 (uri (cran-uri "abbyyR" version))
1892 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1893 (properties `((upstream-name . "abbyyR")))
1894 (build-system r-build-system)
1896 `(("r-curl" ,r-curl)
1899 ("r-progress" ,r-progress)
1900 ("r-readr" ,r-readr)
1902 (home-page "https://github.com/soodoku/abbyyR")
1903 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1905 "This package provides tools to get text from images of text using Abbyy
1906 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1907 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1908 passports and get the results in a variety of formats including plain text and
1909 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1910 (license license:expat)))
1912 (define-public r-colorspace
1914 (name "r-colorspace")
1919 (uri (cran-uri "colorspace" version))
1921 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1922 (build-system r-build-system)
1923 (home-page "https://cran.r-project.org/web/packages/colorspace")
1924 (synopsis "Color space manipulation")
1926 "This package carries out a mapping between assorted color spaces
1927 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1928 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1929 colors are provided.")
1930 (license license:bsd-3)))
1932 (define-public r-glue
1939 (uri (cran-uri "glue" version))
1942 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
1943 (build-system r-build-system)
1944 ;; knitr depends on glue, so we can't add knitr here to build the
1948 `(("r-knitr" ,r-knitr)))
1949 (home-page "https://github.com/tidyverse/glue")
1950 (synopsis "Interpreted string literals")
1952 "This package provides an implementation of interpreted string literals,
1953 inspired by Python's Literal String Interpolation (PEP-0498) and
1954 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1955 (license license:expat)))
1957 (define-public r-pastecs
1963 (uri (cran-uri "pastecs" version))
1966 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1967 (build-system r-build-system)
1969 `(("r-boot" ,r-boot)))
1970 (home-page "http://www.sciviews.org/pastecs")
1971 (synopsis "Analysis of space-time ecological series")
1973 "This package provides functions for regulation, decomposition and analysis
1974 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1975 initiative to bring PASSTEC 2000 functionalities to R.")
1976 (license license:gpl2+)))
1978 (define-public r-partykit
1984 (uri (cran-uri "partykit" version))
1987 "1jg68rqhk2r0h2hk50xl99zp56b1nfdcam06kfvssqrkgkavkswf"))))
1988 (build-system r-build-system)
1990 `(("r-formula" ,r-formula)
1992 ("r-libcoin" ,r-libcoin)
1993 ("r-mvtnorm" ,r-mvtnorm)
1994 ("r-rpart" ,r-rpart)
1995 ("r-survival" ,r-survival)))
1996 (home-page "http://partykit.R-Forge.R-project.org/partykit")
1997 (synopsis "Toolkit for recursive partytioning")
1999 "This package provides a toolkit with infrastructure for representing,
2000 summarizing, and visualizing tree-structured regression and classification
2002 (license license:gpl2+)))
2004 (define-public r-plogr
2011 (uri (cran-uri "plogr" version))
2014 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2015 (build-system r-build-system)
2016 (home-page "https://github.com/krlmlr/plogr")
2017 (synopsis "R bindings for the plog C++ logging library")
2019 "This package provides the header files for a stripped-down version of
2020 the plog header-only C++ logging library, and a method to log to R's standard
2022 (license license:expat)))
2024 (define-public r-pls
2031 (uri (cran-uri "pls" version))
2033 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2034 (build-system r-build-system)
2035 (home-page "https://mevik.net/work/software/pls.html")
2036 (synopsis "Partial Least Squares and Principal Component Regression")
2038 "The pls package implements multivariate regression methods: Partial Least
2039 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2040 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2043 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2044 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2045 @item multi-response models (or @dfn{PLS2})
2046 @item flexible cross-validation
2047 @item Jackknife variance estimates of regression coefficients
2048 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2049 (R)MSEP, R², and correlation loadings
2050 @item formula interface, modelled after @code{lm()}, with methods for predict,
2051 print, summary, plot, update, etc.
2052 @item extraction functions for coefficients, scores, and loadings
2053 @item MSEP, RMSEP, and R² estimates
2054 @item multiplicative scatter correction (@dfn{MSC})
2056 (license license:gpl2)))
2065 (uri (cran-uri "ps" version))
2067 (base32 "0yns03ffd2a2cs4b6dsjjlqhv46vq2g094m8psmhf3h9i52awyaz"))))
2068 (build-system r-build-system)
2069 (home-page "https://ps.r-lib.org")
2070 (synopsis "List, query, and manipulate system processes")
2072 "The ps package implements an API to list, query, and manipulate system
2073 processes. Most of its code is based on the @code{psutil} Python package.")
2074 (license license:bsd-3)))
2076 (define-public r-pkgbuild
2083 (uri (cran-uri "pkgbuild" version))
2085 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk"))))
2086 (build-system r-build-system)
2088 `(("r-callr" ,r-callr)
2090 ("r-crayon" ,r-crayon)
2092 ("r-prettyunits" ,r-prettyunits)
2094 ("r-rprojroot" ,r-rprojroot)
2095 ("r-withr" ,r-withr)))
2096 (home-page "https://github.com/r-pkgs/pkgbuild")
2097 (synopsis "Find tools needed to build R packages")
2099 "This package provides functions used to build R packages. It locates
2100 compilers needed to build R packages on various platforms and ensures the PATH
2101 is configured appropriately so R can use them.")
2102 (license license:gpl3)))
2104 (define-public r-pkgload
2111 (uri (cran-uri "pkgload" version))
2114 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2115 (build-system r-build-system)
2118 ("r-crayon" ,r-crayon)
2120 ("r-pkgbuild" ,r-pkgbuild)
2121 ("r-rlang" ,r-rlang)
2122 ("r-rprojroot" ,r-rprojroot)
2123 ("r-rstudioapi" ,r-rstudioapi)
2124 ("r-withr" ,r-withr)))
2125 (home-page "https://github.com/r-lib/pkgload")
2126 (synopsis "Simulate package installation and attach")
2128 "This package simulates the process of installing a package and then
2129 attaching it. This is a key part of the @code{devtools} package as it allows
2130 you to rapidly iterate while developing a package.")
2131 (license license:gpl3)))
2133 (define-public r-rcpp
2140 (uri (cran-uri "Rcpp" version))
2142 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2143 (build-system r-build-system)
2144 (home-page "http://www.rcpp.org")
2145 (synopsis "Seamless R and C++ integration")
2147 "The Rcpp package provides R functions as well as C++ classes which offer
2148 a seamless integration of R and C++. Many R data types and objects can be
2149 mapped back and forth to C++ equivalents which facilitates both writing of new
2150 code as well as easier integration of third-party libraries. Documentation
2151 about Rcpp is provided by several vignettes included in this package, via the
2152 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2153 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2154 @code{citation(\"Rcpp\")} for details on these last two.")
2155 (license license:gpl2+)))
2157 (define-public r-bindr
2164 (uri (cran-uri "bindr" version))
2167 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2168 (build-system r-build-system)
2169 (home-page "https://github.com/krlmlr/bindr")
2170 (synopsis "Parametrized active bindings")
2172 "This package provides a simple interface for creating active bindings
2173 where the bound function accepts additional arguments.")
2174 (license license:expat)))
2176 (define-public r-bindrcpp
2183 (uri (cran-uri "bindrcpp" version))
2186 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2187 (build-system r-build-system)
2189 `(("r-bindr" ,r-bindr)
2190 ("r-plogr" ,r-plogr)
2191 ("r-rcpp" ,r-rcpp)))
2192 (home-page "https://github.com/krlmlr/bindrcpp")
2193 (synopsis "Rcpp interface to active bindings")
2195 "This package provides an easy way to fill an environment with active
2196 bindings that call a C++ function.")
2197 (license license:expat)))
2199 (define-public r-bisquerna
2201 (name "r-bisquerna")
2205 (uri (cran-uri "BisqueRNA" version))
2208 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2209 (properties `((upstream-name . "BisqueRNA")))
2210 (build-system r-build-system)
2212 `(("r-biobase" ,r-biobase)
2213 ("r-limsolve" ,r-limsolve)))
2214 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2215 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2216 (description "This package provides tools to accurately estimate cell type
2217 abundances from heterogeneous bulk expression. A reference-based method
2218 utilizes single-cell information to generate a signature matrix and
2219 transformation of bulk expression for accurate regression based estimates.
2220 A marker-based method utilizes known cell-specific marker genes to measure
2221 relative abundances across samples.")
2222 (license license:gpl3)))
2224 (define-public r-auc
2231 (uri (cran-uri "AUC" version))
2234 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2235 (properties `((upstream-name . "AUC")))
2236 (build-system r-build-system)
2237 (home-page "https://cran.r-project.org/web/packages/AUC")
2238 (synopsis "Compute the area under the curve of selected measures")
2240 "This package includes functions to compute the area under the curve of
2241 selected measures: the area under the sensitivity curve (AUSEC), the area
2242 under the specificity curve (AUSPC), the area under the accuracy
2243 curve (AUACC), and the area under the receiver operating characteristic
2244 curve (AUROC). The curves can also be visualized. Support for partial areas
2246 (license license:gpl2+)))
2248 (define-public r-calibrate
2250 (name "r-calibrate")
2255 (uri (cran-uri "calibrate" version))
2257 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2258 (build-system r-build-system)
2260 `(("r-mass" ,r-mass)))
2261 (home-page "https://cran.r-project.org/web/packages/calibrate")
2262 (synopsis "Calibration of scatterplot and biplot axes")
2264 "This is a package for drawing calibrated scales with tick marks
2265 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2266 (license license:gpl2)))
2268 (define-public r-shape
2275 (uri (cran-uri "shape" version))
2278 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2279 (build-system r-build-system)
2280 (home-page "https://cran.r-project.org/web/packages/shape")
2281 (synopsis "Functions for plotting graphical shapes")
2283 "This package provides functions for plotting graphical shapes such as
2284 ellipses, circles, cylinders, arrows, ...")
2285 (license license:gpl3+)))
2287 (define-public r-globaloptions
2289 (name "r-globaloptions")
2294 (uri (cran-uri "GlobalOptions" version))
2296 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2297 (properties `((upstream-name . "GlobalOptions")))
2298 (build-system r-build-system)
2300 `(("r-knitr" ,r-knitr)))
2301 (home-page "https://github.com/jokergoo/GlobalOptions")
2302 (synopsis "Generate functions to get or set global options")
2304 "This package provides more controls on the option values such as
2305 validation and filtering on the values, making options invisible or private.")
2306 (license license:gpl2+)))
2308 (define-public r-circlize
2315 (uri (cran-uri "circlize" version))
2318 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2319 (build-system r-build-system)
2321 `(("r-colorspace" ,r-colorspace)
2322 ("r-globaloptions" ,r-globaloptions)
2323 ("r-shape" ,r-shape)))
2325 `(("r-knitr" ,r-knitr)))
2326 (home-page "https://github.com/jokergoo/circlize")
2327 (synopsis "Circular visualization")
2329 "Circular layout is an efficient way to visualise huge amounts of
2330 information. This package provides an implementation of circular layout
2331 generation in R as well as an enhancement of available software. Its
2332 flexibility is based on the usage of low-level graphics functions such that
2333 self-defined high-level graphics can be easily implemented by users for
2334 specific purposes. Together with the seamless connection between the powerful
2335 computational and visual environment in R, it gives users more convenience and
2336 freedom to design figures for better understanding complex patterns behind
2337 multi-dimensional data.")
2338 (license license:gpl2+)))
2340 (define-public r-powerlaw
2347 (uri (cran-uri "poweRlaw" version))
2349 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2350 (properties `((upstream-name . "poweRlaw")))
2351 (build-system r-build-system)
2353 `(("r-pracma" ,r-pracma)))
2355 `(("r-knitr" ,r-knitr)))
2356 (home-page "https://github.com/csgillespie/poweRlaw")
2357 (synopsis "Tools for the analysis of heavy tailed distributions")
2359 "This package provides an implementation of maximum likelihood estimators
2360 for a variety of heavy tailed distributions, including both the discrete and
2361 continuous power law distributions. Additionally, a goodness-of-fit based
2362 approach is used to estimate the lower cut-off for the scaling region.")
2363 ;; Any of these GPL versions.
2364 (license (list license:gpl2 license:gpl3))))
2366 (define-public r-compare
2373 (uri (cran-uri "compare" version))
2376 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2377 (build-system r-build-system)
2378 (home-page "https://cran.r-project.org/web/packages/compare")
2379 (synopsis "Comparing objects for differences")
2381 "This package provides functions to compare a model object to a
2382 comparison object. If the objects are not identical, the functions can be
2383 instructed to explore various modifications of the objects (e.g., sorting
2384 rows, dropping names) to see if the modified versions are identical.")
2385 (license license:gpl2+)))
2387 (define-public r-dendextend
2389 (name "r-dendextend")
2394 (uri (cran-uri "dendextend" version))
2397 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2398 (build-system r-build-system)
2400 `(("r-ggplot2" ,r-ggplot2)
2401 ("r-magrittr" ,r-magrittr)
2402 ("r-viridis" ,r-viridis)))
2404 `(("r-knitr" ,r-knitr)))
2405 (home-page "https://cran.r-project.org/web/packages/dendextend")
2406 (synopsis "Extending 'dendrogram' functionality in R")
2408 "This package offers a set of functions for extending @code{dendrogram}
2409 objects in R, letting you visualize and compare trees of hierarchical
2410 clusterings. You can adjust a tree's graphical parameters (the color, size,
2411 type, etc of its branches, nodes and labels) and visually and statistically
2412 compare different dendrograms to one another.")
2413 ;; Any of these versions
2414 (license (list license:gpl2 license:gpl3))))
2416 (define-public r-getoptlong
2418 (name "r-getoptlong")
2423 (uri (cran-uri "GetoptLong" version))
2426 "0l9pa9dx8pcg3j7jn4b9k98g7r5vdsvnmf6apnifzm57mc0vlkg6"))))
2427 (properties `((upstream-name . "GetoptLong")))
2428 (build-system r-build-system)
2432 `(("r-crayon" ,r-crayon)
2433 ("r-globaloptions" ,r-globaloptions)
2434 ("r-rjson" ,r-rjson)))
2436 `(("r-knitr" ,r-knitr)))
2437 (home-page "https://github.com/jokergoo/GetoptLong")
2438 (synopsis "Parsing command-line arguments and variable interpolation")
2440 "This is yet another command-line argument parser which wraps the
2441 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2442 use in R. It also provides a simple way for variable interpolation in R.")
2443 (license license:gpl2+)))
2445 (define-public r-fastmatch
2447 (name "r-fastmatch")
2452 (uri (cran-uri "fastmatch" version))
2455 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2456 (build-system r-build-system)
2457 (home-page "https://www.rforge.net/fastmatch")
2458 (synopsis "Fast match function")
2460 "This package provides a fast @code{match} replacement for cases that
2461 require repeated look-ups. It is slightly faster that R's built-in
2462 @code{match} function on first match against a table, but extremely fast on
2463 any subsequent lookup as it keeps the hash table in memory.")
2464 (license license:gpl2)))
2473 (uri (cran-uri "ff" version))
2476 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
2477 (build-system r-build-system)
2478 (propagated-inputs `(("r-bit" ,r-bit)))
2479 (home-page "http://ff.r-forge.r-project.org/")
2480 (synopsis "Memory-efficient storage of large data on disk and access functions")
2482 "This package provides data structures that are stored on disk but
2483 behave (almost) as if they were in RAM by transparently mapping only a section
2485 ;; error Architecture not supported.
2486 (supported-systems (delete "aarch64-linux" %supported-systems))
2487 (license license:gpl2)))
2489 (define-public r-ffbase
2496 (uri (cran-uri "ffbase" version))
2499 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2500 (build-system r-build-system)
2503 ("r-fastmatch" ,r-fastmatch)
2505 (home-page "https://github.com/edwindj/ffbase")
2506 (synopsis "Basic statistical functions for package 'ff'")
2508 "This package extends the out of memory vectors of @code{ff} with
2509 statistical functions and other utilities to ease their usage.")
2510 (license license:gpl3)))
2512 (define-public r-prettyunits
2514 (name "r-prettyunits")
2519 (uri (cran-uri "prettyunits" version))
2522 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2523 (build-system r-build-system)
2524 (home-page "https://github.com/gaborcsardi/prettyunits")
2525 (synopsis "Pretty, human readable formatting of quantities")
2527 "This package provides tools for pretty, human readable formatting of
2529 (license license:expat)))
2531 (define-public r-reshape
2538 (uri (cran-uri "reshape" version))
2541 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2542 (build-system r-build-system)
2544 `(("r-plyr" ,r-plyr)
2545 ("r-rcpp" ,r-rcpp)))
2546 (home-page "http://had.co.nz/reshape")
2547 (synopsis "Flexibly reshape data")
2549 "Flexibly restructure and aggregate data using just two functions:
2550 @code{melt} and @code{cast}. This package provides them.")
2551 (license license:expat)))
2553 (define-public r-progress
2560 (uri (cran-uri "progress" version))
2563 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2564 (build-system r-build-system)
2566 `(("r-crayon" ,r-crayon)
2568 ("r-prettyunits" ,r-prettyunits)
2570 (home-page "https://github.com/gaborcsardi/progress")
2571 (synopsis "Terminal progress bars")
2573 "This package provides configurable progress bars. They may include
2574 percentage, elapsed time, and/or the estimated completion time. They work in
2575 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2576 package also provides a C++ API, that works with or without Rcpp.")
2577 (license license:expat)))
2579 (define-public r-ggally
2586 (uri (cran-uri "GGally" version))
2589 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2590 (properties `((upstream-name . "GGally")))
2591 (build-system r-build-system)
2593 `(("libressl" ,libressl)))
2595 `(("r-ggplot2" ,r-ggplot2)
2596 ("r-gtable" ,r-gtable)
2597 ("r-lifecycle" ,r-lifecycle)
2599 ("r-progress" ,r-progress)
2600 ("r-rcolorbrewer" ,r-rcolorbrewer)
2601 ("r-reshape" ,r-reshape)
2602 ("r-rlang" ,r-rlang)
2603 ("r-scales" ,r-scales)))
2604 (home-page "https://ggobi.github.io/ggally")
2605 (synopsis "Extension to ggplot2")
2607 "The R package ggplot2 is a plotting system based on the grammar of
2608 graphics. GGally extends ggplot2 by adding several functions to reduce the
2609 complexity of combining geometric objects with transformed data. Some of
2610 these functions include a pairwise plot matrix, a two group pairwise plot
2611 matrix, a parallel coordinates plot, a survival plot, and several functions to
2613 (license license:gpl2+)))
2615 (define-public r-proxy
2622 (uri (cran-uri "proxy" version))
2625 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2626 (build-system r-build-system)
2627 (home-page "https://cran.r-project.org/web/packages/proxy")
2628 (synopsis "Distance and similarity measures")
2630 "This package provides an extensible framework for the efficient
2631 calculation of auto- and cross-proximities, along with implementations of the
2632 most popular ones.")
2633 (license license:gpl2)))
2642 (uri (cran-uri "sp" version))
2644 (base32 "0zzw1gfic5b311vrbkmmmaap3yllgd192af067l5ymm885jqm1zs"))))
2645 (build-system r-build-system)
2647 `(("r-lattice" ,r-lattice)))
2648 (home-page "https://cran.r-project.org/web/packages/sp")
2649 (synopsis "Classes and methods for spatial data")
2651 "This package provides classes and methods for spatial data; the classes
2652 document where the spatial location information resides, for 2D or 3D data.
2653 Utility functions are provided, e.g. for plotting data as maps, spatial
2654 selection, as well as methods for retrieving coordinates, for subsetting,
2655 print, summary, etc.")
2656 (license license:gpl2+)))
2658 (define-public r-laplacesdemon
2660 (name "r-laplacesdemon")
2665 (uri (cran-uri "LaplacesDemon" version))
2667 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
2668 (properties `((upstream-name . "LaplacesDemon")))
2669 (build-system r-build-system)
2670 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
2671 (synopsis "Complete environment for Bayesian inference")
2673 "This package provides a complete environment for Bayesian inference using
2674 a variety of different samplers.")
2675 (license license:expat)))
2677 (define-public r-rmtstat
2684 (uri (cran-uri "RMTstat" version))
2687 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2688 (properties `((upstream-name . "RMTstat")))
2689 (build-system r-build-system)
2690 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2691 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2693 "This package provides functions for working with the Tracy-Widom laws
2694 and other distributions related to the eigenvalues of large Wishart
2696 (license license:bsd-3)))
2698 (define-public r-rmpi
2704 (uri (cran-uri "Rmpi" version))
2707 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2708 (properties `((upstream-name . "Rmpi")))
2709 (build-system r-build-system)
2711 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2712 #:phases (modify-phases %standard-phases
2713 (add-before 'install 'mpi-setup
2716 `(("openmpi" ,openmpi)))
2718 `(("pkg-config" ,pkg-config)))
2719 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2720 (synopsis "R interface to message-passing interface (MPI)")
2722 "This package provides an interface (wrapper) to MPI APIs. It also
2723 provides an interactive R manager and worker environment.")
2724 (license license:gpl2+)))
2726 (define-public r-lmoments
2733 (uri (cran-uri "Lmoments" version))
2736 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2737 (properties `((upstream-name . "Lmoments")))
2738 (build-system r-build-system)
2740 `(("r-rcpp" ,r-rcpp)
2741 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2742 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2743 (synopsis "L-moments and quantile mixtures")
2745 "This package contains functions to estimate L-moments and trimmed
2746 L-moments from the data. It also contains functions to estimate the
2747 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2748 quantile mixture from L-moments and trimmed L-moments.")
2749 (license license:gpl2)))
2751 (define-public r-distillery
2753 (name "r-distillery")
2758 (uri (cran-uri "distillery" version))
2761 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
2762 (build-system r-build-system)
2763 (home-page "https://ral.ucar.edu/staff/ericg/")
2764 (synopsis "Functions for confidence intervals and object information")
2766 "This package provides some very simple method functions for confidence
2767 interval calculation and to distill pertinent information from a potentially
2768 complex object; primarily used in common with the packages extRemes and
2770 (license license:gpl2+)))
2772 (define-public r-extremes
2779 (uri (cran-uri "extRemes" version))
2782 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2783 (properties `((upstream-name . "extRemes")))
2784 (build-system r-build-system)
2786 `(("r-distillery" ,r-distillery)
2787 ("r-lmoments" ,r-lmoments)))
2788 (home-page "https://www.assessment.ucar.edu/toolkit/")
2789 (synopsis "Extreme value analysis")
2791 "ExtRemes is a suite of functions for carrying out analyses on the
2792 extreme values of a process of interest; be they block maxima over long blocks
2793 or excesses over a high threshold.")
2794 (license license:gpl2+)))
2796 (define-public r-lmtest
2803 (uri (cran-uri "lmtest" version))
2806 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
2807 (build-system r-build-system)
2809 `(("r-zoo" ,r-zoo)))
2811 `(("gfortran" ,gfortran)))
2812 (home-page "https://cran.r-project.org/web/packages/lmtest")
2813 (synopsis "Testing linear regression models")
2815 "This package provides a collection of tests, data sets, and examples for
2816 diagnostic checking in linear regression models. Furthermore, some generic
2817 tools for inference in parametric models are provided.")
2818 ;; Either version is okay
2819 (license (list license:gpl2 license:gpl3))))
2821 (define-public r-idr
2827 (uri (cran-uri "idr" version))
2830 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2831 (build-system r-build-system)
2832 (home-page "https://cran.r-project.org/web/packages/idr/")
2833 (synopsis "Irreproducible discovery rate")
2835 "This is a package for estimating the copula mixture model and plotting
2836 correspondence curves in \"Measuring reproducibility of high-throughput
2837 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2838 by Li, Brown, Huang, and Bickel")
2839 (license license:gpl2+)))
2841 (define-public r-inline
2847 (uri (cran-uri "inline" version))
2850 "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj"))))
2851 (build-system r-build-system)
2852 (home-page "https://cran.r-project.org/web/packages/inline")
2853 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2855 "This package provides functionality to dynamically define R functions
2856 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2857 @code{.Call} calling conventions.")
2858 ;; Any version of the LGPL.
2859 (license license:lgpl3+)))
2861 (define-public r-inum
2867 (uri (cran-uri "inum" version))
2870 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2871 (build-system r-build-system)
2873 `(("r-libcoin" ,r-libcoin)))
2874 (home-page "https://cran.r-project.org/web/packages/inum/")
2875 (synopsis "Interval and enum-type representation of vectors")
2877 "This package provides an enum-type representation of vectors and
2878 representation of intervals, including a method of coercing variables
2880 (license license:gpl2)))
2882 (define-public r-bdsmatrix
2884 (name "r-bdsmatrix")
2889 (uri (cran-uri "bdsmatrix" version))
2892 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2893 (properties `((upstream-name . "bdsmatrix")))
2894 (build-system r-build-system)
2895 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2896 (synopsis "Routines for block diagonal symmetric matrices")
2898 "This package provides procedures to work with block diagonal symmetric
2899 matrices, a special case of sparse matrices.")
2900 (license license:lgpl2.0)))
2902 (define-public r-bbmle
2905 (version "1.0.23.1")
2909 (uri (cran-uri "bbmle" version))
2912 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2913 (build-system r-build-system)
2915 `(("r-bdsmatrix" ,r-bdsmatrix)
2916 ("r-lattice" ,r-lattice)
2918 ("r-matrix" ,r-matrix)
2919 ("r-mvtnorm" ,r-mvtnorm)
2920 ("r-numderiv" ,r-numderiv)))
2921 (home-page "https://cran.r-project.org/web/packages/bbmle")
2922 (synopsis "Tools for General Maximum Likelihood Estimation")
2924 "This package provides methods and functions for fitting maximum
2925 likelihood models in R. This package modifies and extends the @code{mle}
2926 classes in the @code{stats4} package.")
2927 ;; Any version of the GPL
2928 (license license:gpl2+)))
2930 (define-public r-emdbook
2937 (uri (cran-uri "emdbook" version))
2940 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2941 (build-system r-build-system)
2943 `(("r-bbmle" ,r-bbmle)
2945 ("r-lattice" ,r-lattice)
2947 ("r-plyr" ,r-plyr)))
2948 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2949 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2951 "This package provides auxiliary functions and data sets for \"Ecological
2952 Models and Data\", a book presenting maximum likelihood estimation and related
2953 topics for ecologists (ISBN 978-0-691-12522-0).")
2955 (license (list license:gpl2 license:gpl3))))
2957 (define-public r-lpsolve
2964 (uri (cran-uri "lpSolve" version))
2967 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2968 (properties `((upstream-name . "lpSolve")))
2969 (build-system r-build-system)
2970 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2971 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2973 "Lp_solve is software for solving linear, integer and mixed integer
2974 programs. This implementation supplies a \"wrapper\" function in C and some R
2975 functions that solve general linear/integer problems, assignment problems, and
2976 transportation problems.")
2977 (license license:lgpl2.0)))
2979 (define-public r-limsolve
2986 (uri (cran-uri "limSolve" version))
2989 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2990 (properties `((upstream-name . "limSolve")))
2991 (build-system r-build-system)
2993 `(("r-lpsolve" ,r-lpsolve)
2995 ("r-quadprog" ,r-quadprog)))
2996 (native-inputs `(("gfortran" ,gfortran)))
2997 (home-page "https://cran.r-project.org/web/packages/limSolve")
2998 (synopsis "Solving linear inverse models")
3000 "This package provides functions that:
3003 @item find the minimum/maximum of a linear or quadratic function,
3004 @item sample an underdetermined or overdetermined system,
3005 @item solve a linear system Ax=B for the unknown x.
3008 It includes banded and tridiagonal linear systems. The package calls Fortran
3009 functions from LINPACK.")
3011 (license (list license:gpl2+ license:gpl3+))))
3013 (define-public r-fitdistrplus
3015 (name "r-fitdistrplus")
3020 (uri (cran-uri "fitdistrplus" version))
3023 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
3024 (build-system r-build-system)
3026 `(("r-mass" ,r-mass)
3027 ("r-survival" ,r-survival)))
3029 `(("r-knitr" ,r-knitr)))
3030 (home-page "http://riskassessment.r-forge.r-project.org")
3031 (synopsis "Fitting a parametric distribution from data")
3033 "This package extends the @code{fitdistr} function of the MASS package
3034 with several functions to help the fit of a parametric distribution to
3035 non-censored or censored data. Censored data may contain left-censored,
3036 right-censored and interval-censored values, with several lower and upper
3037 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3038 provides moment matching (MME), quantile matching (QME) and maximum
3039 goodness-of-fit estimation (MGE) methods (available only for non-censored
3040 data). Weighted versions of MLE, MME and QME are available.")
3041 (license license:gpl2+)))
3043 (define-public r-energy
3050 (uri (cran-uri "energy" version))
3053 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3054 (build-system r-build-system)
3056 `(("r-boot" ,r-boot)
3057 ("r-rcpp" ,r-rcpp)))
3058 (home-page "https://cran.r-project.org/web/packages/energy")
3059 (synopsis "Multivariate inference via the energy of data")
3061 "This package provides e-statistics (energy) tests and statistics for
3062 multivariate and univariate inference, including distance correlation,
3063 one-sample, two-sample, and multi-sample tests for comparing multivariate
3064 distributions, are implemented. Measuring and testing multivariate
3065 independence based on distance correlation, partial distance correlation,
3066 multivariate goodness-of-fit tests, clustering based on energy distance,
3067 testing for multivariate normality, distance components (disco) for
3068 non-parametric analysis of structured data, and other energy
3069 statistics/methods are implemented.")
3070 (license license:gpl2+)))
3072 (define-public r-suppdists
3074 (name "r-suppdists")
3079 (uri (cran-uri "SuppDists" version))
3082 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3083 (properties `((upstream-name . "SuppDists")))
3084 (build-system r-build-system)
3085 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3086 (synopsis "Supplementary distributions")
3088 "This package provides ten distributions supplementing those built into
3089 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3090 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3091 coefficient, Johnson distributions, normal scores and generalized
3092 hypergeometric distributions. In addition two random number generators of
3093 George Marsaglia are included.")
3094 (license license:gpl2+)))
3096 (define-public r-ksamples
3103 (uri (cran-uri "kSamples" version))
3106 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3107 (properties `((upstream-name . "kSamples")))
3108 (build-system r-build-system)
3110 `(("r-suppdists" ,r-suppdists)))
3111 (home-page "https://cran.r-project.org/web/packages/kSamples")
3112 (synopsis "K-Sample rank tests and their combinations")
3114 "This package provides tools to compares k samples using the
3115 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3116 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3117 test. It computes asymptotic, simulated or (limited) exact P-values, all
3118 valid under randomization, with or without ties, or conditionally under random
3119 sampling from populations, given the observed tie pattern. Except for Steel's
3120 test and the JT test it also combines these tests across several blocks of
3122 (license license:gpl2+)))
3124 (define-public r-cvst
3131 (uri (cran-uri "CVST" version))
3134 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3135 (properties `((upstream-name . "CVST")))
3136 (build-system r-build-system)
3138 `(("r-kernlab" ,r-kernlab)
3139 ("r-matrix" ,r-matrix)))
3140 (home-page "https://cran.r-project.org/web/packages/CVST")
3141 (synopsis "Fast cross-validation via sequential testing")
3143 "This package implements the fast cross-validation via sequential
3144 testing (CVST) procedure. CVST is an improved cross-validation procedure
3145 which uses non-parametric testing coupled with sequential analysis to
3146 determine the best parameter set on linearly increasing subsets of the data.
3147 Additionally to the CVST the package contains an implementation of the
3148 ordinary k-fold cross-validation with a flexible and powerful set of helper
3149 objects and methods to handle the overall model selection process. The
3150 implementations of the Cochran's Q test with permutations and the sequential
3151 testing framework of Wald are generic and can therefore also be used in other
3153 (license license:gpl2+)))
3155 (define-public r-squarem
3162 (uri (cran-uri "SQUAREM" version))
3165 "1f0j5pbsz2wi7dfl8h8gvdl991bjywiwkd2f6z0xgkh87kl5y0b4"))))
3166 (properties `((upstream-name . "SQUAREM")))
3167 (build-system r-build-system)
3168 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3169 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3171 "This package provides algorithms for accelerating the convergence of
3172 slow, monotone sequences from smooth, contraction mapping such as the EM
3173 algorithm. It can be used to accelerate any smooth, linearly convergent
3174 acceleration scheme. A tutorial style introduction to this package is
3175 available in a vignette.")
3176 (license license:gpl2+)))
3178 (define-public r-lava
3185 (uri (cran-uri "lava" version))
3188 "0jdmjjs894mfncswmzz7sa6cy7hqbqii5fcvl3zqkmzpbadb2za2"))))
3189 (build-system r-build-system)
3191 `(("r-numderiv" ,r-numderiv)
3192 ("r-squarem" ,r-squarem)
3193 ("r-survival" ,r-survival)))
3195 `(("r-knitr" ,r-knitr)))
3196 (home-page "https://github.com/kkholst/lava")
3197 (synopsis "Latent variable models")
3199 "This package provides tools for the estimation and simulation of latent
3201 (license license:gpl3)))
3203 (define-public r-drr
3210 (uri (cran-uri "DRR" version))
3213 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3214 (properties `((upstream-name . "DRR")))
3215 (build-system r-build-system)
3217 `(("r-cvst" ,r-cvst)
3218 ("r-kernlab" ,r-kernlab)
3219 ("r-matrix" ,r-matrix)))
3220 (home-page "https://cran.r-project.org/web/packages/DRR")
3221 (synopsis "Dimensionality reduction via regression")
3223 "This package provides an implementation of dimensionality reduction via
3224 regression using Kernel Ridge Regression.")
3225 (license license:gpl3)))
3227 (define-public r-prodlim
3230 (version "2019.11.13")
3234 (uri (cran-uri "prodlim" version))
3237 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3238 (build-system r-build-system)
3240 `(("r-kernsmooth" ,r-kernsmooth)
3243 ("r-survival" ,r-survival)))
3244 (home-page "https://cran.r-project.org/web/packages/prodlim")
3245 (synopsis "Product-limit estimation for censored event history analysis")
3247 "This package provides a fast and user-friendly implementation of
3248 nonparametric estimators for censored event history (survival) analysis with
3249 the Kaplan-Meier and Aalen-Johansen methods.")
3250 (license license:gpl2+)))
3252 (define-public r-dimred
3259 (uri (cran-uri "dimRed" version))
3262 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3263 (properties `((upstream-name . "dimRed")))
3264 (build-system r-build-system)
3267 ("r-magrittr" ,r-magrittr)))
3268 (home-page "https://github.com/gdkrmr/dimRed")
3269 (synopsis "Framework for dimensionality reduction")
3271 "This package provides a collection of dimensionality reduction
3272 techniques from R packages and provides a common interface for calling the
3274 (license license:gpl3)))
3276 (define-public r-timedate
3279 (version "3043.102")
3283 (uri (cran-uri "timeDate" version))
3286 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3287 (properties `((upstream-name . "timeDate")))
3288 (build-system r-build-system)
3289 (home-page "https://www.rmetrics.org")
3290 (synopsis "Chronological and calendar objects")
3292 "This package provides an environment for teaching \"Financial
3293 Engineering and Computational Finance\" and for managing chronological and
3295 (license license:gpl2+)))
3297 (define-public r-magic
3304 (uri (cran-uri "magic" version))
3307 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3308 (build-system r-build-system)
3310 `(("r-abind" ,r-abind)))
3311 (home-page "https://github.com/RobinHankin/magic.git")
3312 (synopsis "Create and investigate magic squares")
3314 "This package provides a collection of efficient, vectorized algorithms
3315 for the creation and investigation of magic squares and hypercubes, including
3316 a variety of functions for the manipulation and analysis of arbitrarily
3317 dimensioned arrays.")
3318 (license license:gpl2)))
3320 (define-public r-rmysql
3327 (uri (cran-uri "RMySQL" version))
3330 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3331 (properties `((upstream-name . "RMySQL")))
3332 (build-system r-build-system)
3334 `(("mariadb" ,mariadb "lib")
3335 ("mariadb-dev" ,mariadb "dev")
3338 `(("r-dbi" ,r-dbi)))
3339 (home-page "https://github.com/r-dbi/RMySQL")
3340 (synopsis "Database interface and MySQL driver for R")
3342 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3343 package contains an old implementation based on legacy code from S-PLUS which
3344 is being phased out. A modern MySQL client based on Rcpp is available from
3345 the RMariaDB package.")
3346 (license license:gpl2)))
3348 (define-public r-rpostgresql
3350 (name "r-rpostgresql")
3355 (uri (cran-uri "RPostgreSQL" version))
3358 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3359 (properties `((upstream-name . "RPostgreSQL")))
3360 (build-system r-build-system)
3362 `(("postgresql" ,postgresql)))
3364 `(("r-dbi" ,r-dbi)))
3365 (home-page "https://github.com/tomoakin/RPostgreSQL")
3366 (synopsis "R interface to the PostgreSQL database system")
3368 "This package provides a Database Interface (DBI) compliant driver for R
3369 to access PostgreSQL database systems.")
3370 ;; The whole package is released under GPL version 2. It includes code
3371 ;; under the PostgreSQL license.
3372 (license license:gpl2)))
3374 (define-public r-linprog
3381 (uri (cran-uri "linprog" version))
3384 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3385 (build-system r-build-system)
3386 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3387 (home-page "http://linprog.r-forge.r-project.org/")
3388 (synopsis "Linear programming and optimization")
3390 "This package can be used to solve Linear Programming / Linear
3391 Optimization problems by using the simplex algorithm.")
3392 (license license:gpl2+)))
3394 (define-public r-geometry
3401 (uri (cran-uri "geometry" version))
3404 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3405 (build-system r-build-system)
3407 `(("r-magic" ,r-magic)
3408 ("r-linprog" ,r-linprog)
3409 ("r-lpsolve" ,r-lpsolve)
3411 ("r-rcppprogress" ,r-rcppprogress)))
3412 (home-page "http://geometry.r-forge.r-project.org/")
3413 (synopsis "Mesh generator and surface tessellator")
3415 "This package makes the qhull library available in R, in a similar manner
3416 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3417 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3418 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3419 and higher dimensions. It implements the Quickhull algorithm for computing
3420 the convex hull. Qhull does not support constrained Delaunay triangulations,
3421 or mesh generation of non-convex objects, but the package does include some R
3422 functions that allow for this. Currently the package only gives access to
3423 Delaunay triangulation and convex hull computation.")
3424 ;; The Qhull sources are included and are distributed under a custom
3425 ;; non-copyleft license. The R sources are released under GPL version 2.
3426 (license (list license:gpl2
3427 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3429 (define-public r-ddalpha
3436 (uri (cran-uri "ddalpha" version))
3439 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3440 (build-system r-build-system)
3443 ("r-class" ,r-class)
3444 ("r-geometry" ,r-geometry)
3447 ("r-robustbase" ,r-robustbase)
3448 ("r-sfsmisc" ,r-sfsmisc)))
3450 `(("gfortran" ,gfortran)))
3451 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3452 (synopsis "Depth-Based classification and calculation of data depth")
3454 "This package contains procedures for depth-based supervised learning,
3455 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3456 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3457 statistical depth function to a compact low-dimensional space, where the final
3458 classification is done. It also offers an extension to functional data and
3459 routines for calculating certain notions of statistical depth functions. 50
3460 multivariate and 5 functional classification problems are included.")
3461 (license license:gpl2)))
3463 (define-public r-gower
3470 (uri (cran-uri "gower" version))
3473 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3474 (build-system r-build-system)
3475 (home-page "https://github.com/markvanderloo/gower")
3476 (synopsis "Gower's distance")
3478 "This package provides tools to compute Gower's distance (or similarity)
3479 coefficient between records, and to compute the top-n matches between records.
3480 Core algorithms are executed in parallel on systems supporting OpenMP.")
3481 (license license:gpl3)))
3483 (define-public r-rcpproll
3490 (uri (cran-uri "RcppRoll" version))
3493 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3494 (properties `((upstream-name . "RcppRoll")))
3495 (build-system r-build-system)
3497 `(("r-rcpp" ,r-rcpp)))
3498 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3499 (synopsis "Efficient rolling and windowed operations")
3501 "This package provides fast and efficient routines for common rolling /
3502 windowed operations. Routines for the efficient computation of windowed mean,
3503 median, sum, product, minimum, maximum, standard deviation and variance are
3505 (license license:gpl2+)))
3507 (define-public r-ipred
3514 (uri (cran-uri "ipred" version))
3517 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3518 (build-system r-build-system)
3520 `(("r-class" ,r-class)
3523 ("r-prodlim" ,r-prodlim)
3524 ("r-rpart" ,r-rpart)
3525 ("r-survival" ,r-survival)))
3526 (home-page "https://cran.r-project.org/web/packages/ipred")
3527 (synopsis "Improved predictors")
3529 "This package provides improved predictive models by indirect
3530 classification and bagging for classification, regression and survival
3531 problems as well as resampling based estimators of prediction error.")
3532 (license license:gpl2+)))
3534 (define-public r-psych
3541 (uri (cran-uri "psych" version))
3544 "0wdh580a0psbdil28n0d85hnp42wmn11hcbnihjq8r7h54drgzpn"))))
3545 (build-system r-build-system)
3547 `(("r-lattice" ,r-lattice)
3548 ("r-mnormt" ,r-mnormt)
3549 ("r-nlme" ,r-nlme)))
3550 (home-page "https://cran.r-project.org/web/packages/psych/")
3551 (synopsis "Procedures for psychological, psychometric, and personality research")
3553 "This package provides a general purpose toolbox for personality,
3554 psychometric theory and experimental psychology. Functions are primarily for
3555 multivariate analysis and scale construction using factor analysis, principal
3556 component analysis, cluster analysis and reliability analysis, although others
3557 provide basic descriptive statistics. Item Response Theory is done using
3558 factor analysis of tetrachoric and polychoric correlations. Functions for
3559 analyzing data at multiple levels include within and between group statistics,
3560 including correlations and factor analysis. Functions for simulating and
3561 testing particular item and test structures are included. Several functions
3562 serve as a useful front end for structural equation modeling. Graphical
3563 displays of path diagrams, factor analysis and structural equation models are
3564 created using basic graphics.")
3565 (license license:gpl2+)))
3567 (define-public r-generics
3574 (uri (cran-uri "generics" version))
3577 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3578 (build-system r-build-system)
3579 (home-page "https://github.com/r-lib/generics")
3580 (synopsis "Common S3 generics not provided by base R methods")
3582 "In order to reduce potential package dependencies and conflicts,
3583 generics provides a number of commonly used S3 generics that are not provided
3584 by base R methods related to model fitting.")
3585 (license license:gpl2)))
3587 (define-public r-broom
3594 (uri (cran-uri "broom" version))
3597 "18qkgw5f46cfr8sc7r9a261ivn3s4w88sdj653gaa20723179300"))))
3598 (build-system r-build-system)
3600 `(("r-backports" ,r-backports)
3601 ("r-dplyr" ,r-dplyr)
3602 ("r-ellipsis" ,r-ellipsis)
3603 ("r-generics" ,r-generics)
3605 ("r-purrr" ,r-purrr)
3606 ("r-rlang" ,r-rlang)
3607 ("r-stringr" ,r-stringr)
3608 ("r-tibble" ,r-tibble)
3609 ("r-tidyr" ,r-tidyr)))
3611 `(("r-knitr" ,r-knitr)))
3612 (home-page "https://github.com/tidyverse/broom")
3613 (synopsis "Convert statistical analysis objects into tidy data frames")
3615 "This package provides tools to convert statistical analysis objects from
3616 R into tidy data frames, so that they can more easily be combined, reshaped
3617 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3618 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3619 summarizes a model's statistical findings such as coefficients of a
3620 regression; @code{augment}, which adds columns to the original data such as
3621 predictions, residuals and cluster assignments; and @code{glance}, which
3622 provides a one-row summary of model-level statistics.")
3623 (license license:expat)))
3625 (define-public r-recipes
3632 (uri (cran-uri "recipes" version))
3635 "0ix678aj71ml5cmfhy1j0b2ddhf5wlb1d74bjc9djr6r86xsqmcz"))))
3636 (build-system r-build-system)
3638 `(("r-dplyr" ,r-dplyr)
3639 ("r-generics" ,r-generics)
3641 ("r-gower" ,r-gower)
3642 ("r-ipred" ,r-ipred)
3643 ("r-lifecycle" ,r-lifecycle)
3644 ("r-lubridate" ,r-lubridate)
3645 ("r-magrittr" ,r-magrittr)
3646 ("r-matrix" ,r-matrix)
3647 ("r-purrr" ,r-purrr)
3648 ("r-rlang" ,r-rlang)
3649 ("r-tibble" ,r-tibble)
3650 ("r-tidyr" ,r-tidyr)
3651 ("r-tidyselect" ,r-tidyselect)
3652 ("r-timedate" ,r-timedate)
3653 ("r-withr" ,r-withr)))
3655 `(("r-knitr" ,r-knitr)))
3656 (home-page "https://github.com/topepo/recipes")
3657 (synopsis "Preprocessing tools to create design matrices")
3659 "Recipes is an extensible framework to create and preprocess design
3660 matrices. Recipes consist of one or more data manipulation and analysis
3661 \"steps\". Statistical parameters for the steps can be estimated from an
3662 initial data set and then applied to other data sets. The resulting design
3663 matrices can then be used as inputs into statistical or machine learning
3665 (license license:gpl2)))
3667 (define-public r-pdist
3674 (uri (cran-uri "pdist" version))
3677 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3678 (build-system r-build-system)
3679 (home-page "https://github.com/jeffwong/pdist")
3680 (synopsis "Partitioned distance function")
3682 "Pdist computes the euclidean distance between rows of a matrix X and
3683 rows of another matrix Y. Previously, this could be done by binding the two
3684 matrices together and calling @code{dist}, but this creates unnecessary
3685 computation by computing the distances between a row of X and another row of
3686 X, and likewise for Y. Pdist strictly computes distances across the two
3687 matrices, not within the same matrix, making computations significantly faster
3688 for certain use cases.")
3689 (license license:gpl3+)))
3691 (define-public r-ggrepel
3698 (uri (cran-uri "ggrepel" version))
3701 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3702 (build-system r-build-system)
3704 `(("r-ggplot2" ,r-ggplot2)
3706 ("r-scales" ,r-scales)))
3708 `(("r-knitr" ,r-knitr))) ; for vignettes
3709 (home-page "https://github.com/slowkow/ggrepel")
3710 (synopsis "Repulsive text and label geometries for ggplot2")
3712 "This package provides text and label geometries for ggplot2 that help to
3713 avoid overlapping text labels. Labels repel away from each other and away
3714 from the data points.")
3715 (license license:gpl3)))
3717 (define-public r-corrplot
3724 (uri (cran-uri "corrplot" version))
3727 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3728 (build-system r-build-system)
3729 (home-page "https://github.com/taiyun/corrplot")
3730 (synopsis "Visualization of a correlation matrix")
3732 "This package provides a graphical display of a correlation matrix or
3733 general matrix. It also contains some algorithms to do matrix reordering. In
3734 addition, corrplot is good at details, including choosing color, text labels,
3735 color labels, layout, etc.")
3736 ;; Any version of the GPL
3737 (license license:gpl2+)))
3739 (define-public r-stringdist
3741 (name "r-stringdist")
3746 (uri (cran-uri "stringdist" version))
3748 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
3749 (build-system r-build-system)
3750 (home-page "https://github.com/markvanderloo/stringdist")
3751 (synopsis "Approximate string matching and string distance functions")
3753 "This package implements an approximate string matching version of R's
3754 native @code{match} function. It can calculate various string distances based
3755 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
3756 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3757 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3758 can be computed between character vectors while taking proper care of encoding
3759 or between integer vectors representing generic sequences.")
3760 (license license:gpl3+)))
3762 (define-public r-ucminf
3769 (uri (cran-uri "ucminf" version))
3772 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3773 (build-system r-build-system)
3774 (native-inputs `(("gfortran" ,gfortran)))
3775 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3776 (synopsis "General-purpose unconstrained non-linear optimization")
3778 "This package provides an implementation of an algorithm for
3779 general-purpose unconstrained non-linear optimization. The algorithm is of
3780 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3781 search with a trust region type monitoring of the input to the line search
3782 algorithm. The interface of @code{ucminf} is designed for easy interchange
3783 with the package @code{optim}.")
3784 (license license:gpl2+)))
3786 (define-public r-useful
3792 (uri (cran-uri "useful" version))
3795 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
3796 (properties `((upstream-name . "useful")))
3797 (build-system r-build-system)
3799 `(("r-assertthat" ,r-assertthat)
3800 ("r-dplyr" ,r-dplyr)
3801 ("r-ggplot2" ,r-ggplot2)
3802 ("r-magrittr" ,r-magrittr)
3803 ("r-matrix" ,r-matrix)
3805 ("r-purrr" ,r-purrr)
3806 ("r-scales" ,r-scales)))
3807 (home-page "https://github.com/jaredlander/useful")
3808 (synopsis "Collection of handy, useful functions")
3809 (description "This package provides a set of little functions that have been
3810 found useful to do little odds and ends such as plotting the results of K-means
3811 clustering, substituting special text characters, viewing parts of a
3812 @code{data.frame}, constructing formulas from text and building design and
3813 response matrices.")
3814 (license license:bsd-3)))
3816 (define-public r-ordinal
3819 (version "2019.12-10")
3823 (uri (cran-uri "ordinal" version))
3826 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3827 (build-system r-build-system)
3829 `(("r-mass" ,r-mass)
3830 ("r-matrix" ,r-matrix)
3831 ("r-numderiv" ,r-numderiv)
3832 ("r-ucminf" ,r-ucminf)))
3833 (home-page "https://github.com/runehaubo/ordinal")
3834 (synopsis "Regression models for ordinal data")
3836 "This package provides an implementation of cumulative link (mixed)
3837 models also known as ordered regression models, proportional odds models,
3838 proportional hazards models for grouped survival times and ordered models.
3839 Estimation is via maximum likelihood and mixed models are fitted with the
3840 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3841 (license license:gpl2+)))
3843 (define-public r-jomo
3850 (uri (cran-uri "jomo" version))
3853 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
3854 (build-system r-build-system)
3856 `(("r-lme4" ,r-lme4)
3858 ("r-ordinal" ,r-ordinal)
3859 ("r-survival" ,r-survival)))
3860 (home-page "https://cran.r-project.org/web/packages/jomo/")
3861 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3863 "Similarly to Schafer's package pan, jomo is a package for multilevel
3864 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3865 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3866 possibility of handling binary and categorical data through latent normal
3867 variables, the option to use cluster-specific covariance matrices and to
3868 impute compatibly with the substantive model.")
3869 (license license:gpl2)))
3871 (define-public r-pan
3878 (uri (cran-uri "pan" version))
3881 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3882 (build-system r-build-system)
3883 (native-inputs `(("gfortran" ,gfortran)))
3884 (home-page "https://cran.r-project.org/web/packages/pan/")
3885 (synopsis "Multiple imputation for multivariate panel or clustered data")
3887 "This package implements multiple imputation for multivariate panel or
3889 (license license:gpl3)))
3891 (define-public r-mitml
3898 (uri (cran-uri "mitml" version))
3901 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3902 (build-system r-build-system)
3904 `(("r-haven" ,r-haven)
3907 (home-page "https://cran.r-project.org/web/packages/mitml/")
3908 (synopsis "Tools for multiple imputation in multilevel modeling")
3910 "This package provides tools for multiple imputation of missing data in
3911 multilevel modeling. It includes a user-friendly interface to the packages
3912 pan and jomo, and several functions for visualization, data management and the
3913 analysis of multiply imputed data sets.")
3914 (license license:gpl2+)))
3916 (define-public r-mice
3923 (uri (cran-uri "mice" version))
3926 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
3927 (build-system r-build-system)
3929 `(("r-broom" ,r-broom)
3930 ("r-dplyr" ,r-dplyr)
3931 ("r-generics" ,r-generics)
3932 ("r-lattice" ,r-lattice)
3934 ("r-tidyr" ,r-tidyr)))
3935 (home-page "https://cran.r-project.org/web/packages/mice/")
3936 (synopsis "Multivariate imputation by chained equations")
3938 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3939 implemented by the MICE algorithm as described in @url{Van Buuren and
3940 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3941 variable has its own imputation model. Built-in imputation models are
3942 provided for continuous data (predictive mean matching, normal), binary
3943 data (logistic regression), unordered categorical data (polytomous logistic
3944 regression) and ordered categorical data (proportional odds). MICE can also
3945 impute continuous two-level data (normal model, pan, second-level variables).
3946 Passive imputation can be used to maintain consistency between variables.
3947 Various diagnostic plots are available to inspect the quality of the
3949 ;; Any of these two versions.
3950 (license (list license:gpl2 license:gpl3))))
3952 (define-public r-truncnorm
3954 (name "r-truncnorm")
3959 (uri (cran-uri "truncnorm" version))
3962 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3963 (build-system r-build-system)
3964 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3965 (synopsis "Truncated normal distribution")
3966 (description "This package provides functions for the truncated normal
3967 distribution with mean equal to @code{mean} and standard deviation equal to
3968 @code{sd}. It includes density, distribution, quantile, and expected value
3969 functions, as well as a random generation function.")
3970 (license license:gpl2)))
3972 (define-public r-rsolnp
3979 (uri (cran-uri "Rsolnp" version))
3982 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3983 (properties `((upstream-name . "Rsolnp")))
3984 (build-system r-build-system)
3986 `(("r-truncnorm" ,r-truncnorm)))
3987 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3988 (synopsis "General non-linear optimization")
3989 (description "The Rsolnp package implements a general non-linear augmented
3990 Lagrange multiplier method solver, a @dfn{sequential quadratic
3991 programming} (SQP) based solver).")
3992 ;; Any version of the GPL.
3993 (license license:gpl2+)))
3995 (define-public r-hardyweinberg
3997 (name "r-hardyweinberg")
4002 (uri (cran-uri "HardyWeinberg" version))
4005 "0b6j1mkpr7ck2nr9fmpnsjdv29jc6vg4b91cg50skmcgky1j0zi7"))))
4006 (properties `((upstream-name . "HardyWeinberg")))
4007 (build-system r-build-system)
4009 `(("r-mice" ,r-mice)
4011 ("r-rsolnp" ,r-rsolnp)))
4012 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4013 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4015 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4016 diallelic genetic marker data. All classical tests (chi-square, exact,
4017 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4018 included in the package, as well as functions for power computation and for
4019 the simulation of marker data under equilibrium and disequilibrium. Routines
4020 for dealing with markers on the X-chromosome are included. Functions for
4021 testing equilibrium in the presence of missing data by using multiple
4022 imputation are also provided. Implements several graphics for exploring the
4023 equilibrium status of a large set of diallelic markers: ternary plots with
4024 acceptance regions, log-ratio plots and Q-Q plots.")
4025 (license license:gpl2+)))
4034 (uri (cran-uri "sm" version))
4037 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4038 (build-system r-build-system)
4039 (native-inputs `(("gfortran" ,gfortran)))
4040 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4041 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4043 "This is software accompanying the book 'Applied Smoothing Techniques for
4044 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4045 University Press. It provides smoothing methods for nonparametric regression
4046 and density estimation")
4047 (license license:gpl2+)))
4049 (define-public r-venndiagram
4051 (name "r-venndiagram")
4055 (uri (cran-uri "VennDiagram" version))
4058 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4059 (properties `((upstream-name . "VennDiagram")))
4060 (build-system r-build-system)
4062 `(("r-futile-logger" ,r-futile-logger)))
4063 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4064 (synopsis "Generate High-Resolution Venn and Euler Plots")
4066 "This package provides a set of functions to generate high-resolution
4067 Venn and Euler plots. It includes handling for several special cases,
4068 including two-case scaling, and extensive customization of plot shape and
4070 (license license:gpl2+)))
4072 (define-public r-vioplot
4079 (uri (cran-uri "vioplot" version))
4082 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4083 (build-system r-build-system)
4088 `(("r-knitr" ,r-knitr)))
4089 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4090 (synopsis "Violin plot")
4092 "This package provides a violin plot, which is a combination of a box
4093 plot and a kernel density plot.")
4094 (license license:bsd-3)))
4096 (define-public r-rsofia
4102 ;; This package has been removed from CRAN, so we can
4103 ;; only fetch it from the archives.
4104 (uri (string-append "https://cran.r-project.org/src/"
4105 "contrib/Archive/RSofia/RSofia_"
4109 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4110 (properties `((upstream-name . "RSofia")))
4111 (build-system r-build-system)
4113 `(("r-rcpp" ,r-rcpp)))
4114 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4115 (synopsis "Port of sofia-ml to R")
4116 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4117 suite of fast incremental algorithms for machine learning that can be used for
4118 training models for classification or ranking.")
4119 (license license:asl2.0)))
4121 (define-public r-xts
4128 (uri (cran-uri "xts" version))
4131 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4132 (build-system r-build-system)
4133 (propagated-inputs `(("r-zoo" ,r-zoo)))
4134 (home-page "https://github.com/joshuaulrich/xts")
4135 (synopsis "Extensible time series")
4137 "This package provides for uniform handling of R's different time-based
4138 data classes by extending @code{zoo}, maximizing native format information
4139 preservation and allowing for user-level customization and extension, while
4140 simplifying cross-class interoperability.")
4141 (license license:gpl2+)))
4143 (define-public r-performanceanalytics
4145 (name "r-performanceanalytics")
4150 (uri (cran-uri "PerformanceAnalytics" version))
4153 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4155 `((upstream-name . "PerformanceAnalytics")))
4156 (build-system r-build-system)
4158 `(("r-quadprog" ,r-quadprog)
4161 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4162 (synopsis "Econometric tools for performance and risk analysis")
4163 (description "This is a collection of econometric functions for
4164 performance and risk analysis. This package aims to aid practitioners and
4165 researchers in utilizing the latest research in analysis of non-normal return
4166 streams. In general, it is most tested on return (rather than price) data on
4167 a regular scale, but most functions will work with irregular return data as
4168 well, and increasing numbers of functions will work with P&L or price data
4170 ;; Either version may be picked.
4171 (license (list license:gpl2 license:gpl3))))
4173 (define-public r-laeken
4180 (uri (cran-uri "laeken" version))
4183 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4184 (build-system r-build-system)
4186 `(("r-boot" ,r-boot)
4187 ("r-mass" ,r-mass)))
4188 (home-page "https://cran.r-project.org/web/packages/laeken/")
4189 (synopsis "Estimation of indicators on social exclusion and poverty")
4190 (description "This package provides tools for the estimation of indicators
4191 on social exclusion and poverty, as well as an implementation of Pareto tail
4192 modeling for empirical income distributions.")
4193 (license license:gpl2+)))
4195 (define-public r-vcd
4202 (uri (cran-uri "vcd" version))
4205 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4206 (build-system r-build-system)
4208 `(("r-colorspace" ,r-colorspace)
4209 ("r-lmtest" ,r-lmtest)
4210 ("r-mass" ,r-mass)))
4211 (home-page "https://cran.r-project.org/web/packages/vcd/")
4212 (synopsis "Visualizing categorical data")
4213 (description "This package provides visualization techniques, data sets,
4214 summary and inference procedures aimed particularly at categorical data.
4215 Special emphasis is given to highly extensible grid graphics. The package was
4216 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4217 Friendly and is now the main support package for a new book, \"Discrete Data
4218 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4219 (license license:gpl2)))
4221 (define-public r-ica
4228 (uri (cran-uri "ica" version))
4231 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4232 (build-system r-build-system)
4233 (home-page "https://cran.r-project.org/web/packages/ica/")
4234 (synopsis "Independent component analysis")
4235 (description "This package provides tools for @dfn{Independent Component
4236 Analysis} (ICA) using various algorithms: FastICA,
4237 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4238 of Eigenmatrices} (JADE).")
4239 (license license:gpl2+)))
4241 (define-public r-dtw
4248 (uri (cran-uri "dtw" version))
4251 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4252 (build-system r-build-system)
4253 (propagated-inputs `(("r-proxy" ,r-proxy)))
4254 (home-page "http://dtw.r-forge.r-project.org/")
4255 (synopsis "Dynamic Time Warping Algorithms")
4256 (description "This package provides a comprehensive implementation of
4257 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4258 optimal (least cumulative distance) alignment between points of two time
4259 series. Common DTW variants covered include local (slope) and global (window)
4260 constraints, subsequence matches, arbitrary distance definitions,
4261 normalizations, minimum variance matching, and so on.")
4262 (license license:gpl2+)))
4264 (define-public r-sdmtools
4267 (version "1.1-221.2")
4271 (uri (cran-uri "SDMTools" version))
4274 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4275 (properties `((upstream-name . "SDMTools")))
4276 (build-system r-build-system)
4277 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4278 (home-page "https://www.rforge.net/SDMTools/")
4279 (synopsis "Species distribution modelling tools")
4280 (description "This package provides a set of tools for post processing
4281 the outcomes of species distribution modeling exercises. It includes novel
4282 methods for comparing models and tracking changes in distributions through
4283 time. It further includes methods for visualizing outcomes, selecting
4284 thresholds, calculating measures of accuracy and landscape fragmentation
4286 (license license:gpl3+)))
4288 (define-public r-scatterplot3d
4290 (name "r-scatterplot3d")
4295 (uri (cran-uri "scatterplot3d" version))
4298 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4299 (build-system r-build-system)
4300 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4301 (synopsis "3D scatter plot")
4302 (description "This package provides an implementation of scatter plots for
4303 plotting. a three dimensional point cloud.")
4304 (license license:gpl2)))
4306 (define-public r-ggridges
4313 (uri (cran-uri "ggridges" version))
4316 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4317 (build-system r-build-system)
4319 `(("r-ggplot2" ,r-ggplot2)
4321 ("r-scales" ,r-scales)
4322 ("r-withr" ,r-withr)))
4323 (home-page "https://github.com/clauswilke/ggridges")
4324 (synopsis "Ridgeline plots in ggplot2")
4326 "Ridgeline plots provide a convenient way of visualizing changes in
4327 distributions over time or space. This package enables the creation of such
4328 plots in @code{ggplot2}.")
4329 (license license:gpl2)))
4331 (define-public r-ggjoy
4338 (uri (cran-uri "ggjoy" version))
4341 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4342 (build-system r-build-system)
4344 `(("r-ggplot2" ,r-ggplot2)
4345 ("r-ggridges" ,r-ggridges)))
4346 (home-page "https://github.com/clauswilke/ggjoy")
4347 (synopsis "Joyplots in ggplot2")
4348 (description "Joyplots provide a convenient way of visualizing changes in
4349 distributions over time or space. This package enables the creation of such
4350 plots in @code{ggplot2}.")
4351 (license license:gpl2)))
4353 (define-public r-cli
4360 (uri (cran-uri "cli" version))
4363 "03zaq9yhz6gw49qdnhc66b3sw9i916ahkzyg2cgh17dhf31d2acq"))))
4364 (build-system r-build-system)
4366 `(("r-assertthat" ,r-assertthat)
4367 ("r-crayon" ,r-crayon)
4368 ("r-fansi" ,r-fansi)
4369 ("r-glue" ,r-glue)))
4370 (home-page "https://github.com/r-lib/cli#readme")
4371 (synopsis "Helpers for developing command line interfaces")
4372 (description "This package provides a suite of tools designed to build
4373 attractive command line interfaces (CLIs). It includes tools for drawing
4374 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4375 (license license:expat)))
4377 (define-public r-argparser
4379 (name "r-argparser")
4384 (uri (cran-uri "argparser" version))
4387 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4388 (build-system r-build-system)
4389 (home-page "https://bitbucket.org/djhshih/argparser")
4390 (synopsis "Command-line argument parser")
4392 "This package provides a cross-platform command-line argument parser
4393 written purely in R with no external dependencies. It is useful with the
4394 Rscript front-end and facilitates turning an R script into an executable
4396 (license license:gpl3+)))
4398 (define-public r-debugme
4405 (uri (cran-uri "debugme" version))
4408 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4409 (build-system r-build-system)
4410 (propagated-inputs `(("r-crayon" ,r-crayon)))
4411 (home-page "https://github.com/r-lib/debugme#readme")
4412 (synopsis "Debug R packages")
4414 "This package allows the user to specify debug messages as special string
4415 constants, and control debugging of packages via environment variables.")
4416 (license license:expat)))
4418 (define-public r-processx
4425 (uri (cran-uri "processx" version))
4427 (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a"))))
4428 (build-system r-build-system)
4432 (home-page "https://github.com/r-lib/processx3")
4433 (synopsis "Execute and control system processes")
4435 "This package provides portable tools to run system processes in the
4436 background. It can check if a background process is running; wait on a
4437 background process to finish; get the exit status of finished processes; kill
4438 background processes and their children; restart processes. It can read the
4439 standard output and error of the processes, using non-blocking connections.
4440 @code{processx} can poll a process for standard output or error, with a
4441 timeout. It can also poll several processes at once.")
4442 (license license:expat)))
4444 (define-public r-tsp
4451 (uri (cran-uri "TSP" version))
4454 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4455 (properties `((upstream-name . "TSP")))
4456 (build-system r-build-system)
4457 (propagated-inputs `(("r-foreach" ,r-foreach)))
4458 (home-page "https://cran.r-project.org/web/packages/TSP/")
4459 (synopsis "Traveling salesperson problem (TSP)")
4460 (description "This package provides basic infrastructure and some
4461 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4462 traveling salesman problem).")
4463 (license license:gpl3)))
4465 (define-public r-qap
4472 (uri (cran-uri "qap" version))
4475 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4476 (build-system r-build-system)
4477 (native-inputs `(("gfortran" ,gfortran)))
4478 (home-page "https://cran.r-project.org/web/packages/qap/")
4479 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4480 (description "This package implements heuristics for the @dfn{quadratic
4481 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4483 (license license:gpl3)))
4485 (define-public r-gclus
4492 (uri (cran-uri "gclus" version))
4495 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4496 (build-system r-build-system)
4497 (propagated-inputs `(("r-cluster" ,r-cluster)))
4498 (home-page "https://cran.r-project.org/web/packages/gclus/")
4499 (synopsis "Clustering graphics")
4500 (description "This package orders panels in scatterplot matrices and
4501 parallel coordinate displays by some merit index. It contains various indices
4502 of merit, ordering functions, and enhanced versions of @code{pairs} and
4503 @code{parcoord} which color panels according to their merit level.")
4504 (license license:gpl2+)))
4506 (define-public r-webshot
4513 (uri (cran-uri "webshot" version))
4516 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4517 (build-system r-build-system)
4519 `(("r-callr" ,r-callr)
4520 ("r-jsonlite" ,r-jsonlite)
4521 ("r-magrittr" ,r-magrittr)))
4522 (home-page "https://github.com/wch/webshot/")
4523 (synopsis "Take screenshots of web pages")
4525 "Webshot makes it easy to take screenshots of web pages from within R.
4526 It can also run Shiny applications locally and take screenshots of the
4527 application; and it can render and screenshot static as well as interactive R
4528 Markdown documents.")
4529 (license license:gpl2)))
4531 (define-public r-seriation
4533 (name "r-seriation")
4538 (uri (cran-uri "seriation" version))
4541 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
4542 (build-system r-build-system)
4544 `(("r-cluster" ,r-cluster)
4545 ("r-colorspace" ,r-colorspace)
4546 ("r-dendextend" ,r-dendextend)
4547 ("r-gclus" ,r-gclus)
4548 ("r-gplots" ,r-gplots)
4551 ("r-registry" ,r-registry)
4553 (native-inputs `(("gfortran" ,gfortran)))
4554 (home-page "https://s2.smu.edu/IDA/seriation/")
4555 (synopsis "Infrastructure for ordering objects using seriation")
4557 "This package provides infrastructure for seriation with an
4558 implementation of several seriation/sequencing techniques to reorder matrices,
4559 dissimilarity matrices, and dendrograms. It also provides (optimally)
4560 reordered heatmaps, color images and clustering visualizations like
4561 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4563 (license license:gpl3)))
4565 (define-public r-xfun
4572 (uri (cran-uri "xfun" version))
4574 (base32 "15yyigkl1g9w9d7097hrm94dxn1af333ywr5xdw78qqrw6npn0iv"))))
4575 (build-system r-build-system)
4576 ;; knitr itself depends on xfun
4579 `(("r-knitr" ,r-knitr)))
4580 (home-page "https://github.com/yihui/xfun")
4581 (synopsis "Miscellaneous functions")
4583 "This package provides miscellaneous functions commonly used in other
4584 packages maintained by Yihui Xie.")
4585 (license license:expat)))
4587 (define-public r-utf8
4594 (uri (cran-uri "utf8" version))
4597 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4598 (build-system r-build-system)
4599 (home-page "https://github.com/patperry/r-utf8")
4600 (synopsis "Unicode text processing")
4602 "This package provides tools to process and print UTF-8 encoded
4603 international text (Unicode). Input, validate, normalize, encode, format, and
4605 (license license:asl2.0)))
4607 (define-public r-zeallot
4614 (uri (cran-uri "zeallot" version))
4617 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4618 (build-system r-build-system)
4619 (home-page "https://github.com/nteetor/zeallot")
4620 (synopsis "Multiple, unpacking, and destructuring assignment")
4622 "This package provides a @code{%<-%} operator to perform multiple,
4623 unpacking, and destructuring assignment in R. The operator unpacks the
4624 right-hand side of an assignment into multiple values and assigns these values
4625 to variables on the left-hand side of the assignment.")
4626 (license license:expat)))
4628 (define-public r-vctrs
4635 (uri (cran-uri "vctrs" version))
4638 "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
4639 (build-system r-build-system)
4641 `(("r-digest" ,r-digest)
4642 ("r-ellipsis" ,r-ellipsis)
4644 ("r-rlang" ,r-rlang)))
4646 `(("r-knitr" ,r-knitr)))
4647 (home-page "https://github.com/r-lib/vctrs")
4648 (synopsis "Vector helpers")
4650 "There are three main goals to the @code{vctrs} package:
4653 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4654 @code{length()} and @code{class()}. These definitions are paired with a
4655 framework for type-coercion and size-recycling.
4656 @item To define type- and size-stability as desirable function properties, use
4657 them to analyse existing base function, and to propose better alternatives.
4658 This work has been particularly motivated by thinking about the ideal
4659 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4660 @item To provide a new @code{vctr} base class that makes it easy to create new
4661 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4662 a few new @code{vctrs} generics, making implementation considerably simpler
4665 (license license:gpl3)))
4667 (define-public r-pillar
4674 (uri (cran-uri "pillar" version))
4677 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4678 (build-system r-build-system)
4681 ("r-crayon" ,r-crayon)
4682 ("r-ellipsis" ,r-ellipsis)
4683 ("r-fansi" ,r-fansi)
4684 ("r-lifecycle" ,r-lifecycle)
4685 ("r-rlang" ,r-rlang)
4687 ("r-vctrs" ,r-vctrs)))
4688 (home-page "https://github.com/r-lib/pillar")
4689 (synopsis "Coloured formatting for columns")
4691 "This package provides a @code{pillar} generic designed for formatting
4692 columns of data using the full range of colours provided by modern
4694 (license license:gpl3)))
4696 (define-public r-uuid
4703 (uri (cran-uri "uuid" version))
4706 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4707 (build-system r-build-system)
4708 (home-page "https://www.rforge.net/uuid")
4709 (synopsis "Tools for generating and handling of UUIDs")
4711 "This package provides tools for generating and handling of
4712 @dfn{Universally Unique Identifiers} (UUIDs).")
4713 (license license:expat)))
4715 (define-public r-tinytex
4722 (uri (cran-uri "tinytex" version))
4725 "02b0v8ydbfspma3rgsdpkf2cm6jl9qm3l9jsrl0xng482b06bb0q"))))
4726 (build-system r-build-system)
4728 `(("r-xfun" ,r-xfun)))
4729 (home-page "https://github.com/yihui/tinytex")
4730 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4732 "This package provides helper functions to install and maintain the LaTeX
4733 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4734 easy-to-maintain version of TeX Live. This package also contains helper
4735 functions to compile LaTeX documents, and install missing LaTeX packages
4737 (license license:expat)))
4739 (define-public r-network
4746 (uri (cran-uri "network" version))
4749 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
4750 (build-system r-build-system)
4752 `(("r-magrittr" ,r-magrittr)
4753 ("r-tibble" ,r-tibble)))
4754 (home-page "https://statnet.org/")
4755 (synopsis "Classes for relational data")
4757 "This package provides tools to create and modify network objects. The
4758 @code{network} class can represent a range of relational data types, and
4759 supports arbitrary vertex/edge/graph attributes.")
4760 (license license:gpl2+)))
4762 (define-public r-stabs
4769 (uri (cran-uri "stabs" version))
4772 "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
4773 (build-system r-build-system)
4774 (home-page "https://github.com/hofnerb/stabs")
4775 (synopsis "Stability selection with error control")
4777 "This package provides resampling procedures to assess the stability of
4778 selected variables with additional finite sample error control for
4779 high-dimensional variable selection procedures such as Lasso or boosting.
4780 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
4781 complementary pairs stability selection with improved error bounds
4782 (Shah & Samworth, 2013) are implemented. The package can be combined with
4783 arbitrary user specified variable selection approaches.")
4784 (license license:gpl2)))
4786 (define-public r-rle
4793 (uri (cran-uri "rle" version))
4796 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
4797 (properties `((upstream-name . "rle")))
4798 (build-system r-build-system)
4799 (home-page "https://cran.r-project.org/web/packages/rle/")
4800 (synopsis "Common functions for run-length encoded vectors")
4802 "This package provides common @code{base} and @code{stats} methods for
4803 @code{rle} objects, aiming to make it possible to treat them transparently as
4805 (license license:gpl3)))
4807 (define-public r-statnet-common
4809 (name "r-statnet-common")
4814 (uri (cran-uri "statnet.common" version))
4817 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
4819 `((upstream-name . "statnet.common")))
4820 (build-system r-build-system)
4822 `(("r-coda" ,r-coda)
4824 (home-page "https://statnet.org")
4825 (synopsis "R scripts and utilities used by the Statnet software")
4826 (description "This package provides non-statistical utilities used by the
4827 software developed by the Statnet Project.")
4828 (license license:gpl3)))
4830 (define-public r-statcheck
4832 (name "r-statcheck")
4837 (uri (cran-uri "statcheck" version))
4840 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4841 (build-system r-build-system)
4843 `(("r-ggplot2" ,r-ggplot2)
4845 ("r-rmarkdown" ,r-rmarkdown)))
4846 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4847 (synopsis "Extract statistics from articles and recompute p-values")
4848 (description "This package can automatically extract statistical
4849 null-hypothesis significant testing (NHST) results from articles and recompute
4850 the p-values based on the reported test statistic and degrees of freedom to
4851 detect possible inconsistencies.")
4852 (license license:gpl2)))
4854 (define-public r-sna
4861 (uri (cran-uri "sna" version))
4864 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
4865 (build-system r-build-system)
4867 `(("r-network" ,r-network)
4868 ("r-statnet-common" ,r-statnet-common)))
4869 (home-page "https://statnet.org")
4870 (synopsis "Tools for social network analysis")
4872 "This package provides a range of tools for social network analysis,
4873 including node and graph-level indices, structural distance and covariance
4874 methods, structural equivalence detection, network regression, random graph
4875 generation, and 2D/3D network visualization.")
4876 (license license:gpl2+)))
4878 (define-public r-tfisher
4885 (uri (cran-uri "TFisher" version))
4888 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4889 (properties `((upstream-name . "TFisher")))
4890 (build-system r-build-system)
4892 `(("r-matrix" ,r-matrix)
4893 ("r-mvtnorm" ,r-mvtnorm)
4895 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4896 (synopsis "Optimal thresholding Fisher's p-value combination method")
4898 "This package provides the @dfn{cumulative distribution function} (CDF),
4899 quantile, and statistical power calculator for a collection of thresholding
4900 Fisher's p-value combination methods, including Fisher's p-value combination
4901 method, truncated product method and, in particular, soft-thresholding
4902 Fisher's p-value combination method which is proven to be optimal in some
4903 context of signal detection. The p-value calculator for the omnibus version
4904 of these tests are also included.")
4905 (license license:gpl2)))
4907 (define-public r-ttr
4914 (uri (cran-uri "TTR" version))
4917 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
4918 (properties `((upstream-name . "TTR")))
4919 (build-system r-build-system)
4921 `(("r-curl" ,r-curl)
4924 (home-page "https://github.com/joshuaulrich/TTR")
4925 (synopsis "Technical trading rules")
4927 "This package provides functions and data to construct technical trading
4929 (license license:gpl2)))
4931 (define-public r-leaps
4938 (uri (cran-uri "leaps" version))
4941 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4942 (build-system r-build-system)
4943 (native-inputs `(("gfortran" ,gfortran)))
4944 (home-page "https://cran.r-project.org/web/packages/leaps/")
4945 (synopsis "Regression subset selection")
4947 "This package provides tools for regression subset selection, including
4948 exhaustive search.")
4949 (license license:gpl2+)))
4951 (define-public r-splus2r
4958 (uri (cran-uri "splus2R" version))
4961 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4962 (properties `((upstream-name . "splus2R")))
4963 (build-system r-build-system)
4964 (native-inputs `(("gfortran" ,gfortran)))
4965 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4966 (synopsis "Supplemental S-PLUS functionality in R")
4968 "Currently there are many functions in S-PLUS that are missing in R. To
4969 facilitate the conversion of S-PLUS packages to R packages, this package
4970 provides some missing S-PLUS functionality in R.")
4971 (license license:gpl2)))
4973 (define-public r-ifultools
4975 (name "r-ifultools")
4980 (uri (cran-uri "ifultools" version))
4983 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4984 (build-system r-build-system)
4986 `(("r-mass" ,r-mass)
4987 ("r-splus2r" ,r-splus2r)))
4988 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4989 (synopsis "Insightful research tools")
4990 (description "This package provides C code used by the wmtsa, fractal, and
4992 (license license:gpl2)))
4994 (define-public r-sapa
5001 (uri (cran-uri "sapa" version))
5004 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5005 (build-system r-build-system)
5007 `(("r-ifultools" ,r-ifultools)
5008 ("r-splus2r" ,r-splus2r)))
5009 (home-page "https://cran.r-project.org/web/packages/sapa/")
5010 (synopsis "Spectral analysis for physical applications")
5011 (description "This package provides software for the book Spectral
5012 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5013 Cambridge University Press, 1993.")
5014 (license license:gpl2)))
5016 (define-public r-aggregation
5018 (name "r-aggregation")
5023 (uri (cran-uri "aggregation" version))
5026 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5027 (build-system r-build-system)
5028 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5029 (synopsis "Methods for p-value aggregation")
5031 "This package contains functionality for performing the following methods
5032 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5033 Fisher's method), and Sidak correction.")
5034 (license license:gpl3)))
5036 (define-public r-quantmod
5043 (uri (cran-uri "quantmod" version))
5046 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
5047 (build-system r-build-system)
5049 `(("r-curl" ,r-curl)
5053 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5054 (synopsis "Quantitative financial modelling framework")
5055 (description "This package provides a quantitative financial modelling
5056 framework to allow users to specify, build, trade, and analyse quantitative
5057 financial trading strategies.")
5058 (license license:gpl3)))
5060 (define-public r-tseries
5067 (uri (cran-uri "tseries" version))
5070 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
5071 (build-system r-build-system)
5073 `(("r-quadprog" ,r-quadprog)
5074 ("r-quantmod" ,r-quantmod)
5077 `(("gfortran" ,gfortran)))
5078 (home-page "https://cran.r-project.org/web/packages/tseries/")
5079 (synopsis "Time series analysis and computational finance")
5081 "This package provides functions relating to time series analysis and
5082 computational finance.")
5083 (license license:gpl2)))
5085 (define-public r-wmtsa
5092 (uri (cran-uri "wmtsa" version))
5095 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5096 (build-system r-build-system)
5098 `(("r-ifultools" ,r-ifultools)
5100 ("r-splus2r" ,r-splus2r)))
5101 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5102 (synopsis "Wavelet methods for time series analysis")
5104 "This package provides software to accompany the book \"Wavelet Methods
5105 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5106 University Press, 2000.")
5107 (license license:gpl2)))
5109 (define-public r-tsa
5116 (uri (cran-uri "TSA" version))
5119 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5120 (properties `((upstream-name . "TSA")))
5121 (build-system r-build-system)
5123 `(("r-leaps" ,r-leaps)
5124 ("r-locfit" ,r-locfit)
5126 ("r-tseries" ,r-tseries)))
5127 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5128 (synopsis "Time series analysis")
5130 "This package contains R functions and datasets detailed in the book
5131 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5132 Cryer and Kung-Sik Chan.")
5133 (license license:gpl2+)))
5135 (define-public r-extradistr
5137 (name "r-extradistr")
5142 (uri (cran-uri "extraDistr" version))
5145 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5146 (properties `((upstream-name . "extraDistr")))
5147 (build-system r-build-system)
5149 `(("r-rcpp" ,r-rcpp)))
5150 (home-page "https://github.com/twolodzko/extraDistr")
5151 (synopsis "Additional univariate and multivariate distributions")
5153 "This package implements density, distribution functions, quantile
5154 functions and random generation functions for a large number of univariate and
5155 multivariate distributions.")
5156 (license license:gpl2)))
5158 (define-public r-fractal
5165 (uri (cran-uri "fractal" version))
5168 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5169 (build-system r-build-system)
5171 `(("r-ifultools" ,r-ifultools)
5174 ("r-scatterplot3d" ,r-scatterplot3d)
5175 ("r-splus2r" ,r-splus2r)
5176 ("r-wmtsa" ,r-wmtsa)))
5177 (home-page "https://cran.r-project.org/web/packages/fractal/")
5178 (synopsis "Fractal time series modeling and analysis")
5180 "This package provides tools for stochastic fractal and deterministic
5181 chaotic time series analysis.")
5182 (license license:gpl2)))
5184 (define-public r-urca
5191 (uri (cran-uri "urca" version))
5194 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5195 (build-system r-build-system)
5196 (propagated-inputs `(("r-nlme" ,r-nlme)))
5197 (native-inputs `(("gfortran" ,gfortran)))
5198 (home-page "https://cran.r-project.org/web/packages/urca/")
5199 (synopsis "Unit root and cointegration tests for time series data")
5201 "This package provides unit root and cointegration tests encountered in
5202 applied econometric analysis.")
5203 (license license:gpl2+)))
5205 (define-public r-cubature
5212 (uri (cran-uri "cubature" version))
5215 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5216 (build-system r-build-system)
5218 `(("r-rcpp" ,r-rcpp)))
5220 `(("r-knitr" ,r-knitr)))
5221 (home-page "https://github.com/bnaras/cubature")
5222 (synopsis "Adaptive multivariate integration over hypercubes")
5224 "This package is an R wrapper around the cubature C library for adaptive
5225 multivariate integration over hypercubes. This version provides both
5226 @code{hcubature} and @code{pcubature} routines in addition to a vector
5228 ;; The included cubature C library is released under GPLv2+, but the
5229 ;; wrapper declares the license to be GPLv3+.
5230 (license (list license:gpl2+ license:gpl3+))))
5232 (define-public r-trend
5239 (uri (cran-uri "trend" version))
5242 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5243 (build-system r-build-system)
5245 `(("r-extradistr" ,r-extradistr)))
5247 `(("gfortran" ,gfortran)))
5248 (home-page "https://cran.r-project.org/web/packages/trend/")
5249 (synopsis "Non-parametric trend tests and change-point detection")
5251 "The analysis of environmental data often requires the detection of
5252 trends and change-points. This package includes tests for trend
5253 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5254 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5255 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5256 correlation trend test), change-point detection (Lanzante's test procedures,
5257 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5258 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5259 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5260 sample Robust Rank-Order Distributional Test.")
5261 (license license:gpl3)))
5263 (define-public r-expm
5270 (uri (cran-uri "expm" version))
5273 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5274 (build-system r-build-system)
5275 (propagated-inputs `(("r-matrix" ,r-matrix)))
5276 (native-inputs `(("gfortran" ,gfortran)))
5277 (home-page "https://r-forge.r-project.org/projects/expm/")
5278 (synopsis "Tools for matrix exponentials and related quantities")
5280 "This package provides tools for the computation of the matrix
5281 exponential, logarithm, square root, and related quantities.")
5282 (license license:gpl2+)))
5284 (define-public r-complexplus
5286 (name "r-complexplus")
5291 (uri (cran-uri "complexplus" version))
5294 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5295 (build-system r-build-system)
5297 `(("r-expm" ,r-expm)
5298 ("r-matrix" ,r-matrix)))
5299 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5300 (synopsis "Functions of complex or real variables")
5302 "This package extends several functions to the complex domain, including
5303 the matrix exponential and logarithm, and the determinant.")
5304 (license license:gpl2)))
5306 (define-public r-phontools
5308 (name "r-phontools")
5313 (uri (cran-uri "phonTools" version))
5316 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5317 (properties `((upstream-name . "phonTools")))
5318 (build-system r-build-system)
5319 (home-page "http://www.santiagobarreda.com/rscripts.html")
5320 (synopsis "Tools for phonetic and acoustic analyses")
5322 "This package contains tools for the organization, display, and analysis
5323 of the sorts of data frequently encountered in phonetics research and
5324 experimentation, including the easy creation of IPA vowel plots, and the
5325 creation and manipulation of WAVE audio files.")
5326 (license license:bsd-2)))
5335 (uri (cran-uri "np" version))
5338 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5339 (build-system r-build-system)
5341 `(("r-boot" ,r-boot)
5342 ("r-cubature" ,r-cubature)
5343 ("r-quadprog" ,r-quadprog)
5344 ("r-quantreg" ,r-quantreg)))
5345 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5346 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5347 (description "This package provides non-parametric (and semi-parametric)
5348 kernel methods that seamlessly handle a mix of continuous, unordered, and
5349 ordered factor data types.")
5350 ;; Any version of the GPL.
5351 (license license:gpl3+)))
5353 (define-public r-powerplus
5355 (name "r-powerplus")
5360 (uri (cran-uri "powerplus" version))
5363 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5364 (build-system r-build-system)
5366 `(("r-complexplus" ,r-complexplus)
5369 ("r-matrix" ,r-matrix)
5370 ("r-phontools" ,r-phontools)))
5371 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5372 (synopsis "Exponentiation operations")
5374 "This package provides tools for the computation of matrix and scalar
5376 (license license:gpl2)))
5378 (define-public r-egg
5385 (uri (cran-uri "egg" version))
5388 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5389 (properties `((upstream-name . "egg")))
5390 (build-system r-build-system)
5392 `(("r-ggplot2" ,r-ggplot2)
5393 ("r-gridextra" ,r-gridextra)
5394 ("r-gtable" ,r-gtable)))
5395 (home-page "https://cran.r-project.org/web/packages/egg")
5396 (synopsis "Extensions for ggplot2")
5398 "This package provides miscellaneous functions to help customize ggplot2
5399 objects. High-level functions are provided to post-process ggplot2 layouts
5400 and allow alignment between plot panels, as well as setting panel sizes to
5401 fixed values. Other functions include a custom @code{geom}, and helper
5402 functions to enforce symmetric scales or add tags to facetted plots.")
5403 (license license:gpl3)))
5405 (define-public r-heatmaply
5407 (name "r-heatmaply")
5412 (uri (cran-uri "heatmaply" version))
5415 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
5416 (build-system r-build-system)
5418 `(("r-assertthat" ,r-assertthat)
5419 ("r-colorspace" ,r-colorspace)
5420 ("r-dendextend" ,r-dendextend)
5422 ("r-ggplot2" ,r-ggplot2)
5423 ("r-htmlwidgets" ,r-htmlwidgets)
5424 ("r-magrittr" ,r-magrittr)
5425 ("r-plotly" ,r-plotly)
5426 ("r-rcolorbrewer" ,r-rcolorbrewer)
5427 ("r-reshape2" ,r-reshape2)
5428 ("r-scales" ,r-scales)
5429 ("r-seriation" ,r-seriation)
5430 ("r-viridis" ,r-viridis)
5431 ("r-webshot" ,r-webshot)))
5433 `(("r-knitr" ,r-knitr)))
5434 (home-page "https://cran.r-project.org/package=heatmaply")
5435 (synopsis "Interactive cluster heat maps using plotly")
5437 "This package enables you to create interactive cluster heatmaps that can
5438 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5439 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5440 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5441 a popular graphical method for visualizing high-dimensional data, in which a
5442 table of numbers is encoded as a grid of colored cells. The rows and columns
5443 of the matrix are ordered to highlight patterns and are often accompanied by
5445 ;; Either version of the license.
5446 (license (list license:gpl2 license:gpl3))))
5455 (uri (cran-uri "h5" version))
5458 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5459 (build-system r-build-system)
5464 `(("which" ,which)))
5466 `(("r-rcpp" ,r-rcpp)))
5467 (home-page "https://github.com/mannau/h5")
5468 (synopsis "Interface to the HDF5 Library")
5470 "This package provides an S4 interface to the HDF5 library supporting
5471 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5472 binary files in a language independent format. The HDF5 format can therefore
5473 be used as an alternative to R's save/load mechanism. Since h5 is able to
5474 access only subsets of stored data it can also handle data sets which do not
5476 (license license:bsd-2)))
5478 (define-public r-cgdsr
5485 (uri (cran-uri "cgdsr" version))
5488 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5489 (build-system r-build-system)
5491 `(("r-httr" ,r-httr)
5492 ("r-r-methodss3" ,r-r-methodss3)
5493 ("r-r-oo" ,r-r-oo)))
5494 (home-page "https://github.com/cBioPortal/cgdsr")
5495 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5497 "This package provides a basic set of R functions for querying the Cancer
5498 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5499 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5500 (license license:lgpl3)))
5502 (define-public r-import
5509 (uri (cran-uri "import" version))
5512 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
5513 (build-system r-build-system)
5515 `(("r-knitr" ,r-knitr)))
5516 (home-page "https://github.com/smbache/import")
5517 (synopsis "Import mechanism for R")
5519 "This is an alternative mechanism for importing objects from packages.
5520 The syntax allows for importing multiple objects from a package with a single
5521 command in an expressive way. The import package bridges some of the gap
5522 between using @code{library} (or @code{require}) and direct (single-object)
5523 imports. Furthermore the imported objects are not placed in the current
5524 environment. It is also possible to import objects from stand-alone @code{.R}
5526 (license license:expat)))
5528 (define-public r-shinyace
5535 (uri (cran-uri "shinyAce" version))
5538 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5539 (properties `((upstream-name . "shinyAce")))
5540 (build-system r-build-system)
5542 `(("r-shiny" ,r-shiny)
5543 ("r-jsonlite" ,r-jsonlite)))
5544 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5545 (synopsis "Ace editor bindings for Shiny")
5547 "This package provides Ace editor bindings to enable a rich text editing
5548 environment within Shiny.")
5549 (license license:expat)))
5551 (define-public r-randomizr
5553 (name "r-randomizr")
5558 (uri (cran-uri "randomizr" version))
5561 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5562 (properties `((upstream-name . "randomizr")))
5563 (build-system r-build-system)
5565 `(("r-knitr" ,r-knitr)))
5566 (home-page "https://declaredesign.org/r/randomizr/")
5567 (synopsis "Tools for common forms of random assignment and sampling")
5569 "This package provides tools for generating random assignments for common
5570 experimental designs and random samples for common sampling designs.")
5571 (license license:expat)))
5573 (define-public r-base64url
5575 (name "r-base64url")
5580 (uri (cran-uri "base64url" version))
5583 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5584 (build-system r-build-system)
5586 `(("r-backports" ,r-backports)))
5587 (home-page "https://github.com/mllg/base64url")
5588 (synopsis "Fast and URL-safe base64 encoder and decoder")
5590 "This package provides a URL-safe base64 encoder and decoder. In
5591 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5592 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5593 encoder does not fill the string with trailing @code{=}. The resulting
5594 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5595 and thus are safe to use in URLs or for file names. The package also comes
5596 with a simple base32 encoder/decoder suited for case insensitive file
5598 (license license:gpl3)))
5600 (define-public r-radiant-data
5602 (name "r-radiant-data")
5607 (uri (cran-uri "radiant.data" version))
5610 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
5611 (modules '((guix build utils)))
5614 ;; Delete files that are under CC-NC-SA.
5615 (delete-file-recursively "inst/app/tools/help")
5617 (properties `((upstream-name . "radiant.data")))
5618 (build-system r-build-system)
5620 `(("r-base64enc" ,r-base64enc)
5621 ("r-broom" ,r-broom)
5624 ("r-dplyr" ,r-dplyr)
5627 ("r-ggplot2" ,r-ggplot2)
5628 ("r-import" ,r-import)
5629 ("r-jsonlite" ,r-jsonlite)
5630 ("r-knitr" ,r-knitr)
5631 ("r-lubridate" ,r-lubridate)
5632 ("r-magrittr" ,r-magrittr)
5633 ("r-markdown" ,r-markdown)
5635 ("r-patchwork" ,r-patchwork)
5636 ("r-plotly" ,r-plotly)
5637 ("r-psych" ,r-psych)
5638 ("r-randomizr" ,r-randomizr)
5639 ("r-readr" ,r-readr)
5640 ("r-readxl" ,r-readxl)
5641 ("r-rlang" ,r-rlang)
5642 ("r-rmarkdown" ,r-rmarkdown)
5643 ("r-rstudioapi" ,r-rstudioapi)
5644 ("r-scales" ,r-scales)
5645 ("r-shiny" ,r-shiny)
5646 ("r-shinyfiles" ,r-shinyfiles)
5647 ("r-shinyace" ,r-shinyace)
5648 ("r-stringi" ,r-stringi)
5649 ("r-tibble" ,r-tibble)
5650 ("r-tidyr" ,r-tidyr)
5651 ("r-writexl" ,r-writexl)))
5652 (home-page "https://github.com/radiant-rstats/radiant.data")
5653 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5655 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5656 visualizing, summarizing, transforming, and combining data. It also contains
5657 functionality to generate reproducible reports of the analyses conducted in
5659 (license license:agpl3)))
5661 (define-public r-algdesign
5663 (name "r-algdesign")
5668 (uri (cran-uri "AlgDesign" version))
5670 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5671 (properties `((upstream-name . "AlgDesign")))
5672 (build-system r-build-system)
5673 (home-page "https://github.com/jvbraun/AlgDesign")
5674 (synopsis "Algorithmic experimental design")
5676 "This package provides tools to calculate exact and approximate theory
5677 experimental designs for D, A, and I criteria. Very large designs may be
5678 created. Experimental designs may be blocked or blocked designs created from
5679 a candidate list, using several criteria. The blocking can be done when whole
5680 and within plot factors interact.")
5681 (license license:gpl2+)))
5683 (define-public r-signal
5690 (uri (cran-uri "signal" version))
5693 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5694 (build-system r-build-system)
5695 (propagated-inputs `(("r-mass" ,r-mass)))
5696 (native-inputs `(("gfortran" ,gfortran)))
5697 (home-page "https://cran.r-project.org/web/packages/signal/")
5698 (synopsis "Signal processing")
5700 "This package provides a set of signal processing functions originally
5701 written for Matlab and GNU Octave. It includes filter generation utilities,
5702 filtering functions, resampling routines, and visualization of filter models.
5703 It also includes interpolation functions.")
5704 (license license:gpl2)))
5706 (define-public r-gsubfn
5713 (uri (cran-uri "gsubfn" version))
5716 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5717 (build-system r-build-system)
5718 (propagated-inputs `(("r-proto" ,r-proto)))
5719 (home-page "https://code.google.com/archive/p/gsubfn/")
5720 (synopsis "Utilities for strings and function arguments.")
5722 "This package provides @code{gsubfn} which is like @code{gsub} but can
5723 take a replacement function or certain other objects instead of the
5724 replacement string. Matches and back references are input to the replacement
5725 function and replaced by the function output. @code{gsubfn} can be used to
5726 split strings based on content rather than delimiters and for quasi-perl-style
5727 string interpolation. The package also has facilities for translating
5728 formulas to functions and allowing such formulas in function calls instead of
5730 (license license:gpl2+)))
5732 (define-public r-sqldf
5739 (uri (cran-uri "sqldf" version))
5742 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5743 (build-system r-build-system)
5745 `(("r-chron" ,r-chron)
5747 ("r-gsubfn" ,r-gsubfn)
5748 ("r-proto" ,r-proto)
5749 ("r-rsqlite" ,r-rsqlite)))
5750 (home-page "https://github.com/ggrothendieck/sqldf")
5751 (synopsis "Manipulate R data frames using SQL")
5753 "The @code{sqldf} function is typically passed a single argument which is
5754 an SQL select statement where the table names are ordinary R data frame names.
5755 @code{sqldf} transparently sets up a database, imports the data frames into
5756 that database, performs the SQL statement and returns the result using a
5757 heuristic to determine which class to assign to each column of the returned
5758 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5759 used to read filtered files into R even if the original files are larger than
5760 R itself can handle.")
5761 (license license:gpl2)))
5763 (define-public r-abind
5770 (uri (cran-uri "abind" version))
5773 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5774 (build-system r-build-system)
5775 (home-page "https://cran.r-project.org/web/packages/abind/")
5776 (synopsis "Combine multidimensional arrays")
5778 "This package provides tools to combine multidimensional arrays into a
5779 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5780 works with vectors, matrices, and higher-dimensional arrays. It also provides
5781 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5782 extracting and replacing data in arrays.")
5783 (license license:lgpl2.0+)))
5785 (define-public r-prroc
5792 (uri (cran-uri "PRROC" version))
5795 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5796 (properties `((upstream-name . "PRROC")))
5797 (build-system r-build-system)
5798 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5799 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5801 "This package computes the areas under the @dfn{precision-recall} (PR)
5802 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5803 contrast to other implementations, the interpolation between points of the PR
5804 curve is done by a non-linear piecewise function. In addition to the areas
5805 under the curves, the curves themselves can also be computed and plotted by a
5806 specific S3-method.")
5807 (license license:gpl3)))
5809 (define-public r-vim
5816 (uri (cran-uri "VIM" version))
5819 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5820 (properties `((upstream-name . "VIM")))
5821 (build-system r-build-system)
5824 ("r-colorspace" ,r-colorspace)
5825 ("r-data-table" ,r-data-table)
5826 ("r-e1071" ,r-e1071)
5827 ("r-laeken" ,r-laeken)
5828 ("r-magrittr" ,r-magrittr)
5831 ("r-ranger" ,r-ranger)
5833 ("r-robustbase" ,r-robustbase)
5837 `(("r-knitr" ,r-knitr)))
5838 (home-page "https://github.com/alexkowa/VIM")
5839 (synopsis "Visualization and imputation of missing values")
5841 "This package provides tools for the visualization of missing and/or
5842 imputed values are introduced, which can be used for exploring the data and
5843 the structure of the missing and/or imputed values. Depending on this
5844 structure of the missing values, the corresponding methods may help to
5845 identify the mechanism generating the missing values and explore the
5846 data including missing values. In addition, the quality of imputation can be
5847 visually explored using various univariate, bivariate, multiple and
5848 multivariate plot methods.")
5849 (license license:gpl2+)))
5851 (define-public r-fnn
5858 (uri (cran-uri "FNN" version))
5861 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5862 (properties `((upstream-name . "FNN")))
5863 (build-system r-build-system)
5864 (home-page "https://cran.r-project.org/web/packages/FNN")
5865 (synopsis "Fast nearest neighbor search algorithms and applications")
5867 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5868 search algorithms. Related applications including KNN classification,
5869 regression and information measures are implemented.")
5870 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5871 ;; later can be used.
5872 (license license:gpl2+)))
5874 (define-public r-smoother
5881 (uri (cran-uri "smoother" version))
5884 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5885 (build-system r-build-system)
5887 `(("r-ttr" ,r-ttr)))
5888 (home-page "https://cran.r-project.org/web/packages/smoother")
5889 (synopsis "Functions relating to the smoothing of numerical data")
5891 "This package provides a collection of methods for smoothing numerical
5892 data, commencing with a port of the Matlab gaussian window smoothing function.
5893 In addition, several functions typically used in smoothing of financial data
5895 (license license:gpl2)))
5897 (define-public r-riverplot
5899 (name "r-riverplot")
5904 (uri (cran-uri "riverplot" version))
5907 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5908 (build-system r-build-system)
5909 (home-page "https://logfc.wordpress.com")
5910 (synopsis "Sankey or ribbon plots")
5912 "Sankey plots are a type of diagram that is convenient to illustrate how
5913 flow of information, resources etc. separates and joins, much like observing
5914 how rivers split and merge. For example, they can be used to compare
5915 different clusterings. This package provides an implementation of Sankey
5917 (license license:gpl2+)))
5919 (define-public r-dyn
5926 (uri (cran-uri "dyn" version))
5929 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5930 (build-system r-build-system)
5932 `(("r-zoo" ,r-zoo)))
5933 (home-page "https://cran.r-project.org/web/packages/dyn")
5934 (synopsis "Time series regression")
5936 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5937 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5938 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5939 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5940 @code{randomForest::randomForest()} and other regression functions, allowing
5941 those functions to be used with time series including specifications that may
5942 contain lags, diffs and missing values.")
5944 (license license:gpl2+)))
5946 (define-public r-catdap
5953 (uri (cran-uri "catdap" version))
5956 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5957 (build-system r-build-system)
5959 `(("gfortran" ,gfortran)))
5960 (home-page "https://cran.r-project.org/web/packages/catdap/")
5961 (synopsis "Tools for categorical data analysis")
5963 "This package provides functions for analyzing multivariate data.
5964 Dependencies of the distribution of the specified variable (response
5965 variable) to other variables (explanatory variables) are derived and
5966 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5967 (license license:gpl2+)))
5969 (define-public r-arules
5976 (uri (cran-uri "arules" version))
5979 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5980 (build-system r-build-system)
5982 `(("r-matrix" ,r-matrix)))
5983 (home-page "https://github.com/mhahsler/arules")
5984 (synopsis "Mining association rules and frequent itemsets")
5986 "This package provides an infrastructure for representing, manipulating
5987 and analyzing transaction data and patterns (frequent itemsets and association rules).
5988 It also provides C implementations of the association mining algorithms Apriori
5990 (license license:gpl3)))
5992 (define-public r-parsedate
5994 (name "r-parsedate")
5999 (uri (cran-uri "parsedate" version))
6002 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6003 (build-system r-build-system)
6005 `(("r-rematch2" ,r-rematch2)))
6006 (home-page "https://github.com/gaborcsardi/parsedate")
6008 "Recognize and parse dates in various formats")
6010 "This package provides three functions for dealing with dates:
6011 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6012 time formats, @code{parse_date} parses dates in unspecified formats,
6013 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6014 (license license:gpl2)))
6016 (define-public r-abc-data
6023 (uri (cran-uri "abc.data" version))
6026 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6027 (properties `((upstream-name . "abc.data")))
6028 (build-system r-build-system)
6029 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6030 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6032 "This package contains data which are used by functions of the abc
6033 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6034 algorithms for performing parameter estimation, model selection, and
6036 (license license:gpl3+)))
6038 (define-public r-abc
6045 (uri (cran-uri "abc" version))
6048 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6049 (build-system r-build-system)
6051 `(("r-abc-data" ,r-abc-data)
6052 ("r-locfit" ,r-locfit)
6055 ("r-quantreg" ,r-quantreg)))
6056 (home-page "https://cran.r-project.org/web/packages/abc/")
6057 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6059 "This package implements several @dfn{Approximate Bayesian
6060 Computation} (ABC) algorithms for performing parameter estimation, model
6061 selection, and goodness-of-fit. Cross-validation tools are also available for
6062 measuring the accuracy of ABC estimates, and to calculate the
6063 misclassification probabilities of different models.")
6064 (license license:gpl3+)))
6066 (define-public r-zip
6073 (uri (cran-uri "zip" version))
6076 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6077 (build-system r-build-system)
6078 (home-page "https://github.com/gaborcsardi/zip")
6079 (synopsis "Cross-platform Zip compression")
6081 "This package provides a cross-platform Zip compression library for R.
6082 It is a replacement for the @code{zip} function, that does not require any
6083 additional external tools on any platform.")
6084 (license license:cc0)))
6086 (define-public r-openxlsx
6093 (uri (cran-uri "openxlsx" version))
6096 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6097 (build-system r-build-system)
6099 `(("r-rcpp" ,r-rcpp)
6100 ("r-stringi" ,r-stringi)
6103 `(("r-knitr" ,r-knitr)))
6104 (home-page "https://github.com/awalker89/openxlsx")
6105 (synopsis "Read, write and edit XLSX files")
6107 "This package simplifies the creation of Excel @code{.xlsx} files by
6108 providing a high level interface to writing, styling and editing worksheets.
6109 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6110 and @code{XLConnect} packages with the added benefit of removing the
6111 dependency on Java.")
6112 (license license:gpl3)))
6114 (define-public r-rio
6121 (uri (cran-uri "rio" version))
6124 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6125 (build-system r-build-system)
6127 `(("r-curl" ,r-curl)
6128 ("r-data-table" ,r-data-table)
6129 ("r-foreign" ,r-foreign)
6130 ("r-haven" ,r-haven)
6131 ("r-openxlsx" ,r-openxlsx)
6132 ("r-readxl" ,r-readxl)
6133 ("r-tibble" ,r-tibble)))
6134 (home-page "https://github.com/leeper/rio")
6135 (synopsis "Swiss-army knife for data I/O")
6137 "This package provides streamlined data import and export infrastructure
6138 by making assumptions that the user is probably willing to make: @code{import}
6139 and @code{export} determine the data structure from the file extension,
6140 reasonable defaults are used for data import and export (e.g.,
6141 @code{stringsAsFactors=FALSE}), web-based import is natively
6142 supported (including from SSL/HTTPS), compressed files can be read directly
6143 without explicit decompression, and fast import packages are used where
6144 appropriate. An additional convenience function, @code{convert}, provides a
6145 simple method for converting between file types.")
6146 (license license:gpl2)))
6148 (define-public r-maptools
6155 (uri (cran-uri "maptools" version))
6158 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6159 (build-system r-build-system)
6161 `(("r-foreign" ,r-foreign)
6162 ("r-lattice" ,r-lattice)
6164 (home-page "https://r-forge.r-project.org/projects/maptools/")
6165 (synopsis "Tools for reading and handling spatial objects")
6167 "This package provides a set of tools for manipulating and reading
6168 geographic data, in particular ESRI Shapefiles. It includes binary access to
6169 GSHHG shoreline files. The package also provides interface wrappers for
6170 exchanging spatial objects with other R packages.")
6171 ;; The C source files from shapelib are released under the Expat license.
6172 ;; The R code is released under GPL version 2 or later.
6173 (license (list license:gpl2+
6176 (define-public r-later
6183 (uri (cran-uri "later" version))
6186 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6187 (build-system r-build-system)
6191 ("r-rlang" ,r-rlang)))
6193 `(("r-knitr" ,r-knitr)))
6194 (home-page "https://github.com/r-lib/later")
6195 (synopsis "Utilities for delaying function execution")
6197 "This package provides tools to execute arbitrary R or C functions some
6198 time after the current time, after the R execution stack has emptied.")
6199 (license license:gpl2+)))
6201 (define-public r-promises
6208 (uri (cran-uri "promises" version))
6211 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6212 (build-system r-build-system)
6214 `(("r-later" ,r-later)
6215 ("r-magrittr" ,r-magrittr)
6218 ("r-rlang" ,r-rlang)))
6220 `(("r-knitr" ,r-knitr)))
6221 (home-page "https://rstudio.github.io/promises")
6222 (synopsis "Abstractions for promise-based asynchronous programming")
6224 "This package provides fundamental abstractions for doing asynchronous
6225 programming in R using promises. Asynchronous programming is useful for
6226 allowing a single R process to orchestrate multiple tasks in the background
6227 while also attending to something else. Semantics are similar to JavaScript
6228 promises, but with a syntax that is idiomatic R.")
6229 (license license:expat)))
6231 (define-public r-dosnow
6238 (uri (cran-uri "doSNOW" version))
6241 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6242 (properties `((upstream-name . "doSNOW")))
6243 (build-system r-build-system)
6245 `(("r-foreach" ,r-foreach)
6246 ("r-iterators" ,r-iterators)
6247 ("r-snow" ,r-snow)))
6248 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6249 (synopsis "Foreach parallel adaptor for the snow package")
6251 "This package provides a parallel backend for the @code{%dopar%} function
6252 using the @code{snow} package.")
6253 (license license:gpl2)))
6255 (define-public r-snowfall
6258 (version "1.84-6.1")
6261 (uri (cran-uri "snowfall" version))
6263 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6264 (build-system r-build-system)
6266 `(("r-snow" ,r-snow)))
6267 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6268 (synopsis "Easier cluster computing")
6269 (description "This package is a usability wrapper around snow for easier
6270 development of parallel R programs. This package offers e.g. extended error
6271 checks, and additional functions. All functions work in sequential mode, too,
6272 if no cluster is present or wished. The package is also designed as connector
6273 to the cluster management tool @code{sfCluster}, but can also used without
6275 (license license:gpl2+)))
6277 (define-public r-rappdirs
6284 (uri (cran-uri "rappdirs" version))
6287 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6288 (build-system r-build-system)
6289 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6290 (synopsis "Determine where to save data, caches, and logs")
6292 "This package provides an easy way to determine which directories on the
6293 user's computer should be used to save data, caches and logs. It is a port of
6294 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6295 (license license:expat)))
6297 (define-public r-renv
6304 (uri (cran-uri "renv" version))
6307 "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
6308 (properties `((upstream-name . "renv")))
6309 (build-system r-build-system)
6311 `(("r-knitr" ,r-knitr)))
6312 (home-page "https://rstudio.github.io/renv")
6313 (synopsis "Project environments")
6315 "This package provides a dependency management toolkit for R. Using
6316 renv, you can create and manage project-local R libraries, save the state of
6317 these libraries to a lockfile, and later restore your library as required.
6318 Together, these tools can help make your projects more isolated, portable, and
6320 (license license:expat)))
6322 (define-public r-learnr
6329 (uri (cran-uri "learnr" version))
6332 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6333 (build-system r-build-system)
6335 `(("r-checkmate" ,r-checkmate)
6336 ("r-ellipsis" ,r-ellipsis)
6337 ("r-evaluate" ,r-evaluate)
6338 ("r-htmltools" ,r-htmltools)
6339 ("r-htmlwidgets" ,r-htmlwidgets)
6340 ("r-jsonlite" ,r-jsonlite)
6341 ("r-knitr" ,r-knitr)
6342 ("r-markdown" ,r-markdown)
6343 ("r-rappdirs" ,r-rappdirs)
6345 ("r-rmarkdown" ,r-rmarkdown)
6346 ("r-rprojroot" ,r-rprojroot)
6347 ("r-shiny" ,r-shiny)
6348 ("r-withr" ,r-withr)))
6349 (home-page "https://rstudio.github.io/learnr/")
6350 (synopsis "Interactive tutorials for R")
6352 "This package provides tools to create interactive tutorials using R
6353 Markdown. Use a combination of narrative, figures, videos, exercises, and
6354 quizzes to create self-paced tutorials for learning about R and R packages.")
6355 (license license:asl2.0)))
6357 (define-public r-analytics
6359 (name "r-analytics")
6364 (uri (cran-uri "analytics" version))
6367 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6368 (build-system r-build-system)
6371 ("r-cluster" ,r-cluster)
6372 ("r-fractal" ,r-fractal)
6373 ("r-lmtest" ,r-lmtest)
6376 ("r-powerplus" ,r-powerplus)
6377 ("r-robust" ,r-robust)
6378 ("r-trend" ,r-trend)
6382 (home-page "https://cran.r-project.org/web/packages/analytics/")
6383 (synopsis "Collection of data analysis tools")
6385 "This package is a collection of data analysis tools. It includes tools
6386 for regression outlier detection in a fitted linear model, stationary
6387 bootstrap using a truncated geometric distribution, a comprehensive test for
6388 weak stationarity, column means by group, weighted biplots, and a heuristic to
6389 obtain a better initial configuration in non-metric MDS.")
6390 (license license:gpl2)))
6392 (define-public r-reticulate
6394 (name "r-reticulate")
6399 (uri (cran-uri "reticulate" version))
6402 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
6403 (build-system r-build-system)
6404 (inputs `(("python" ,python)))
6406 `(("r-rappdirs" ,r-rappdirs)
6407 ("r-jsonlite" ,r-jsonlite)
6408 ("r-matrix" ,r-matrix)
6409 ("r-rcpp" ,r-rcpp)))
6411 `(("r-knitr" ,r-knitr)))
6412 (home-page "https://github.com/rstudio/reticulate")
6413 (synopsis "R interface to Python")
6415 "This package provides an interface from R to Python modules, classes,
6416 and functions. When calling into Python, R data types are automatically
6417 converted to their equivalent Python types. When values are returned from
6418 Python to R they are converted back to R types.")
6419 (license license:asl2.0)))
6421 (define-public r-bibtex
6428 (uri (cran-uri "bibtex" version))
6431 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
6432 (build-system r-build-system)
6433 (propagated-inputs `(("r-stringr" ,r-stringr)))
6434 (home-page "https://github.com/romainfrancois/bibtex")
6435 (synopsis "Bibtex parser")
6436 (description "This package provides a utility for R to parse a bibtex
6438 (license license:gpl2+)))
6440 (define-public r-ggseqlogo
6442 (name "r-ggseqlogo")
6447 (uri (cran-uri "ggseqlogo" version))
6450 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6451 (build-system r-build-system)
6452 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6453 (home-page "https://github.com/omarwagih/ggseqlogo")
6454 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6456 "The range of functions provided by this package makes it possible to
6457 draw highly versatile genomic sequence logos. Features include, but are not
6458 limited to, modifying colour schemes and fonts used to draw the logo,
6459 generating multiple logo plots, and aiding the visualisation with annotations.
6460 Sequence logos can easily be combined with other ggplot2 plots.")
6461 ;; Unspecified version of the LGPL.
6462 (license license:lgpl3+)))
6464 (define-public r-ggsci
6471 (uri (cran-uri "ggsci" version))
6474 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6475 (build-system r-build-system)
6477 `(("r-ggplot2" ,r-ggplot2)
6478 ("r-scales" ,r-scales)))
6479 (home-page "https://nanx.me/ggsci/")
6480 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6482 "This package provides a collection of ggplot2 color palettes inspired by
6483 plots in scientific journals, data visualization libraries, science fiction
6484 movies, and TV shows.")
6485 (license license:gpl3)))
6487 (define-public r-ggsignif
6494 (uri (cran-uri "ggsignif" version))
6497 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6498 (build-system r-build-system)
6500 `(("r-knitr" ,r-knitr)))
6502 `(("r-ggplot2" ,r-ggplot2)))
6503 (home-page "https://github.com/const-ae/ggsignif")
6504 (synopsis "Significance brackets for ggplot2")
6506 "Enrich your ggplots with group-wise comparisons. This package provides
6507 an easy way to indicate if two groups are significantly different. Commonly
6508 this is shown by a bracket on top connecting the groups of interest which
6509 itself is annotated with the level of significance. The package provides a
6510 single layer that takes the groups for comparison and the test as arguments
6511 and adds the annotation to the plot.")
6512 (license license:gpl3)))
6514 (define-public r-rstatix
6521 (uri (cran-uri "rstatix" version))
6524 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6525 (properties `((upstream-name . "rstatix")))
6526 (build-system r-build-system)
6528 `(("r-broom" ,r-broom)
6530 ("r-corrplot" ,r-corrplot)
6531 ("r-dplyr" ,r-dplyr)
6532 ("r-generics" ,r-generics)
6533 ("r-magrittr" ,r-magrittr)
6534 ("r-purrr" ,r-purrr)
6535 ("r-rlang" ,r-rlang)
6536 ("r-tibble" ,r-tibble)
6537 ("r-tidyr" ,r-tidyr)
6538 ("r-tidyselect" ,r-tidyselect)))
6539 (home-page "https://rpkgs.datanovia.com/rstatix/")
6540 (synopsis "Pipe-friendly framework for basic statistical tests")
6542 "This package provides a simple and intuitive pipe-friendly framework,
6543 coherent with the @code{tidyverse} design philosophy, for performing basic
6544 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6545 correlation analyses. The output of each test is automatically transformed
6546 into a tidy data frame to facilitate visualization. Additional functions are
6547 available for reshaping, reordering, manipulating and visualizing correlation
6549 (license license:gpl2)))
6551 (define-public r-ggpubr
6558 (uri (cran-uri "ggpubr" version))
6561 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6562 (build-system r-build-system)
6564 `(("r-cowplot" ,r-cowplot)
6565 ("r-dplyr" ,r-dplyr)
6566 ("r-ggplot2" ,r-ggplot2)
6567 ("r-ggrepel" ,r-ggrepel)
6568 ("r-ggsci" ,r-ggsci)
6569 ("r-ggsignif" ,r-ggsignif)
6571 ("r-gridextra" ,r-gridextra)
6572 ("r-magrittr" ,r-magrittr)
6573 ("r-polynom" ,r-polynom)
6574 ("r-purrr" ,r-purrr)
6575 ("r-rlang" ,r-rlang)
6576 ("r-scales" ,r-scales)
6577 ("r-rstatix" ,r-rstatix)
6578 ("r-tibble" ,r-tibble)
6579 ("r-tidyr" ,r-tidyr)))
6580 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6581 (synopsis "ggplot2-based publication-ready plots")
6583 "The ggplot2 package is an excellent and flexible package for elegant
6584 data visualization in R. However the default generated plots require some
6585 formatting before we can send them for publication. The ggpubr package
6586 provides some easy-to-use functions for creating and customizing ggplot2-based
6587 publication-ready plots.")
6588 (license license:gpl2)))
6590 (define-public r-ellipse
6597 (uri (cran-uri "ellipse" version))
6600 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6601 (build-system r-build-system)
6602 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6603 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6605 "This package contains various routines for drawing ellipses and
6606 ellipse-like confidence regions, implementing the plots described in Murdoch
6607 and Chow (1996), A graphical display of large correlation matrices, The
6608 American Statistician 50, 178-180. There are also routines implementing the
6609 profile plots described in Bates and Watts (1988), Nonlinear Regression
6610 Analysis and its Applications.")
6611 (license license:gpl2+)))
6613 (define-public r-flashclust
6615 (name "r-flashclust")
6620 (uri (cran-uri "flashClust" version))
6623 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6624 (properties `((upstream-name . "flashClust")))
6625 (build-system r-build-system)
6626 (native-inputs `(("gfortran" ,gfortran)))
6627 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6628 (synopsis "Implementation of optimal hierarchical clustering")
6630 "This package provides a fast implementation of hierarchical
6632 (license license:gpl2+)))
6634 (define-public r-factominer
6636 (name "r-factominer")
6641 (uri (cran-uri "FactoMineR" version))
6644 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6645 (properties `((upstream-name . "FactoMineR")))
6646 (build-system r-build-system)
6649 ("r-cluster" ,r-cluster)
6650 ("r-ellipse" ,r-ellipse)
6651 ("r-flashclust" ,r-flashclust)
6652 ("r-ggplot2" ,r-ggplot2)
6653 ("r-ggrepel" ,r-ggrepel)
6654 ("r-lattice" ,r-lattice)
6655 ("r-leaps" ,r-leaps)
6657 ("r-scatterplot3d" ,r-scatterplot3d)))
6658 (home-page "http://factominer.free.fr")
6659 (synopsis "Multivariate exploratory data analysis and data mining")
6661 "This package provides exploratory data analysis methods to summarize,
6662 visualize and describe datasets. The main principal component methods are
6663 available, those with the largest potential in terms of applications:
6664 principal component analysis (PCA) when variables are quantitative,
6665 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6666 variables are categorical, Multiple Factor Analysis when variables are
6667 structured in groups, etc. and hierarchical cluster analysis.")
6668 (license license:gpl2+)))
6670 (define-public r-factoextra
6672 (name "r-factoextra")
6677 (uri (cran-uri "factoextra" version))
6680 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6681 (build-system r-build-system)
6683 `(("r-abind" ,r-abind)
6684 ("r-cluster" ,r-cluster)
6685 ("r-dendextend" ,r-dendextend)
6686 ("r-factominer" ,r-factominer)
6687 ("r-ggplot2" ,r-ggplot2)
6688 ("r-ggpubr" ,r-ggpubr)
6689 ("r-ggrepel" ,r-ggrepel)
6690 ("r-reshape2" ,r-reshape2)
6691 ("r-tidyr" ,r-tidyr)))
6692 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6693 (synopsis "Extract and visualize the results of multivariate data analyses")
6695 "This package provides some easy-to-use functions to extract and
6696 visualize the output of multivariate data analyses, including
6697 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6698 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6699 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6700 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6701 packages. It contains also functions for simplifying some clustering analysis
6702 steps and provides ggplot2-based elegant data visualization.")
6703 (license license:gpl2)))
6705 (define-public r-fansi
6712 (uri (cran-uri "fansi" version))
6715 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6716 (build-system r-build-system)
6718 `(("r-knitr" ,r-knitr))) ; for vignettes
6719 (home-page "https://github.com/brodieG/fansi")
6720 (synopsis "ANSI control sequence aware string functions")
6722 "This package provides counterparts to R string manipulation functions
6723 that account for the effects of ANSI text formatting control sequences.")
6724 (license license:gpl2+)))
6726 (define-public r-nbclust
6733 (uri (cran-uri "NbClust" version))
6736 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6737 (properties `((upstream-name . "NbClust")))
6738 (build-system r-build-system)
6739 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6740 (synopsis "Determine the best number of clusters in a data set")
6742 "NbClust provides 30 indexes for determining the optimal number of
6743 clusters in a data set and offers the best clustering scheme from different
6744 results to the user.")
6745 (license license:gpl2)))
6747 (define-public r-hdf5r
6754 (uri (cran-uri "hdf5r" version))
6757 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6758 (build-system r-build-system)
6763 `(("r-bit64" ,r-bit64)
6766 `(("r-knitr" ,r-knitr)))
6767 (home-page "https://hhoeflin.github.io/hdf5r")
6768 (synopsis "Interface to the HDF5 binary data format")
6770 "HDF5 is a data model, library and file format for storing and managing
6771 large amounts of data. This package provides a nearly feature complete,
6772 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6773 functionality is added so that HDF5 objects behave very similar to their
6774 corresponding R counterparts.")
6775 (license license:asl2.0)))
6777 (define-public r-itertools
6779 (name "r-itertools")
6784 (uri (cran-uri "itertools" version))
6787 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6788 (build-system r-build-system)
6790 `(("r-iterators" ,r-iterators)))
6791 (home-page "https://cran.r-project.org/web/packages/itertools/")
6792 (synopsis "Iterator tools")
6794 "This package provides various tools for creating iterators, many
6795 patterned after functions in the Python @code{itertools} module, and others
6796 patterned after functions in the snow package.")
6797 (license license:gpl2)))
6799 (define-public r-polynom
6806 (uri (cran-uri "polynom" version))
6809 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6810 (build-system r-build-system)
6811 (home-page "https://cran.r-project.org/web/packages/polynom/")
6812 (synopsis "Functions for univariate polynomial manipulations")
6814 "This package provides a collection of functions to implement a class for
6815 univariate polynomial manipulations.")
6816 (license license:gpl2)))
6818 (define-public r-gbrd
6825 (uri (cran-uri "gbRd" version))
6828 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6829 (properties `((upstream-name . "gbRd")))
6830 (build-system r-build-system)
6831 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6832 (synopsis "Utilities for processing Rd objects and files")
6834 "This package provides utilities for processing Rd objects and files.
6835 Extract argument descriptions and other parts of the help pages of
6837 (license license:gpl2+)))
6839 (define-public r-rjags
6846 (uri (cran-uri "rjags" version))
6849 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6850 (build-system r-build-system)
6852 `(("r-coda" ,r-coda)))
6856 `(("pkg-config" ,pkg-config)))
6857 (home-page "http://mcmc-jags.sourceforge.net")
6858 (synopsis "Bayesian graphical models using MCMC")
6860 "This package provides an R interface to the JAGS MCMC library. JAGS is
6861 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6862 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6863 (license license:gpl2)))
6865 (define-public r-rbibutils
6867 (name "r-rbibutils")
6872 (uri (cran-uri "rbibutils" version))
6875 "1i000czyd059dczd2nn1cb0d4n0bjykrfh51rs85s8r2zlaydn6i"))))
6876 (properties `((upstream-name . "rbibutils")))
6877 (build-system r-build-system)
6878 (propagated-inputs `(("r-xml2" ,r-xml2)))
6879 (home-page "https://geobosh.github.io/rbibutils/")
6880 (synopsis "Convert between bibliography formats")
6882 "This package converts between a number of bibliography formats,
6883 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
6884 utilities and supports all bibliography formats and character encodings
6885 implemented in bibutils.")
6886 (license license:gpl2)))
6888 (define-public r-rdpack
6895 (uri (cran-uri "Rdpack" version))
6898 "04gk68y3cxlqhfl1aarjwz2mvx934ka0yxfgzrnw03ykhvb47fpi"))))
6899 (properties `((upstream-name . "Rdpack")))
6900 (build-system r-build-system)
6902 `(("r-rbibutils" ,r-rbibutils)
6903 ("r-gbrd" ,r-gbrd)))
6904 (home-page "https://github.com/GeoBosh/Rdpack")
6905 (synopsis "Update and manipulate Rd documentation objects")
6907 "This package provides functions for manipulation of R documentation
6908 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6909 updating Rd documentation for functions, methods and classes; it also includes
6910 Rd macros for citations and import of references from bibtex files for use in
6911 Rd files and roxygen2 comments, as well as many functions for manipulation of
6912 references and Rd files.")
6913 (license license:gpl2+)))
6915 (define-public r-officer
6922 (uri (cran-uri "officer" version))
6925 "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h"))))
6926 (build-system r-build-system)
6928 `(("r-magrittr" ,r-magrittr)
6934 `(("r-knitr" ,r-knitr)))
6935 (home-page "https://davidgohel.github.io/officer")
6936 (synopsis "Manipulation of Word and PowerPoint documents")
6938 "This package provides tools to access and manipulate Word and PowerPoint
6939 documents from R. The package focuses on tabular and graphical reporting from
6940 R; it also provides two functions that let users get document content into
6941 data objects. A set of functions lets add and remove images, tables and
6942 paragraphs of text in new or existing documents. When working with PowerPoint
6943 presentations, slides can be added or removed; shapes inside slides can also
6944 be added or removed. When working with Word documents, a cursor can be used
6945 to help insert or delete content at a specific location in the document.")
6946 (license license:gpl3)))
6948 (define-public r-profilemodel
6950 (name "r-profilemodel")
6955 (uri (cran-uri "profileModel" version))
6958 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6959 (properties `((upstream-name . "profileModel")))
6960 (build-system r-build-system)
6961 (home-page "https://github.com/ikosmidis/profileModel")
6962 (synopsis "Profiling inference functions for various model classes")
6964 "This package provides tools that can be used to calculate, evaluate,
6965 plot and use for inference the profiles of *arbitrary* inference functions for
6966 arbitrary @code{glm}-like fitted models with linear predictors. More information
6967 on the methods that are implemented can be found in Kosmidis (2008)
6968 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6969 (license license:gpl2+)))
6971 (define-public r-brglm
6978 (uri (cran-uri "brglm" version))
6981 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
6982 (properties `((upstream-name . "brglm")))
6983 (build-system r-build-system)
6985 `(("r-profilemodel" ,r-profilemodel)))
6986 (home-page "https://github.com/ikosmidis/brglm")
6987 (synopsis "Bias reduction in binomial-response generalized linear models")
6989 "Fit generalized linear models with binomial responses using either an
6990 adjusted-score approach to bias reduction or maximum penalized likelihood
6991 where penalization is by Jeffreys invariant prior. These procedures return
6992 estimates with improved frequentist properties (bias, mean squared error) that
6993 are always finite even in cases where the maximum likelihood estimates are
6994 infinite (data separation). Fitting takes place by fitting generalized linear
6995 models on iteratively updated pseudo-data. The interface is essentially the
6996 same as @code{glm}. More flexibility is provided by the fact that custom
6997 pseudo-data representations can be specified and used for model fitting.
6998 Functions are provided for the construction of confidence intervals for the
6999 reduced-bias estimates.")
7000 (license license:gpl2+)))
7002 (define-public r-entropy
7009 (uri (cran-uri "entropy" version))
7012 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
7013 (properties `((upstream-name . "entropy")))
7014 (build-system r-build-system)
7015 (home-page "https://www.strimmerlab.org/software/entropy/")
7016 (synopsis "Estimation of entropy, mutual information and related quantities")
7018 "This package implements various estimators of entropy, such as the
7019 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
7020 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
7021 estimator. It also offers an R interface to the NSB estimator. Furthermore,
7022 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
7023 mutual information, and chi-squared statistic of independence. In addition
7024 there are functions for discretizing continuous random variables.")
7025 (license license:gpl3+)))
7027 (define-public r-abn
7034 (uri (cran-uri "abn" version))
7037 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
7038 (build-system r-build-system)
7042 `(("r-lme4" ,r-lme4)
7045 ("r-rcpparmadillo" ,r-rcpparmadillo)
7046 ("r-rjags" ,r-rjags)))
7047 (home-page "https://r-bayesian-networks.org/")
7048 (synopsis "Modelling multivariate data with additive bayesian networks")
7050 "Bayesian network analysis is a form of probabilistic graphical models
7051 which derives from empirical data a directed acyclic graph, DAG, describing
7052 the dependency structure between random variables. An additive Bayesian
7053 network model consists of a form of a DAG where each node comprises a
7054 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
7055 equivalent to Bayesian multivariate regression using graphical modelling, they
7056 generalises the usual multivariable regression, GLM, to multiple dependent
7057 variables. This package provides routines to help determine optimal Bayesian
7058 network models for a given data set, where these models are used to identify
7059 statistical dependencies in messy, complex data.")
7060 (license license:gpl2+)))
7062 (define-public r-acd
7069 (uri (cran-uri "ACD" version))
7072 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
7073 (properties `((upstream-name . "ACD")))
7074 (build-system r-build-system)
7075 (home-page "https://cran.r-project.org/web/packages/ACD/")
7076 (synopsis "Categorical data analysis with complete or missing responses")
7078 "This package provides tools for categorical data analysis with complete
7079 or missing responses.")
7080 (license license:gpl2+)))
7082 (define-public r-acdm
7089 (uri (cran-uri "ACDm" version))
7092 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
7093 (properties `((upstream-name . "ACDm")))
7094 (build-system r-build-system)
7096 `(("r-dplyr" ,r-dplyr)
7097 ("r-ggplot2" ,r-ggplot2)
7099 ("r-rsolnp" ,r-rsolnp)
7101 (home-page "https://cran.r-project.org/web/packages/ACDm/")
7102 (synopsis "Tools for Autoregressive Conditional Duration Models")
7104 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
7105 and Russell, 1998) models. It creates trade, price or volume durations from
7106 transactions (tic) data, performs diurnal adjustments, fits various ACD models
7108 (license license:gpl2+)))
7110 (define-public r-overlap
7117 (uri (cran-uri "overlap" version))
7120 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
7121 (build-system r-build-system)
7122 (home-page "https://cran.r-project.org/web/packages/overlap/")
7123 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
7125 "This package provides functions to fit kernel density functions to data
7126 on temporal activity patterns of animals; estimate coefficients of overlapping
7127 of densities for two species; and calculate bootstrap estimates of confidence
7129 (license license:gpl3+)))
7131 (define-public r-snakecase
7133 (name "r-snakecase")
7138 (uri (cran-uri "snakecase" version))
7141 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
7142 (build-system r-build-system)
7144 `(("r-stringi" ,r-stringi)
7145 ("r-stringr" ,r-stringr)))
7146 (home-page "https://github.com/Tazinho/snakecase")
7147 (synopsis "Convert strings into any case")
7149 "This package provides a consistent, flexible and easy to use tool to
7150 parse and convert strings into cases like snake or camel among others.")
7151 (license license:gpl3)))
7153 (define-public r-prediction
7155 (name "r-prediction")
7160 (uri (cran-uri "prediction" version))
7163 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
7164 (build-system r-build-system)
7166 `(("r-data-table" ,r-data-table)))
7167 (home-page "https://github.com/leeper/prediction")
7168 (synopsis "Tidy, type-safe prediction methods")
7170 "This package provides the @code{prediction()} function, a type-safe
7171 alternative to @code{predict()} that always returns a data frame. The package
7172 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
7173 from the @code{stats} package, as well as numerous other model classes from
7174 other add-on packages.")
7175 (license license:expat)))
7177 (define-public r-insight
7184 (uri (cran-uri "insight" version))
7187 "1r4val3hvc43zailfmq6wcbg366s0bi0ysib476a49k1x6h8b6ji"))))
7188 (build-system r-build-system)
7190 `(("r-knitr" ,r-knitr)))
7191 (home-page "https://easystats.github.io/insight/")
7192 (synopsis "Easy access to model information for various model objects")
7194 "This package provides a tool to provide an easy, intuitive and
7195 consistent access to information contained in various R models, like model
7196 formulas, model terms, information about random effects, data that was used to
7197 fit the model or data from response variables. The package mainly revolves
7198 around two types of functions: Functions that find (the names of) information,
7199 starting with @code{find_}, and functions that get the underlying data,
7200 starting with @code{get_}. The package has a consistent syntax and works with
7201 many different model objects, where otherwise functions to access these
7202 information are missing.")
7203 (license license:gpl3)))
7205 (define-public r-sjlabelled
7207 (name "r-sjlabelled")
7212 (uri (cran-uri "sjlabelled" version))
7215 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
7216 (build-system r-build-system)
7218 `(("r-insight" ,r-insight)))
7220 `(("r-knitr" ,r-knitr)))
7221 (home-page "https://github.com/strengejacke/sjlabelled")
7222 (synopsis "Labelled data utility functions")
7224 "This package provides a collection of functions dealing with labelled
7225 data, like reading and writing data between R and other statistical software
7226 packages. This includes easy ways to get, set or change value and variable
7227 label attributes, to convert labelled vectors into factors or numeric (and
7228 vice versa), or to deal with multiple declared missing values.")
7229 (license license:gpl3)))
7231 (define-public r-sjmisc
7238 (uri (cran-uri "sjmisc" version))
7241 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
7242 (build-system r-build-system)
7244 `(("r-dplyr" ,r-dplyr)
7245 ("r-insight" ,r-insight)
7246 ("r-magrittr" ,r-magrittr)
7247 ("r-purrr" ,r-purrr)
7248 ("r-rlang" ,r-rlang)
7249 ("r-sjlabelled" ,r-sjlabelled)
7250 ("r-tidyselect" ,r-tidyselect)))
7252 `(("r-knitr" ,r-knitr)))
7253 (home-page "https://github.com/strengejacke/sjmisc")
7254 (synopsis "Data and variable transformation functions")
7256 "This package is a collection of miscellaneous utility functions,
7257 supporting data transformation tasks like recoding, dichotomizing or grouping
7258 variables, setting and replacing missing values. The data transformation
7259 functions also support labelled data, and all integrate seamlessly into a
7260 tidyverse workflow.")
7261 (license license:gpl3)))
7263 (define-public r-nortest
7270 (uri (cran-uri "nortest" version))
7273 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7274 (build-system r-build-system)
7275 (home-page "https://cran.r-project.org/web/packages/nortest/")
7276 (synopsis "Tests for normality")
7278 "This package provides five omnibus tests for testing the composite
7279 hypothesis of normality.")
7280 (license license:gpl2+)))
7282 (define-public r-moonbook
7289 (uri (cran-uri "moonBook" version))
7292 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7293 (properties `((upstream-name . "moonBook")))
7294 (build-system r-build-system)
7296 `(("r-magrittr" ,r-magrittr)
7297 ("r-nortest" ,r-nortest)
7298 ("r-purrr" ,r-purrr)
7299 ("r-sjmisc" ,r-sjmisc)
7300 ("r-stringr" ,r-stringr)
7301 ("r-survival" ,r-survival)))
7302 (home-page "https://github.com/cardiomoon/moonBook")
7303 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7305 "This package provides several analysis-related functions for the book
7306 entitled \"R statistics and graph for medical articles\" (written in Korean),
7307 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7309 (license license:gpl2)))
7311 (define-public r-flextable
7313 (name "r-flextable")
7318 (uri (cran-uri "flextable" version))
7321 "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4"))))
7322 (build-system r-build-system)
7324 `(("r-base64enc" ,r-base64enc)
7325 ("r-data-table" ,r-data-table)
7326 ("r-gdtools" ,r-gdtools)
7327 ("r-htmltools" ,r-htmltools)
7328 ("r-knitr" ,r-knitr)
7329 ("r-officer" ,r-officer)
7330 ("r-rlang" ,r-rlang)
7331 ("r-rmarkdown" ,r-rmarkdown)
7333 ("r-xml2" ,r-xml2)))
7334 (home-page "https://davidgohel.github.io/flextable")
7335 (synopsis "Functions for tabular reporting")
7337 "This package provides tools to create pretty tables for HTML documents
7338 and other formats. Functions are provided to let users create tables, modify
7339 and format their content. It extends the @code{officer} package and can be
7340 used within R markdown documents when rendering to HTML and to Word
7342 (license license:gpl3)))
7344 (define-public r-writexl
7351 (uri (cran-uri "writexl" version))
7354 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
7355 (build-system r-build-system)
7356 (inputs `(("zlib" ,zlib)))
7357 (home-page "https://github.com/ropensci/writexl")
7358 (synopsis "Export data frames to xlsx format")
7360 "This package provides a data frame to xlsx exporter based on
7362 (license license:bsd-2)))
7364 (define-public r-biasedurn
7366 (name "r-biasedurn")
7371 (uri (cran-uri "BiasedUrn" version))
7374 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7375 (properties `((upstream-name . "BiasedUrn")))
7376 (build-system r-build-system)
7377 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7378 (synopsis "Biased Urn model distributions")
7380 "This package provides statistical models of biased sampling in the form
7381 of univariate and multivariate noncentral hypergeometric distributions,
7382 including Wallenius' noncentral hypergeometric distribution and Fisher's
7383 noncentral hypergeometric distribution (also called extended hypergeometric
7385 (license license:gpl3)))
7387 (define-public r-goplot
7394 (uri (cran-uri "GOplot" version))
7397 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7398 (properties `((upstream-name . "GOplot")))
7399 (build-system r-build-system)
7401 `(("r-ggdendro" ,r-ggdendro)
7402 ("r-ggplot2" ,r-ggplot2)
7403 ("r-gridextra" ,r-gridextra)
7404 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7405 (home-page "https://github.com/wencke/wencke.github.io")
7406 (synopsis "Visualization of functional analysis data")
7408 "This package provides an implementation of multilayered visualizations
7409 for enhanced graphical representation of functional analysis data. It
7410 combines and integrates omics data derived from expression and functional
7411 annotation enrichment analyses. Its plotting functions have been developed
7412 with an hierarchical structure in mind: starting from a general overview to
7413 identify the most enriched categories (modified bar plot, bubble plot) to a
7414 more detailed one displaying different types of relevant information for the
7415 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7416 Venn diagram, heatmap).")
7417 (license license:gpl2)))
7419 (define-public r-getopt
7426 (uri (cran-uri "getopt" version))
7429 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7430 (build-system r-build-system)
7431 (home-page "https://github.com/trevorld/getopt")
7432 (synopsis "Command-line option processor for R")
7434 "This package is designed to be used with Rscript to write shebang
7435 scripts that accept short and long options. Many users will prefer to
7436 use the packages @code{optparse} or @code{argparse} which add extra
7437 features like automatically generated help options and usage texts,
7438 support for default values, positional argument support, etc.")
7439 (license license:gpl2+)))
7441 (define-public r-findpython
7443 (name "r-findpython")
7448 (uri (cran-uri "findpython" version))
7451 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7452 (build-system r-build-system)
7453 (home-page "https://github.com/trevorld/findpython")
7454 (synopsis "Functions to find an acceptable Python binary")
7456 "This package was designed to find an acceptable Python binary that
7457 matches version and feature constraints.")
7458 (license license:expat)))
7460 ;; This in not the same as "r-argparser"
7461 (define-public r-argparse
7468 (uri (cran-uri "argparse" version))
7471 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
7472 (build-system r-build-system)
7473 (inputs `(("python" ,python)))
7475 `(("r-findpython" ,r-findpython)
7476 ("r-jsonlite" ,r-jsonlite)
7479 `(("r-knitr" ,r-knitr)))
7480 (home-page "https://github.com/trevorld/argparse")
7481 (synopsis "Command line optional and positional argument parser")
7483 "This package provides a command line parser to be used with Rscript to
7484 write shebang scripts that gracefully accept positional and optional arguments
7485 and automatically generate usage notices.")
7486 (license license:gpl2+)))
7488 (define-public r-hash
7495 (uri (cran-uri "hash" version))
7498 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7499 (build-system r-build-system)
7500 (home-page "https://cran.r-project.org/web/packages/hash/")
7501 (synopsis "Implementation of hash/associated arrays/dictionaries")
7503 "This package implements a data structure similar to hashes in Perl and
7504 dictionaries in Python but with a purposefully R flavor. For objects of
7505 appreciable size, access using hashes outperforms native named lists and
7507 (license license:gpl2+)))
7509 (define-public r-orddom
7516 (uri (cran-uri "orddom" version))
7519 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7520 (build-system r-build-system)
7521 (propagated-inputs `(("r-psych" ,r-psych)))
7522 (home-page "https://cran.r-project.org/web/packages/orddom/")
7523 (synopsis "Ordinal dominance statistics")
7525 "This package provides tools to compute ordinal, statistics and effect
7526 sizes as an alternative to mean comparison: Cliff's delta or success rate
7527 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7528 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7529 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7530 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7531 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7532 Group (Non-)Overlap considerations.")
7533 (license license:gpl2)))
7535 (define-public r-deriv
7542 (uri (cran-uri "Deriv" version))
7545 "1fzchsignpb7cpizbf6l8v9k1nkmaf4r4j3mnxz0csl2g2npi1xc"))))
7546 (properties `((upstream-name . "Deriv")))
7547 (build-system r-build-system)
7548 (home-page "https://cran.r-project.org/web/packages/Deriv")
7549 (synopsis "Symbolic differentiation")
7551 "This package provides an R-based solution for symbolic differentiation.
7552 It admits user-defined functions as well as function substitution in arguments
7553 of functions to be differentiated. Some symbolic simplification is part of
7555 (license license:gpl3+)))
7557 (define-public r-doby
7564 (uri (cran-uri "doBy" version))
7567 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7568 (properties `((upstream-name . "doBy")))
7569 (build-system r-build-system)
7571 `(("r-broom" ,r-broom)
7572 ("r-deriv" ,r-deriv)
7573 ("r-dplyr" ,r-dplyr)
7574 ("r-ggplot2" ,r-ggplot2)
7575 ("r-magrittr" ,r-magrittr)
7577 ("r-matrix" ,r-matrix)
7578 ("r-pbkrtest" ,r-pbkrtest)
7579 ("r-tibble" ,r-tibble)))
7581 `(("r-knitr" ,r-knitr)))
7582 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7583 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7585 "This package contains:
7588 @item facilities for working with grouped data: @code{do}
7589 something to data stratified @code{by} some variables.
7590 @item implementations of least-squares means, general linear contrasts, and
7591 @item miscellaneous other utilities.
7593 (license license:gpl2+)))
7595 (define-public r-refgenome
7597 (name "r-refgenome")
7602 (uri (cran-uri "refGenome" version))
7605 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7606 (properties `((upstream-name . "refGenome")))
7607 (build-system r-build-system)
7611 ("r-rsqlite" ,r-rsqlite)))
7612 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7614 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7616 "This package contains functionality for importing and managing of
7617 downloaded genome annotation data from the Ensembl genome browser (European
7618 Bioinformatics Institute) and from the UCSC genome browser (University of
7619 California, Santa Cruz) and annotation routines for genomic positions and
7620 splice site positions.")
7621 (license license:gpl2)))
7623 (define-public r-basix
7630 (uri (cran-uri "BASIX" version))
7633 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7634 (properties `((upstream-name . "BASIX")))
7635 (build-system r-build-system)
7636 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7637 (synopsis "Efficient C/C++ toolset for R")
7639 "BASIX provides some efficient C/C++ implementations of native R
7640 procedures to speed up calculations in R.")
7641 (license license:gpl2)))
7643 (define-public r-blockfest
7645 (name "r-blockfest")
7650 (uri (cran-uri "BlockFeST" version))
7653 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7654 (properties `((upstream-name . "BlockFeST")))
7655 (build-system r-build-system)
7656 (propagated-inputs `(("r-basix" ,r-basix)))
7657 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7658 (synopsis "Bayesian calculation of region-specific fixation index")
7660 "This package provides an R implementation of an extension of the
7661 BayeScan software for codominant markers, adding the option to group
7662 individual SNPs into pre-defined blocks. A typical application of this new
7663 approach is the identification of genomic regions, genes, or gene sets
7664 containing one or more SNPs that evolved under directional selection.")
7665 (license license:gpl2)))
7667 (define-public r-proc
7674 (uri (cran-uri "pROC" version))
7677 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7678 (properties `((upstream-name . "pROC")))
7679 (build-system r-build-system)
7681 `(("r-plyr" ,r-plyr)
7682 ("r-rcpp" ,r-rcpp)))
7683 (home-page "https://web.expasy.org/pROC/")
7684 (synopsis "Display and analyze ROC curves")
7686 "This package provides tools for visualizing, smoothing and comparing
7687 receiver operating characteristic (ROC curves). The area under the
7688 curve (AUC) can be compared with statistical tests based on U-statistics or
7689 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7690 (license license:gpl3+)))
7692 (define-public r-rootsolve
7694 (name "r-rootsolve")
7699 (uri (cran-uri "rootSolve" version))
7702 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7703 (properties `((upstream-name . "rootSolve")))
7704 (build-system r-build-system)
7705 (native-inputs `(("gfortran" ,gfortran)))
7706 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7707 (synopsis "Tools for the analysis of ordinary differential equations")
7709 "This package provides routines to find the root of nonlinear functions,
7710 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7711 differential equations} (ODE). It includes routines that:
7714 @item generate gradient and jacobian matrices (full and banded),
7715 @item find roots of non-linear equations by the Newton-Raphson method,
7716 @item estimate steady-state conditions of a system of (differential) equations
7717 in full, banded or sparse form, using the Newton-Raphson method, or by
7718 dynamically running,
7719 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7720 and 3-D partial differential equations, that have been converted to ordinary
7721 differential equations by numerical differencing (using the method-of-lines
7724 (license license:gpl2+)))
7726 (define-public r-abcanalysis
7728 (name "r-abcanalysis")
7733 (uri (cran-uri "ABCanalysis" version))
7735 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7736 (properties `((upstream-name . "ABCanalysis")))
7737 (build-system r-build-system)
7738 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7739 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7740 (synopsis "Computed ABC Analysis")
7742 "Multivariate data sets often differ in several factors or derived statistical
7743 parameters, which have to be selected for a valid interpretation. Basing this
7744 selection on traditional statistical limits leads occasionally to the perception
7745 of losing information from a data set. This package provides tools to calculate
7746 these limits on the basis of the mathematical properties of the distribution of
7747 the analyzed items.")
7748 (license license:gpl3)))
7750 (define-public r-slam
7757 (uri (cran-uri "slam" version))
7759 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7760 (build-system r-build-system)
7761 (home-page "https://cran.r-project.org/web/packages/slam/")
7762 (synopsis "Sparse lightweight arrays and matrices")
7764 "This package contains data structures and algorithms for sparse arrays and matrices,
7765 based on index arrays and simple triplet representations, respectively.")
7766 (license license:gpl2)))
7768 (define-public r-manipulatewidget
7770 (name "r-manipulatewidget")
7775 (uri (cran-uri "manipulateWidget" version))
7777 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7779 `((upstream-name . "manipulateWidget")))
7780 (build-system r-build-system)
7782 `(("r-base64enc" ,r-base64enc)
7783 ("r-codetools" ,r-codetools)
7784 ("r-htmltools" ,r-htmltools)
7785 ("r-htmlwidgets" ,r-htmlwidgets)
7786 ("r-knitr" ,r-knitr)
7787 ("r-miniui" ,r-miniui)
7788 ("r-shiny" ,r-shiny)
7789 ("r-webshot" ,r-webshot)))
7790 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7791 (synopsis "Add even more interactivity to interactive charts")
7793 "This package lets you create in just a few lines of R code a nice user interface to
7794 modify the data or the graphical parameters of one or multiple interactive
7795 charts. It is useful to quickly explore visually some data or for package
7796 developers to generate user interfaces easy to maintain.")
7797 (license license:gpl2+)))
7806 (uri (cran-uri "A3" version))
7808 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7809 (properties `((upstream-name . "A3")))
7810 (build-system r-build-system)
7812 `(("r-pbapply" ,r-pbapply)
7813 ("r-xtable" ,r-xtable)))
7814 (home-page "https://cran.r-project.org/web/packages/A3/")
7815 (synopsis "Error metrics for predictive models")
7817 "This package supplies tools for tabulating and analyzing the results of predictive
7818 models. The methods employed are applicable to virtually any predictive model
7819 and make comparisons between different methodologies straightforward.")
7820 (license license:gpl2+)))
7822 (define-public r-infotheo
7829 (uri (cran-uri "infotheo" version))
7832 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7833 (build-system r-build-system)
7834 (home-page "http://homepage.meyerp.com/software")
7835 (synopsis "Information-theoretic measures")
7837 "This package implements various measures of information theory based on
7838 several entropy estimators.")
7839 (license license:gpl3+)))
7841 (define-public r-abcoptim
7848 (uri (cran-uri "ABCoptim" version))
7850 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7851 (properties `((upstream-name . "ABCoptim")))
7852 (build-system r-build-system)
7853 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7854 (home-page "https://github.com/gvegayon/ABCoptim/")
7855 (synopsis "Optimization of Artificial Bee Colony algorithm")
7857 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7858 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7859 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7860 algorithms, and uses only common control parameters such as colony size and
7861 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7862 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7863 This version is a work-in-progress and is written in R code.")
7864 (license license:expat)))
7866 (define-public r-abcp2
7873 (uri (cran-uri "ABCp2" version))
7875 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7876 (properties `((upstream-name . "ABCp2")))
7877 (build-system r-build-system)
7878 (propagated-inputs `(("r-mass" ,r-mass)))
7879 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7880 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7882 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7883 Poisson, and Gamma distribution and estimates the proportional paternity of the
7884 second male (P2) based on the best fit distribution.")
7885 (license license:gpl2)))
7887 (define-public r-abcrf
7894 (uri (cran-uri "abcrf" version))
7896 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7897 (build-system r-build-system)
7899 `(("r-doparallel" ,r-doparallel)
7900 ("r-foreach" ,r-foreach)
7902 ("r-matrixstats" ,r-matrixstats)
7903 ("r-ranger" ,r-ranger)
7905 ("r-rcpparmadillo" ,r-rcpparmadillo)
7906 ("r-readr" ,r-readr)
7907 ("r-stringr" ,r-stringr)))
7908 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7909 (synopsis "Approximate bayesian computation via random forests")
7911 "This package performs approximate bayesian computation (ABC) model choice and
7912 parameter inference via random forests. This machine learning tool named random
7913 forests (RF) can conduct selection among the highly complex models covered by
7915 (license license:gpl2+)))
7917 (define-public r-abctools
7924 (uri (cran-uri "abctools" version))
7926 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7927 (build-system r-build-system)
7930 ("r-abind" ,r-abind)
7931 ("r-hmisc" ,r-hmisc)
7932 ("r-plyr" ,r-plyr)))
7933 (home-page "https://github.com/dennisprangle/abctools/")
7934 (synopsis "Tools for ABC analyses")
7936 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7937 including summary statistic selection and assessing coverage. This includes
7938 recent dimension reduction algorithms to tune the choice of summary statistics,
7939 and coverage methods to tune the choice of threshold.")
7940 (license license:gpl2+)))
7942 (define-public r-ggstance
7949 (uri (cran-uri "ggstance" version))
7951 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7952 (build-system r-build-system)
7954 `(("r-ggplot2" ,r-ggplot2)
7956 ("r-rlang" ,r-rlang)
7957 ("r-withr" ,r-withr)))
7958 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7959 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7961 "This package is a @code{r-ggplot2} extension that provides flipped components:
7963 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7964 @item vertical versions of @code{r-ggplot2} positions.
7966 (license license:gpl3)))
7968 (define-public r-mosaiccore
7970 (name "r-mosaiccore")
7975 (uri (cran-uri "mosaicCore" version))
7977 (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj"))))
7978 (properties `((upstream-name . "mosaicCore")))
7979 (build-system r-build-system)
7981 `(("r-dplyr" ,r-dplyr)
7983 ("r-rlang" ,r-rlang)
7984 ("r-tidyr" ,r-tidyr)))
7985 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7986 (synopsis "Common utilities for mosaic family packages")
7988 "Common utilities used in other Mosaic family packages are collected here.")
7989 (license license:gpl2+)))
7991 (define-public r-ggformula
7993 (name "r-ggformula")
7998 (uri (cran-uri "ggformula" version))
8000 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
8001 (build-system r-build-system)
8003 `(("r-ggforce" ,r-ggforce)
8004 ("r-ggplot2" ,r-ggplot2)
8005 ("r-ggstance" ,r-ggstance)
8006 ("r-magrittr" ,r-magrittr)
8007 ("r-mosaiccore" ,r-mosaiccore)
8008 ("r-rlang" ,r-rlang)
8009 ("r-stringr" ,r-stringr)
8010 ("r-tibble" ,r-tibble)))
8011 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
8012 (synopsis "Formula interface for the @code{r-ggplot2}")
8014 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
8015 gf_density(), and so on, bring the formula interface to ggplot(). This captures
8016 and extends the excellent simplicity of the lattice-graphics formula interface,
8017 while providing the intuitive capabilities of @code{r-ggplot2}.")
8018 (license license:expat)))
8020 (define-public r-mosaicdata
8022 (name "r-mosaicdata")
8027 (uri (cran-uri "mosaicData" version))
8029 (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji"))))
8030 (properties `((upstream-name . "mosaicData")))
8031 (build-system r-build-system)
8032 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
8033 (synopsis "Data sets for project Mosaic")
8035 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
8036 used to teach mathematics, statistics, computation and modeling.")
8037 (license license:gpl2+)))
8039 (define-public r-raster
8046 (uri (cran-uri "raster" version))
8049 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
8050 (build-system r-build-system)
8052 `(("r-rcpp" ,r-rcpp)
8054 (home-page "https://www.rspatial.org/")
8055 (synopsis "Geographic data analysis and modeling")
8057 "The package implements basic and high-level functions for reading,
8058 writing, manipulating, analyzing and modeling of gridded spatial data.
8059 Processing of very large files is supported.")
8060 (license license:gpl3+)))
8062 (define-public r-mosaic
8069 (uri (cran-uri "mosaic" version))
8071 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8072 (build-system r-build-system)
8074 `(("r-broom" ,r-broom)
8075 ("r-dplyr" ,r-dplyr)
8076 ("r-ggdendro" ,r-ggdendro)
8077 ("r-ggformula" ,r-ggformula)
8078 ("r-ggplot2" ,r-ggplot2)
8079 ("r-ggrepel" ,r-ggrepel)
8081 ("r-gridextra" ,r-gridextra)
8082 ("r-lattice" ,r-lattice)
8083 ("r-latticeextra" ,r-latticeextra)
8084 ("r-lazyeval" ,r-lazyeval)
8086 ("r-matrix" ,r-matrix)
8087 ("r-mosaiccore" ,r-mosaiccore)
8088 ("r-mosaicdata" ,r-mosaicdata)
8089 ("r-readr" ,r-readr)
8090 ("r-tidyr" ,r-tidyr)))
8092 `(("r-knitr" ,r-knitr)))
8093 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8094 (synopsis "Mathematics, statistics, and computation teaching utilities")
8096 "This package contain data sets and utilities from
8097 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8098 statistics, computation and modeling. Project MOSAIC is a community of
8099 educators working to tie together aspects of quantitative work that students
8100 in science, technology, engineering and mathematics will need in their
8101 professional lives, but which are usually taught in isolation, if at all.")
8102 (license license:gpl2+)))
8104 (define-public r-abd
8111 (uri (cran-uri "abd" version))
8113 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8114 (build-system r-build-system)
8116 `(("r-lattice" ,r-lattice)
8117 ("r-mosaic" ,r-mosaic)
8118 ("r-nlme" ,r-nlme)))
8119 (home-page "https://cran.r-project.org/web/packages/abd/")
8120 (synopsis "Analysis of biological data")
8122 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8123 biological data by Michael Whitlock and Dolph Schluter.")
8124 (license license:gpl2)))
8126 (define-public r-svgui
8133 (uri (cran-uri "svGUI" version))
8135 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8136 (properties `((upstream-name . "svGUI")))
8137 (build-system r-build-system)
8138 (home-page "https://github.com/SciViews/svGUI/")
8139 (synopsis "Functions for managing GUI clients in R")
8141 "The SciViews @code{svGUI} package eases the management of Graphical User
8142 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8143 centralizes info about GUI elements currently used, and it dispatches GUI
8144 calls to the particular toolkits in use in function of the context.")
8145 (license license:gpl2)))
8147 (define-public r-svdialogs
8149 (name "r-svdialogs")
8154 (uri (cran-uri "svDialogs" version))
8156 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8157 (properties `((upstream-name . "svDialogs")))
8158 (build-system r-build-system)
8161 ("zenity" ,zenity)))
8163 `(("r-rstudioapi" ,r-rstudioapi)
8164 ("r-svgui" ,r-svgui)))
8165 (home-page "https://github.com/SciViews/svDialogs/")
8166 (synopsis "Portable dialog boxes")
8168 "This package helps to construct standard dialog boxes for your GUI, including
8169 message boxes, input boxes, list, file or directory selection, and others. In
8170 case R cannot display GUI dialog boxes, a simpler command line version of these
8171 interactive elements is also provided as a fallback solution.")
8172 (license license:gpl2)))
8174 (define-public r-abe
8181 (uri (cran-uri "abe" version))
8184 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8185 (build-system r-build-system)
8186 (home-page "https://cran.r-project.org/web/packages/abe/")
8187 (synopsis "Augmented backward elimination")
8189 "This package performs augmented backward elimination and checks the
8190 stability of the obtained model. Augmented backward elimination combines
8191 significance or information based criteria with the change in estimate to
8192 either select the optimal model for prediction purposes or to serve as a tool
8193 to obtain a practically sound, highly interpretable model.")
8194 (license license:gpl2+)))
8196 (define-public r-abf2
8203 (uri (cran-uri "abf2" version))
8205 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8206 (build-system r-build-system)
8207 (home-page "https://cran.r-project.org/web/packages/abf2/")
8208 (synopsis "Load gap-free axon @code{r-abf2} files")
8210 "This package loads electrophysiology data from ABF2 files, as created by
8211 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8212 mode are currently supported.")
8213 (license license:artistic2.0)))
8215 (define-public r-abhgenotyper
8217 (name "r-abhgenotyper")
8222 (uri (cran-uri "ABHgenotypeR" version))
8224 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8225 (properties `((upstream-name . "ABHgenotypeR")))
8226 (build-system r-build-system)
8228 `(("r-ggplot2" ,r-ggplot2)
8229 ("r-reshape2" ,r-reshape2)))
8230 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8231 (synopsis "Visualize and manipulate ABH genotypes")
8233 "The @code{r-abhgenotyper} package provides simple imputation,
8234 error-correction and plotting capacities for genotype data. The package is
8235 supposed to serve as an intermediate but independent analysis tool between the
8236 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8237 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8238 genotypes as \"graphical genotypes\".")
8239 (license license:gpl3)))
8241 (define-public r-furrr
8248 (uri (cran-uri "furrr" version))
8251 "16s6sgfgh1ayzhf3kvpy9vhsd5h6p57waj1xgbksgdmf4j1wkcq7"))))
8252 (build-system r-build-system)
8254 `(("r-ellipsis" ,r-ellipsis)
8255 ("r-future" ,r-future)
8256 ("r-globals" ,r-globals)
8257 ("r-lifecycle" ,r-lifecycle)
8258 ("r-purrr" ,r-purrr)
8259 ("r-rlang" ,r-rlang)
8260 ("r-vctrs" ,r-vctrs)))
8261 (home-page "https://github.com/DavisVaughan/furrr")
8262 (synopsis "Apply mapping functions in parallel using futures")
8264 "This package provides implementations of the family of @code{map()}
8265 functions from the @code{purrr} package that can be resolved using any
8266 @code{future}-supported backend, e.g. parallel on the local machine or
8267 distributed on a compute cluster.")
8268 (license license:lgpl2.1+)))
8270 (define-public r-abjutils
8277 (uri (cran-uri "abjutils" version))
8279 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8280 (build-system r-build-system)
8282 `(("r-dplyr" ,r-dplyr)
8283 ("r-magrittr" ,r-magrittr)
8284 ("r-purrr" ,r-purrr)
8285 ("r-rlang" ,r-rlang)
8286 ("r-rstudioapi" ,r-rstudioapi)
8287 ("r-stringi" ,r-stringi)
8288 ("r-stringr" ,r-stringr)
8289 ("r-tidyr" ,r-tidyr)))
8290 (home-page "https://github.com/abjur/abjutils/")
8291 (synopsis "Collection of tools for jurimetrical analysis")
8293 "This package implements general purpose tools, such as functions for
8294 sampling and basic manipulation of Brazilian lawsuits identification number.
8295 It also implements functions for text cleaning, such as accentuation
8297 (license license:expat)))
8299 (define-public r-abnormality
8301 (name "r-abnormality")
8306 (uri (cran-uri "abnormality" version))
8308 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8309 (build-system r-build-system)
8311 `(("r-mass" ,r-mass)
8312 ("r-matrix" ,r-matrix)))
8313 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8314 (synopsis "Measure a subject's abnormality with respect to a reference population")
8316 "This package contains functions to implement the methodology and
8317 considerations laid out by Marks et al. in the article \"Measuring abnormality
8318 in high dimensional spaces: applications in biomechanical gait analysis\".
8319 Using high-dimensional datasets to measure a subject's overall level of
8320 abnormality as compared to a reference population is often needed in outcomes
8322 (license license:expat)))
8324 (define-public r-abodoutlier
8326 (name "r-abodoutlier")
8331 (uri (cran-uri "abodOutlier" version))
8333 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8334 (properties `((upstream-name . "abodOutlier")))
8335 (build-system r-build-system)
8337 `(("r-cluster" ,r-cluster)))
8338 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8339 (synopsis "Angle-based outlier detection")
8341 "This package performs angle-based outlier detection on a given data
8342 frame. It offers three methods to process data:
8344 @item full but slow implementation using all the data that has cubic
8346 @item a fully randomized method;
8347 @item a method using k-nearest neighbours.
8349 These algorithms are well suited for high dimensional data outlier
8351 (license license:expat)))
8353 (define-public r-abps
8360 (uri (cran-uri "ABPS" version))
8362 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8363 (properties `((upstream-name . "ABPS")))
8364 (build-system r-build-system)
8365 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8366 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8367 (synopsis "Abnormal blood profile score to detect blood doping")
8369 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8370 The ABPS is a part of the Athlete biological passport program of the World
8371 anti-doping agency, which combines several blood parameters into a single
8372 score in order to detect blood doping. The package also contains functions to
8373 calculate other scores used in anti-doping programs, such as the ratio of
8374 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8375 (license license:gpl2+)))
8377 (define-public r-parmigene
8379 (name "r-parmigene")
8384 (uri (cran-uri "parmigene" version))
8387 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8388 (build-system r-build-system)
8389 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8390 (synopsis "Mutual information estimation for gene network reconstruction")
8392 "This package provides a parallel estimation of the mutual information
8393 based on entropy estimates from k-nearest neighbors distances and algorithms
8394 for the reconstruction of gene regulatory networks.")
8395 (license license:agpl3+)))
8397 (define-public r-pscl
8404 (uri (cran-uri "pscl" version))
8406 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8407 (build-system r-build-system)
8409 `(("r-mass" ,r-mass)))
8410 (home-page "https://github.com/atahk/pscl/")
8411 (synopsis "Political science computational laboratory")
8413 "The @code{pscl} is an R package providing classes and methods for:
8415 @item Bayesian analysis of roll call data (item-response models);
8416 @item elementary Bayesian statistics;
8417 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8419 @item utility functions.
8421 (license license:gpl2)))
8423 (define-public r-accelmissing
8425 (name "r-accelmissing")
8430 (uri (cran-uri "accelmissing" version))
8432 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8433 (build-system r-build-system)
8435 `(("r-mice" ,r-mice)
8436 ("r-pscl" ,r-pscl)))
8437 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8438 (synopsis "Missing value imputation for accelerometer data")
8440 "This package provides a statistical method to impute the missing values in
8441 accelerometer data. The methodology includes both parametric and
8442 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8443 model. It also provides multiple functions to preprocess the accelerometer data
8444 previous to the missing data imputation. These include detecting the wearing
8445 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8446 (license license:gpl2+)))
8448 (define-public r-mhsmm
8455 (uri (cran-uri "mhsmm" version))
8457 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8458 (build-system r-build-system)
8459 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8460 (home-page "https://github.com/jaredo/mhsmm/")
8461 (synopsis "Inference for hidden Markov and semi-Markov models")
8463 "The @code{r-mhsmm} package implements estimation and prediction methods for
8464 hidden Markov and semi-Markov models for multiple observation sequences. Such
8465 techniques are of interest when observed data is thought to be dependent on some
8466 unobserved (or hidden) state. Also, this package is suitable for equidistant
8467 time series data, with multivariate and/or missing data. Allows user defined
8468 emission distributions.")
8469 (license license:gpl2+)))
8471 (define-public r-nleqslv
8478 (uri (cran-uri "nleqslv" version))
8480 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8481 (build-system r-build-system)
8482 (native-inputs `(("gfortran" ,gfortran)))
8483 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8484 (synopsis "Solve systems of nonlinear equations")
8486 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8487 Broyden or a Newton method with a choice of global strategies such as line
8488 search and trust region. There are options for using a numerical or user
8489 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8490 singular or ill-conditioned Jacobian.")
8491 (license license:gpl2+)))
8493 (define-public r-physicalactivity
8495 (name "r-physicalactivity")
8500 (uri (cran-uri "PhysicalActivity" version))
8502 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8504 `((upstream-name . "PhysicalActivity")))
8505 (build-system r-build-system)
8506 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8507 (synopsis "Procesing accelerometer data for physical activity measurement")
8509 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8510 for classification of monitor wear and nonwear time intervals in accelerometer
8511 data collected to assess physical activity. The package also contains functions
8512 for making plots of accelerometer data and obtaining the summary of various
8513 information including daily monitor wear time and the mean monitor wear time
8514 during valid days. The revised package version 0.2-1 improved the functions
8515 regarding speed, robustness and add better support for time zones and daylight
8516 saving. In addition, several functions were added:
8518 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8519 @item the @code{markPAI} can categorize physical activity intensity level based
8520 on user-defined cut-points of accelerometer counts.
8522 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8523 @code{queryActigraph} functions.")
8524 (license license:gpl3+)))
8526 (define-public r-acc
8533 (uri (cran-uri "acc" version))
8535 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8536 (build-system r-build-system)
8538 `(("r-circlize" ,r-circlize)
8540 ("r-ggplot2" ,r-ggplot2)
8541 ("r-iterators" ,r-iterators)
8542 ("r-mhsmm" ,r-mhsmm)
8543 ("r-nleqslv" ,r-nleqslv)
8544 ("r-physicalactivity" ,r-physicalactivity)
8546 ("r-r-utils" ,r-r-utils)
8548 ("r-rcpparmadillo" ,r-rcpparmadillo)
8549 ("r-rsqlite" ,r-rsqlite)
8551 (home-page "https://cran.r-project.org/web/packages/acc/")
8552 (synopsis "Exploring accelerometer data")
8554 "This package processes accelerometer data from uni-axial and tri-axial devices
8555 and generates data summaries. Also, includes functions to plot, analyze, and
8556 simulate accelerometer data.")
8557 (license license:gpl2+)))
8559 (define-public r-rbenchmark
8561 (name "r-rbenchmark")
8566 (uri (cran-uri "rbenchmark" version))
8568 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8569 (build-system r-build-system)
8570 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8571 (synopsis "Benchmarking routine for R")
8573 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8574 and is intended to facilitate benchmarking of arbitrary R code. The library
8575 consists of just one function, benchmark, which is a simple wrapper around
8576 system.time. Given a specification of the benchmarking process (counts of
8577 replications, evaluation environment) and an arbitrary number of expressions,
8578 benchmark evaluates each of the expressions in the specified environment,
8579 replicating the evaluation as many times as specified, and returning the results
8580 conveniently wrapped into a data frame.")
8581 (license license:gpl2+)))
8583 (define-public r-mitools
8590 (uri (cran-uri "mitools" version))
8593 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8594 (build-system r-build-system)
8595 (propagated-inputs `(("r-dbi" ,r-dbi)))
8596 (home-page "https://cran.r-project.org/web/packages/mitools/")
8597 (synopsis "Tools for multiple imputation of missing data")
8599 "This package provides tools to perform analyses and combine results from
8600 multiple-imputation datasets.")
8601 (license license:gpl2)))
8603 (define-public r-magick
8610 (uri (cran-uri "magick" version))
8613 "1fhwr34xff6793ifbzqmij8b8qg7hrnr4birqpg33ib0mdd6flkf"))))
8614 (build-system r-build-system)
8616 `(("imagemagick" ,imagemagick)
8619 `(("r-curl" ,r-curl)
8620 ("r-magrittr" ,r-magrittr)
8621 ("r-rcpp" ,r-rcpp)))
8623 `(("pkg-config" ,pkg-config)
8624 ("r-knitr" ,r-knitr)))
8625 (home-page "https://github.com/ropensci/magick")
8626 (synopsis "Advanced graphics and image-processing in R")
8628 "This package provides bindings to ImageMagick, a comprehensive image
8629 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8630 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8631 operations are vectorized via the Magick++ STL meaning they operate either on
8632 a single frame or a series of frames for working with layers, collages, or
8633 animation. In RStudio, images are automatically previewed when printed to the
8634 console, resulting in an interactive editing environment.")
8635 (license license:expat)))
8637 (define-public r-survey
8644 (uri (cran-uri "survey" version))
8647 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8648 (build-system r-build-system)
8650 `(("r-lattice" ,r-lattice)
8651 ("r-matrix" ,r-matrix)
8652 ("r-minqa" ,r-minqa)
8653 ("r-mitools" ,r-mitools)
8654 ("r-numderiv" ,r-numderiv)
8655 ("r-survival" ,r-survival)))
8656 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8657 (synopsis "Analysis of complex survey samples")
8659 "This package provides tools for the analysis of complex survey samples.
8660 The provided features include: summary statistics, two-sample tests, rank
8661 tests, generalised linear models, cumulative link models, Cox models,
8662 loglinear models, and general maximum pseudolikelihood estimation for
8663 multistage stratified, cluster-sampled, unequally weighted survey samples;
8664 variances by Taylor series linearisation or replicate weights;
8665 post-stratification, calibration, and raking; two-phase subsampling designs;
8666 graphics; PPS sampling without replacement; principal components, and factor
8668 ;; Either version of the GPL.
8669 (license (list license:gpl2 license:gpl3))))
8671 (define-public r-gee
8678 (uri (cran-uri "gee" version))
8681 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8682 (properties `((upstream-name . "gee")))
8683 (build-system r-build-system)
8685 `(("gfortran" ,gfortran)))
8686 (home-page "https://cran.r-project.org/web/packages/gee/")
8687 (synopsis "Generalized estimation equation solver")
8689 "This package provides a solver for generalized estimation equations.")
8690 (license license:gpl2)))
8692 (define-public r-tab
8699 (uri (cran-uri "tab" version))
8702 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8703 (properties `((upstream-name . "tab")))
8704 (build-system r-build-system)
8706 `(("r-dplyr" ,r-dplyr)
8708 ("r-knitr" ,r-knitr)
8710 ("r-survey" ,r-survey)
8711 ("r-survival" ,r-survival)
8712 ("r-xtable" ,r-xtable)))
8713 (home-page "https://cran.r-project.org/web/packages/tab/")
8714 (synopsis "Create summary tables for statistical reports")
8716 "This package contains functions for creating various types of summary
8717 tables, e.g. comparing characteristics across levels of a categorical variable
8718 and summarizing fitted generalized linear models, generalized estimating
8719 equations, and Cox proportional hazards models. Functions are available to
8720 handle data from simple random samples as well as complex surveys.")
8721 (license license:gpl3+)))
8723 (define-public r-dvmisc
8730 (uri (cran-uri "dvmisc" version))
8732 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8733 (build-system r-build-system)
8735 `(("r-cubature" ,r-cubature)
8736 ("r-data-table" ,r-data-table)
8737 ("r-dplyr" ,r-dplyr)
8738 ("r-ggplot2" ,r-ggplot2)
8740 ("r-mvtnorm" ,r-mvtnorm)
8741 ("r-pracma" ,r-pracma)
8742 ("r-rbenchmark" ,r-rbenchmark)
8744 ("r-survey" ,r-survey)
8746 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8747 (synopsis "Faster computation of common statistics and miscellaneous functions")
8749 "This package implements faster versions of base R functions (e.g. mean, standard
8750 deviation, covariance, weighted mean), mostly written in C++, along with
8751 miscellaneous functions for various purposes (e.g. create the histogram with
8752 fitted probability density function or probability mass function curve, create
8753 the body mass index groups, assess the linearity assumption in logistic
8755 (license license:gpl2)))
8757 (define-public r-accelerometry
8759 (name "r-accelerometry")
8764 (uri (cran-uri "accelerometry" version))
8766 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8767 (build-system r-build-system)
8769 `(("r-dvmisc" ,r-dvmisc)
8770 ("r-rcpp" ,r-rcpp)))
8771 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8772 (synopsis "Functions for processing accelerometer data")
8774 "This package provides a collection of functions that perform operations on
8775 time-series accelerometer data, such as identify the non-wear time, flag minutes
8776 that are part of an activity bout, and find the maximum 10-minute average count
8777 value. The functions are generally very flexible, allowing for a variety of
8778 algorithms to be implemented.")
8779 (license license:gpl3)))
8781 (define-public r-absim
8788 (uri (cran-uri "AbSim" version))
8790 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8791 (properties `((upstream-name . "AbSim")))
8792 (build-system r-build-system)
8795 ("r-powerlaw" ,r-powerlaw)))
8796 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8797 (synopsis "Time resolved simulations of antibody repertoires")
8799 "This package provides simulation methods for the evolution of antibody repertoires.
8800 The heavy and light chain variable region of both human and C57BL/6 mice can
8801 be simulated in a time-dependent fashion. Both single lineages using one set of
8802 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8803 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8804 Upon completion, the main loop of the algorithm begins, with each iteration
8805 representing one simulated time step. Various mutation events are possible at
8806 each time step, contributing to a diverse final repertoire.")
8807 (license license:gpl2)))
8809 (define-public r-quic
8816 (uri (cran-uri "QUIC" version))
8818 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8819 (properties `((upstream-name . "QUIC")))
8820 (build-system r-build-system)
8821 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8822 (synopsis "Regularized sparse inverse covariance matrix estimation")
8824 "This package implements the regularized Gaussian maximum likelihood
8825 estimation of the inverse of a covariance matrix. It uses Newton's method and
8826 coordinate descent to solve the regularized inverse covariance matrix
8827 estimation problem.")
8828 ;; The project home page states that the release is under GPLv3 or later.
8829 ;; The CRAN page only says GPL-3.
8830 (license license:gpl3+)))
8832 (define-public r-abundant
8839 (uri (cran-uri "abundant" version))
8841 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8842 (build-system r-build-system)
8844 `(("r-quic" ,r-quic)))
8845 (home-page "https://cran.r-project.org/web/packages/abundant/")
8846 (synopsis "Abundant regression and high-dimensional principal fitted components")
8848 "This package provides tools to fit and predict with the high-dimensional
8849 principal fitted components model. This model is described by Cook, Forzani,
8850 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8851 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8852 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8853 (license license:gpl2+)))
8855 (define-public r-ac3net
8862 (uri (cran-uri "Ac3net" version))
8864 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8865 (properties `((upstream-name . "Ac3net")))
8866 (build-system r-build-system)
8868 `(("r-data-table" ,r-data-table)))
8869 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8870 (synopsis "Inferring directional conservative causal core gene networks")
8871 (description "This package infers directional Conservative causal core
8872 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8873 directional network.")
8874 (license license:gpl3+)))
8876 (define-public r-aca
8883 (uri (cran-uri "ACA" version))
8885 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8886 (properties `((upstream-name . "ACA")))
8887 (build-system r-build-system)
8888 (home-page "https://cran.r-project.org/web/packages/ACA/")
8889 (synopsis "Abrupt change-point or aberration detection in point series")
8891 "This package offers an interactive function for the detection of breakpoints in
8893 ;; Any version of the GPL
8894 (license (list license:gpl2+ license:gpl3+))))
8896 (define-public r-acceptancesampling
8898 (name "r-acceptancesampling")
8903 (uri (cran-uri "AcceptanceSampling" version))
8905 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8907 `((upstream-name . "AcceptanceSampling")))
8908 (build-system r-build-system)
8909 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8910 (synopsis "Creation and evaluation of acceptance sampling plans")
8912 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8913 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8914 in quality control and improvement. International standards of acceptance
8915 sampling provide sampling plans for specific circumstances. The aim of this
8916 package is to provide an easy-to-use interface to visualize single, double or
8917 multiple sampling plans. In addition, methods have been provided to enable the
8918 user to assess sampling plans against pre-specified levels of performance, as
8919 measured by the probability of acceptance for a given level of quality in the
8921 (license license:gpl3+)))
8923 (define-public r-acclma
8930 (uri (cran-uri "ACCLMA" version))
8932 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8933 (properties `((upstream-name . "ACCLMA")))
8934 (build-system r-build-system)
8935 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8936 (synopsis "ACC & LMA graph plotting")
8938 "This package contains a function that imports data from a @acronym{CSV,
8939 Comma-Separated Values} file, or uses manually entered data from the format (x,
8940 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8941 Curve} vs @acronym{LOI, Line of Independence} graph and
8942 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8943 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8944 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8945 string) was passed, a manual data entry window is opened. The header parameter
8946 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8947 a header row or not. The dataset should contain only one independent variable
8948 (x) and one dependent variable (y) and can contain a weight for each
8950 (license license:gpl2)))
8952 (define-public r-aspi
8959 (uri (cran-uri "aspi" version))
8961 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8962 (build-system r-build-system)
8964 "https://cran.r-project.org/web/packages/aspi/")
8966 "Analysis of symmetry of parasitic infections")
8968 "This package provides tools for the analysis and visualization of bilateral
8969 asymmetry in parasitic infections.")
8970 (license license:gpl3+)))
8972 (define-public r-sandwich
8979 (uri (cran-uri "sandwich" version))
8982 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
8983 (build-system r-build-system)
8985 `(("r-zoo" ,r-zoo)))
8986 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8987 (synopsis "Robust Covariance Matrix Estimators")
8989 "This package provides model-robust standard error estimators for
8990 cross-sectional, time series, clustered, panel, and longitudinal data.")
8991 ;; Either version of the license.
8992 (license (list license:gpl2 license:gpl3))))
8994 (define-public r-th-data
9001 (uri (cran-uri "TH.data" version))
9004 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
9005 (properties `((upstream-name . "TH.data")))
9006 (build-system r-build-system)
9008 `(("r-mass" ,r-mass)
9009 ("r-survival" ,r-survival)))
9010 (home-page "https://cran.r-project.org/web/packages/TH.data/")
9011 (synopsis "Shared data sets")
9013 "This package contains supporting data sets that are used in other
9014 packages maintained by Torsten Hothorn.")
9015 (license license:gpl3)))
9017 (define-public r-multcomp
9024 (uri (cran-uri "multcomp" version))
9027 "14a55isy1sp745s109nirlk5fryy144cri6dl8y9d9wjhfxz336a"))))
9028 (build-system r-build-system)
9030 `(("r-codetools" ,r-codetools)
9031 ("r-mvtnorm" ,r-mvtnorm)
9032 ("r-sandwich" ,r-sandwich)
9033 ("r-survival" ,r-survival)
9034 ("r-th-data" ,r-th-data)))
9035 (home-page "https://cran.r-project.org/web/packages/multcomp/")
9036 (synopsis "Simultaneous inference in general parametric models")
9038 "Simultaneous tests and confidence intervals for general linear
9039 hypotheses in parametric models, including linear, generalized linear, linear
9040 mixed effects, and survival models. The package includes demos reproducing
9041 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
9042 Hothorn, Westfall, 2010, CRC Press).")
9043 (license license:gpl2)))
9045 (define-public r-emmeans
9052 (uri (cran-uri "emmeans" version))
9055 "0ndbjhglycdycppz9lbj3vhiqv2mp0z6h4w8fbyjziqx15ai5h59"))))
9056 (build-system r-build-system)
9058 `(("r-estimability" ,r-estimability)
9059 ("r-mvtnorm" ,r-mvtnorm)
9060 ("r-numderiv" ,r-numderiv)
9062 ("r-xtable" ,r-xtable)))
9064 `(("r-knitr" ,r-knitr)))
9065 (home-page "https://github.com/rvlenth/emmeans")
9066 (synopsis "Estimated marginal means, aka least-squares means")
9068 "This package provides tools to obtain @dfn{estimated marginal
9069 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9070 be used to compute contrasts or linear functions of EMMs, trends, and
9071 comparisons of slopes.")
9072 ;; Either version of the license.
9073 (license (list license:gpl2 license:gpl3))))
9075 (define-public r-pwr
9082 (uri (cran-uri "pwr" version))
9085 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9086 (build-system r-build-system)
9088 `(("r-knitr" ,r-knitr)))
9089 (home-page "https://github.com/heliosdrm/pwr")
9090 (synopsis "Basic functions for power analysis")
9092 "This package provides power analysis functions along the lines of
9094 (license license:gpl3+)))
9096 (define-public r-libcoin
9103 (uri (cran-uri "libcoin" version))
9105 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
9106 (build-system r-build-system)
9107 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9108 (home-page "https://cran.r-project.org/web/packages/libcoin")
9109 (synopsis "Linear test statistics for permutation inference")
9111 "This package provides basic infrastructure for linear test statistics
9112 and permutation inference in the framework of Strasser and Weber (1999).")
9113 (license license:gpl2)))
9115 (define-public r-coin
9122 (uri (cran-uri "coin" version))
9125 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
9126 (build-system r-build-system)
9128 `(("r-libcoin" ,r-libcoin)
9129 ("r-matrixstats" ,r-matrixstats)
9130 ("r-modeltools" ,r-modeltools)
9131 ("r-multcomp" ,r-multcomp)
9132 ("r-mvtnorm" ,r-mvtnorm)
9133 ("r-survival" ,r-survival)))
9134 (home-page "http://coin.r-forge.r-project.org")
9135 (synopsis "Conditional inference procedures in a permutation test framework")
9137 "This package provides conditional inference procedures for the general
9138 independence problem including two-sample, K-sample (non-parametric ANOVA),
9139 correlation, censored, ordered and multivariate problems.")
9140 (license license:gpl2)))
9142 (define-public r-bayesplot
9144 (name "r-bayesplot")
9149 (uri (cran-uri "bayesplot" version))
9152 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
9153 (build-system r-build-system)
9155 `(("pandoc" ,pandoc)
9156 ("pandoc-citeproc" ,pandoc-citeproc)))
9158 `(("r-knitr" ,r-knitr)))
9160 `(("r-dplyr" ,r-dplyr)
9161 ("r-ggplot2" ,r-ggplot2)
9162 ("r-ggridges" ,r-ggridges)
9164 ("r-reshape2" ,r-reshape2)
9165 ("r-rlang" ,r-rlang)
9166 ("r-tibble" ,r-tibble)
9167 ("r-tidyselect" ,r-tidyselect)))
9168 (home-page "https://mc-stan.org/bayesplot")
9169 (synopsis "Plotting for Bayesian models")
9171 "This package provides plotting functions for posterior analysis, model
9172 checking, and MCMC diagnostics. The package is designed not only to provide
9173 convenient functionality for users, but also a common set of functions that
9174 can be easily used by developers working on a variety of R packages for
9175 Bayesian modeling.")
9176 (license license:gpl3+)))
9178 (define-public r-tmb
9185 (uri (cran-uri "TMB" version))
9188 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
9189 (properties `((upstream-name . "TMB")))
9190 (build-system r-build-system)
9192 `(("r-matrix" ,r-matrix)
9193 ("r-rcppeigen" ,r-rcppeigen)))
9194 (home-page "http://tmb-project.org")
9195 (synopsis "Template model builder: a general random effect tool")
9197 "With this tool, a user should be able to quickly implement complex
9198 random effect models through simple C++ templates. The package combines
9199 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9200 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9201 from R) to obtain an efficient implementation of the applied Laplace
9202 approximation with exact derivatives. Key features are: Automatic sparseness
9203 detection, parallelism through BLAS and parallel user templates.")
9204 (license license:gpl2)))
9206 (define-public r-sjstats
9213 (uri (cran-uri "sjstats" version))
9215 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
9216 (build-system r-build-system)
9218 `(("r-bayestestr" ,r-bayestestr)
9219 ("r-broom" ,r-broom)
9220 ("r-dplyr" ,r-dplyr)
9221 ("r-effectsize" ,r-effectsize)
9222 ("r-emmeans" ,r-emmeans)
9223 ("r-insight" ,r-insight)
9225 ("r-magrittr" ,r-magrittr)
9227 ("r-modelr" ,r-modelr)
9228 ("r-parameters" ,r-parameters)
9229 ("r-performance" ,r-performance)
9230 ("r-purrr" ,r-purrr)
9231 ("r-rlang" ,r-rlang)
9232 ("r-sjlabelled" ,r-sjlabelled)
9233 ("r-sjmisc" ,r-sjmisc)
9234 ("r-tidyr" ,r-tidyr)))
9235 (home-page "https://github.com/strengejacke/sjstats")
9236 (synopsis "Functions for common statistical computations")
9238 "This package provides a collection of convenient functions for common
9239 statistical computations, which are not directly provided by R's @code{base}
9240 or @code{stats} packages. This package aims at providing, first, shortcuts
9241 for statistical measures, which otherwise could only be calculated with
9242 additional effort. Second, these shortcut functions are generic, and can be
9243 applied not only to vectors, but also to other objects as well. The focus of
9244 most functions lies on summary statistics or fit measures for regression
9245 models, including generalized linear models, mixed effects models and Bayesian
9247 (license license:gpl3)))
9249 (define-public r-glmmtmb
9256 (uri (cran-uri "glmmTMB" version))
9259 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9260 (properties `((upstream-name . "glmmTMB")))
9261 (build-system r-build-system)
9263 `(("r-lme4" ,r-lme4)
9264 ("r-matrix" ,r-matrix)
9266 ("r-rcppeigen" ,r-rcppeigen)
9269 `(("r-knitr" ,r-knitr))) ; for vignettes
9270 (home-page "https://github.com/glmmTMB")
9271 (synopsis "Generalized linear mixed models")
9273 "Fit linear and generalized linear mixed models with various extensions,
9274 including zero-inflation. The models are fitted using maximum likelihood
9275 estimation via the Template Model Builder. Random effects are assumed to be
9276 Gaussian on the scale of the linear predictor and are integrated out using the
9277 Laplace approximation. Gradients are calculated using automatic
9279 (license license:agpl3+)))
9281 (define-public r-bayestestr
9283 (name "r-bayestestr")
9288 (uri (cran-uri "bayestestR" version))
9291 "0l6q7v96m9asqa0p55k0gpzy8hddf8srkhc9r7zf4hv0dscbi9dv"))))
9292 (properties `((upstream-name . "bayestestR")))
9293 (build-system r-build-system)
9295 `(("r-insight" ,r-insight)))
9297 `(("r-knitr" ,r-knitr)))
9298 (home-page "https://github.com/easystats/bayestestR")
9299 (synopsis "Describe Bayesian models and posterior distributions")
9301 "This package provides utilities to understand and describe posterior
9302 distributions and Bayesian models. It includes point-estimates such as
9303 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9304 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9305 ROPE percentage and pd).")
9306 (license license:gpl3)))
9308 (define-public r-performance
9310 (name "r-performance")
9315 (uri (cran-uri "performance" version))
9318 "1vkc87vbhw7l626pdnpiravnpsa5j0iv73lbwy3m309lnfvv0cqx"))))
9319 (build-system r-build-system)
9321 `(("r-bayestestr" ,r-bayestestr)
9322 ("r-insight" ,r-insight)))
9323 (home-page "https://easystats.github.io/performance/")
9324 (synopsis "Assessment of regression models performance")
9326 "This package provides utilities for computing measures to assess model
9327 quality, which are not directly provided by R's @code{base} or @code{stats}
9328 packages. These include e.g. measures like r-squared, intraclass correlation
9329 coefficient, root mean squared error or functions to check models for
9330 overdispersion, singularity or zero-inflation and more. Functions apply to a
9331 large variety of regression models, including generalized linear models, mixed
9332 effects models and Bayesian models.")
9333 (license license:gpl3)))
9335 (define-public r-ggeffects
9337 (name "r-ggeffects")
9342 (uri (cran-uri "ggeffects" version))
9345 "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5"))))
9346 (build-system r-build-system)
9348 `(("r-insight" ,r-insight)
9350 ("r-sjlabelled" ,r-sjlabelled)))
9352 `(("r-knitr" ,r-knitr)))
9353 (home-page "https://github.com/strengejacke/ggeffects")
9354 (synopsis "Create tidy data frames of marginal effects for ggplot")
9356 "This package provides tools to compute marginal effects from statistical
9357 models and return the result as tidy data frames. These data frames are ready
9358 to use with the @code{ggplot2} package. Marginal effects can be calculated
9359 for many different models. Interaction terms, splines and polynomial terms
9360 are also supported. The two main functions are @code{ggpredict()} and
9361 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9362 results using @code{ggplot2}.")
9363 (license license:gpl3)))
9365 (define-public r-effectsize
9367 (name "r-effectsize")
9372 (uri (cran-uri "effectsize" version))
9375 "0shx19ahw13wrn7jlyyvzvngqk66d6jiw9i51mx3psdn3hdnhy9s"))))
9376 (properties `((upstream-name . "effectsize")))
9377 (build-system r-build-system)
9379 `(("r-bayestestr" ,r-bayestestr)
9380 ("r-insight" ,r-insight)
9381 ("r-parameters" ,r-parameters)))
9383 `(("r-knitr" ,r-knitr)))
9384 (home-page "https://github.com/easystats/effectsize")
9385 (synopsis "Indices of effect size and standardized parameters")
9387 "This package provides utilities to work with indices of effect size and
9388 standardized parameters for a wide variety of models, allowing computation and
9389 conversion of indices such as Cohen's d, r, odds, etc.")
9390 (license license:gpl3)))
9392 (define-public r-sjplot
9399 (uri (cran-uri "sjPlot" version))
9401 (base32 "1dn9nvvp4jd45kwr4rpp2abf7xdpdmiv41rr3fkdb32a136bzx4b"))))
9402 (properties `((upstream-name . "sjPlot")))
9403 (build-system r-build-system)
9405 `(("r-bayestestr" ,r-bayestestr)
9406 ("r-dplyr" ,r-dplyr)
9407 ("r-effectsize" ,r-effectsize)
9408 ("r-ggeffects" ,r-ggeffects)
9409 ("r-ggplot2" ,r-ggplot2)
9410 ("r-insight" ,r-insight)
9411 ("r-knitr" ,r-knitr)
9413 ("r-parameters" ,r-parameters)
9414 ("r-performance" ,r-performance)
9415 ("r-purrr" ,r-purrr)
9416 ("r-rlang" ,r-rlang)
9417 ("r-scales" ,r-scales)
9418 ("r-sjlabelled" ,r-sjlabelled)
9419 ("r-sjmisc" ,r-sjmisc)
9420 ("r-sjstats" ,r-sjstats)
9421 ("r-tidyr" ,r-tidyr)))
9423 `(("r-knitr" ,r-knitr)))
9424 (home-page "https://strengejacke.github.io/sjPlot/")
9425 (synopsis "Data visualization for statistics in social science")
9427 "This package represents a collection of plotting and table output
9428 functions for data visualization. Results of various statistical
9429 analyses (that are commonly used in social sciences) can be visualized using
9430 this package, including simple and cross tabulated frequencies, histograms,
9431 box plots, (generalized) linear models, mixed effects models, principal
9432 component analysis and correlation matrices, cluster analyses, scatter plots,
9433 stacked scales, effects plots of regression models (including interaction
9434 terms) and much more. This package supports labelled data.")
9435 (license license:gpl3)))
9437 (define-public r-ini
9444 (uri (cran-uri "ini" version))
9447 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9448 (build-system r-build-system)
9449 (home-page "https://github.com/dvdscripter/ini")
9450 (synopsis "Read and write configuration files")
9452 "This package provides tools to parse simple @code{.ini} configuration
9453 files to an structured list. Users can manipulate this resulting list with
9454 @code{lapply()} functions. This same structured list can be used to write
9455 back to file after modifications.")
9456 (license license:gpl3)))
9465 (uri (cran-uri "gh" version))
9468 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9469 (build-system r-build-system)
9474 ("r-jsonlite" ,r-jsonlite)))
9475 (home-page "https://github.com/r-lib/gh#readme")
9476 (synopsis "Access the GitHub API via R")
9478 "This package provides a minimal R client to access the GitHub API.")
9479 (license license:expat)))
9488 (uri (cran-uri "fs" version))
9491 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9492 (build-system r-build-system)
9494 `(("r-knitr" ,r-knitr)))
9495 (home-page "https://fs.r-lib.org")
9496 (synopsis "Cross-platform file system operations based on libuv")
9498 "This package provides a cross-platform interface to file system
9499 operations, built on top of the libuv C library.")
9500 (license license:gpl3)))
9502 (define-public r-clisymbols
9504 (name "r-clisymbols")
9509 (uri (cran-uri "clisymbols" version))
9512 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9513 (build-system r-build-system)
9514 (home-page "https://github.com/gaborcsardi/clisymbols")
9515 (synopsis "Unicode symbols at the R prompt")
9517 "This package provides a small subset of Unicode symbols, that are useful
9518 when building command line applications. They fall back to alternatives on
9519 terminals that do not support Unicode.")
9520 (license license:expat)))
9522 (define-public r-usethis
9529 (uri (cran-uri "usethis" version))
9532 "09lk04kycvf5x9ggrb6pwc7bx5mzqxwialm2w9vn1a0w0gh2gcfc"))))
9533 (build-system r-build-system)
9536 ("r-clipr" ,r-clipr)
9537 ("r-crayon" ,r-crayon)
9542 ("r-git2r" ,r-git2r)
9544 ("r-purrr" ,r-purrr)
9545 ("r-rematch2" ,r-rematch2)
9546 ("r-rlang" ,r-rlang)
9547 ("r-rprojroot" ,r-rprojroot)
9548 ("r-rstudioapi" ,r-rstudioapi)
9549 ("r-whisker" ,r-whisker)
9550 ("r-withr" ,r-withr)
9551 ("r-yaml" ,r-yaml)))
9552 (home-page "https://github.com/r-lib/usethis")
9553 (synopsis "Automate R package and project setup")
9555 "This package helps you to automate R package and project setup tasks
9556 that are otherwise performed manually. This includes setting up unit testing,
9557 test coverage, continuous integration, Git, GitHub integration, licenses,
9558 Rcpp, RStudio projects, and more.")
9559 (license license:gpl3)))
9561 (define-public r-sessioninfo
9563 (name "r-sessioninfo")
9568 (uri (cran-uri "sessioninfo" version))
9571 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9572 (build-system r-build-system)
9575 ("r-withr" ,r-withr)))
9576 (home-page "https://github.com/r-lib/sessioninfo#readme")
9577 (synopsis "R session information")
9579 "This package provides tools to query and print information about the
9580 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9581 more information about packages, and where they were installed from.")
9582 (license license:gpl2)))
9584 (define-public r-remotes
9591 (uri (cran-uri "remotes" version))
9594 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9595 (build-system r-build-system)
9597 `(("r-knitr" ,r-knitr)))
9598 (home-page "https://github.com/r-lib/remotes#readme")
9599 (synopsis "R package installation from remote repositories")
9601 "Download and install R packages stored in GitHub, BitBucket, or plain
9602 subversion or git repositories. This package is a lightweight replacement of
9603 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9604 the code was copied over from @code{devtools}.")
9605 (license license:gpl2+)))
9607 (define-public r-xopen
9614 (uri (cran-uri "xopen" version))
9617 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9618 (build-system r-build-system)
9620 `(("r-processx" ,r-processx)))
9621 (home-page "https://github.com/r-lib/xopen#readme")
9622 (synopsis "Open system files, URLs, anything")
9624 "This package provides a cross-platform solution to open files,
9625 directories or URLs with their associated programs.")
9626 (license license:expat)))
9628 (define-public r-rcmdcheck
9630 (name "r-rcmdcheck")
9635 (uri (cran-uri "rcmdcheck" version))
9638 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9639 (build-system r-build-system)
9641 `(("r-callr" ,r-callr)
9643 ("r-crayon" ,r-crayon)
9645 ("r-digest" ,r-digest)
9646 ("r-pkgbuild" ,r-pkgbuild)
9647 ("r-prettyunits" ,r-prettyunits)
9649 ("r-rprojroot" ,r-rprojroot)
9650 ("r-sessioninfo" ,r-sessioninfo)
9651 ("r-withr" ,r-withr)
9652 ("r-xopen" ,r-xopen)))
9653 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9654 (synopsis "Run R CMD check from R and capture results")
9656 "Run @code{R CMD check} from R programmatically, and capture the results
9657 of the individual checks.")
9658 (license license:expat)))
9660 (define-public r-rapportools
9662 (name "r-rapportools")
9667 (uri (cran-uri "rapportools" version))
9670 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9671 (build-system r-build-system)
9673 `(("r-pander" ,r-pander)
9675 ("r-reshape" ,r-reshape)))
9676 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9677 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9679 "This package provides helper functions that act as wrappers to more
9680 advanced statistical methods with the advantage of having sane defaults for
9682 (license license:agpl3+)))
9684 (define-public r-pander
9691 (uri (cran-uri "pander" version))
9694 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9695 (build-system r-build-system)
9697 `(("r-digest" ,r-digest)
9698 ("r-rcpp" ,r-rcpp)))
9699 (home-page "https://rapporter.github.io/pander")
9700 (synopsis "Render R objects into Pandoc's markdown")
9702 "The main aim of the pander R package is to provide a minimal and easy
9703 tool for rendering R objects into Pandoc's markdown. The package is also
9704 capable of exporting/converting complex Pandoc documents (reports) in various
9706 ;; This package is licensed under either the AGPLv3+ or the very rarely
9708 (license license:agpl3+)))
9710 (define-public r-summarytools
9712 (name "r-summarytools")
9717 (uri (cran-uri "summarytools" version))
9720 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9721 (build-system r-build-system)
9723 `(("r-base64enc" ,r-base64enc)
9724 ("r-checkmate" ,r-checkmate)
9725 ("r-dplyr" ,r-dplyr)
9726 ("r-htmltools" ,r-htmltools)
9727 ("r-lubridate" ,r-lubridate)
9728 ("r-magick" ,r-magick)
9729 ("r-matrixstats" ,r-matrixstats)
9730 ("r-pander" ,r-pander)
9732 ("r-rapportools" ,r-rapportools)
9733 ("r-tibble" ,r-tibble)
9734 ("r-tidyr" ,r-tidyr)))
9735 (home-page "https://github.com/dcomtois/summarytools")
9736 (synopsis "Tools to quickly and neatly summarize data")
9738 "This package provides tools for data frame summaries, cross-tabulations,
9739 weight-enabled frequency tables and common univariate statistics in concise
9740 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9741 good point-of-entry for exploring data, both for experienced and new R
9743 (license license:gpl2)))
9745 (define-public r-lsei
9752 (uri (cran-uri "lsei" version))
9755 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
9756 (build-system r-build-system)
9758 `(("gfortran" ,gfortran)))
9759 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9760 (synopsis "Solve regression problems under equality/inequality constraints")
9762 "It contains functions that solve least squares linear regression
9763 problems under linear equality/inequality constraints. Functions for solving
9764 quadratic programming problems are also available, which transform such
9765 problems into least squares ones first.")
9766 (license license:gpl2+)))
9768 (define-public r-npsurv
9775 (uri (cran-uri "npsurv" version))
9778 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
9779 (build-system r-build-system)
9781 `(("r-lsei" ,r-lsei)))
9782 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9783 (synopsis "Nonparametric survival analysis")
9785 "This package contains functions for non-parametric survival analysis of
9786 exact and interval-censored observations.")
9787 (license license:gpl2+)))
9789 (define-public r-clusteval
9791 (name "r-clusteval")
9796 (uri (cran-uri "clusteval" version))
9799 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9800 (build-system r-build-system)
9802 `(("r-mvtnorm" ,r-mvtnorm)
9803 ("r-rcpp" ,r-rcpp)))
9804 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9805 (synopsis "Evaluation of clustering algorithms")
9807 "This R package provides a suite of tools to evaluate clustering
9808 algorithms, clusterings, and individual clusters.")
9809 (license license:expat)))
9811 (define-public r-tweedie
9818 (uri (cran-uri "tweedie" version))
9821 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9822 (build-system r-build-system)
9823 (native-inputs `(("gfortran" ,gfortran)))
9824 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9825 (synopsis "Evaluation of Tweedie exponential family models")
9827 "Maximum likelihood computations for Tweedie families, including the
9828 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9829 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9830 and related methods.")
9831 (license license:gpl2+)))
9833 (define-public r-rcppgsl
9840 (uri (cran-uri "RcppGSL" version))
9842 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9843 (properties `((upstream-name . "RcppGSL")))
9844 (build-system r-build-system)
9846 `(("r-rcpp" ,r-rcpp)
9848 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9849 (synopsis "Rcpp integration for GSL vectors and matrices")
9851 "The GNU Scientific Library (or GSL) is a collection of numerical
9852 routines for scientific computing. It is particularly useful for C and C++
9853 programs as it provides a standard C interface to a wide range of mathematical
9854 routines. There are over 1000 functions in total with an extensive test
9855 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9856 structures and R using concepts from Rcpp which is itself a package that eases
9857 the interfaces between R and C++.")
9858 (license license:gpl2+)))
9860 (define-public r-mvabund
9867 (uri (cran-uri "mvabund" version))
9870 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9871 (build-system r-build-system)
9873 `(("r-mass" ,r-mass)
9875 ("r-rcppgsl" ,r-rcppgsl)
9876 ("r-statmod" ,r-statmod)
9877 ("r-tweedie" ,r-tweedie)))
9878 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9879 (synopsis "Statistical methods for analysing multivariate abundance data")
9881 "This package provides a set of tools for displaying, modeling and
9882 analysing multivariate abundance data in community ecology.")
9883 (license license:lgpl2.1+)))
9885 (define-public r-afex
9892 (uri (cran-uri "afex" version))
9895 "0c47bq2llzw2b4avhkxyhmf1m2zjh9jsjiw2kww9n1bhwqsyr4ci"))))
9896 (build-system r-build-system)
9900 ("r-lmertest" ,r-lmertest)
9901 ("r-pbkrtest" ,r-pbkrtest)
9902 ("r-reshape2" ,r-reshape2)))
9904 `(("r-knitr" ,r-knitr)))
9905 (home-page "https://afex.singmann.science/")
9906 (synopsis "Analysis of factorial experiments")
9908 "This package provides convenience functions for analyzing factorial
9909 experiments using ANOVA or mixed models.")
9910 (license license:gpl2+)))
9912 (define-public r-lmertest
9919 (uri (cran-uri "lmerTest" version))
9922 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
9923 (properties `((upstream-name . "lmerTest")))
9924 (build-system r-build-system)
9926 `(("r-ggplot2" ,r-ggplot2)
9929 ("r-numderiv" ,r-numderiv)))
9930 (home-page "https://github.com/runehaubo/lmerTestR")
9931 (synopsis "Tests in linear mixed effects models")
9933 "This package provides p-values in type I, II or III anova and summary
9934 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9935 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9936 package. Model selection methods include step, drop1 and anova-like tables
9937 for random effects (ranova). Methods for Least-Square means (LS-means) and
9938 tests of linear contrasts of fixed effects are also available.")
9939 (license license:gpl2+)))
9941 (define-public r-r2glmm
9948 (uri (cran-uri "r2glmm" version))
9951 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9952 (build-system r-build-system)
9954 `(("r-afex" ,r-afex)
9955 ("r-data-table" ,r-data-table)
9956 ("r-dplyr" ,r-dplyr)
9957 ("r-ggplot2" ,r-ggplot2)
9958 ("r-gridextra" ,r-gridextra)
9959 ("r-lmertest" ,r-lmertest)
9961 ("r-matrix" ,r-matrix)
9963 ("r-pbkrtest" ,r-pbkrtest)))
9964 (home-page "https://github.com/bcjaeger/r2glmm")
9965 (synopsis "Compute R squared for mixed (multilevel) models")
9967 "This package computes model and semi partial R squared with confidence
9968 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9969 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9970 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9972 (license license:gpl2)))
9974 (define-public r-weights
9981 (uri (cran-uri "weights" version))
9984 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9985 (build-system r-build-system)
9987 `(("r-gdata" ,r-gdata)
9988 ("r-hmisc" ,r-hmisc)
9989 ("r-mice" ,r-mice)))
9991 "https://cran.r-project.org/web/packages/weights/")
9992 (synopsis "Weighting and weighted statistics")
9993 (description "This package Provides a variety of functions for producing
9994 simple weighted statistics, such as weighted Pearson's correlations, partial
9995 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9996 includes some software for quickly recoding survey data and plotting point
9997 estimates from interaction terms in regressions (and multiply imputed
9998 regressions). NOTE: Weighted partial correlation calculations pulled to
10000 (license license:gpl2+)))
10002 (define-public r-rcppannoy
10004 (name "r-rcppannoy")
10009 (uri (cran-uri "RcppAnnoy" version))
10012 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
10013 (properties `((upstream-name . "RcppAnnoy")))
10014 (build-system r-build-system)
10016 `(("r-rcpp" ,r-rcpp)))
10017 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
10018 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
10020 "Annoy is a small C++ library for Approximate Nearest Neighbors written
10021 for efficient memory usage as well an ability to load from and save to disk.
10022 This package provides an R interface.")
10023 ;; Annoy is released under ASL 2.0, but this wrapper is released under
10025 (license (list license:gpl2+ license:asl2.0))))
10027 (define-public r-rcpphnsw
10029 (name "r-rcpphnsw")
10034 (uri (cran-uri "RcppHNSW" version))
10037 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
10038 (properties `((upstream-name . "RcppHNSW")))
10039 (build-system r-build-system)
10040 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10041 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
10042 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
10044 "Hnswlib is a C++ library for approximate nearest neighbors. This
10045 package provides a minimal R interface by relying on the Rcpp package.")
10046 ;; hnswlib is released under Version 2.0 of the Apache License.
10047 (license (list license:gpl3 license:asl2.0))))
10049 (define-public r-rcppparallel
10051 (name "r-rcppparallel")
10056 (uri (cran-uri "RcppParallel" version))
10059 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10060 (properties `((upstream-name . "RcppParallel")))
10061 (build-system r-build-system)
10062 (home-page "https://rcppcore.github.io/RcppParallel/")
10063 (synopsis "Parallel programming tools for Rcpp")
10065 "This package provides high level functions for parallel programming with
10066 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10067 the work of a standard serial @code{for} loop into a parallel one and the
10068 @code{parallelReduce()} function can be used for accumulating aggregates or
10070 (license license:gpl2)))
10072 (define-public r-ncdf4
10079 (uri (cran-uri "ncdf4" version))
10082 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10083 (build-system r-build-system)
10085 `(("netcdf" ,netcdf)
10087 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10088 (synopsis "R interface to Unidata netCDF format data files")
10090 "This package provides a high-level R interface to data files written
10091 using Unidata's netCDF library (version 4 or earlier), which are binary data
10092 files that are portable across platforms and include metadata information in
10093 addition to the data sets. Using this package, netCDF files can be opened and
10094 data sets read in easily. It is also easy to create new netCDF dimensions,
10095 variables, and files, in either version 3 or 4 format, and manipulate existing
10097 (license license:gpl3+)))
10099 (define-public r-biocmanager
10101 (name "r-biocmanager")
10102 (version "1.30.10")
10106 (uri (cran-uri "BiocManager" version))
10108 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10109 (properties `((upstream-name . "BiocManager")))
10110 (build-system r-build-system)
10111 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10112 (synopsis "Access the Bioconductor project package repository")
10114 "This package provides a convenient tool to install and update
10115 Bioconductor packages.")
10116 (license license:artistic2.0)))
10118 (define-public r-rgl
10121 (version "0.100.54")
10125 (uri (cran-uri "rgl" version))
10128 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
10129 (build-system r-build-system)
10131 `(("pkg-config" ,pkg-config)))
10133 `(("freetype" ,freetype)
10140 `(("r-crosstalk" ,r-crosstalk)
10141 ("r-htmltools" ,r-htmltools)
10142 ("r-htmlwidgets" ,r-htmlwidgets)
10143 ("r-jsonlite" ,r-jsonlite)
10144 ("r-knitr" ,r-knitr)
10145 ("r-magrittr" ,r-magrittr)
10146 ("r-manipulatewidget" ,r-manipulatewidget)
10147 ("r-shiny" ,r-shiny)))
10148 (home-page "https://r-forge.r-project.org/projects/rgl/")
10149 (synopsis "3D visualization using OpenGL")
10151 "This package provides medium to high level functions for 3D interactive graphics,
10152 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
10153 as functions for constructing representations of geometric
10154 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
10155 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
10156 image formats, including PNG, Postscript, SVG, PGF.")
10157 ;; Any version of the GPL.
10158 (license (list license:gpl2+ license:gpl3+))))
10160 (define-public r-multicool
10162 (name "r-multicool")
10167 (uri (cran-uri "multicool" version))
10170 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
10171 (build-system r-build-system)
10172 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10173 (home-page "https://cran.r-project.org/web/packages/multicool/")
10174 (synopsis "Permutations of multisets in cool-lex order")
10176 "This package provides a set of tools to permute multisets without loops
10177 or hash tables and to generate integer partitions. Cool-lex order is similar
10178 to colexicographical order.")
10179 (license license:gpl2)))
10181 (define-public r-misc3d
10188 (uri (cran-uri "misc3d" version))
10191 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
10192 (build-system r-build-system)
10193 (home-page "https://cran.r-project.org/web/packages/misc3d/")
10194 (synopsis "Miscellaneous 3D Plots")
10196 "This package provides a collection of miscellaneous 3d plots, including
10198 ;; Any version of the GPL.
10199 (license (list license:gpl2+ license:gpl3+))))
10201 (define-public r-ks
10208 (uri (cran-uri "ks" version))
10210 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
10211 (build-system r-build-system)
10214 ("r-kernlab" ,r-kernlab)
10215 ("r-kernsmooth" ,r-kernsmooth)
10216 ("r-matrix" ,r-matrix)
10217 ("r-mclust" ,r-mclust)
10219 ("r-multicool" ,r-multicool)
10220 ("r-mvtnorm" ,r-mvtnorm)))
10221 (home-page "http://www.mvstat.net/tduong/")
10222 (synopsis "Kernel smoothing")
10224 "This package provides kernel smoothers for univariate and multivariate
10225 data, including density functions, density derivatives, cumulative
10226 distributions, modal clustering, discriminant analysis, and two-sample
10227 hypothesis testing.")
10228 ;; Either version of the GPL.
10229 (license (list license:gpl2 license:gpl3))))
10231 (define-public r-feature
10238 (uri (cran-uri "feature" version))
10241 "1c12rny9nx8dynzxbcf49h76a7wlmsk1m131wh0jiyqx3c3y41y1"))))
10242 (build-system r-build-system)
10246 `(("r-knitr" ,r-knitr)))
10247 (home-page "http://www.mvstat.net/tduong/")
10248 (synopsis "Inferential feature significance for kernel density estimation")
10250 "The feature package contains functions to display and compute kernel
10251 density estimates, significant gradient and significant curvature regions.
10252 Significant gradient and/or curvature regions often correspond to significant
10253 features (e.g. local modes).")
10254 ;; Either version of the GPL.
10255 (license (list license:gpl2 license:gpl3))))
10257 (define-public r-arm
10264 (uri (cran-uri "arm" version))
10267 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10268 (build-system r-build-system)
10270 `(("r-abind" ,r-abind)
10272 ("r-hmisc" ,r-hmisc)
10275 ("r-matrix" ,r-matrix)
10276 ("r-nlme" ,r-nlme)))
10277 (home-page "https://cran.r-project.org/web/packages/arm/")
10278 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10280 "This package provides functions to accompany A. Gelman and J. Hill,
10281 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10282 University Press, 2007.")
10283 (license license:gpl3+)))
10285 (define-public r-circular
10287 (name "r-circular")
10292 (uri (cran-uri "circular" version))
10295 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10296 (build-system r-build-system)
10298 `(("r-boot" ,r-boot)
10299 ("r-mvtnorm" ,r-mvtnorm)))
10301 `(("gfortran" ,gfortran)))
10302 (home-page "https://cran.r-project.org/web/packages/circular/")
10303 (synopsis "Circular statistics")
10305 "This package provides tools for circular statistics, from \"Topics in
10306 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10308 (license license:gpl2+)))
10310 (define-public r-activity
10312 (name "r-activity")
10317 (uri (cran-uri "activity" version))
10320 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10321 (build-system r-build-system)
10323 `(("r-circular" ,r-circular)
10324 ("r-insol" ,r-insol)
10325 ("r-pbapply" ,r-pbapply)))
10326 (home-page "https://cran.r-project.org/web/packages/activity/")
10327 (synopsis "Animal activity statistics")
10329 "This package provides functions to fit kernel density functions to
10330 animal activity time data; plot activity distributions; quantify overall
10331 levels of activity; statistically compare activity metrics through
10332 bootstrapping; and evaluate variation in linear variables with time (or other
10333 circular variables).")
10334 (license license:gpl3)))
10336 (define-public r-ouch
10343 (uri (cran-uri "ouch" version))
10346 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10347 (build-system r-build-system)
10348 (propagated-inputs `(("r-subplex" ,r-subplex)))
10349 (home-page "https://kingaa.github.io/ouch/")
10350 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10352 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10353 for evolution along a phylogenetic tree.")
10354 (license license:gpl2+)))
10356 (define-public r-fmsb
10363 (uri (cran-uri "fmsb" version))
10366 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10367 (build-system r-build-system)
10368 (home-page "http://minato.sip21c.org/msb/")
10369 (synopsis "Functions for medical statistics book with demographic data")
10371 "This package provides several utility functions for the book entitled
10372 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10373 Japan, 2007) with Japanese demographic data and some demographic analysis
10374 related functions.")
10375 (license license:gpl2+)))
10377 (define-public r-stabledist
10379 (name "r-stabledist")
10384 (uri (cran-uri "stabledist" version))
10387 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10388 (build-system r-build-system)
10389 (home-page "https://www.rmetrics.org")
10390 (synopsis "Stable distribution functions")
10392 "This package provides density, probability and quantile functions, and
10393 random number generation for (skew) stable distributions, using the
10394 parametrizations of Nolan.")
10395 (license license:gpl2+)))
10397 (define-public r-gsl
10404 (uri (cran-uri "gsl" version))
10407 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10408 (build-system r-build-system)
10411 (home-page "https://cran.r-project.org/web/packages/gsl")
10412 (synopsis "Wrapper for the GNU Scientific Library")
10414 "This package provides an R wrapper for the special functions and quasi
10415 random number generators of the GNU Scientific Library.")
10416 (license license:gpl2+)))
10418 (define-public r-adgoftest
10420 (name "r-adgoftest")
10425 (uri (cran-uri "ADGofTest" version))
10428 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10429 (properties `((upstream-name . "ADGofTest")))
10430 (build-system r-build-system)
10431 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10432 (synopsis "Anderson-Darling GoF test")
10434 "This package provides an implementation of the Anderson-Darling GoF test
10435 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10436 Anderson-Darling Distribution\".")
10437 ;; Any version of the GPL.
10438 (license license:gpl3+)))
10440 (define-public r-softimpute
10442 (name "r-softimpute")
10447 (uri (cran-uri "softImpute" version))
10450 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10451 (properties `((upstream-name . "softImpute")))
10452 (build-system r-build-system)
10454 `(("r-matrix" ,r-matrix)))
10456 `(("gfortran" ,gfortran)))
10457 (home-page "https://cran.r-project.org/web/packages/softImpute")
10458 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10460 "This package provides iterative methods for matrix completion that use
10461 nuclear-norm regularization. The package includes procedures for centering
10462 and scaling rows, columns or both, and for computing low-rank @dfn{single
10463 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10465 (license license:gpl2)))
10467 (define-public r-fftwtools
10469 (name "r-fftwtools")
10474 (uri (cran-uri "fftwtools" version))
10477 "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9"))))
10478 (build-system r-build-system)
10479 (inputs `(("fftw" ,fftw)))
10480 (home-page "https://github.com/krahim/fftwtools")
10481 (synopsis "Wrapper for FFTW3")
10483 "This package provides a wrapper for several FFTW functions. It provides
10484 access to the two-dimensional FFT, the multivariate FFT, and the
10485 one-dimensional real to complex FFT using the FFTW3 library. The package
10486 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10487 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10488 The FFT functions have a parameter that allows them to not return the
10489 redundant complex conjugate when the input is real data.")
10490 (license license:gpl2+)))
10492 (define-public r-tiff
10499 (uri (cran-uri "tiff" version))
10502 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10503 (build-system r-build-system)
10505 `(("libtiff" ,libtiff)
10506 ("libjpeg" ,libjpeg-turbo)
10508 (home-page "https://www.rforge.net/tiff/")
10509 (synopsis "Read and write TIFF images")
10511 "This package provides an easy and simple way to read, write and display
10512 bitmap images stored in the TIFF format. It can read and write both files and
10513 in-memory raw vectors.")
10514 ;; Either of these two license versions.
10515 (license (list license:gpl2 license:gpl3))))
10517 (define-public r-nlp
10524 (uri (cran-uri "NLP" version))
10527 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
10528 (properties `((upstream-name . "NLP")))
10529 (build-system r-build-system)
10530 (home-page "https://cran.r-project.org/web/packages/NLP/")
10531 (synopsis "Natural language processing infrastructure")
10533 "This package provides basic classes and methods for Natural Language
10535 (license license:gpl3)))
10537 (define-public r-tm
10544 (uri (cran-uri "tm" version))
10547 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10548 (properties `((upstream-name . "tm")))
10549 (build-system r-build-system)
10555 ("r-xml2" ,r-xml2)))
10556 (home-page "http://tm.r-forge.r-project.org/")
10557 (synopsis "Text mining package")
10559 "This package provides a framework for text mining applications within R.")
10560 (license license:gpl3)))
10562 (define-public r-waveslim
10564 (name "r-waveslim")
10569 (uri (cran-uri "waveslim" version))
10572 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10573 (build-system r-build-system)
10575 `(("gfortran" ,gfortran)))
10576 (home-page "http://waveslim.blogspot.com")
10577 (synopsis "Basic wavelet routines for signal processing")
10579 "This package provides basic wavelet routines for time series (1D),
10580 image (2D) and array (3D) analysis. The code provided here is based on
10581 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10582 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10583 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10584 pairs (Selesnick 2001, 2002).")
10585 (license license:bsd-3)))
10587 (define-public r-wordcloud
10589 (name "r-wordcloud")
10594 (uri (cran-uri "wordcloud" version))
10597 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10598 (build-system r-build-system)
10600 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10602 ;; The "tm" package is only "suggested" according to CRAN, but the
10603 ;; wordcloud package cannot be loaded without it.
10605 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10606 (synopsis "Word clouds")
10608 "This package provides functionality to create pretty word clouds,
10609 visualize differences and similarity between documents, and avoid
10610 over-plotting in scatter plots with text.")
10611 (license license:lgpl2.1)))
10613 (define-public r-colorramps
10615 (name "r-colorramps")
10620 (uri (cran-uri "colorRamps" version))
10623 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10624 (properties `((upstream-name . "colorRamps")))
10625 (build-system r-build-system)
10626 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10627 (synopsis "Build color tables")
10628 (description "This package provides features to build gradient color
10630 ;; Any version of the GPL
10631 (license license:gpl3+)))
10633 (define-public r-tidytree
10635 (name "r-tidytree")
10640 (uri (cran-uri "tidytree" version))
10642 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10643 (build-system r-build-system)
10646 ("r-dplyr" ,r-dplyr)
10647 ("r-lazyeval" ,r-lazyeval)
10648 ("r-magrittr" ,r-magrittr)
10649 ("r-rlang" ,r-rlang)
10650 ("r-tibble" ,r-tibble)))
10652 `(("r-knitr" ,r-knitr)))
10653 (home-page "https://github.com/GuangchuangYu/tidytree")
10654 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10656 "Phylogenetic trees generally contain multiple components including nodes,
10657 edges, branches and associated data. This package provides an approach to
10658 convert tree objects to tidy data frames. It also provides tidy interfaces to
10659 manipulate tree data.")
10660 (license license:artistic2.0)))
10662 (define-public r-rvcheck
10669 (uri (cran-uri "rvcheck" version))
10671 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10672 (build-system r-build-system)
10674 `(("r-biocmanager" ,r-biocmanager)
10675 ("r-rlang" ,r-rlang)))
10676 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10677 (synopsis "R package version check")
10679 "This package provides tools to check the latest release version of R and
10680 R packages (on CRAN, Bioconductor or Github).")
10681 (license license:artistic2.0)))
10683 (define-public r-docopt
10690 (uri (cran-uri "docopt" version))
10693 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10694 (build-system r-build-system)
10695 (home-page "https://github.com/docopt/docopt.R")
10696 (synopsis "Command-line interface specification language")
10698 "This package enables you to define a command-line interface by just
10699 giving it a description in the specific format.")
10700 (license license:expat)))
10702 (define-public r-sparsesvd
10704 (name "r-sparsesvd")
10709 (uri (cran-uri "sparsesvd" version))
10712 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10713 (build-system r-build-system)
10714 (propagated-inputs `(("r-matrix" ,r-matrix)))
10715 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10716 (synopsis "Sparse truncated singular value decomposition")
10718 "This package provides a Wrapper around the SVDLIBC library
10719 for (truncated) singular value decomposition of a sparse matrix. Currently,
10720 only sparse real matrices in Matrix package format are supported.")
10721 ;; SVDLIBC is released under BSD-2. The R interface is released under
10723 (license (list license:bsd-3 license:bsd-2))))
10725 (define-public r-speedglm
10727 (name "r-speedglm")
10732 (uri (cran-uri "speedglm" version))
10735 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10736 (build-system r-build-system)
10738 `(("r-mass" ,r-mass)
10739 ("r-matrix" ,r-matrix)))
10740 (home-page "https://cran.r-project.org/web/packages/speedglm")
10741 (synopsis "Fit linear and generalized linear models to large data sets")
10743 "This package provides tools for fitting linear models and generalized
10744 linear models to large data sets by updating algorithms.")
10745 ;; Any version of the GPL
10746 (license license:gpl2+)))
10748 (define-public r-densityclust
10750 (name "r-densityclust")
10755 (uri (cran-uri "densityClust" version))
10758 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10759 (properties `((upstream-name . "densityClust")))
10760 (build-system r-build-system)
10763 ("r-ggplot2" ,r-ggplot2)
10764 ("r-ggrepel" ,r-ggrepel)
10765 ("r-gridextra" ,r-gridextra)
10766 ("r-rcolorbrewer" ,r-rcolorbrewer)
10768 ("r-rtsne" ,r-rtsne)))
10769 (home-page "https://cran.r-project.org/web/packages/densityClust")
10770 (synopsis "Clustering by fast search and find of density peaks")
10772 "This package provides an improved implementation (based on k-nearest
10773 neighbors) of the density peak clustering algorithm, originally described by
10774 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10775 large datasets (> 100,000 samples) very efficiently.")
10776 (license license:gpl2+)))
10778 (define-public r-combinat
10780 (name "r-combinat")
10785 (uri (cran-uri "combinat" version))
10788 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10789 (build-system r-build-system)
10790 (home-page "https://cran.r-project.org/web/packages/combinat")
10791 (synopsis "Combinatorics utilities")
10792 (description "This package provides assorted routines for combinatorics.")
10793 (license license:gpl2)))
10795 (define-public r-qlcmatrix
10797 (name "r-qlcmatrix")
10802 (uri (cran-uri "qlcMatrix" version))
10805 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10806 (properties `((upstream-name . "qlcMatrix")))
10807 (build-system r-build-system)
10809 `(("r-docopt" ,r-docopt)
10810 ("r-matrix" ,r-matrix)
10812 ("r-sparsesvd" ,r-sparsesvd)))
10813 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10814 (synopsis "Sparse matrix functions for quantitative language comparison")
10816 "This package provides an extension of the functionality of the Matrix
10817 package for using sparse matrices. Some of the functions are very general,
10818 while other are highly specific for the special data format used for
10819 @dfn{quantitative language comparison} (QLC).")
10820 (license license:gpl3)))
10822 (define-public r-ddrtree
10829 (uri (cran-uri "DDRTree" version))
10832 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10833 (properties `((upstream-name . "DDRTree")))
10834 (build-system r-build-system)
10837 ("r-irlba" ,r-irlba)
10839 ("r-rcppeigen" ,r-rcppeigen)))
10840 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10841 (synopsis "Learning principal graphs with DDRTree")
10843 "This package provides an implementation of the framework of
10844 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10845 dimensional space while constructs a principal tree which passes through the
10846 middle of the data simultaneously. DDRTree shows superiority to
10847 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10848 intrinsic structure of single cell genomics data. In general, it could be
10849 used to reconstruct the temporal progression as well as the bifurcation
10850 structure of any data type.")
10851 (license license:asl2.0)))
10853 (define-public r-corpcor
10860 (uri (cran-uri "corpcor" version))
10863 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10864 (build-system r-build-system)
10865 (home-page "http://strimmerlab.org/software/corpcor/")
10866 (synopsis "Efficient estimation of covariance and (partial) correlation")
10868 "This package implements a James-Stein-type shrinkage estimator for the
10869 covariance matrix, with separate shrinkage for variances and correlations.
10870 Furthermore, functions are available for fast singular value decomposition,
10871 for computing the pseudoinverse, and for checking the rank and positive
10872 definiteness of a matrix.")
10873 (license license:gpl3+)))
10875 (define-public r-rspectra
10877 (name "r-rspectra")
10882 (uri (cran-uri "RSpectra" version))
10885 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10886 (properties `((upstream-name . "RSpectra")))
10887 (build-system r-build-system)
10889 `(("r-matrix" ,r-matrix)
10891 ("r-rcppeigen" ,r-rcppeigen)))
10892 (home-page "https://github.com/yixuan/RSpectra")
10893 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10895 "This package provides an R interface to the Spectra library for
10896 large-scale eigenvalue and SVD problems. It is typically used to compute a
10897 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10898 which is usually more efficient than @code{eigen()} if k << n.")
10900 (license license:mpl2.0)))
10902 (define-public r-vbsr
10909 (uri (cran-uri "vbsr" version))
10912 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10913 (build-system r-build-system)
10914 (home-page "https://cran.r-project.org/web/packages/vbsr")
10915 (synopsis "Variational Bayes spike regression regularized linear models")
10917 "This package provides an efficient algorithm for solving ultra-sparse
10918 regularized regression models using a variational Bayes algorithm with a spike
10919 prior. The algorithm is solved on a path, with coordinate updates, and is
10920 capable of generating very sparse models. Very general model
10921 diagnostics for controlling type-1 errors are also provided.")
10922 (license license:gpl2)))
10924 (define-public r-flare
10927 (version "1.6.0.2")
10931 (uri (cran-uri "flare" version))
10934 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10935 (build-system r-build-system)
10937 `(("r-igraph" ,r-igraph)
10938 ("r-lattice" ,r-lattice)
10940 ("r-matrix" ,r-matrix)))
10941 (home-page "https://cran.r-project.org/web/packages/flare")
10942 (synopsis "Family of Lasso regression implementations")
10944 "This package provides implementations of a family of Lasso variants
10945 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10946 high dimensional sparse linear models.")
10947 (license license:gpl2)))
10949 (define-public r-lassopv
10956 (uri (cran-uri "lassopv" version))
10959 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10960 (build-system r-build-system)
10961 (propagated-inputs `(("r-lars" ,r-lars)))
10962 (home-page "https://github.com/lingfeiwang/lassopv")
10963 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10965 "This package enables you to estimate the p-values for predictors x
10966 against target variable y in Lasso regression, using the regularization
10967 strength when each predictor enters the active set of regularization path for
10968 the first time as the statistic.")
10969 (license license:gpl3)))
10971 (define-public r-splitstackshape
10973 (name "r-splitstackshape")
10978 (uri (cran-uri "splitstackshape" version))
10981 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10982 (build-system r-build-system)
10984 `(("r-data-table" ,r-data-table)))
10985 (home-page "https://github.com/mrdwab/splitstackshape")
10986 (synopsis "Stack and reshape datasets after splitting concatenated values")
10988 "Online data collection tools like Google Forms often export
10989 multiple-response questions with data concatenated in cells. The
10990 @code{concat.split} (cSplit) family of functions provided by this package
10991 splits such data into separate cells. This package also includes functions to
10992 stack groups of columns and to reshape wide data, even when the data are
10993 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10994 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10996 (license license:gpl3)))
10998 (define-public r-tfmpvalue
11000 (name "r-tfmpvalue")
11005 (uri (cran-uri "TFMPvalue" version))
11008 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
11009 (properties `((upstream-name . "TFMPvalue")))
11010 (build-system r-build-system)
11011 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11012 (home-page "https://github.com/ge11232002/TFMPvalue")
11013 (synopsis "P-value computation for position weight matrices")
11015 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
11016 identification from sequence/alignments, we are interested in the significance
11017 of certain match scores. TFMPvalue provides the accurate calculation of a
11018 p-value with a score threshold for position weight matrices, or the score with
11019 a given p-value. It is an interface to code originally made available by
11020 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
11021 Touzet and Varre (2007).")
11022 (license license:gpl2)))
11024 (define-public r-rnifti
11031 (uri (cran-uri "RNifti" version))
11034 "02jdxz3w423k9b5wldky4pnnq0cs2zlfi52jxjw1mk24z756j692"))))
11035 (properties `((upstream-name . "RNifti")))
11036 (build-system r-build-system)
11037 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11038 (home-page "https://github.com/jonclayden/RNifti")
11039 (synopsis "Fast R and C++ access to NIfTI images")
11041 "This package provides very fast read and write access to images stored
11042 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
11043 compiled C and interpreted R code. It also provides a C/C++ API that can be
11044 used by other packages.")
11045 (license license:gpl2)))
11047 (define-public r-shades
11054 (uri (cran-uri "shades" version))
11057 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
11058 (build-system r-build-system)
11059 (home-page "https://github.com/jonclayden/shades")
11060 (synopsis "Simple color manipulation")
11062 "This package provides functions for easily manipulating colors,
11063 creating color scales and calculating color distances.")
11064 (license license:bsd-3)))
11066 (define-public r-ore
11073 (uri (cran-uri "ore" version))
11075 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11076 (build-system r-build-system)
11077 (home-page "https://github.com/jonclayden/ore")
11078 (synopsis "R interface to the Onigmo regular expression library")
11080 "This package provides an alternative to R's built-in functionality for
11081 handling regular expressions, based on the Onigmo library. It offers
11082 first-class compiled regex objects, partial matching and function-based
11083 substitutions, amongst other features.")
11084 (license license:bsd-3)))
11086 (define-public r-reportr
11093 (uri (cran-uri "reportr" version))
11096 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11097 (build-system r-build-system)
11098 (propagated-inputs `(("r-ore" ,r-ore)))
11099 (home-page "https://github.com/jonclayden/reportr")
11100 (synopsis "General message and error reporting system")
11102 "This package provides a system for reporting messages, which offers
11103 certain useful features over the standard R system, such as the incorporation
11104 of output consolidation, message filtering, assertions, expression
11105 substitution, automatic generation of stack traces for debugging, and
11106 conditional reporting based on the current \"output level\".")
11107 (license license:gpl2)))
11109 (define-public r-tractor-base
11111 (name "r-tractor-base")
11116 (uri (cran-uri "tractor.base" version))
11119 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
11120 (properties `((upstream-name . "tractor.base")))
11121 (build-system r-build-system)
11124 ("r-reportr" ,r-reportr)
11125 ("r-rnifti" ,r-rnifti)
11126 ("r-shades" ,r-shades)))
11127 (home-page "https://www.tractor-mri.org.uk")
11128 (synopsis "Read, manipulate and visualize magnetic resonance images")
11130 "This package provides functions for working with magnetic resonance
11131 images. It supports reading and writing of popular file formats (DICOM,
11132 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
11133 visualization; flexible image manipulation; metadata and sparse image
11135 (license license:gpl2)))
11137 (define-public r-grimport
11139 (name "r-grimport")
11144 (uri (cran-uri "grImport" version))
11147 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
11148 (properties `((upstream-name . "grImport")))
11149 (build-system r-build-system)
11151 `(("ghostscript" ,ghostscript)))
11153 `(("r-xml" ,r-xml)))
11154 (home-page "https://cran.r-project.org/web/packages/grImport")
11155 (synopsis "Convert, import, and draw PostScript pictures")
11157 "This package provides functions for converting, importing, and drawing
11158 PostScript pictures in R plots.")
11159 (license license:gpl2+)))
11161 (define-public r-grimport2
11163 (name "r-grimport2")
11168 (uri (cran-uri "grImport2" version))
11171 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
11172 (properties `((upstream-name . "grImport2")))
11173 (build-system r-build-system)
11175 `(("r-base64enc" ,r-base64enc)
11179 (home-page "https://cran.r-project.org/web/packages/grImport2/")
11180 (synopsis "Import SVG graphics")
11182 "This package provides functions for importing external vector images and
11183 drawing them as part of R plots. This package is different from the
11184 @code{grImport} package because, where that package imports PostScript format
11185 images, this package imports SVG format images. Furthermore, this package
11186 imports a specific subset of SVG, so external images must be preprocessed
11187 using a package like @code{rsvg} to produce SVG that this package can import.
11188 SVG features that are not supported by R graphics, such as gradient fills, can
11189 be imported and then exported via the @code{gridSVG} package.")
11190 (license license:gpl2+)))
11192 (define-public r-kohonen
11199 (uri (cran-uri "kohonen" version))
11202 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
11203 (build-system r-build-system)
11205 `(("r-rcpp" ,r-rcpp)))
11206 (home-page "https://cran.r-project.org/web/packages/kohonen")
11207 (synopsis "Supervised and unsupervised self-organising maps")
11209 "This package provides functions to train @dfn{self-organising
11210 maps} (SOMs). Also interrogation of the maps and prediction using trained
11211 maps are supported. The name of the package refers to Teuvo Kohonen, the
11212 inventor of the SOM.")
11213 (license license:gpl2+)))
11215 (define-public r-nnls
11222 (uri (cran-uri "nnls" version))
11225 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
11226 (build-system r-build-system)
11227 (native-inputs `(("gfortran" ,gfortran)))
11228 (home-page "https://cran.r-project.org/web/packages/nnls")
11229 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
11231 "This package provides an R interface to the Lawson-Hanson implementation
11232 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
11233 the combination of non-negative and non-positive constraints.")
11234 (license license:gpl2+)))
11236 (define-public r-iso
11239 (version "0.0-18.1")
11243 (uri (cran-uri "Iso" version))
11246 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11247 (properties `((upstream-name . "Iso")))
11248 (build-system r-build-system)
11249 (native-inputs `(("gfortran" ,gfortran)))
11250 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11251 (synopsis "Functions to perform isotonic regression")
11253 "This package provides support for linear order and unimodal
11254 order (univariate) isotonic regression and bivariate isotonic regression with
11255 linear order on both variables.")
11256 (license license:gpl2+)))
11258 (define-public r-chemometricswithr
11260 (name "r-chemometricswithr")
11265 (uri (cran-uri "ChemometricsWithR" version))
11268 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11270 `((upstream-name . "ChemometricsWithR")))
11271 (build-system r-build-system)
11273 `(("r-devtools" ,r-devtools)
11274 ("r-kohonen" ,r-kohonen)
11277 (home-page "https://github.com/rwehrens/CWR")
11278 (synopsis "Chemometrics with R")
11280 "This package provides functions and scripts used in the book
11281 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11282 Life Sciences\" by Ron Wehrens, Springer (2011).")
11283 (license license:gpl2+)))
11285 (define-public r-als
11292 (uri (cran-uri "ALS" version))
11295 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11296 (properties `((upstream-name . "ALS")))
11297 (build-system r-build-system)
11300 ("r-nnls" ,r-nnls)))
11301 (home-page "https://cran.r-project.org/web/packages/ALS")
11302 (synopsis "Multivariate curve resolution alternating least squares")
11304 "Alternating least squares is often used to resolve components
11305 contributing to data with a bilinear structure; the basic technique may be
11306 extended to alternating constrained least squares. This package provides an
11307 implementation of @dfn{multivariate curve resolution alternating least
11308 squares} (MCR-ALS).
11310 Commonly applied constraints include unimodality, non-negativity, and
11311 normalization of components. Several data matrices may be decomposed
11312 simultaneously by assuming that one of the two matrices in the bilinear
11313 decomposition is shared between datasets.")
11314 (license license:gpl2+)))
11316 (define-public r-strucchange
11318 (name "r-strucchange")
11323 (uri (cran-uri "strucchange" version))
11326 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11327 (build-system r-build-system)
11329 `(("r-sandwich" ,r-sandwich)
11331 (home-page "https://cran.r-project.org/web/packages/strucchange")
11332 (synopsis "Testing, monitoring, and dating structural changes")
11334 "This package provides tools for testing, monitoring and dating
11335 structural changes in (linear) regression models. It features tests/methods
11336 from the generalized fluctuation test framework as well as from the F
11337 test (Chow test) framework. This includes methods to fit, plot and test
11338 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11339 statistics, respectively. It is possible to monitor incoming data online
11340 using fluctuation processes. Finally, the breakpoints in regression models
11341 with structural changes can be estimated together with confidence intervals.
11342 Emphasis is always given to methods for visualizing the data.")
11343 ;; Either of these two GPL versions
11344 (license (list license:gpl2 license:gpl3))))
11346 (define-public r-pixmap
11353 (uri (cran-uri "pixmap" version))
11356 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11357 (build-system r-build-system)
11358 (home-page "https://cran.r-project.org/web/packages/pixmap")
11359 (synopsis "Tools for bitmap images")
11361 "This package provides functions for importing, exporting, plotting and
11362 other manipulations of bitmapped images.")
11363 (license license:gpl2)))
11365 (define-public r-rapidjsonr
11367 (name "r-rapidjsonr")
11372 (uri (cran-uri "rapidjsonr" version))
11375 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11376 (build-system r-build-system)
11377 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11378 (synopsis "JSON parser")
11380 "This package provides JSON parsing capability through the Rapidjson
11382 (license license:expat)))
11384 (define-public r-ontologyindex
11386 (name "r-ontologyindex")
11391 (uri (cran-uri "ontologyIndex" version))
11394 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11395 (properties `((upstream-name . "ontologyIndex")))
11396 (build-system r-build-system)
11397 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11398 (synopsis "Functions for processing ontologies in R")
11400 "This package provides functions for reading ontologies into R as lists
11401 and manipulating sets of ontological terms.")
11402 (license license:gpl2+)))
11404 (define-public r-gargle
11411 (uri (cran-uri "gargle" version))
11414 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11415 (build-system r-build-system)
11420 ("r-jsonlite" ,r-jsonlite)
11421 ("r-rlang" ,r-rlang)
11422 ("r-withr" ,r-withr)))
11424 `(("r-knitr" ,r-knitr)))
11425 (home-page "https://gargle.r-lib.org")
11426 (synopsis "Utilities for working with Google APIs")
11428 "This package provides utilities for working with Google APIs. This
11429 includes functions and classes for handling common credential types and for
11430 preparing, executing, and processing HTTP requests.")
11431 (license license:expat)))
11433 (define-public r-bigrquery
11435 (name "r-bigrquery")
11440 (uri (cran-uri "bigrquery" version))
11443 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
11444 (build-system r-build-system)
11446 `(("r-assertthat" ,r-assertthat)
11447 ("r-bit64" ,r-bit64)
11450 ("r-gargle" ,r-gargle)
11453 ("r-jsonlite" ,r-jsonlite)
11454 ("r-prettyunits" ,r-prettyunits)
11455 ("r-progress" ,r-progress)
11456 ("r-rapidjsonr" ,r-rapidjsonr)
11458 ("r-rlang" ,r-rlang)
11459 ("r-tibble" ,r-tibble)))
11460 (home-page "https://github.com/rstats-db/bigrquery")
11461 (synopsis "R interface to Google's BigQuery API")
11463 "This package provides an R interface to Google's BigQuery database.")
11464 (license license:gpl3)))
11466 (define-public r-gmp
11473 (uri (cran-uri "gmp" version))
11476 "11rl7qmfrpp1974f0vzsi3zjyx147wlb82ydxak2b60khfvhrn90"))))
11477 (build-system r-build-system)
11480 (modify-phases %standard-phases
11481 (add-after 'unpack 'set-CC
11482 (lambda _ (setenv "CC" "gcc") #t)))))
11483 (inputs `(("gmp" ,gmp)))
11484 (home-page "https://cran.r-project.org/web/packages/gmp")
11485 (synopsis "Multiple precision arithmetic")
11487 "This package supports multiple precision arithmetic (big integers and
11488 rationals, prime number tests, matrix computation), \"arithmetic without
11489 limitations\" using the GNU Multiple Precision library.")
11490 ;; Any version of the GPL.
11491 (license license:gpl3+)))
11493 (define-public r-rmpfr
11500 (uri (cran-uri "Rmpfr" version))
11503 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11504 (properties `((upstream-name . "Rmpfr")))
11505 (build-system r-build-system)
11510 `(("r-gmp" ,r-gmp)))
11512 `(("pkg-config" ,pkg-config)))
11513 (home-page "http://rmpfr.r-forge.r-project.org/")
11514 (synopsis "R bindings to the MPFR library")
11516 "This package supports arithmetic (via S4 classes and methods) for
11517 arbitrary precision floating point numbers, including transcendental
11518 functions. To this end, the package interfaces with the @dfn{Multiple
11519 Precision Floating-Point Reliable} (MPFR) library.")
11520 (license license:gpl2+)))
11522 (define-public r-assertive-base
11524 (name "r-assertive-base")
11529 (uri (cran-uri "assertive.base" version))
11532 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11534 `((upstream-name . "assertive.base")))
11535 (build-system r-build-system)
11536 (home-page "https://bitbucket.org/richierocks/assertive.base")
11537 (synopsis "Core of the assertive package")
11539 "This package provides a minimal set of predicates and assertions used by
11540 the assertive package. This is mainly for use by other package developers who
11541 want to include run-time testing features in their own packages.")
11542 (license license:gpl3+)))
11544 (define-public r-assertive-properties
11546 (name "r-assertive-properties")
11551 (uri (cran-uri "assertive.properties" version))
11554 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11556 `((upstream-name . "assertive.properties")))
11557 (build-system r-build-system)
11559 `(("r-assertive-base" ,r-assertive-base)))
11560 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11561 (synopsis "Assertions to check properties of variables")
11563 "This package provides a set of predicates and assertions for checking
11564 the properties of variables, such as length, names and attributes. This is
11565 mainly for use by other package developers who want to include run-time
11566 testing features in their own packages.")
11567 (license license:gpl3+)))
11569 (define-public r-assertive-numbers
11571 (name "r-assertive-numbers")
11576 (uri (cran-uri "assertive.numbers" version))
11579 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11581 `((upstream-name . "assertive.numbers")))
11582 (build-system r-build-system)
11584 `(("r-assertive-base" ,r-assertive-base)))
11585 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11586 (synopsis "Assertions to check properties of numbers")
11588 "This package provides a set of predicates and assertions for checking
11589 the properties of numbers. This is mainly for use by other package developers
11590 who want to include run-time testing features in their own packages.")
11591 (license license:gpl3+)))
11593 (define-public r-assertive-sets
11595 (name "r-assertive-sets")
11600 (uri (cran-uri "assertive.sets" version))
11603 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11605 `((upstream-name . "assertive.sets")))
11606 (build-system r-build-system)
11608 `(("r-assertive-base" ,r-assertive-base)))
11609 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11610 (synopsis "Assertions to check properties of sets")
11612 "This package provides a set of predicates and assertions for checking
11613 the properties of sets. This is mainly for use by other package developers
11614 who want to include run-time testing features in their own packages.")
11615 (license license:gpl3+)))
11617 (define-public r-assertive-matrices
11619 (name "r-assertive-matrices")
11624 (uri (cran-uri "assertive.matrices" version))
11627 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11629 `((upstream-name . "assertive.matrices")))
11630 (build-system r-build-system)
11632 `(("r-assertive-base" ,r-assertive-base)))
11633 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11634 (synopsis "Assertions to check properties of matrices")
11636 "This package provides a set of predicates and assertions for checking
11637 the properties of matrices. This is mainly for use by other package
11638 developers who want to include run-time testing features in their own
11640 (license license:gpl3+)))
11642 (define-public r-assertive-models
11644 (name "r-assertive-models")
11649 (uri (cran-uri "assertive.models" version))
11652 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11654 `((upstream-name . "assertive.models")))
11655 (build-system r-build-system)
11657 `(("r-assertive-base" ,r-assertive-base)))
11658 (home-page "https://bitbucket.org/richierocks/assertive.models")
11659 (synopsis "Assertions to check properties of models")
11661 "This package provides a set of predicates and assertions for checking
11662 the properties of models. This is mainly for use by other package developers
11663 who want to include run-time testing features in their own packages.")
11664 (license license:gpl3+)))
11666 (define-public r-assertive-reflection
11668 (name "r-assertive-reflection")
11673 (uri (cran-uri "assertive.reflection" version))
11676 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11678 `((upstream-name . "assertive.reflection")))
11679 (build-system r-build-system)
11681 `(("r-assertive-base" ,r-assertive-base)))
11682 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11683 (synopsis "Assertions for checking the state of R")
11685 "This package provides a set of predicates and assertions for checking
11686 the state and capabilities of R, the operating system it is running on, and
11687 the IDE being used. This is mainly for use by other package developers who
11688 want to include run-time testing features in their own packages.")
11689 (license license:gpl3+)))
11691 (define-public r-assertive-types
11693 (name "r-assertive-types")
11698 (uri (cran-uri "assertive.types" version))
11701 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11703 `((upstream-name . "assertive.types")))
11704 (build-system r-build-system)
11706 `(("r-assertive-base" ,r-assertive-base)
11707 ("r-assertive-properties" ,r-assertive-properties)
11708 ("r-codetools" ,r-codetools)))
11709 (home-page "https://bitbucket.org/richierocks/assertive.types")
11710 (synopsis "Assertions to check types of variables")
11712 "This package provides a set of predicates and assertions for checking
11713 the types of variables. This is mainly for use by other package developers
11714 who want to include run-time testing features in their own packages.")
11715 (license license:gpl3+)))
11717 (define-public r-assertive-files
11719 (name "r-assertive-files")
11724 (uri (cran-uri "assertive.files" version))
11727 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11729 `((upstream-name . "assertive.files")))
11730 (build-system r-build-system)
11732 `(("r-assertive-base" ,r-assertive-base)
11733 ("r-assertive-numbers" ,r-assertive-numbers)))
11734 (home-page "https://bitbucket.org/richierocks/assertive.files")
11735 (synopsis "Assertions to check properties of files")
11737 "This package provides a set of predicates and assertions for checking
11738 the properties of files and connections. This is mainly for use by other
11739 package developers who want to include run-time testing features in their own
11741 (license license:gpl3+)))
11743 (define-public r-assertive-code
11745 (name "r-assertive-code")
11750 (uri (cran-uri "assertive.code" version))
11753 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11755 `((upstream-name . "assertive.code")))
11756 (build-system r-build-system)
11758 `(("r-assertive-base" ,r-assertive-base)
11759 ("r-assertive-properties" ,r-assertive-properties)
11760 ("r-assertive-types" ,r-assertive-types)))
11761 (home-page "https://bitbucket.org/richierocks/assertive.code")
11762 (synopsis "Assertions to check properties of code")
11764 "This package provides a set of predicates and assertions for checking
11765 the properties of code. This is mainly for use by other package developers
11766 who want to include run-time testing features in their own packages.")
11767 (license license:gpl3+)))
11769 (define-public r-assertive-datetimes
11771 (name "r-assertive-datetimes")
11776 (uri (cran-uri "assertive.datetimes" version))
11779 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11781 `((upstream-name . "assertive.datetimes")))
11782 (build-system r-build-system)
11784 `(("r-assertive-base" ,r-assertive-base)
11785 ("r-assertive-types" ,r-assertive-types)))
11786 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11787 (synopsis "Assertions to check properties of dates and times")
11789 "This package provides a set of predicates and assertions for checking
11790 the properties of dates and times. This is mainly for use by other package
11791 developers who want to include run-time testing features in their own
11793 (license license:gpl3+)))
11795 (define-public r-assertive-strings
11797 (name "r-assertive-strings")
11802 (uri (cran-uri "assertive.strings" version))
11805 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11807 `((upstream-name . "assertive.strings")))
11808 (build-system r-build-system)
11810 `(("r-assertive-base" ,r-assertive-base)
11811 ("r-assertive-types" ,r-assertive-types)
11812 ("r-stringi" ,r-stringi)))
11813 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11814 (synopsis "Assertions to check properties of strings")
11816 "This package provides a set of predicates and assertions for checking
11817 the properties of strings. This is mainly for use by other package developers
11818 who want to include run-time testing features in their own packages.")
11819 (license license:gpl3+)))
11821 (define-public r-assertive-data-us
11823 (name "r-assertive-data-us")
11828 (uri (cran-uri "assertive.data.us" version))
11831 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11833 `((upstream-name . "assertive.data.us")))
11834 (build-system r-build-system)
11836 `(("r-assertive-base" ,r-assertive-base)
11837 ("r-assertive-strings" ,r-assertive-strings)))
11838 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11839 (synopsis "Assertions to check properties of strings")
11841 "This package provides a set of predicates and assertions for checking
11842 the properties of US-specific complex data types. This is mainly for use by
11843 other package developers who want to include run-time testing features in
11844 their own packages.")
11845 (license license:gpl3+)))
11847 (define-public r-assertive-data-uk
11849 (name "r-assertive-data-uk")
11854 (uri (cran-uri "assertive.data.uk" version))
11857 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11859 `((upstream-name . "assertive.data.uk")))
11860 (build-system r-build-system)
11862 `(("r-assertive-base" ,r-assertive-base)
11863 ("r-assertive-strings" ,r-assertive-strings)))
11864 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11865 (synopsis "Assertions to check properties of strings")
11867 "This package provides a set of predicates and assertions for checking
11868 the properties of UK-specific complex data types. This is mainly for use by
11869 other package developers who want to include run-time testing features in
11870 their own packages.")
11871 (license license:gpl3+)))
11873 (define-public r-assertive-data
11875 (name "r-assertive-data")
11880 (uri (cran-uri "assertive.data" version))
11883 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11885 `((upstream-name . "assertive.data")))
11886 (build-system r-build-system)
11888 `(("r-assertive-base" ,r-assertive-base)
11889 ("r-assertive-strings" ,r-assertive-strings)))
11890 (home-page "https://bitbucket.org/richierocks/assertive.data")
11891 (synopsis "Assertions to check properties of data")
11893 "This package provides a set of predicates and assertions for checking
11894 the properties of (country independent) complex data types. This is mainly
11895 for use by other package developers who want to include run-time testing
11896 features in their own packages.")
11897 (license license:gpl3+)))
11899 (define-public r-assertive
11901 (name "r-assertive")
11906 (uri (cran-uri "assertive" version))
11909 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11910 (build-system r-build-system)
11912 `(("r-assertive-base" ,r-assertive-base)
11913 ("r-assertive-code" ,r-assertive-code)
11914 ("r-assertive-data" ,r-assertive-data)
11915 ("r-assertive-data-uk" ,r-assertive-data-uk)
11916 ("r-assertive-data-us" ,r-assertive-data-us)
11917 ("r-assertive-datetimes" ,r-assertive-datetimes)
11918 ("r-assertive-files" ,r-assertive-files)
11919 ("r-assertive-matrices" ,r-assertive-matrices)
11920 ("r-assertive-models" ,r-assertive-models)
11921 ("r-assertive-numbers" ,r-assertive-numbers)
11922 ("r-assertive-properties" ,r-assertive-properties)
11923 ("r-assertive-reflection" ,r-assertive-reflection)
11924 ("r-assertive-sets" ,r-assertive-sets)
11925 ("r-assertive-strings" ,r-assertive-strings)
11926 ("r-assertive-types" ,r-assertive-types)
11927 ("r-knitr" ,r-knitr)))
11929 `(("r-knitr" ,r-knitr)))
11930 (home-page "https://bitbucket.org/richierocks/assertive")
11931 (synopsis "Readable check functions to ensure code integrity")
11933 "This package provides lots of predicates (@code{is_*} functions) to
11934 check the state of your variables, and assertions (@code{assert_*} functions)
11935 to throw errors if they aren't in the right form.")
11936 (license license:gpl3+)))
11938 (define-public r-dotcall64
11940 (name "r-dotcall64")
11945 (uri (cran-uri "dotCall64" version))
11948 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11949 (properties `((upstream-name . "dotCall64")))
11950 (build-system r-build-system)
11951 (native-inputs `(("gfortran" ,gfortran)))
11952 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11953 (synopsis "Enhanced foreign function interface supporting long vectors")
11955 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11956 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11957 supports long vectors, arguments of type 64-bit integer, and provides a
11958 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11959 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11960 (license license:gpl2+)))
11962 (define-public r-spam
11969 (uri (cran-uri "spam" version))
11971 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11972 (build-system r-build-system)
11974 `(("r-dotcall64" ,r-dotcall64)))
11975 (native-inputs `(("gfortran" ,gfortran)))
11976 (home-page "https://www.math.uzh.ch/pages/spam/")
11977 (synopsis "Sparse matrix algebra")
11979 "This package provides a set of functions for sparse matrix algebra.
11980 Differences with other sparse matrix packages are:
11983 @item it only supports (essentially) one sparse matrix format;
11984 @item it is based on transparent and simple structure(s);
11985 @item it is tailored for MCMC calculations within G(M)RF;
11986 @item and it is fast and scalable (with the extension package @code{spam64}).
11988 ;; Either of these licenses
11989 (license (list license:bsd-3 license:lgpl2.0))))
11991 (define-public r-fields
11998 (uri (cran-uri "fields" version))
12000 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
12001 (build-system r-build-system)
12003 `(("r-maps" ,r-maps)
12004 ("r-spam" ,r-spam)))
12006 `(("gfortran" ,gfortran)))
12007 (home-page "https://www.image.ucar.edu/fields")
12008 (synopsis "Tools for spatial data")
12010 "This is a package for curve, surface and function fitting with an
12011 emphasis on splines, spatial data and spatial statistics. The major methods
12012 include cubic, and thin plate splines, Kriging, and compactly supported
12013 covariance functions for large data sets.")
12014 (license license:gpl2+)))
12016 (define-public r-spatialextremes
12018 (name "r-spatialextremes")
12023 (uri (cran-uri "SpatialExtremes" version))
12026 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
12028 `((upstream-name . "SpatialExtremes")))
12029 (build-system r-build-system)
12031 `(("r-fields" ,r-fields)
12032 ("r-maps" ,r-maps)))
12033 (home-page "http://spatialextremes.r-forge.r-project.org/")
12034 (synopsis "Modelling spatial extremes")
12036 "This package provides tools for the statistical modelling of spatial
12037 extremes using max-stable processes, copula or Bayesian hierarchical models.
12038 More precisely, this package allows (conditional) simulations from various
12039 parametric max-stable models, analysis of the extremal spatial dependence, the
12040 fitting of such processes using composite likelihoods or least square (simple
12041 max-stable processes only), model checking and selection and prediction.")
12042 (license license:gpl2+)))
12044 (define-public r-drc
12051 (uri (cran-uri "drc" version))
12054 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
12055 (build-system r-build-system)
12058 ("r-gtools" ,r-gtools)
12060 ("r-multcomp" ,r-multcomp)
12061 ("r-plotrix" ,r-plotrix)
12062 ("r-scales" ,r-scales)))
12063 (home-page "https://cran.r-project.org/web/packages/drc")
12064 (synopsis "Analysis of dose-response curves")
12066 "This package provides a suite of flexible and versatile model fitting
12067 and after-fitting functions for the analysis of dose-response data.")
12068 (license license:gpl2+)))
12070 (define-public r-rmeta
12077 (uri (cran-uri "rmeta" version))
12080 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12081 (build-system r-build-system)
12082 (home-page "https://cran.r-project.org/web/packages/rmeta")
12083 (synopsis "Tools for meta-analysis")
12085 "This package provides functions for simple fixed and random effects
12086 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12087 draws standard summary plots, funnel plots, and computes summaries and tests
12088 for association and heterogeneity.")
12089 (license license:gpl2)))
12091 (define-public r-bootstrap
12093 (name "r-bootstrap")
12098 (uri (cran-uri "bootstrap" version))
12101 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
12102 (build-system r-build-system)
12103 (native-inputs `(("gfortran" ,gfortran)))
12104 (home-page "https://cran.r-project.org/web/packages/bootstrap")
12105 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
12107 "This package provides software and data for the book \"An Introduction
12108 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
12109 This package is primarily provided for projects already based on it, and for
12110 support of the book. New projects should preferentially use the recommended
12111 package \"boot\".")
12112 (license license:bsd-3)))
12114 (define-public r-survivalroc
12116 (name "r-survivalroc")
12121 (uri (cran-uri "survivalROC" version))
12124 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
12125 (properties `((upstream-name . "survivalROC")))
12126 (build-system r-build-system)
12127 (home-page "https://cran.r-project.org/web/packages/survivalROC")
12128 (synopsis "Time-dependent ROC curve estimation from censored survival data")
12130 "Compute time-dependent ROC curve from censored survival data using
12131 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
12132 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
12133 (license license:gpl2+)))
12135 (define-public r-longitudinal
12137 (name "r-longitudinal")
12142 (uri (cran-uri "longitudinal" version))
12145 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
12146 (build-system r-build-system)
12147 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
12148 (home-page "http://strimmerlab.org/software/longitudinal/")
12149 (synopsis "Analysis of multiple time course data")
12151 "This package contains general data structures and functions for
12152 longitudinal data with multiple variables, repeated measurements, and
12153 irregularly spaced time points. It also implements a shrinkage estimator of
12154 dynamical correlation and dynamical covariance.")
12155 (license license:gpl3+)))
12157 (define-public r-genenet
12164 (uri (cran-uri "GeneNet" version))
12167 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
12168 (properties `((upstream-name . "GeneNet")))
12169 (build-system r-build-system)
12171 `(("r-corpcor" ,r-corpcor)
12172 ("r-fdrtool" ,r-fdrtool)
12173 ("r-longitudinal" ,r-longitudinal)))
12174 (home-page "http://strimmerlab.org/software/genenet/")
12175 (synopsis "Modeling and inferring gene networks")
12177 "This package analyzes gene expression (time series) data with focus on
12178 the inference of gene networks. In particular, GeneNet implements the methods
12179 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
12180 for learning large-scale gene association networks (including assignment of
12181 putative directions).")
12182 (license license:gpl3+)))
12184 (define-public r-rbamtools
12186 (name "r-rbamtools")
12187 (version "2.16.17")
12191 (uri (cran-uri "rbamtools" version))
12194 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
12195 (build-system r-build-system)
12196 (inputs `(("zlib" ,zlib)))
12198 `(("r-refgenome" ,r-refgenome)))
12199 (home-page "https://cran.r-project.org/web/packages/rbamtools")
12200 (synopsis "Read and write BAM (binary alignment) files")
12202 "This package provides an R interface to functions of the SAMtools
12204 (license license:artistic2.0)))
12206 (define-public r-protviz
12213 (uri (cran-uri "protViz" version))
12216 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
12217 (properties `((upstream-name . "protViz")))
12218 (build-system r-build-system)
12219 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12220 (home-page "https://github.com/protViz/protViz/")
12221 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
12223 "This package helps with quality checks, visualizations and analysis of
12224 mass spectrometry data, coming from proteomics experiments. The package is
12225 developed, tested and used at the Functional Genomics Center Zurich, where it
12226 is used mainly for prototyping, teaching, and having fun with proteomics data.
12227 But it can also be used to do data analysis for small scale data sets.")
12228 (license license:gpl3)))
12230 (define-public r-cmprsk
12237 (uri (cran-uri "cmprsk" version))
12239 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
12240 (build-system r-build-system)
12242 `(("r-survival" ,r-survival)))
12244 `(("gfortran" ,gfortran)))
12245 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12246 (synopsis "Subdistribution analysis of competing risks")
12248 "This package provides tool for estimation, testing and regression
12249 modeling of subdistribution functions in competing risks, as described in
12250 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12251 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12252 A proportional hazards model for the subdistribution of a competing risk,
12253 JASA, 94:496-509.")
12254 (license license:gpl2+)))
12256 (define-public r-etm
12263 (uri (cran-uri "etm" version))
12266 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
12267 (build-system r-build-system)
12269 `(("r-data-table" ,r-data-table)
12270 ("r-lattice" ,r-lattice)
12272 ("r-rcpparmadillo" ,r-rcpparmadillo)
12273 ("r-survival" ,r-survival)))
12274 (home-page "https://cran.r-project.org/web/packages/etm")
12275 (synopsis "Empirical transition matrix")
12277 "The @dfn{empirical transition matrix} (etm) package estimates
12278 the matrix of transition probabilities for any time-inhomogeneous multistate
12279 model with finite state space using the Aalen-Johansen estimator.")
12280 (license license:expat)))
12282 (define-public r-epi
12289 (uri (cran-uri "Epi" version))
12292 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12293 (properties `((upstream-name . "Epi")))
12294 (build-system r-build-system)
12296 `(("r-cmprsk" ,r-cmprsk)
12297 ("r-data-table" ,r-data-table)
12300 ("r-matrix" ,r-matrix)
12302 ("r-numderiv" ,r-numderiv)
12304 ("r-survival" ,r-survival)
12306 (home-page "https://BendixCarstensen.com/Epi/")
12307 (synopsis "Statistical analysis in epidemiology")
12309 "This package provides functions for demographic and epidemiological
12310 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12311 particular representation, manipulation and simulation of multistate data -
12312 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12313 @code{etm} and @code{cmprsk} packages. It also contains functions for
12314 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12315 data and some useful functions for tabulation and plotting, as well as a
12316 number of epidemiological data sets.")
12317 (license license:gpl2)))
12319 (define-public r-ppls
12322 (version "1.6-1.1")
12326 (uri (cran-uri "ppls" version))
12329 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12330 (build-system r-build-system)
12331 (propagated-inputs `(("r-mass" ,r-mass)))
12332 (home-page "https://cran.r-project.org/web/packages/ppls")
12333 (synopsis "Penalized partial least squares")
12335 "This package contains linear and nonlinear regression methods based on
12336 partial least squares and penalization techniques. Model parameters are
12337 selected via cross-validation, and confidence intervals ans tests for the
12338 regression coefficients can be conducted via jackknifing.")
12339 (license license:gpl2+)))
12341 (define-public r-huge
12344 (version "1.3.4.1")
12348 (uri (cran-uri "huge" version))
12350 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12351 (build-system r-build-system)
12353 `(("r-igraph" ,r-igraph)
12355 ("r-matrix" ,r-matrix)
12357 ("r-rcppeigen" ,r-rcppeigen)))
12358 (home-page "https://cran.r-project.org/web/packages/huge")
12359 (synopsis "High-dimensional undirected graph estimation")
12361 "This package provides a general framework for high-dimensional
12362 undirected graph estimation. It integrates data preprocessing, neighborhood
12363 screening, graph estimation, and model selection techniques into a pipeline.")
12364 (license license:gpl2)))
12366 (define-public r-parcor
12373 (uri (cran-uri "parcor" version))
12376 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12377 (build-system r-build-system)
12380 ("r-genenet" ,r-genenet)
12381 ("r-glmnet" ,r-glmnet)
12383 ("r-ppls" ,r-ppls)))
12384 (home-page "https://cran.r-project.org/web/packages/parcor")
12385 (synopsis "Regularized estimation of partial correlation matrices")
12387 "This package estimates the matrix of partial correlations based on
12388 different regularized regression methods: lasso, adaptive lasso, PLS, and
12389 Ridge Regression. In addition, the package provides model selection for
12390 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12391 (license license:gpl2+)))
12393 (define-public r-mcmc
12400 (uri (cran-uri "mcmc" version))
12403 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12404 (build-system r-build-system)
12405 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12406 (synopsis "Markov chain Monte Carlo")
12408 "This package simulates continuous distributions of random vectors using
12409 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12410 function that evaluates the log unnormalized density. Algorithms are random
12411 walk Metropolis algorithm (function @code{metrop}), simulated
12412 tempering (function @code{temper}), and morphometric random walk
12413 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12414 by change of variable.")
12415 (license license:expat)))
12417 (define-public r-listenv
12424 (uri (cran-uri "listenv" version))
12427 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12428 (build-system r-build-system)
12430 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12431 (home-page "https://github.com/HenrikBengtsson/listenv")
12432 (synopsis "Environments behaving (almost) as lists")
12434 "This package implements list environments. List environments are
12435 environments that have list-like properties. For instance, the elements of a
12436 list environment are ordered and can be accessed and iterated over using index
12438 (license license:lgpl2.1+)))
12440 (define-public r-globals
12447 (uri (cran-uri "globals" version))
12450 "1ch9m7fxclfhfa38b743wcm7w1bkx9kmivc6l7phpbgs6h9jhrcc"))))
12451 (build-system r-build-system)
12453 `(("r-codetools" ,r-codetools)))
12454 (home-page "https://github.com/HenrikBengtsson/globals")
12455 (synopsis "Identify global objects in R expressions")
12457 "This package provides tools to identify global (\"unknown\" or \"free\")
12458 objects in R expressions by code inspection using various strategies, e.g.
12459 conservative or liberal. The objective of this package is to make it as
12460 simple as possible to identify global objects for the purpose of exporting
12461 them in distributed compute environments.")
12462 (license license:lgpl2.1+)))
12464 (define-public r-future
12471 (uri (cran-uri "future" version))
12474 "12f483h7g172ygafbg7h43vykv0f7xz9miwqf5q8dyv7gpgqi5fl"))))
12475 (build-system r-build-system)
12477 `(("r-digest" ,r-digest)
12478 ("r-globals" ,r-globals)
12479 ("r-listenv" ,r-listenv)))
12481 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12482 (home-page "https://github.com/HenrikBengtsson/future")
12483 (synopsis "Unified parallel and distributed processing in R")
12485 "The purpose of this package is to provide a lightweight and unified
12486 Future API for sequential and parallel processing of R expression via futures.
12487 This package implements sequential, multicore, multisession, and cluster
12488 futures. With these, R expressions can be evaluated on the local machine, in
12489 parallel a set of local machines, or distributed on a mix of local and remote
12490 machines. Extensions to this package implement additional backends for
12491 processing futures via compute cluster schedulers etc. Because of its unified
12492 API, there is no need to modify any code in order to switch from sequential on
12493 the local machine to, say, distributed processing on a remote compute cluster.")
12494 (license license:lgpl2.1+)))
12496 (define-public r-future-apply
12498 (name "r-future-apply")
12503 (uri (cran-uri "future.apply" version))
12506 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12507 (properties `((upstream-name . "future.apply")))
12508 (build-system r-build-system)
12510 `(("r-future" ,r-future)
12511 ("r-globals" ,r-globals)))
12513 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12514 (home-page "https://github.com/HenrikBengtsson/future.apply")
12515 (synopsis "Apply function to elements in parallel using futures")
12517 "This package provides implementations of @code{apply()},
12518 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12519 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12520 can be resolved using any future-supported backend, e.g. parallel on the local
12521 machine or distributed on a compute cluster.")
12522 (license license:gpl2+)))
12524 (define-public r-rsvd
12531 (uri (cran-uri "rsvd" version))
12534 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12535 (build-system r-build-system)
12537 `(("r-matrix" ,r-matrix)))
12538 (home-page "https://github.com/erichson/rSVD")
12539 (synopsis "Randomized singular value decomposition")
12541 "Low-rank matrix decompositions are fundamental tools and widely used for
12542 data analysis, dimension reduction, and data compression. Classically, highly
12543 accurate deterministic matrix algorithms are used for this task. However, the
12544 emergence of large-scale data has severely challenged our computational
12545 ability to analyze big data. The concept of randomness has been demonstrated
12546 as an effective strategy to quickly produce approximate answers to familiar
12547 problems such as the @dfn{singular value decomposition} (SVD). This package
12548 provides several randomized matrix algorithms such as the randomized singular
12549 value decomposition (@code{rsvd}), randomized principal component
12550 analysis (@code{rpca}), randomized robust principal component
12551 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12552 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12553 functions are provided.")
12554 (license license:gpl3+)))
12556 (define-public r-sloop
12563 (uri (cran-uri "sloop" version))
12566 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12567 (build-system r-build-system)
12569 `(("r-codetools" ,r-codetools)
12570 ("r-crayon" ,r-crayon)
12571 ("r-purrr" ,r-purrr)
12572 ("r-rlang" ,r-rlang)
12573 ("r-tibble" ,r-tibble)))
12574 (home-page "https://github.com/r-lib/sloop")
12575 (synopsis "Helpers for object-oriented programming in R")
12577 "This package provides a collection of helper functions designed to
12578 help you to better understand object oriented programming in R, particularly
12580 (license license:gpl3)))
12582 (define-public r-capushe
12589 (uri (cran-uri "capushe" version))
12592 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12593 (build-system r-build-system)
12594 (propagated-inputs `(("r-mass" ,r-mass)))
12595 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12596 (synopsis "Calibrating penalties using slope heuristics")
12598 "This package provides tools for the calibration of penalized criteria
12599 for model selection. The calibration methods available are based on the slope
12601 (license license:gpl2+)))
12603 (define-public r-dorng
12610 (uri (cran-uri "doRNG" version))
12613 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12614 (properties `((upstream-name . "doRNG")))
12615 (build-system r-build-system)
12617 `(("r-foreach" ,r-foreach)
12618 ("r-iterators" ,r-iterators)
12619 ("r-rngtools" ,r-rngtools)))
12620 (home-page "https://renozao.github.io/doRNG/")
12621 (synopsis "Generic reproducible parallel backend for foreach loops")
12623 "This package provides functions to perform reproducible parallel
12624 @code{foreach} loops, using independent random streams as generated by
12625 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12626 convert standard @code{%dopar%} loops into fully reproducible loops,
12627 independently of the number of workers, the task scheduling strategy, or the
12628 chosen parallel environment and associated foreach backend.")
12629 (license license:gpl2+)))
12631 (define-public r-blockmodeling
12633 (name "r-blockmodeling")
12638 (uri (cran-uri "blockmodeling" version))
12641 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12642 (build-system r-build-system)
12644 `(("r-matrix" ,r-matrix)))
12645 (native-inputs `(("gfortran" ,gfortran)))
12646 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12647 (synopsis "Generalized and classical blockmodeling of valued networks")
12649 "This package is primarily meant as an implementation of generalized
12650 blockmodeling for valued networks. In addition, measures of similarity or
12651 dissimilarity based on structural equivalence and regular equivalence (REGE
12652 algorithms) can be computed and partitioned matrices can be plotted.")
12653 (license license:gpl2+)))
12655 (define-public r-upsetr
12662 (uri (cran-uri "UpSetR" version))
12665 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12666 (properties `((upstream-name . "UpSetR")))
12667 (build-system r-build-system)
12669 `(("r-ggplot2" ,r-ggplot2)
12670 ("r-gridextra" ,r-gridextra)
12672 ("r-scales" ,r-scales)))
12673 (home-page "https://github.com/hms-dbmi/UpSetR")
12674 (synopsis "Visualize intersecting sets")
12676 "This package provides a more scalable alternative to Venn and Euler
12677 diagrams for visualizing intersecting sets. Create visualizations of
12678 intersecting sets using a novel matrix design, along with visualizations of
12679 several common set, element and attribute related tasks.")
12680 (license license:expat)))
12682 ;; This package includes a JavaScript file, which is not minified. When
12683 ;; upgrading please check that there are no new minified JavaScript files.
12684 (define-public r-shinybs
12691 (uri (cran-uri "shinyBS" version))
12694 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12695 (properties `((upstream-name . "shinyBS")))
12696 (build-system r-build-system)
12697 ;; The tests spawn Shiny browser apps. They cannot be run
12698 ;; non-interactively.
12699 (arguments '(#:tests? #f))
12701 `(("r-htmltools" ,r-htmltools)
12702 ("r-shiny" ,r-shiny)))
12703 (home-page "https://ebailey78.github.io/shinyBS/")
12704 (synopsis "Twitter Bootstrap components for Shiny")
12706 "This package adds additional Twitter Bootstrap components to Shiny.")
12707 (license license:gpl3)))
12709 (define-public r-outliers
12711 (name "r-outliers")
12716 (uri (cran-uri "outliers" version))
12719 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12720 (build-system r-build-system)
12721 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12722 (synopsis "Tests for outliers")
12724 "This package provides a collection of some tests commonly used for
12725 identifying outliers.")
12726 (license license:gpl2+)))
12728 (define-public r-bayesm
12735 (uri (cran-uri "bayesm" version))
12737 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12738 (build-system r-build-system)
12740 `(("r-rcpp" ,r-rcpp)
12741 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12742 (home-page "http://www.perossi.org/home/bsm-1")
12743 (synopsis "Bayesian inference for marketing/micro-econometrics")
12745 "This package covers many important models used in marketing and
12746 micro-econometrics applications, including Bayes Regression (univariate or
12747 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12748 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12749 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12750 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12751 Estimation with normal base, Hierarchical Linear Models with normal prior and
12752 covariates, Hierarchical Linear Models with a mixture of normals prior and
12753 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12754 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12755 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12756 analysis of choice-based conjoint data, Bayesian treatment of linear
12757 instrumental variables models, Analysis of Multivariate Ordinal survey data
12758 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12759 Coefficient Logit Models.")
12760 (license license:gpl2+)))
12762 (define-public r-tensora
12769 (uri (cran-uri "tensorA" version))
12772 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12773 (properties `((upstream-name . "tensorA")))
12774 (build-system r-build-system)
12775 (home-page "http://www.stat.boogaart.de/tensorA")
12776 (synopsis "Advanced tensor arithmetic with named indices")
12778 "This package provides convenience functions for advanced linear algebra
12779 with tensors and computation with datasets of tensors on a higher level
12780 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12781 co- and contravariate indices, and parallel computations on sequences of
12783 (license license:gpl2+)))
12785 (define-public r-rarpack
12792 (uri (cran-uri "rARPACK" version))
12795 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12796 (properties `((upstream-name . "rARPACK")))
12797 (build-system r-build-system)
12798 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12799 (home-page "https://github.com/yixuan/rARPACK")
12800 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12802 "This package was previously an R wrapper of the ARPACK library, and now
12803 a shell of the R package RSpectra, an R interface to the Spectra library for
12804 solving large scale eigenvalue/vector problems. The current version of
12805 rARPACK simply imports and exports the functions provided by RSpectra. New
12806 users of rARPACK are advised to switch to the RSpectra package.")
12807 (license license:bsd-3)))
12809 (define-public r-compositions
12811 (name "r-compositions")
12816 (uri (cran-uri "compositions" version))
12819 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12820 (build-system r-build-system)
12822 `(("r-bayesm" ,r-bayesm)
12824 ("r-robustbase" ,r-robustbase)
12825 ("r-tensora" ,r-tensora)))
12827 `(("r-knitr" ,r-knitr)))
12828 (home-page "http://www.stat.boogaart.de/compositions")
12829 (synopsis "Compositional data analysis")
12831 "This package provides functions for the consistent analysis of
12832 compositional data (e.g. portions of substances) and positive
12833 numbers (e.g. concentrations).")
12834 (license license:gpl2+)))
12836 (define-public r-cobs
12843 (uri (cran-uri "cobs" version))
12846 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12847 (build-system r-build-system)
12849 `(("r-quantreg" ,r-quantreg)
12850 ("r-sparsem" ,r-sparsem)))
12851 (home-page "https://cran.r-project.org/web/packages/cobs")
12852 (synopsis "Constrained B-Splines (sparse matrix based)")
12854 "This package provides qualitatively constrained (regression) smoothing
12855 splines via linear programming and sparse matrices.")
12856 (license license:gpl2+)))
12858 (define-public r-drimpute
12860 (name "r-drimpute")
12865 (uri (cran-uri "DrImpute" version))
12868 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12869 (properties `((upstream-name . "DrImpute")))
12870 (build-system r-build-system)
12872 `(("r-rcpp" ,r-rcpp)
12873 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12874 (home-page "https://github.com/ikwak2/DrImpute")
12875 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12877 "This is an R package for imputing dropout events. Many statistical
12878 methods in cell type identification, visualization and lineage reconstruction
12879 do not account for dropout events. DrImpute can improve the performance of
12880 such software by imputing dropout events.")
12881 (license license:gpl3)))
12883 (define-public r-gamlss-dist
12885 (name "r-gamlss-dist")
12890 (uri (cran-uri "gamlss.dist" version))
12892 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12893 (properties `((upstream-name . "gamlss.dist")))
12894 (build-system r-build-system)
12895 (propagated-inputs `(("r-mass" ,r-mass)))
12896 (home-page "http://www.gamlss.org/")
12897 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12899 "This package provides a set of distributions which can be used for
12900 modelling the response variables in Generalized Additive Models for Location
12901 Scale and Shape. The distributions can be continuous, discrete or mixed
12902 distributions. Extra distributions can be created, by transforming, any
12903 continuous distribution defined on the real line, to a distribution defined on
12904 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12905 transformation, respectively.")
12906 ;; Either version of the GPL.
12907 (license (list license:gpl2 license:gpl3))))
12909 ;; This package includes JavaScript files, which are not minified. When
12910 ;; upgrading please check that there are no new minified JavaScript files.
12911 (define-public r-shinyjs
12918 (uri (cran-uri "shinyjs" version))
12921 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
12922 (build-system r-build-system)
12924 `(("r-digest" ,r-digest)
12925 ("r-htmltools" ,r-htmltools)
12926 ("r-jsonlite" ,r-jsonlite)
12927 ("r-shiny" ,r-shiny)))
12929 `(("r-knitr" ,r-knitr)))
12930 (home-page "https://deanattali.com/shinyjs")
12931 (synopsis "Improve the user experience of your Shiny apps")
12933 "Perform common useful JavaScript operations in Shiny apps that will
12934 greatly improve your apps without having to know any JavaScript. Examples
12935 include: hiding an element, disabling an input, resetting an input back to its
12936 original value, delaying code execution by a few seconds, and many more useful
12937 functions for both the end user and the developer. Shinyjs can also be used
12938 to easily call your own custom JavaScript functions from R.")
12939 (license license:agpl3+)))
12941 ;; This package includes minified JavaScript files. When upgrading please
12942 ;; check that there are no new minified JavaScript files.
12943 (define-public r-colourpicker
12945 (name "r-colourpicker")
12950 (uri (cran-uri "colourpicker" version))
12953 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
12954 (build-system r-build-system)
12956 `(#:modules ((guix build utils)
12957 (guix build r-build-system)
12961 (modify-phases %standard-phases
12962 (add-after 'unpack 'process-javascript
12963 (lambda* (#:key inputs #:allow-other-keys)
12964 (with-directory-excursion "inst"
12968 `((,(assoc-ref inputs "js-salvattore")
12969 "examples/colourInput/www/salvattore.min.js")
12970 (,(assoc-ref inputs "js-jquery")
12971 "htmlwidgets/lib/jquery/jquery.min.js")
12972 ("www/shared/colourpicker/js/colourpicker.js"
12973 "www/shared/colourpicker/js/colourpicker.min.js"))))
12974 (lambda (sources targets)
12975 (for-each (lambda (source target)
12976 (format #t "Processing ~a --> ~a~%"
12978 (delete-file target)
12979 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12980 (call-with-output-file target
12982 (dump-port minified port)))))
12983 sources targets))))
12986 `(("r-ggplot2" ,r-ggplot2)
12987 ("r-htmltools" ,r-htmltools)
12988 ("r-htmlwidgets" ,r-htmlwidgets)
12989 ("r-jsonlite" ,r-jsonlite)
12990 ("r-miniui" ,r-miniui)
12991 ("r-shiny" ,r-shiny)
12992 ("r-shinyjs" ,r-shinyjs)))
12994 `(("r-knitr" ,r-knitr)
12995 ("uglify-js" ,uglify-js)
12999 (uri "https://code.jquery.com/jquery-3.3.1.js")
13002 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
13006 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
13009 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
13010 (home-page "https://github.com/daattali/colourpicker")
13011 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
13013 "This package provides a color picker that can be used as an input in
13014 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
13015 custom color palettes, and many more options. A plot color helper tool is
13016 available as an RStudio Addin, which helps you pick colors to use in your
13017 plots. A more generic color picker RStudio Addin is also provided to let you
13018 select colors to use in your R code.")
13019 (license license:expat)))
13021 (define-public r-ggextra
13028 (uri (cran-uri "ggExtra" version))
13031 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
13032 (properties `((upstream-name . "ggExtra")))
13033 (build-system r-build-system)
13035 `(("r-colourpicker" ,r-colourpicker)
13036 ("r-ggplot2" ,r-ggplot2)
13037 ("r-gtable" ,r-gtable)
13038 ("r-miniui" ,r-miniui)
13040 ("r-scales" ,r-scales)
13041 ("r-shiny" ,r-shiny)
13042 ("r-shinyjs" ,r-shinyjs)))
13044 `(("r-knitr" ,r-knitr)))
13045 (home-page "https://github.com/daattali/ggExtra")
13046 (synopsis "Marginal histograms for ggplot2 and other enhancements")
13048 "This package is a collection of functions and layers to enhance ggplot2.
13049 The flagship function is @code{ggMarginal()}, which can be used to add
13050 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
13051 (license license:expat)))
13053 (define-public r-minpack-lm
13055 (name "r-minpack-lm")
13060 (uri (cran-uri "minpack.lm" version))
13063 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
13064 (properties `((upstream-name . "minpack.lm")))
13065 (build-system r-build-system)
13066 (native-inputs `(("gfortran" ,gfortran)))
13067 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
13068 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
13070 "The @code{nls.lm} function provides an R interface to @code{lmder} and
13071 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
13072 problems by a modification of the Levenberg-Marquardt algorithm, with support
13073 for lower and upper parameter bounds. The implementation can be used via
13074 @code{nls}-like calls using the @code{nlsLM} function.")
13075 (license license:gpl3)))
13077 (define-public r-moments
13084 (uri (cran-uri "moments" version))
13087 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
13088 (build-system r-build-system)
13089 (home-page "https://cran.r-project.org/web/packages/moments")
13090 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
13092 "This package provides functions to calculate: moments, Pearson's
13093 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
13094 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
13095 (license license:gpl2+)))
13097 (define-public r-msir
13104 (uri (cran-uri "msir" version))
13107 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
13108 (build-system r-build-system)
13110 `(("r-mclust" ,r-mclust)))
13111 (home-page "https://cran.r-project.org/web/packages/msir")
13112 (synopsis "Model-based sliced inverse regression")
13114 "This is an R package for dimension reduction based on finite Gaussian
13115 mixture modeling of inverse regression.")
13116 (license license:gpl2+)))
13118 (define-public r-pbivnorm
13120 (name "r-pbivnorm")
13125 (uri (cran-uri "pbivnorm" version))
13128 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
13129 (build-system r-build-system)
13130 (native-inputs `(("gfortran" ,gfortran)))
13131 (home-page "https://github.com/brentonk/pbivnorm")
13132 (synopsis "Vectorized bivariate normal CDF")
13134 "This package provides a vectorized R function for calculating
13135 probabilities from a standard bivariate normal CDF.")
13136 (license license:gpl2+)))
13138 (define-public r-lavaan
13145 (uri (cran-uri "lavaan" version))
13148 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
13149 (build-system r-build-system)
13151 `(("r-mass" ,r-mass)
13152 ("r-mnormt" ,r-mnormt)
13153 ("r-numderiv" ,r-numderiv)
13154 ("r-pbivnorm" ,r-pbivnorm)))
13155 (home-page "http://lavaan.ugent.be")
13156 (synopsis "Latent variable analysis")
13158 "This package provides tools to fit a variety of latent variable models,
13159 including confirmatory factor analysis, structural equation modeling and
13160 latent growth curve models.")
13161 (license license:gpl2+)))
13163 (define-public r-nonnest2
13165 (name "r-nonnest2")
13170 (uri (cran-uri "nonnest2" version))
13173 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
13174 (build-system r-build-system)
13176 `(("r-compquadform" ,r-compquadform)
13177 ("r-lavaan" ,r-lavaan)
13178 ("r-mvtnorm" ,r-mvtnorm)
13179 ("r-sandwich" ,r-sandwich)))
13181 `(("r-knitr" ,r-knitr)))
13182 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
13183 (synopsis "Tests of non-nested models")
13185 "This package allows for testing of non-nested models. It includes tests
13186 of model distinguishability and of model fit that can be applied to both
13187 nested and non-nested models. The package also includes functionality to
13188 obtain confidence intervals associated with AIC and BIC.")
13189 ;; Either version of the GPL.
13190 (license (list license:gpl2 license:gpl3))))
13192 (define-public r-penalized
13194 (name "r-penalized")
13199 (uri (cran-uri "penalized" version))
13202 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
13203 (build-system r-build-system)
13205 `(("r-rcpp" ,r-rcpp)
13206 ("r-rcpparmadillo" ,r-rcpparmadillo)
13207 ("r-survival" ,r-survival)))
13208 (home-page "https://cran.r-project.org/web/packages/penalized/")
13209 (synopsis "Penalized estimation in GLMs and in the Cox model")
13211 "This package provides tools for fitting possibly high dimensional
13212 penalized regression models. The penalty structure can be any combination of
13213 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
13214 constraint on the regression coefficients. The supported regression models
13215 are linear, logistic and Poisson regression and the Cox Proportional Hazards
13216 model. Cross-validation routines allow optimization of the tuning
13218 (license license:gpl2+)))
13220 (define-public r-zim
13227 (uri (cran-uri "ZIM" version))
13230 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
13231 (properties `((upstream-name . "ZIM")))
13232 (build-system r-build-system)
13233 (propagated-inputs `(("r-mass" ,r-mass)))
13234 (home-page "https://github.com/biostatstudio/ZIM")
13235 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
13237 "Analyze count time series with excess zeros. Two types of statistical
13238 models are supported: Markov regression and state-space models. They are also
13239 known as observation-driven and parameter-driven models respectively in the
13240 time series literature. The functions used for Markov regression or
13241 observation-driven models can also be used to fit ordinary regression models
13242 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
13243 negative binomial (ZINB) assumption. The package also contains miscellaneous
13244 functions to compute density, distribution, quantile, and generate random
13245 numbers from ZIP and ZINB distributions.")
13246 (license license:gpl3)))
13248 (define-public r-nor1mix
13255 (uri (cran-uri "nor1mix" version))
13258 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13259 (build-system r-build-system)
13260 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13261 (synopsis "Normal (1-d) mixture models")
13263 "This package provides S3 classes and methods for one-dimensional normal
13264 mixture models, for, e.g., density estimation or clustering algorithms
13265 research and teaching; it provides the widely used Marron-Wand densities. It
13266 also provides tools for efficient random number generation and graphics.")
13267 (license license:gpl2+)))
13269 (define-public r-beanplot
13271 (name "r-beanplot")
13276 (uri (cran-uri "beanplot" version))
13279 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13280 (build-system r-build-system)
13281 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13282 (synopsis "Visualization via beanplots")
13284 "This package provides beanplots, an alternative to
13285 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13287 (license license:gpl2)))
13289 (define-public r-pbdzmq
13292 (version "0.3-3.1")
13296 (uri (cran-uri "pbdZMQ" version))
13299 "08qmrzazadkyxlqc8830r0pckaq10l3fgj1f198xy6wwrm2lf0wy"))))
13300 (properties `((upstream-name . "pbdZMQ")))
13301 (build-system r-build-system)
13303 `(("zeromq" ,zeromq)
13306 `(("pkg-config" ,pkg-config)))
13307 (home-page "https://pbdr.org/")
13308 (synopsis "R interface to ZeroMQ")
13310 "ZeroMQ is a well-known library for high-performance asynchronous
13311 messaging in scalable, distributed applications. This package provides high
13312 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13313 interactive client/server programming frameworks. A few wrapper functions
13314 compatible with @code{rzmq} are also provided.")
13315 (license license:gpl3)))
13317 (define-public r-repr
13324 (uri (cran-uri "repr" version))
13327 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13328 (build-system r-build-system)
13330 `(("r-base64enc" ,r-base64enc)
13331 ("r-htmltools" ,r-htmltools)
13332 ("r-jsonlite" ,r-jsonlite)
13333 ("r-pillar" ,r-pillar)))
13334 (home-page "https://cran.r-project.org/web/packages/repr/")
13335 (synopsis "Serializable representations")
13337 "This package provides string and binary representations of objects for
13338 several formats and MIME types.")
13339 (license license:gpl3)))
13341 (define-public r-irdisplay
13343 (name "r-irdisplay")
13348 (uri (cran-uri "IRdisplay" version))
13351 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13352 (properties `((upstream-name . "IRdisplay")))
13353 (build-system r-build-system)
13355 `(("r-repr" ,r-repr)))
13356 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13357 (synopsis "Jupyter display machinery")
13359 "This package provides an interface to the rich display capabilities of
13360 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13361 running IRkernel session.")
13362 (license license:expat)))
13364 (define-public r-irkernel
13366 (name "r-irkernel")
13371 (uri (cran-uri "IRkernel" version))
13374 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13375 (properties `((upstream-name . "IRkernel")))
13376 (build-system r-build-system)
13379 (modify-phases %standard-phases
13380 (add-after 'install 'install-kernelspec
13381 (lambda* (#:key outputs #:allow-other-keys)
13382 (let ((out (assoc-ref outputs "out")))
13383 (setenv "HOME" "/tmp")
13384 (invoke "jupyter" "kernelspec" "install"
13387 (string-append out "/site-library/IRkernel/kernelspec"))
13388 ;; Record the absolute file name of the 'R' executable in
13390 (substitute* (string-append out "/share/jupyter"
13391 "/kernels/ir/kernel.json")
13393 (string-append "[\"" (which "R") "\",")))
13396 `(("jupyter" ,jupyter)))
13398 `(("r-crayon" ,r-crayon)
13399 ("r-digest" ,r-digest)
13400 ("r-evaluate" ,r-evaluate)
13401 ("r-irdisplay" ,r-irdisplay)
13402 ("r-jsonlite" ,r-jsonlite)
13403 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13404 ("r-minimal" ,r-minimal)
13405 ("r-pbdzmq" ,r-pbdzmq)
13407 ("r-uuid" ,r-uuid)))
13408 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13409 (synopsis "Native R kernel for Jupyter")
13411 "The R kernel for the Jupyter environment executes R code which the
13412 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13414 (license license:expat)))
13416 (define-public r-gmodels
13423 (uri (cran-uri "gmodels" version))
13426 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13427 (build-system r-build-system)
13429 `(("r-gdata" ,r-gdata)
13430 ("r-mass" ,r-mass)))
13431 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13432 (synopsis "Various R programming tools for model fitting")
13434 "This package provides various R programming tools for model fitting.")
13435 (license license:gpl2)))
13437 (define-public r-apcluster
13439 (name "r-apcluster")
13444 (uri (cran-uri "apcluster" version))
13447 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13448 (build-system r-build-system)
13450 `(("r-matrix" ,r-matrix)
13451 ("r-rcpp" ,r-rcpp)))
13452 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13453 (synopsis "Affinity propagation clustering")
13455 "This package implements affinity propagation clustering introduced by
13456 Frey and Dueck (2007). The package further provides leveraged affinity
13457 propagation and an algorithm for exemplar-based agglomerative clustering that
13458 can also be used to join clusters obtained from affinity propagation. Various
13459 plotting functions are available for analyzing clustering results.")
13460 (license license:gpl2+)))
13462 (define-public r-valr
13469 (uri (cran-uri "valr" version))
13472 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
13473 (build-system r-build-system)
13475 `(("r-broom" ,r-broom)
13476 ("r-dplyr" ,r-dplyr)
13477 ("r-ggplot2" ,r-ggplot2)
13479 ("r-readr" ,r-readr)
13480 ("r-rlang" ,r-rlang)
13481 ("r-stringr" ,r-stringr)
13482 ("r-tibble" ,r-tibble)))
13484 `(("r-knitr" ,r-knitr)))
13485 (home-page "https://github.com/rnabioco/valr")
13486 (synopsis "Genome interval arithmetic in R")
13488 "This package enables you to read and manipulate genome intervals and
13489 signals. It provides functionality similar to command-line tool suites within
13490 R, enabling interactive analysis and visualization of genome-scale data.")
13491 (license license:expat)))
13493 (define-public r-rematch2
13495 (name "r-rematch2")
13500 (uri (cran-uri "rematch2" version))
13503 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13504 (build-system r-build-system)
13506 `(("r-tibble" ,r-tibble)))
13507 (home-page "https://github.com/r-lib/rematch2")
13508 (synopsis "Tidy output from regular expression matching")
13510 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13511 return the match results in tidy data frames.")
13512 (license license:expat)))
13514 (define-public r-picante
13521 (uri (cran-uri "picante" version))
13524 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13525 (build-system r-build-system)
13529 ("r-vegan" ,r-vegan)))
13530 (home-page "https://cran.r-project.org/web/packages/picante/")
13531 (synopsis "Integrating phylogenies and ecology")
13533 "This package provides functions for phylocom integration, community
13534 analyses, null-models, traits and evolution. It implements numerous
13535 ecophylogenetic approaches including measures of community phylogenetic and
13536 trait diversity, phylogenetic signal, estimation of trait values for
13537 unobserved taxa, null models for community and phylogeny randomizations, and
13538 utility functions for data input/output and phylogeny plotting. A full
13539 description of package functionality and methods are provided by Kembel et
13541 (license license:gpl2)))
13543 (define-public r-reinforcelearn
13545 (name "r-reinforcelearn")
13550 (uri (cran-uri "reinforcelearn" version))
13553 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13554 (build-system r-build-system)
13556 `(("r-checkmate" ,r-checkmate)
13558 ("r-purrr" ,r-purrr)
13560 (home-page "https://markusdumke.github.io/reinforcelearn")
13561 (synopsis "Reinforcement learning")
13563 "This package implements reinforcement learning environments and
13564 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13565 can be used with function approximation, eligibility traces (Singh & Sutton,
13566 1996) and experience replay (Mnih et al., 2013).")
13567 (license license:expat)))
13569 (define-public r-lemon
13576 (uri (cran-uri "lemon" version))
13579 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13580 (build-system r-build-system)
13582 `(("r-ggplot2" ,r-ggplot2)
13583 ("r-gridextra" ,r-gridextra)
13584 ("r-gtable" ,r-gtable)
13585 ("r-knitr" ,r-knitr)
13586 ("r-lattice" ,r-lattice)
13588 ("r-rlang" ,r-rlang)
13589 ("r-scales" ,r-scales)))
13591 `(("r-knitr" ,r-knitr)))
13592 (home-page "https://github.com/stefanedwards/lemon")
13593 (synopsis "Freshen up your ggplot2 plots")
13595 "This package provides functions for working with legends and axis lines
13596 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13598 (license license:gpl3)))
13600 (define-public r-wgaim
13607 (uri (cran-uri "wgaim" version))
13609 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13610 (build-system r-build-system)
13612 `(("r-ggplot2" ,r-ggplot2)
13614 (home-page "https://cran.r-project.org/web/packages/wgaim")
13615 (synopsis "Whole genome average interval mapping for QTL detection")
13617 "This package integrates sophisticated mixed modelling methods with a
13618 whole genome approach to detecting significant QTL in linkage maps.")
13619 (license license:gpl2+)))
13621 (define-public r-bedr
13628 (uri (cran-uri "bedr" version))
13631 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13632 (build-system r-build-system)
13634 `(("r-data-table" ,r-data-table)
13635 ("r-r-utils" ,r-r-utils)
13636 ("r-testthat" ,r-testthat)
13637 ("r-venndiagram" ,r-venndiagram)
13640 ("bedtools" ,bedtools)
13641 ("htslib" ,htslib))) ; for tabix
13643 `(("r-knitr" ,r-knitr))) ; for vignettes
13644 (home-page "https://cran.r-project.org/web/packages/bedr")
13645 (synopsis "Genomic region processing")
13647 "This package is for genomic regions processing using command line tools
13648 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13649 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13650 The bedr package's API enhances access to these tools as well as offers
13651 additional utilities for genomic regions processing.")
13652 (license license:gpl2)))
13654 (define-public r-sets
13661 (uri (cran-uri "sets" version))
13664 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13665 (properties `((upstream-name . "sets")))
13666 (build-system r-build-system)
13667 (home-page "https://cran.r-project.org/web/packages/sets")
13668 (synopsis "Sets, generalized sets, customizable sets and intervals")
13670 "This package provides data structures and basic operations for ordinary
13671 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13672 customizable sets, and intervals.")
13673 (license license:gpl2)))
13675 (define-public r-partitions
13677 (name "r-partitions")
13682 (uri (cran-uri "partitions" version))
13685 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13686 (build-system r-build-system)
13689 ("r-polynom" ,r-polynom)
13690 ("r-sets" ,r-sets)))
13691 (home-page "https://cran.r-project.org/web/packages/partitions")
13692 (synopsis "Additive partitions of integers")
13694 "This package provides tools to enumerates the partitions, unequal
13695 partitions, and restricted partitions of an integer; the three corresponding
13696 partition functions are also given.")
13697 ;; Any version of the GPL
13698 (license license:gpl2+)))
13700 (define-public r-brobdingnag
13702 (name "r-brobdingnag")
13707 (uri (cran-uri "Brobdingnag" version))
13710 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13711 (properties `((upstream-name . "Brobdingnag")))
13712 (build-system r-build-system)
13713 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13714 (synopsis "Very large numbers in R")
13716 "This package handles very large numbers in R. Real numbers are held
13717 using their natural logarithms, plus a logical flag indicating sign. The
13718 package includes a vignette that gives a step-by-step introduction to using S4
13720 ;; Any version of the GPL
13721 (license license:gpl2+)))
13723 (define-public r-untb
13730 (uri (cran-uri "untb" version))
13733 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13734 (build-system r-build-system)
13736 `(("r-brobdingnag" ,r-brobdingnag)
13737 ("r-partitions" ,r-partitions)
13738 ("r-polynom" ,r-polynom)))
13739 (home-page "https://github.com/RobinHankin/untb.git")
13740 (synopsis "Ecological drift under the UNTB")
13742 "This package provides numerical simulations, and visualizations, of
13743 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13744 (license license:gpl2+)))
13746 (define-public r-stepwise
13748 (name "r-stepwise")
13753 (uri (cran-uri "stepwise" version))
13756 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13757 (build-system r-build-system)
13758 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13759 (synopsis "Stepwise detection of recombination breakpoints")
13761 "This package provides a stepwise approach to identifying recombination
13762 breakpoints in a genomic sequence alignment.")
13763 (license license:gpl2+)))
13765 (define-public r-snpmaxsel
13767 (name "r-snpmaxsel")
13772 (uri (cran-uri "SNPmaxsel" version))
13775 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13776 (properties `((upstream-name . "SNPmaxsel")))
13777 (build-system r-build-system)
13779 `(("r-combinat" ,r-combinat)
13780 ("r-mvtnorm" ,r-mvtnorm)))
13781 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13782 (synopsis "Maximally selected statistics for SNP data")
13784 "This package implements asymptotic methods related to maximally selected
13785 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13787 (license license:gpl2+)))
13789 (define-public r-acsnminer
13791 (name "r-acsnminer")
13792 (version "0.16.8.25")
13795 (uri (cran-uri "ACSNMineR" version))
13798 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13799 (properties `((upstream-name . "ACSNMineR")))
13800 (build-system r-build-system)
13802 `(("r-ggplot2" ,r-ggplot2)
13803 ("r-gridextra" ,r-gridextra)))
13804 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13805 (synopsis "Gene enrichment analysis")
13807 "This package provides tools to compute and represent gene set enrichment
13808 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13809 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13810 enrichment can be run with hypergeometric test or Fisher exact test, and can
13811 use multiple corrections. Visualization of data can be done either by
13812 barplots or heatmaps.")
13813 (license license:gpl2+)))
13815 (define-public r-seqinr
13822 (uri (cran-uri "seqinr" version))
13825 "0pw035h17dmic8m0pb73fbyf6p4jbwggxjk5vpjlybn8dwd0rk93"))))
13826 (build-system r-build-system)
13828 `(("r-ade4" ,r-ade4)
13829 ("r-segmented" ,r-segmented)))
13832 (home-page "http://seqinr.r-forge.r-project.org/")
13833 (synopsis "Biological sequences retrieval and analysis")
13835 "This package provides tools for exploratory data analysis and data
13836 visualization of biological sequence (DNA and protein) data. It also includes
13837 utilities for sequence data management under the ACNUC system.")
13838 (license license:gpl2+)))
13840 (define-public r-units
13847 (uri (cran-uri "units" version))
13850 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13851 (build-system r-build-system)
13853 `(("udunits" ,udunits)))
13855 `(("r-rcpp" ,r-rcpp)))
13857 `(("r-knitr" ,r-knitr)))
13858 (home-page "https://github.com/r-quantities/units/")
13859 (synopsis "Measurement Units for R Vectors")
13861 "This package provides support for measurement units in R vectors,
13862 matrices and arrays: automatic propagation, conversion, derivation and
13863 simplification of units; raising errors in case of unit incompatibility. It
13864 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13866 (license license:gpl2)))
13868 (define-public r-classint
13870 (name "r-classint")
13875 (uri (cran-uri "classInt" version))
13878 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13879 (properties `((upstream-name . "classInt")))
13880 (build-system r-build-system)
13882 `(("r-class" ,r-class)
13883 ("r-e1071" ,r-e1071)
13884 ("r-kernsmooth" ,r-kernsmooth)))
13886 `(("gfortran" ,gfortran)
13887 ("r-knitr" ,r-knitr)))
13888 (home-page "https://github.com/r-spatial/classInt/")
13889 (synopsis "Choose univariate class intervals")
13891 "This package provides selected commonly used methods for choosing
13892 univariate class intervals for mapping or other graphics purposes.")
13893 (license license:gpl2+)))
13895 (define-public r-spdata
13902 (uri (cran-uri "spData" version))
13905 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13906 (properties `((upstream-name . "spData")))
13907 (build-system r-build-system)
13909 `(("r-raster" ,r-raster)
13911 (home-page "https://github.com/Nowosad/spData")
13912 (synopsis "Datasets for spatial analysis")
13914 "This a package containing diverse spatial datasets for demonstrating,
13915 benchmarking and teaching spatial data analysis. It includes R data of class
13916 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13917 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13918 of the datasets are designed to illustrate specific analysis techniques.
13919 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13920 illustrate point pattern analysis techniques.")
13921 (license license:cc0)))
13923 (define-public r-learnbayes
13925 (name "r-learnbayes")
13930 (uri (cran-uri "LearnBayes" version))
13933 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13934 (properties `((upstream-name . "LearnBayes")))
13935 (build-system r-build-system)
13936 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13937 (synopsis "Functions for learning Bayesian inference")
13939 "This package provides a collection of functions helpful in learning the
13940 basic tenets of Bayesian statistical inference. It contains functions for
13941 summarizing basic one and two parameter posterior distributions and predictive
13942 distributions. It contains MCMC algorithms for summarizing posterior
13943 distributions defined by the user. It also contains functions for regression
13944 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13946 (license license:gpl2+)))
13948 (define-public r-deldir
13955 (uri (cran-uri "deldir" version))
13958 "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
13959 (build-system r-build-system)
13960 (native-inputs `(("gfortran" ,gfortran)))
13961 (home-page "https://cran.r-project.org/web/packages/deldir")
13962 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13964 "This package provides tools for calculating the Delaunay triangulation
13965 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13966 of a planar point set. It plots triangulations and tessellations in various
13967 ways, clips tessellations to sub-windows, calculates perimeters of
13968 tessellations, and summarizes information about the tiles of the
13970 (license license:gpl2+)))
13972 (define-public r-sf
13979 (uri (cran-uri "sf" version))
13982 "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9"))))
13983 (build-system r-build-system)
13991 `(("r-classint" ,r-classint)
13993 ("r-magrittr" ,r-magrittr)
13995 ("r-units" ,r-units)))
13997 `(("pkg-config" ,pkg-config)
13998 ("r-knitr" ,r-knitr)))
13999 (home-page "https://github.com/r-spatial/sf/")
14000 (synopsis "Simple features for R")
14002 "This package provides support for simple features, a standardized way to
14003 encode spatial vector data. It binds to GDAL for reading and writing data, to
14004 GEOS for geometrical operations, and to PROJ for projection conversions and
14005 datum transformations.")
14006 ;; Either of these licenses
14007 (license (list license:gpl2 license:expat))))
14009 (define-public r-spdep
14016 (uri (cran-uri "spdep" version))
14019 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
14020 (build-system r-build-system)
14022 `(("r-boot" ,r-boot)
14024 ("r-deldir" ,r-deldir)
14026 ("r-gmodels" ,r-gmodels)
14027 ("r-learnbayes" ,r-learnbayes)
14029 ("r-matrix" ,r-matrix)
14033 ("r-spdata" ,r-spdata)))
14035 `(("r-knitr" ,r-knitr)))
14036 (home-page "https://github.com/r-spatial/spdep/")
14037 (synopsis "Spatial dependence: weighting schemes, statistics and models")
14039 "This package provides a collection of functions to create spatial
14040 weights matrix objects from polygon contiguities, from point patterns by
14041 distance and tessellations, for summarizing these objects, and for permitting
14042 their use in spatial data analysis, including regional aggregation by minimum
14044 (license license:gpl2+)))
14046 (define-public r-adegenet
14048 (name "r-adegenet")
14053 (uri (cran-uri "adegenet" version))
14056 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
14057 (build-system r-build-system)
14059 `(("r-ade4" ,r-ade4)
14062 ("r-dplyr" ,r-dplyr)
14063 ("r-ggplot2" ,r-ggplot2)
14064 ("r-igraph" ,r-igraph)
14066 ("r-reshape2" ,r-reshape2)
14067 ("r-seqinr" ,r-seqinr)
14068 ("r-shiny" ,r-shiny)
14069 ("r-spdep" ,r-spdep)
14070 ("r-vegan" ,r-vegan)))
14071 (home-page "https://github.com/thibautjombart/adegenet")
14072 (synopsis "Exploratory analysis of genetic and genomic data")
14074 "This package provides a toolset for the exploration of genetic and
14075 genomic data. Adegenet provides formal (S4) classes for storing and handling
14076 various genetic data, including genetic markers with varying ploidy and
14077 hierarchical population structure (@code{genind} class), alleles counts by
14078 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
14079 also implements original multivariate methods (DAPC, sPCA), graphics,
14080 statistical tests, simulation tools, distance and similarity measures, and
14081 several spatial methods. A range of both empirical and simulated datasets is
14082 also provided to illustrate various methods.")
14083 (license license:gpl2+)))
14085 (define-public r-pegas
14092 (uri (cran-uri "pegas" version))
14094 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
14095 (build-system r-build-system)
14097 `(("r-adegenet" ,r-adegenet)
14099 (home-page "http://ape-package.ird.fr/pegas.html")
14100 (synopsis "Population and evolutionary genetics analysis system")
14102 "This package provides functions for reading, writing, plotting,
14103 analysing, and manipulating allelic and haplotypic data, including from VCF
14104 files, and for the analysis of population nucleotide sequences and
14105 micro-satellites including coalescent analyses, linkage disequilibrium,
14106 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
14107 minimum spanning tree and network, and median-joining networks.")
14108 (license license:gpl2+)))
14110 (define-public r-rmetasim
14112 (name "r-rmetasim")
14117 (uri (cran-uri "rmetasim" version))
14120 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
14121 (build-system r-build-system)
14123 `(("r-ade4" ,r-ade4)
14124 ("r-adegenet" ,r-adegenet)
14125 ("r-gtools" ,r-gtools)
14126 ("r-pegas" ,r-pegas)))
14127 (home-page "https://cran.r-project.org/web/packages/rmetasim")
14128 (synopsis "Individual-based population genetic simulation environment")
14130 "This package provides an interface between R and the metasim simulation
14131 engine. The simulation environment is documented in: Strand, A.(2002),
14132 Metasim 1.0: an individual-based environment for simulating population
14133 genetics of complex population dynamics.")
14135 (license license:gpl2+)))
14137 (define-public r-genetics
14139 (name "r-genetics")
14140 (version "1.3.8.1.2")
14144 (uri (cran-uri "genetics" version))
14147 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
14148 (build-system r-build-system)
14150 `(("r-combinat" ,r-combinat)
14151 ("r-gdata" ,r-gdata)
14152 ("r-gtools" ,r-gtools)
14154 ("r-mvtnorm" ,r-mvtnorm)))
14155 (home-page "https://cran.r-project.org/web/packages/genetics/")
14156 (synopsis "Population genetics")
14158 "This package provides classes and methods for handling genetic data.
14159 It includes classes to represent genotypes and haplotypes at single markers up
14160 to multiple markers on multiple chromosomes. Function include allele
14161 frequencies, flagging homo/heterozygotes, flagging carriers of certain
14162 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
14163 and testing for linkage disequilibrium, ...")
14164 ;; Any GPL version.
14165 (license license:gpl2+)))
14167 (define-public r-snp-plotter
14169 (name "r-snp-plotter")
14174 (uri (cran-uri "snp.plotter" version))
14177 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
14178 (properties `((upstream-name . "snp.plotter")))
14179 (build-system r-build-system)
14180 (propagated-inputs `(("r-genetics" ,r-genetics)))
14181 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
14182 (synopsis "Plot p-values using single SNP and/or haplotype data")
14184 "This package helps you create plots of p-values using single SNP and/or
14185 haplotype data. Main features of the package include options to display a
14186 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
14187 datasets simultaneously. Plots can be created using global and/or individual
14188 haplotype p-values along with single SNP p-values. Images are created as
14189 either PDF/EPS files.")
14190 (license license:gpl2+)))
14192 (define-public r-polspline
14194 (name "r-polspline")
14199 (uri (cran-uri "polspline" version))
14201 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
14202 (build-system r-build-system)
14203 (native-inputs `(("gfortran" ,gfortran)))
14204 (home-page "https://cran.r-project.org/web/packages/polspline/")
14205 (synopsis "Polynomial spline routines")
14207 "This package provides routines for the polynomial spline fitting
14208 routines hazard regression, hazard estimation with flexible tails, logspline,
14209 lspec, polyclass, and polymars.")
14210 (license license:gpl2+)))
14212 (define-public r-rms
14219 (uri (cran-uri "rms" version))
14221 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
14222 (build-system r-build-system)
14224 `(("r-cluster" ,r-cluster)
14225 ("r-digest" ,r-digest)
14226 ("r-ggplot2" ,r-ggplot2)
14227 ("r-hmisc" ,r-hmisc)
14228 ("r-htmltable" ,r-htmltable)
14229 ("r-htmltools" ,r-htmltools)
14230 ("r-lattice" ,r-lattice)
14232 ("r-multcomp" ,r-multcomp)
14234 ("r-polspline" ,r-polspline)
14235 ("r-quantreg" ,r-quantreg)
14236 ("r-rpart" ,r-rpart)
14237 ("r-sparsem" ,r-sparsem)
14238 ("r-survival" ,r-survival)))
14239 (native-inputs `(("gfortran" ,gfortran)))
14240 (home-page "http://biostat.mc.vanderbilt.edu/rms")
14241 (synopsis "Regression modeling strategies")
14243 "This is a package for regression modeling, testing, estimation,
14244 validation, graphics, prediction, and typesetting by storing enhanced model
14245 design attributes in the fit. The rms package is a collection of functions
14246 that assist with and streamline modeling. It also contains functions for
14247 binary and ordinal logistic regression models, ordinal models for continuous Y
14248 with a variety of distribution families, and the Buckley-James multiple
14249 regression model for right-censored responses, and implements penalized
14250 maximum likelihood estimation for logistic and ordinary linear models. The
14251 package works with almost any regression model, but it was especially written
14252 to work with binary or ordinal regression models, Cox regression, accelerated
14253 failure time models, ordinary linear models, the Buckley-James model,
14254 generalized least squares for serially or spatially correlated observations,
14255 generalized linear models, and quantile regression.")
14256 (license license:gpl2+)))
14258 (define-public r-arsenal
14265 (uri (cran-uri "arsenal" version))
14268 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14269 (properties `((upstream-name . "arsenal")))
14270 (build-system r-build-system)
14271 (propagated-inputs `(("r-knitr" ,r-knitr)))
14272 (native-inputs `(("r-knitr" ,r-knitr)))
14273 (home-page "https://github.com/mayoverse/arsenal")
14274 (synopsis "Functions for large-scale statistical summaries")
14276 "This package provides an arsenal of R functions for large-scale
14277 statistical summaries, which are streamlined to work within the latest
14278 reporting tools in R and RStudio and which use formulas and versatile
14279 summary statistics for summary tables and models. The primary functions
14283 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14284 levels of one or more categorical variables;
14285 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14286 across two time points;
14287 @item @code{modelsum}, which performs simple model fits on one or more
14288 endpoints for many variables (univariate or adjusted for covariates);
14289 @item @code{freqlist}, a powerful frequency table across many categorical
14291 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14292 @item @code{write2}, a function to output tables to a document.
14295 (license license:gpl2+)))
14297 (define-public r-haplo-stats
14299 (name "r-haplo-stats")
14304 (uri (cran-uri "haplo.stats" version))
14307 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
14308 (properties `((upstream-name . "haplo.stats")))
14309 (build-system r-build-system)
14311 `(("r-arsenal" ,r-arsenal)
14314 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14315 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14316 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14318 "This package provides routines for the analysis of indirectly measured
14319 haplotypes. The statistical methods assume that all subjects are unrelated
14320 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14321 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14322 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14323 examples in the vignette.")
14324 (license license:gpl2+)))
14326 (define-public r-bqtl
14333 (uri (cran-uri "bqtl" version))
14336 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14337 (build-system r-build-system)
14338 (native-inputs `(("gfortran" ,gfortran)))
14339 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14340 (synopsis "Bayesian QTL mapping toolkit")
14342 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14343 lines. It includes maximum likelihood and Bayesian tools.")
14344 (license license:gpl2+)))
14346 (define-public r-ibdreg
14353 (uri (cran-uri "ibdreg" version))
14356 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14357 (build-system r-build-system)
14358 (home-page "https://www.mayo.edu/research/labs/\
14359 statistical-genetics-genetic-epidemiology/software")
14360 (synopsis "Regression methods for IBD linkage with covariates")
14362 "This package provides a method to test genetic linkage with covariates
14363 by regression methods with response IBD sharing for relative pairs. Account
14364 for correlations of IBD statistics and covariates for relative pairs within
14365 the same pedigree.")
14366 (license license:gpl2+)))
14368 (define-public r-dlmap
14375 (uri (cran-uri "dlmap" version))
14378 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14379 (build-system r-build-system)
14381 `(("r-ibdreg" ,r-ibdreg)
14385 ("r-wgaim" ,r-wgaim)))
14386 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14387 (synopsis "Detection localization mapping for QTL")
14389 "This is package for QTL mapping in a mixed model framework with separate
14390 detection and localization stages. The first stage detects the number of QTL
14391 on each chromosome based on the genetic variation due to grouped markers on
14392 the chromosome; the second stage uses this information to determine the most
14393 likely QTL positions. The mixed model can accommodate general fixed and
14394 random effects, including spatial effects in field trials and pedigree
14395 effects. It is applicable to backcrosses, doubled haploids, recombinant
14396 inbred lines, F2 intercrosses, and association mapping populations.")
14397 (license license:gpl2)))
14399 (define-public r-ldheatmap
14401 (name "r-ldheatmap")
14406 (uri (cran-uri "LDheatmap" version))
14409 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
14410 (properties `((upstream-name . "LDheatmap")))
14411 (build-system r-build-system)
14413 `(("r-genetics" ,r-genetics)
14415 ("r-snpstats" ,r-snpstats)))
14416 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14417 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14419 "This package provides tools to produce a graphical display, as a heat
14420 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14421 optionally include the physical locations or genetic map distances of each SNP
14423 (license license:gpl3)))
14425 (define-public r-hwde
14432 (uri (cran-uri "hwde" version))
14435 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14436 (build-system r-build-system)
14437 (home-page "https://cran.r-project.org/web/packages/hwde/")
14438 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14440 "This package fits models for genotypic disequilibria, as described in
14441 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14442 terms are available that account for first order interactions between loci.
14443 It also implements, for a single locus in a single population, a conditional
14444 exact test for Hardy-Weinberg equilibrium.")
14445 (license license:gpl2+)))
14447 (define-public r-tdthap
14454 (uri (cran-uri "tdthap" version))
14457 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14458 (build-system r-build-system)
14459 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14460 (synopsis "TDT tests for extended haplotypes")
14462 "Functions and examples are provided for transmission/disequilibrium
14463 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14464 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14465 (license license:artistic2.0)))
14467 (define-public r-sparql
14473 (uri (cran-uri "SPARQL" version))
14476 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14477 (properties `((upstream-name . "SPARQL")))
14478 (build-system r-build-system)
14480 `(("r-rcurl" ,r-rcurl)
14482 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14483 (synopsis "SPARQL client for R")
14484 (description "This package provides an interface to use SPARQL to pose
14485 SELECT or UPDATE queries to an end-point.")
14486 ;; The only license indication is found in the DESCRIPTION file,
14487 ;; which states GPL-3. So we cannot assume GPLv3+.
14488 (license license:gpl3)))
14490 (define-public r-bookdown
14492 (name "r-bookdown")
14496 (uri (cran-uri "bookdown" version))
14499 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
14500 (build-system r-build-system)
14502 `(("r-htmltools" ,r-htmltools)
14503 ("r-knitr" ,r-knitr)
14504 ("r-rmarkdown" ,r-rmarkdown)
14505 ("r-tinytex" ,r-tinytex)
14508 ("pandoc" ,pandoc)))
14509 (home-page "https://github.com/rstudio/bookdown")
14510 (synopsis "Authoring books and technical documents with R markdown")
14511 (description "This package provides output formats and utilities for
14512 authoring books and technical documents with R Markdown.")
14513 (license license:gpl3)))
14515 (define-public r-optparse
14517 (name "r-optparse")
14522 (uri (cran-uri "optparse" version))
14525 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14526 (build-system r-build-system)
14528 `(("r-getopt" ,r-getopt)))
14530 `(("r-knitr" ,r-knitr)))
14531 (home-page "https://github.com/trevorld/optparse")
14532 (synopsis "Command line option parser")
14534 "This package provides a command line parser inspired by Python's
14535 @code{optparse} library to be used with Rscript to write shebang scripts
14536 that accept short and long options.")
14537 (license license:gpl2+)))
14539 (define-public r-kernlab
14546 (uri (cran-uri "kernlab" version))
14548 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14549 (build-system r-build-system)
14550 (home-page "https://cran.r-project.org/web/packages/kernlab")
14551 (synopsis "Kernel-based machine learning tools")
14553 "This package provides kernel-based machine learning methods for
14554 classification, regression, clustering, novelty detection, quantile regression
14555 and dimensionality reduction. Among other methods @code{kernlab} includes
14556 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14558 (license license:gpl2)))
14560 (define-public r-hierfstat
14562 (name "r-hierfstat")
14567 (uri (cran-uri "hierfstat" version))
14570 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14571 (build-system r-build-system)
14573 `(("r-ade4" ,r-ade4)
14574 ("r-adegenet" ,r-adegenet)
14575 ("r-gaston" ,r-gaston)
14576 ("r-gtools" ,r-gtools)))
14578 `(("r-knitr" ,r-knitr)))
14579 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14580 (synopsis "Estimation and tests of hierarchical F-statistics")
14582 "This package allows the estimation of hierarchical F-statistics from
14583 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14584 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14585 are also given to test via randomisations the significance of each F and
14586 variance components, using the likelihood-ratio statistics G.")
14587 (license license:gpl2+)))
14589 (define-public r-hapassoc
14591 (name "r-hapassoc")
14596 (uri (cran-uri "hapassoc" version))
14599 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14600 (build-system r-build-system)
14601 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14602 (synopsis "Inference of trait associations with SNP haplotypes")
14604 "Hapassoc performs likelihood inference of trait associations with
14605 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14606 functions are developed primarily for data collected in cohort or
14607 cross-sectional studies. They can accommodate uncertain haplotype phase and
14608 handle missing genotypes at some SNPs.")
14609 (license license:gpl2)))
14611 (define-public r-sampling
14613 (name "r-sampling")
14618 (uri (cran-uri "sampling" version))
14621 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14622 (build-system r-build-system)
14624 `(("r-lpsolve" ,r-lpsolve)
14625 ("r-mass" ,r-mass)))
14626 (home-page "https://cran.r-project.org/web/packages/sampling/")
14627 (synopsis "Survey sampling")
14629 "This package provides functions for drawing and calibrating samples.")
14630 (license license:gpl2+)))
14632 (define-public r-r2html
14639 (uri (cran-uri "R2HTML" version))
14642 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14643 (properties `((upstream-name . "R2HTML")))
14644 (build-system r-build-system)
14645 (home-page "https://github.com/nalimilan/R2HTML")
14646 (synopsis "HTML export for R objects")
14648 "This package includes HTML functions and methods to write in an HTML
14649 file. Thus, making HTML reports is easy. It includes a function that allows
14650 redirection on the fly, which appears to be very useful for teaching purposes,
14651 as the student can keep a copy of the produced output to keep all that they
14652 did during the course. The package comes with a vignette describing how to
14653 write HTML reports for statistical analysis. Finally, a driver for Sweave
14654 parses HTML flat files containing R code and to automatically write
14655 the corresponding outputs (tables and graphs).")
14656 (license license:gpl2+)))
14658 (define-public r-rjava
14665 (uri (cran-uri "rJava" version))
14668 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14669 (properties `((upstream-name . "rJava")))
14670 (build-system r-build-system)
14672 `(#:modules ((guix build utils)
14673 (guix build r-build-system)
14676 (modify-phases %standard-phases
14677 (add-after 'unpack 'set-JAVA_HOME
14678 (lambda* (#:key inputs #:allow-other-keys)
14679 (let ((jdk (assoc-ref inputs "jdk")))
14680 (setenv "JAVA_HOME" jdk)
14681 (setenv "JAVA" (which "java"))
14682 (setenv "JAR" (which "jar"))
14683 (setenv "JAVAC" (which "javac"))
14684 (setenv "JAVAH" (which "javah"))
14685 (setenv "JAVA_CPPFLAGS"
14686 (string-append "-I" jdk "/include "
14687 "-I" jdk "/include/linux"))
14688 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14689 ((lib) (setenv "JAVA_LIBS" lib))
14690 (_ (error "Could not find libjvm.so"))))
14694 ("jdk" ,icedtea-8 "jdk")
14697 (home-page "https://www.rforge.net/rJava/")
14698 (synopsis "Low-Level R to Java interface")
14700 "This package provides a low-level interface to the Java VM very much
14701 like .C/.Call and friends. It allows the creation of objects, calling methods
14702 and accessing fields.")
14703 (license license:gpl2)))
14705 (define-public r-svmisc
14712 (uri (cran-uri "svMisc" version))
14715 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14716 (properties `((upstream-name . "svMisc")))
14717 (build-system r-build-system)
14718 (home-page "https://github.com/SciViews/svMisc")
14719 (synopsis "Miscellaneous functions for SciViews")
14721 "This package provides miscellaneous functions for SciViews or general
14722 use, including tools to manage a temporary environment attached to the search
14723 path for temporary variables you do not want to @code{save()} or
14724 @code{load()}; test the current platform; showing progress bars, etc.")
14725 (license license:gpl2)))
14727 (define-public r-xyz
14734 (uri (cran-uri "xyz" version))
14737 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14738 (build-system r-build-system)
14740 `(("r-rcpp" ,r-rcpp)))
14741 (home-page "https://cran.r-project.org/web/packages/xyz/")
14742 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14744 "High dimensional interaction search by brute force requires a quadratic
14745 computational cost in the number of variables. The xyz algorithm provably
14746 finds strong interactions in almost linear time. For details of the algorithm
14747 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14748 interaction search in high-dimensional data.")
14749 ;; Any version of the GPL.
14750 (license license:gpl2+)))
14752 (define-public r-rttf2pt1
14754 (name "r-rttf2pt1")
14759 (uri (cran-uri "Rttf2pt1" version))
14762 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14763 (properties `((upstream-name . "Rttf2pt1")))
14764 (build-system r-build-system)
14765 (home-page "https://github.com/wch/Rttf2pt1")
14766 (synopsis "Font conversion utility")
14768 "This package contains the program @code{ttf2pt1}, for use with the
14769 @code{extrafont} package.")
14770 ;; Most of the files are covered under the Expat license. Some files are
14771 ;; covered under BSD-3. Deviations for individual files are recorded in
14772 ;; the LICENSE file.
14773 (license (list license:bsd-3 license:expat
14774 (license:non-copyleft "file://LICENSE")))))
14776 (define-public r-extrafontdb
14778 (name "r-extrafontdb")
14783 (uri (cran-uri "extrafontdb" version))
14786 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14787 (build-system r-build-system)
14788 (home-page "https://github.com/wch/extrafontdb")
14789 (synopsis "Database for the extrafont package")
14791 "This package holds the database for the @code{extrafont} package.")
14792 (license license:gpl2)))
14794 (define-public r-extrafont
14796 (name "r-extrafont")
14801 (uri (cran-uri "extrafont" version))
14804 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14805 (build-system r-build-system)
14807 `(("r-extrafontdb" ,r-extrafontdb)
14808 ("r-rttf2pt1" ,r-rttf2pt1)))
14809 (home-page "https://github.com/wch/extrafont")
14810 (synopsis "Tools for using fonts in R")
14812 "The extrafont package makes it easier to use fonts other than the basic
14813 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14814 used with PDF or PostScript output files. There are two hurdles for using
14815 fonts in PDF (or Postscript) output files:
14818 @item Making R aware of the font and the dimensions of the characters.
14819 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14820 properly on a device that doesn't have the font. This is usually needed if
14821 you want to print the PDF file or share it with others.
14824 The extrafont package makes both of these things easier.")
14825 (license license:gpl2)))
14827 (define-public r-xkcd
14834 (uri (cran-uri "xkcd" version))
14837 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14838 (build-system r-build-system)
14840 `(("r-extrafont" ,r-extrafont)
14841 ("r-ggplot2" ,r-ggplot2)
14842 ("r-hmisc" ,r-hmisc)))
14843 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14844 (synopsis "Plot ggplot2 graphics in the XKCD style")
14846 "This package provides the means to plot ggplot2 graphs in the style of
14847 the XKCD web comic.")
14848 (license license:gpl3)))
14850 (define-public r-msigdbr
14857 (uri (cran-uri "msigdbr" version))
14860 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
14861 (build-system r-build-system)
14863 `(("r-dplyr" ,r-dplyr)
14864 ("r-magrittr" ,r-magrittr)
14865 ("r-rlang" ,r-rlang)
14866 ("r-tibble" ,r-tibble)
14867 ("r-tidyselect" ,r-tidyselect)))
14869 `(("r-knitr" ,r-knitr)))
14870 (home-page "https://github.com/igordot/msigdbr")
14871 (synopsis "MSigDB gene sets for multiple organisms")
14873 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14874 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14875 software in a standard R data frame with key-value pairs. Included are the
14876 original human gene symbols and Entrez IDs as well as the equivalents for
14877 various frequently studied model organisms such as mouse, rat, pig, fly, and
14879 ;; The package is covered under the Expat license, but the upstream MSigDB
14880 ;; files are made available under the Creative Commons Attribution 4.0
14881 ;; International license.
14882 (license (list license:expat license:cc-by4.0))))
14884 (define-public r-gridgraphics
14886 (name "r-gridgraphics")
14891 (uri (cran-uri "gridGraphics" version))
14894 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14895 (properties `((upstream-name . "gridGraphics")))
14896 (build-system r-build-system)
14897 (home-page "https://github.com/pmur002/gridgraphics")
14898 (synopsis "Redraw base graphics using @code{grid} graphics")
14900 "This package provides functions to convert a page of plots drawn with
14901 the @code{graphics} package into identical output drawn with the @code{grid}
14902 package. The result looks like the original @code{graphics}-based plot, but
14903 consists of @code{grid} grobs and viewports that can then be manipulated with
14904 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14905 (license license:gpl2+)))
14907 (define-public r-farver
14914 (uri (cran-uri "farver" version))
14917 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14918 (build-system r-build-system)
14919 (home-page "https://github.com/thomasp85/farver")
14920 (synopsis "Vectorized color conversion and comparison")
14922 "The encoding of color can be handled in many different ways, using
14923 different color spaces. As different color spaces have different uses,
14924 efficient conversion between these representations are important. This
14925 package provides a set of functions that gives access to very fast color space
14926 conversion and comparisons implemented in C++, and offers 100-fold speed
14927 improvements over the @code{convertColor} function in the @code{grDevices}
14929 (license license:expat)))
14931 (define-public r-ggplotify
14933 (name "r-ggplotify")
14938 (uri (cran-uri "ggplotify" version))
14941 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14942 (build-system r-build-system)
14944 `(("r-ggplot2" ,r-ggplot2)
14945 ("r-gridgraphics" ,r-gridgraphics)
14946 ("r-rvcheck" ,r-rvcheck)))
14948 `(("r-knitr" ,r-knitr)))
14949 (home-page "https://github.com/GuangchuangYu/ggplotify")
14950 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14952 "This package provides tools to convert plot function calls (using
14953 expression or formula) to @code{grob} or @code{ggplot} objects that are
14954 compatible with the @code{grid} and @code{ggplot2} environment. With this
14955 package, we are able to e.g. use @code{cowplot} to align plots produced by
14956 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14957 converting them to @code{ggplot} objects.")
14958 (license license:artistic2.0)))
14960 (define-public r-triebeard
14962 (name "r-triebeard")
14967 (uri (cran-uri "triebeard" version))
14970 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14971 (build-system r-build-system)
14972 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14973 (home-page "https://github.com/Ironholds/triebeard/")
14974 (synopsis "Radix trees in Rcpp")
14976 "Radix trees, or tries, are key-value data structures optimized for
14977 efficient lookups, similar in purpose to hash tables. This package provides
14978 an implementation of radix trees for use in R programming and in developing
14979 packages with Rcpp.")
14980 (license license:expat)))
14982 (define-public r-tweenr
14989 (uri (cran-uri "tweenr" version))
14992 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14993 (build-system r-build-system)
14995 `(("r-farver" ,r-farver)
14996 ("r-magrittr" ,r-magrittr)
14998 ("r-rlang" ,r-rlang)))
14999 (home-page "https://github.com/thomasp85/tweenr")
15000 (synopsis "Interpolate data for smooth animations")
15002 "In order to create smooth animation between states of data, tweening is
15003 necessary. This package provides a range of functions for creating tweened
15004 data that can be used as basis for animation. Furthermore it adds a number of
15005 vectorized interpolaters for common R data types such as numeric, date and
15007 (license license:expat)))
15009 (define-public r-polyclip
15011 (name "r-polyclip")
15016 (uri (cran-uri "polyclip" version))
15019 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
15020 (build-system r-build-system)
15021 (native-inputs `(("pkg-config" ,pkg-config)))
15022 (home-page "http://www.angusj.com/delphi/clipper.php")
15023 (synopsis "Polygon clipping")
15025 "This package provides an R port of the library Clipper. It performs
15026 polygon clipping operations (intersection, union, set minus, set difference)
15027 for polygonal regions of arbitrary complexity, including holes. It computes
15028 offset polygons (spatial buffer zones, morphological dilations, Minkowski
15029 dilations) for polygonal regions and polygonal lines. It computes the
15030 Minkowski Sum of general polygons. There is a function for removing
15031 self-intersections from polygon data.")
15032 (license license:boost1.0)))
15034 (define-public r-urltools
15036 (name "r-urltools")
15041 (uri (cran-uri "urltools" version))
15044 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
15045 (build-system r-build-system)
15047 `(("r-rcpp" ,r-rcpp)
15048 ("r-triebeard" ,r-triebeard)))
15049 (home-page "https://github.com/Ironholds/urltools/")
15050 (synopsis "Vectorized tools for URL handling and parsing")
15052 "This package provides a toolkit for all URL-handling needs, including
15053 encoding and decoding, parsing, parameter extraction and modification. All
15054 functions are designed to be both fast and entirely vectorized. It is
15055 intended to be useful for people dealing with web-related datasets, such as
15056 server-side logs, although may be useful for other situations involving large
15058 (license license:expat)))
15060 (define-public r-ggforce
15067 (uri (cran-uri "ggforce" version))
15070 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
15071 (build-system r-build-system)
15073 `(("r-ggplot2" ,r-ggplot2)
15074 ("r-gtable" ,r-gtable)
15076 ("r-polyclip" ,r-polyclip)
15078 ("r-rcppeigen" ,r-rcppeigen)
15079 ("r-rlang" ,r-rlang)
15080 ("r-scales" ,r-scales)
15081 ("r-tidyselect" ,r-tidyselect)
15082 ("r-tweenr" ,r-tweenr)
15083 ("r-withr" ,r-withr)))
15084 (home-page "https://ggforce.data-imaginist.com")
15085 (synopsis "Accelerating ggplot2")
15087 "The aim of the ggplot2 package is to aid in visual data investigations.
15088 This focus has led to a lack of facilities for composing specialized plots.
15089 Thi package aims to be a collection of mainly new statistics and geometries
15090 that fills this gap.")
15091 (license license:expat)))
15093 (define-public r-europepmc
15095 (name "r-europepmc")
15100 (uri (cran-uri "europepmc" version))
15103 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
15104 (build-system r-build-system)
15106 `(("r-dplyr" ,r-dplyr)
15108 ("r-jsonlite" ,r-jsonlite)
15110 ("r-progress" ,r-progress)
15111 ("r-purrr" ,r-purrr)
15112 ("r-rlang" ,r-rlang)
15113 ("r-tibble" ,r-tibble)
15114 ("r-tidyr" ,r-tidyr)
15115 ("r-urltools" ,r-urltools)
15116 ("r-xml2" ,r-xml2)))
15118 `(("r-knitr" ,r-knitr)))
15119 (home-page "https://github.com/ropensci/europepmc/")
15120 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
15122 "This package provides an R Client for the
15123 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
15124 Service}. It gives access to both metadata on life science literature and
15125 open access full texts. Europe PMC indexes all PubMed content and other
15126 literature sources including Agricola, a bibliographic database of citations
15127 to the agricultural literature, or Biological Patents. In addition to
15128 bibliographic metadata, the client allows users to fetch citations and
15129 reference lists. Links between life-science literature and other EBI
15130 databases, including ENA, PDB or ChEMBL are also accessible.")
15131 (license license:gpl3)))
15133 (define-public r-ggraph
15140 (uri (cran-uri "ggraph" version))
15143 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
15144 (build-system r-build-system)
15146 `(("r-digest" ,r-digest)
15147 ("r-dplyr" ,r-dplyr)
15148 ("r-ggforce" ,r-ggforce)
15149 ("r-ggplot2" ,r-ggplot2)
15150 ("r-ggrepel" ,r-ggrepel)
15151 ("r-graphlayouts" ,r-graphlayouts)
15152 ("r-gtable" ,r-gtable)
15153 ("r-igraph" ,r-igraph)
15156 ("r-rlang" ,r-rlang)
15157 ("r-scales" ,r-scales)
15158 ("r-tidygraph" ,r-tidygraph)
15159 ("r-viridis" ,r-viridis)))
15161 `(("r-knitr" ,r-knitr)))
15162 (home-page "https://cran.r-project.org/web/packages/ggraph/")
15163 (synopsis "Implementation of grammar of graphics for graphs and networks")
15165 "The grammar of graphics as implemented in ggplot2 is a poor fit for
15166 graph and network visualizations due to its reliance on tabular data input.
15167 The ggraph package is an extension of the ggplot2 API tailored to graph
15168 visualizations and provides the same flexible approach to building up plots
15170 (license license:gpl3)))
15172 (define-public r-varselrf
15174 (name "r-varselrf")
15179 (uri (cran-uri "varSelRF" version))
15182 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
15183 (properties `((upstream-name . "varSelRF")))
15184 (build-system r-build-system)
15186 `(("r-randomforest" ,r-randomforest)))
15187 (home-page "https://www.ligarto.org/rdiaz/software/software")
15188 (synopsis "Variable selection using random forests")
15190 "This package provides tools for the variable selection from random
15191 forests using both backwards variable elimination (for the selection of small
15192 sets of non-redundant variables) and selection based on the importance
15193 spectrum (somewhat similar to scree plots; for the selection of large,
15194 potentially highly-correlated variables). The main applications are in
15195 high-dimensional data (e.g., microarray data, and other genomics and
15196 proteomics applications).")
15197 (license license:gpl2+)))
15199 (define-public r-pamr
15206 (uri (cran-uri "pamr" version))
15209 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
15210 (build-system r-build-system)
15212 `(("r-cluster" ,r-cluster)
15213 ("r-survival" ,r-survival)))
15214 (native-inputs `(("gfortran" ,gfortran)))
15215 (home-page "https://cran.r-project.org/web/packages/pamr/")
15216 (synopsis "Prediction Analysis for Microarrays")
15218 "This package provides some functions for sample classification in
15220 (license license:gpl2)))
15222 (define-public r-rda
15225 (version "1.0.2-2.1")
15229 (uri (cran-uri "rda" version))
15232 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15233 (build-system r-build-system)
15234 (home-page "https://cran.r-project.org/web/packages/rda/")
15235 (synopsis "Shrunken centroids regularized discriminant analysis")
15237 "This package provides tools for shrunken centroids regularized
15238 discriminant analysis for the purpose of classifying high dimensional data.")
15239 (license license:gpl2+)))
15241 (define-public r-ggvis
15248 (uri (cran-uri "ggvis" version))
15251 "1k40mkfxj66qvwbsp849maihv6vxkdprhhzjkwffwn0lwl78lsz1"))))
15252 (build-system r-build-system)
15254 `(("r-assertthat" ,r-assertthat)
15255 ("r-dplyr" ,r-dplyr)
15256 ("r-htmltools" ,r-htmltools)
15257 ("r-jsonlite" ,r-jsonlite)
15258 ("r-lazyeval" ,r-lazyeval)
15259 ("r-magrittr" ,r-magrittr)
15260 ("r-shiny" ,r-shiny)))
15261 (home-page "https://ggvis.rstudio.com/")
15262 (synopsis "Interactive grammar of graphics")
15264 "This package is a data visualization package for R providing an
15265 implementation of an interactive grammar of graphics, taking the best parts of
15266 ggplot2, combining them with the reactive framework of Shiny and drawing web
15267 graphics using Vega.")
15268 (license license:gpl2)))
15270 (define-public r-gbm
15277 (uri (cran-uri "gbm" version))
15280 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15281 (build-system r-build-system)
15283 `(("r-lattice" ,r-lattice)
15284 ("r-survival" ,r-survival)))
15286 `(("r-knitr" ,r-knitr)))
15287 (home-page "https://github.com/gbm-developers/gbm")
15288 (synopsis "Generalized boosted regression models")
15290 "This package is an implementation of extensions to Freund and Schapire's
15291 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15292 regression methods for least squares, absolute loss, t-distribution loss,
15293 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15294 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15295 and Learning to Rank measures (LambdaMart).")
15296 (license license:gpl2+)))
15298 (define-public r-threejs
15305 (uri (cran-uri "threejs" version))
15308 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15309 (build-system r-build-system)
15311 `(#:modules ((guix build utils)
15312 (guix build r-build-system)
15316 (modify-phases %standard-phases
15317 (add-after 'unpack 'process-javascript
15318 (lambda* (#:key inputs #:allow-other-keys)
15319 (with-directory-excursion "inst"
15323 `((,(assoc-ref inputs "js-jquery")
15324 "htmlwidgets/lib/jquery/jquery.min.js")
15325 (,(assoc-ref inputs "js-threejs-111")
15326 "htmlwidgets/lib/threejs-111/three.min.js"))))
15327 (lambda (sources targets)
15328 (for-each (lambda (source target)
15329 (format #t "Processing ~a --> ~a~%"
15331 (delete-file target)
15332 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15333 (call-with-output-file target
15335 (dump-port minified port)))))
15336 sources targets))))
15339 `(("r-base64enc" ,r-base64enc)
15340 ("r-crosstalk" ,r-crosstalk)
15341 ("r-htmlwidgets" ,r-htmlwidgets)
15342 ("r-igraph" ,r-igraph)))
15344 `(("uglify-js" ,uglify-js)
15348 (uri "https://code.jquery.com/jquery-1.12.4.js")
15351 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15355 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15358 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15359 (home-page "https://bwlewis.github.io/rthreejs")
15360 (synopsis "Interactive 3D scatter plots, networks and globes")
15362 "Create interactive 3D scatter plots, network plots, and globes in R
15363 using the three.js visualization library.")
15364 (license license:expat)))
15366 (define-public r-mlbench
15373 (uri (cran-uri "mlbench" version))
15376 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15377 (build-system r-build-system)
15378 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15379 (synopsis "Machine learning benchmark problems")
15381 "This package provides a collection of artificial and real-world machine
15382 learning benchmark problems, including, e.g., several data sets from the UCI
15384 (license license:gpl2)))
15386 (define-public r-mpm
15393 (uri (cran-uri "mpm" version))
15396 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15397 (build-system r-build-system)
15399 `(("r-kernsmooth" ,r-kernsmooth)
15400 ("r-mass" ,r-mass)))
15401 (home-page "http://mpm.r-forge.r-project.org")
15402 (synopsis "Multivariate projection methods")
15404 "This is a package for exploratory graphical analysis of multivariate
15405 data, specifically gene expression data with different projection methods:
15406 principal component analysis, correspondence analysis, spectral map
15408 (license license:gpl2+)))
15410 (define-public r-png
15416 (uri (cran-uri "png" version))
15419 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15420 (build-system r-build-system)
15422 `(("libpng" ,libpng)
15424 (home-page "https://www.rforge.net/png/")
15425 (synopsis "Read and write PNG images")
15427 "This package provides an easy and simple way to read, write and display
15428 bitmap images stored in the PNG format. It can read and write both files and
15429 in-memory raw vectors.")
15430 ;; Any of these GPL versions.
15431 (license (list license:gpl2 license:gpl3))))
15433 (define-public r-ggcorrplot
15435 (name "r-ggcorrplot")
15440 (uri (cran-uri "ggcorrplot" version))
15443 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15444 (build-system r-build-system)
15446 `(("r-ggplot2" ,r-ggplot2)
15447 ("r-reshape2" ,r-reshape2)))
15448 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15449 (synopsis "Visualization of a correlation matrix using ggplot2")
15451 "The ggcorrplot package can be used to visualize easily a correlation
15452 matrix using ggplot2. It provides a solution for reordering the correlation
15453 matrix and displays the significance level on the plot. It also includes a
15454 function for computing a matrix of correlation p-values.")
15455 (license license:gpl2)))
15457 ;; This package includes minified JavaScript files. When upgrading please
15458 ;; check that there are no new minified JavaScript files.
15459 (define-public r-flexdashboard
15461 (name "r-flexdashboard")
15466 (uri (cran-uri "flexdashboard" version))
15469 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15470 (modules '((guix build utils)))
15473 ;; Delete bundled minified JavaScript files
15474 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15475 (delete-file "inst/www/sly/sly.min.js")
15476 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15477 (delete-file "inst/www/prism/prism.js")
15479 (build-system r-build-system)
15481 `(#:modules ((guix build utils)
15482 (guix build r-build-system)
15486 (ice-9 textual-ports))
15488 (modify-phases %standard-phases
15489 (add-after 'unpack 'process-javascript
15490 (lambda* (#:key inputs #:allow-other-keys)
15491 (with-directory-excursion "inst"
15492 ;; Concatenate all components of prism.js
15493 (let ((contents (string-join
15494 (map (lambda (name)
15495 (call-with-input-file
15496 (assoc-ref inputs name)
15500 "js-prism-line-numbers"))
15502 (call-with-output-file "prism-src.js"
15503 (cut display contents <>)))
15507 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15508 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15510 "www/sly/sly.min.js")
15512 "www/prism/prism.js")
15513 (,(assoc-ref inputs "js-raphael")
15514 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15515 (,(assoc-ref inputs "js-featherlight")
15516 "www/featherlight/featherlight.min.js"))))
15517 (lambda (sources targets)
15518 (for-each (lambda (source target)
15519 (format #t "Processing ~a --> ~a~%"
15521 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15522 (call-with-output-file target
15524 (dump-port minified port)))))
15525 sources targets))))
15528 `(("r-htmltools" ,r-htmltools)
15529 ("r-htmlwidgets" ,r-htmlwidgets)
15530 ("r-jsonlite" ,r-jsonlite)
15531 ("r-knitr" ,r-knitr)
15532 ("r-rmarkdown" ,r-rmarkdown)
15533 ("r-shiny" ,r-shiny)))
15535 `(("uglify-js" ,uglify-js)
15539 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15542 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15546 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15549 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15553 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15556 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15557 ("js-prism-line-numbers"
15560 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15563 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15567 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15570 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15571 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15572 (synopsis "R Markdown format for flexible dashboards")
15574 "This package provides an R Markdown format for converting an R Markdown
15575 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15576 of its components to the containing web page.")
15577 (license license:expat)))
15579 (define-public r-preseqr
15586 (uri (cran-uri "preseqR" version))
15589 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15590 (properties `((upstream-name . "preseqR")))
15591 (build-system r-build-system)
15593 `(("r-polynom" ,r-polynom)))
15594 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15595 (synopsis "Predicting species accumulation curves")
15597 "This package can be used to predict the r-species accumulation
15598 curve (r-SAC), which is the number of species represented at least r times as
15599 a function of the sampling effort. When r = 1, the curve is known as the
15600 species accumulation curve, or the library complexity curve in high-throughput
15601 genomic sequencing. The package includes both parametric and nonparametric
15602 methods, as described by Deng C, et al. (2018).")
15603 (license license:gpl3)))
15605 (define-public r-mapplots
15607 (name "r-mapplots")
15612 (uri (cran-uri "mapplots" version))
15615 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15616 (build-system r-build-system)
15617 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15618 (synopsis "Data visualization on maps")
15620 "This package helps you create simple maps; add sub-plots like pie plots
15621 to a map or any other plot; format, plot and export gridded data. The package
15622 was developed for displaying fisheries data but most functions can be used for
15623 more generic data visualisation.")
15624 (license license:gpl2+)))
15626 (define-public r-pmcmr
15633 (uri (cran-uri "PMCMR" version))
15636 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15637 (properties `((upstream-name . "PMCMR")))
15638 (build-system r-build-system)
15639 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15640 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15642 "This is a deprecated package for calculating pairwise multiple
15643 comparisons of mean rank sums. This package is superseded by the novel
15644 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15645 compatibility of dependent packages for some time.")
15646 (license license:gpl3+)))
15648 (define-public r-downloader
15650 (name "r-downloader")
15655 (uri (cran-uri "downloader" version))
15658 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15659 (build-system r-build-system)
15661 `(("r-digest" ,r-digest)))
15662 (home-page "https://github.com/wch/downloader")
15663 (synopsis "Download files over HTTP and HTTPS")
15665 "This package provides a wrapper for the @code{download.file} function,
15666 making it possible to download files over HTTPS across platforms. The
15667 @code{RCurl} package provides this functionality (and much more) but has
15668 external dependencies. This package has is implemented purely in R.")
15669 (license license:gpl2)))
15671 (define-public r-rex
15678 (uri (cran-uri "rex" version))
15681 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15682 (build-system r-build-system)
15684 `(("r-lazyeval" ,r-lazyeval)))
15686 `(("r-knitr" ,r-knitr)))
15687 (home-page "https://github.com/kevinushey/rex")
15688 (synopsis "Friendly regular expressions")
15690 "This package provides a friendly interface for the construction of
15691 regular expressions. Regular expressions are a very powerful feature, however
15692 they are often difficult to interpret. Rex allows you to build complex
15693 regular expressions from human readable expressions")
15694 (license license:expat)))
15696 (define-public r-xmlparsedata
15698 (name "r-xmlparsedata")
15703 (uri (cran-uri "xmlparsedata" version))
15706 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
15707 (properties `((upstream-name . "xmlparsedata")))
15708 (build-system r-build-system)
15709 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15710 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15712 "This package provides tools to convert the output of
15713 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15714 @code{XPath}, and is easier to manipulate in general.")
15715 (license license:expat)))
15717 (define-public r-cyclocomp
15719 (name "r-cyclocomp")
15724 (uri (cran-uri "cyclocomp" version))
15727 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15728 (properties `((upstream-name . "cyclocomp")))
15729 (build-system r-build-system)
15731 `(("r-callr" ,r-callr)
15732 ("r-crayon" ,r-crayon)
15734 ("r-remotes" ,r-remotes)
15735 ("r-withr" ,r-withr)))
15736 (home-page "https://github.com/MangoTheCat/cyclocomp")
15737 (synopsis "Cyclomatic complexity of R code")
15739 "Cyclomatic complexity is a software metric, used to indicate the
15740 complexity of a program. It is a quantitative measure of the number of
15741 linearly independent paths through a program's source code. This package
15742 provides tools to compute this metric.")
15743 (license license:expat)))
15745 (define-public r-lintr
15752 (uri (cran-uri "lintr" version))
15755 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15756 (properties `((upstream-name . "lintr")))
15757 (build-system r-build-system)
15759 `(("r-codetools" ,r-codetools)
15760 ("r-crayon" ,r-crayon)
15761 ("r-cyclocomp" ,r-cyclocomp)
15762 ("r-digest" ,r-digest)
15764 ("r-jsonlite" ,r-jsonlite)
15765 ("r-knitr" ,r-knitr)
15767 ("r-rstudioapi" ,r-rstudioapi)
15768 ("r-testthat" ,r-testthat)
15770 ("r-xmlparsedata" ,r-xmlparsedata)))
15771 (home-page "https://github.com/jimhester/lintr")
15772 (synopsis "Linter for R code")
15773 (description "This package checks adherence to a given style, syntax
15774 errors and possible semantic issues. It supports on the fly checking of R
15775 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15776 (license license:expat)))
15778 (define-public r-sctransform
15780 (name "r-sctransform")
15785 (uri (cran-uri "sctransform" version))
15788 "0b8ni8dzlcikjm2bx5w8yi9vygx0qqxjrmnsy4kf7d1h03n2sxwa"))))
15789 (build-system r-build-system)
15791 `(("r-future" ,r-future)
15792 ("r-future-apply" ,r-future-apply)
15793 ("r-ggplot2" ,r-ggplot2)
15794 ("r-gridextra" ,r-gridextra)
15796 ("r-matrix" ,r-matrix)
15797 ("r-matrixstats" ,r-matrixstats)
15799 ("r-rcpparmadillo" ,r-rcpparmadillo)
15800 ("r-reshape2" ,r-reshape2)))
15801 (home-page "https://github.com/ChristophH/sctransform")
15802 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15804 "This package provides a normalization method for single-cell UMI count
15805 data using a variance stabilizing transformation. The transformation is based
15806 on a negative binomial regression model with regularized parameters. As part
15807 of the same regression framework, this package also provides functions for
15808 batch correction, and data correction.")
15809 (license license:gpl3)))
15811 (define-public r-styler
15818 (uri (cran-uri "styler" version))
15821 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15822 (build-system r-build-system)
15824 `(("r-backports" ,r-backports)
15826 ("r-magrittr" ,r-magrittr)
15827 ("r-purrr" ,r-purrr)
15828 ("r-r-cache" ,r-r-cache)
15829 ("r-rematch2" ,r-rematch2)
15830 ("r-rlang" ,r-rlang)
15831 ("r-rprojroot" ,r-rprojroot)
15832 ("r-tibble" ,r-tibble)
15833 ("r-withr" ,r-withr)
15834 ("r-xfun" ,r-xfun)))
15835 (home-page "https://github.com/r-lib/styler")
15836 (synopsis "Non-invasive pretty printing of R code")
15838 "This is a package for pretty-printing R code without changing the user's
15839 formatting intent.")
15840 (license license:gpl3)))
15842 (define-public r-scrime
15849 (uri (cran-uri "scrime" version))
15852 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15853 (build-system r-build-system)
15854 (home-page "https://cran.r-project.org/web/packages/scrime/")
15855 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15857 "This package provides tools for the analysis of high-dimensional data
15858 developed/implemented at the group \"Statistical Complexity Reduction In
15859 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15860 the functions can also be applied to other types of categorical data.")
15861 (license license:gpl2)))
15863 (define-public r-pbmcapply
15865 (name "r-pbmcapply")
15870 (uri (cran-uri "pbmcapply" version))
15873 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15874 (build-system r-build-system)
15875 (home-page "https://github.com/kvnkuang/pbmcapply")
15876 (synopsis "Track the progress of apply procedures with a progress bar")
15878 "This light-weight package helps you track and visualize the progress of
15879 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15880 (license license:expat)))
15882 (define-public r-blme
15889 (uri (cran-uri "blme" version))
15892 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15893 (build-system r-build-system)
15894 (propagated-inputs `(("r-lme4" ,r-lme4)))
15895 (home-page "https://github.com/vdorie/blme")
15896 (synopsis "Bayesian linear mixed-effects models")
15898 "This package provides tools for maximum a posteriori estimation for
15899 linear and generalized linear mixed-effects models in a Bayesian setting. It
15900 extends the lme4 package.")
15901 (license license:gpl2+)))
15903 (define-public r-batchtools
15905 (name "r-batchtools")
15910 (uri (cran-uri "batchtools" version))
15913 "1b78r70gm4a0wzjr367hqx2rfphfkbppp14d0l5zs2fvyz166lsx"))))
15914 (build-system r-build-system)
15916 `(("r-backports" ,r-backports)
15917 ("r-base64url" ,r-base64url)
15919 ("r-checkmate" ,r-checkmate)
15920 ("r-data-table" ,r-data-table)
15921 ("r-digest" ,r-digest)
15923 ("r-progress" ,r-progress)
15925 ("r-rappdirs" ,r-rappdirs)
15926 ("r-stringi" ,r-stringi)
15927 ("r-withr" ,r-withr)))
15929 `(("r-knitr" ,r-knitr)))
15930 (home-page "https://github.com/mllg/batchtools")
15931 (synopsis "Tools for computation on batch systems")
15933 "As a successor of the packages BatchJobs and BatchExperiments, this
15934 package provides a parallel implementation of the Map function for high
15935 performance computing systems managed by various schedulers. A multicore and
15936 socket mode allow the parallelization on a local machines, and multiple
15937 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15938 the package provides an abstraction mechanism to define large-scale computer
15939 experiments in a well-organized and reproducible way.")
15940 (license license:lgpl3)))
15942 (define-public r-clue
15949 (uri (cran-uri "clue" version))
15952 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15953 (build-system r-build-system)
15954 (propagated-inputs `(("r-cluster" ,r-cluster)))
15955 (home-page "https://cran.r-project.org/web/packages/clue/")
15956 (synopsis "Tools for analyzing cluster ensembles")
15957 (description "Cluster ensembles are collections of individual solutions to
15958 a given clustering problem which are useful or necessary to consider in a wide
15959 range of applications. This R package provides an extensible computational
15960 environment for creating and analyzing cluster ensembles, with basic data
15961 structures for representing partitions and hierarchies, and facilities for
15962 computing on them, including methods for measuring proximity and obtaining
15963 consensus and secondary clusterings.")
15964 (license license:gpl2)))
15966 (define-public r-sitmo
15973 (uri (cran-uri "sitmo" version))
15976 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15977 (build-system r-build-system)
15978 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15979 (home-page "https://github.com/coatless/sitmo/")
15980 (synopsis "Parallel pseudo random number generator header files")
15982 "This package provides two high quality and fast PPRNGs that may be used
15983 in an OpenMP parallel environment. In addition, there is a generator for one
15984 dimensional low-discrepancy sequence.")
15985 (license license:expat)))
15987 (define-public r-dqrng
15994 (uri (cran-uri "dqrng" version))
15997 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15998 (build-system r-build-system)
16002 ("r-sitmo" ,r-sitmo)))
16003 (home-page "https://www.daqana.org/dqrng")
16004 (synopsis "Fast pseudo random number generators")
16006 "Several fast random number generators are provided as C++ header-only
16007 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
16008 Additionally, fast functions for generating random numbers according to a
16009 uniform, normal and exponential distribution are included. The latter two use
16010 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
16011 functions are exported to R and as a C++ interface and are enabled for use
16012 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
16013 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
16014 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
16015 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
16016 ;; whole is distributed under the terms of the AGPL 3.
16017 (license license:agpl3)))
16019 (define-public r-ingredients
16021 (name "r-ingredients")
16026 (uri (cran-uri "ingredients" version))
16029 "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
16030 (properties `((upstream-name . "ingredients")))
16031 (build-system r-build-system)
16033 `(("r-ggplot2" ,r-ggplot2)
16034 ("r-gridextra" ,r-gridextra)
16035 ("r-scales" ,r-scales)))
16036 (native-inputs `(("r-knitr" ,r-knitr)))
16037 (home-page "https://ModelOriented.github.io/ingredients/")
16038 (synopsis "Effects and importances of model ingredients")
16040 "This is a collection of tools for assessment of feature importance and
16041 feature effects. Key functions are:
16044 @item @code{feature_importance()} for assessment of global level feature
16046 @item @code{ceteris_paribus()} for calculation of the what-if plots,
16047 @item @code{partial_dependence()} for partial dependence plots,
16048 @item @code{conditional_dependence()} for conditional dependence plots,
16049 @item @code{accumulated_dependence()} for accumulated local effects plots,
16050 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
16051 aggregation of ceteris paribus profiles,
16052 @item generic @code{print()} and @code{plot()} for better usability of
16053 selected explainers,
16054 @item generic @code{plotD3()} for interactive, D3 based explanations, and
16055 @item generic @code{describe()} for explanations in natural language.
16057 (license license:gpl3)))
16059 (define-public r-ibreakdown
16061 (name "r-ibreakdown")
16066 (uri (cran-uri "iBreakDown" version))
16069 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
16070 (properties `((upstream-name . "iBreakDown")))
16071 (build-system r-build-system)
16072 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
16073 (native-inputs `(("r-knitr" ,r-knitr)))
16074 (home-page "https://ModelOriented.github.io/iBreakDown/")
16075 (synopsis "Model agnostic instance level variable attributions")
16077 "This package provides a model agnostic tool for decomposition of
16078 predictions from black boxes. It supports additive attributions and
16079 attributions with interactions. The Break Down Table shows contributions of
16080 every variable to a final prediction. The Break Down Plot presents variable
16081 contributions in a concise graphical way. This package works for
16082 classification and regression models.")
16083 (license license:gpl3)))
16085 (define-public r-dae
16092 (uri (cran-uri "dae" version))
16095 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
16096 (build-system r-build-system)
16098 `(("r-ggplot2" ,r-ggplot2)
16099 ("r-plyr" ,r-plyr)))
16101 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
16102 (home-page "http://chris.brien.name")
16103 (synopsis "Functions useful in the design and ANOVA of experiments")
16105 "This package provides functions useful in the design and ANOVA of
16106 experiments. The content falls into the following groupings:
16110 @item factor manipulation functions,
16111 @item design functions,
16112 @item ANOVA functions,
16113 @item matrix functions,
16114 @item projector and canonical efficiency functions, and
16115 @item miscellaneous functions.
16118 There is a vignette called @code{DesignNotes} describing how to use the design
16119 functions for randomizing and assessing designs. The ANOVA functions
16120 facilitate the extraction of information when the @code{Error} function has
16121 been used in the call to @code{aov}.")
16122 (license license:gpl2)))
16124 (define-public r-dalex
16131 (uri (cran-uri "DALEX" version))
16134 "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98"))))
16135 (properties `((upstream-name . "DALEX")))
16136 (build-system r-build-system)
16138 `(("r-ggplot2" ,r-ggplot2)
16139 ("r-ibreakdown" ,r-ibreakdown)
16140 ("r-ingredients" ,r-ingredients)))
16141 (home-page "https://pbiecek.github.io/DALEX/")
16142 (synopsis "Descriptive machine learning explanations")
16144 "Machine Learning models are widely used and have various applications in
16145 classification or regression. Models created with boosting, bagging, stacking
16146 or similar techniques are often used due to their high performance, but such
16147 black-box models usually lack interpretability. The DALEX package contains
16148 various explainers that help to understand the link between input variables
16149 and model output.")
16150 ;; Any version of the GPL
16151 (license license:gpl3+)))
16153 (define-public r-enrichr
16160 (uri (cran-uri "enrichR" version))
16163 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
16164 (properties `((upstream-name . "enrichR")))
16165 (build-system r-build-system)
16167 `(("r-httr" ,r-httr)
16168 ("r-rjson" ,r-rjson)))
16169 (home-page "https://cran.r-project.org/web/packages/enrichR/")
16170 (synopsis "R Interface to Enrichr database for analyzing gene sets")
16172 "This package provides an R interface to all Enrichr databases, a
16173 web-based tool for analyzing gene sets and returns any enrichment of common
16174 annotated biological functions.")
16175 (license license:gpl2+)))
16177 (define-public r-plot3d
16184 (uri (cran-uri "plot3D" version))
16187 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
16188 (properties `((upstream-name . "plot3D")))
16189 (build-system r-build-system)
16190 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
16191 (home-page "https://cran.r-project.org/web/packages/plot3D")
16192 (synopsis "Plot multi-dimensional data")
16194 "This package provides functions for viewing 2D and 3D data, including
16195 perspective plots, slice plots, surface plots, scatter plots, etc. It
16196 includes data sets from oceanography.")
16197 (license license:gpl3+)))
16199 (define-public r-ggfortify
16201 (name "r-ggfortify")
16206 (uri (cran-uri "ggfortify" version))
16209 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
16210 (build-system r-build-system)
16212 `(("r-dplyr" ,r-dplyr)
16213 ("r-ggplot2" ,r-ggplot2)
16214 ("r-gridextra" ,r-gridextra)
16215 ("r-scales" ,r-scales)
16216 ("r-stringr" ,r-stringr)
16217 ("r-tibble" ,r-tibble)
16218 ("r-tidyr" ,r-tidyr)))
16220 `(("r-knitr" ,r-knitr)))
16221 (home-page "https://github.com/sinhrks/ggfortify")
16222 (synopsis "Data visualization tools for statistical analysis results")
16224 "This package provides unified plotting tools for statistics commonly
16225 used, such as GLM, time series, PCA families, clustering and survival
16226 analysis. The package offers a single plotting interface for these analysis
16227 results and plots in a unified style using the @code{ggplot2} package.")
16228 (license license:gpl2)))
16230 (define-public r-refmanager
16232 (name "r-refmanager")
16237 (uri (cran-uri "RefManageR" version))
16240 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16241 (properties `((upstream-name . "RefManageR")))
16242 (build-system r-build-system)
16244 `(("r-bibtex" ,r-bibtex)
16246 ("r-jsonlite" ,r-jsonlite)
16247 ("r-lubridate" ,r-lubridate)
16249 ("r-stringr" ,r-stringr)
16250 ("r-xml2" ,r-xml2)))
16251 (home-page "https://github.com/ropensci/RefManageR/")
16252 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16254 "This package provides tools for importing and working with bibliographic
16255 references. It greatly enhances the @code{bibentry} class by providing a
16256 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16257 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16258 by various formats for name lists (author by last names, translator by full
16259 names, etc.). Entries can be updated, combined, sorted, printed in a number
16260 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16261 into R and converted to @code{BibEntry} objects.")
16262 ;; Any of these licenses may be picked.
16263 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16265 (define-public r-citr
16272 (uri (cran-uri "citr" version))
16275 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16276 (build-system r-build-system)
16278 `(("r-assertthat" ,r-assertthat)
16281 ("r-miniui" ,r-miniui)
16282 ("r-refmanager" ,r-refmanager)
16283 ("r-rstudioapi" ,r-rstudioapi)
16284 ("r-shiny" ,r-shiny)
16285 ("r-shinyjs" ,r-shinyjs)
16286 ("r-yaml" ,r-yaml)))
16287 (home-page "https://github.com/crsh/citr")
16288 (synopsis "RStudio add-in to insert Markdown citations")
16290 "This package provides functions and an RStudio add-in that search a
16291 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16292 the current document.")
16293 (license license:expat)))
16295 (define-public r-xgboost
16298 (version "1.2.0.1")
16302 (uri (cran-uri "xgboost" version))
16305 "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
16306 (build-system r-build-system)
16308 `(("r-data-table" ,r-data-table)
16309 ("r-magrittr" ,r-magrittr)
16310 ("r-matrix" ,r-matrix)
16311 ("r-stringi" ,r-stringi)))
16313 `(("r-knitr" ,r-knitr)))
16314 (home-page "https://github.com/dmlc/xgboost")
16315 (synopsis "Extreme gradient boosting")
16317 "This package provides an R interface to Extreme Gradient Boosting, which
16318 is an efficient implementation of the gradient boosting framework from Chen
16319 and Guestrin (2016). The package includes efficient linear model solver and
16320 tree learning algorithms. The package can automatically do parallel
16321 computation on a single machine. It supports various objective functions,
16322 including regression, classification and ranking. The package is made to be
16323 extensible, so that users are also allowed to define their own objectives
16325 (license license:asl2.0)))
16327 (define-public r-umap
16330 (version "0.2.6.0")
16334 (uri (cran-uri "umap" version))
16337 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16338 (build-system r-build-system)
16340 `(("r-openssl" ,r-openssl)
16342 ("r-reticulate" ,r-reticulate)
16343 ("r-rspectra" ,r-rspectra)))
16345 `(("r-knitr" ,r-knitr)))
16346 (home-page "https://github.com/tkonopka/umap")
16347 (synopsis "Uniform manifold approximation and projection")
16349 "Uniform manifold approximation and projection is a technique for
16350 dimension reduction. This package provides an interface to the UMAP algorithm
16351 in R, including a translation of the original algorithm into R.")
16352 (license license:expat)))
16354 (define-public r-uwot
16361 (uri (cran-uri "uwot" version))
16364 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16365 (build-system r-build-system)
16367 `(("r-dqrng" ,r-dqrng)
16369 ("r-irlba" ,r-irlba)
16370 ("r-matrix" ,r-matrix)
16372 ("r-rcppannoy" ,r-rcppannoy)
16373 ("r-rcppprogress" ,r-rcppprogress)
16374 ("r-rspectra" ,r-rspectra)))
16375 (home-page "https://github.com/jlmelville/uwot")
16376 (synopsis "Uniform manifold approximation and projection")
16378 "This package provides an implementation of the Uniform Manifold
16379 Approximation and Projection dimensionality reduction by McInnes et
16380 al. (2018). It also provides means to transform new data and to carry out
16381 supervised dimensionality reduction. An implementation of the related
16382 LargeVis method of Tang et al. (2016) is also provided.")
16383 (license license:gpl3)))
16385 (define-public r-kableextra
16387 (name "r-kableextra")
16392 (uri (cran-uri "kableExtra" version))
16395 "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf"))))
16396 (properties `((upstream-name . "kableExtra")))
16397 (build-system r-build-system)
16399 `(("r-digest" ,r-digest)
16401 ("r-htmltools" ,r-htmltools)
16402 ("r-knitr" ,r-knitr)
16403 ("r-magrittr" ,r-magrittr)
16404 ("r-rmarkdown" ,r-rmarkdown)
16405 ("r-rstudioapi" ,r-rstudioapi)
16406 ("r-rvest" ,r-rvest)
16407 ("r-scales" ,r-scales)
16408 ("r-stringr" ,r-stringr)
16409 ("r-viridislite" ,r-viridislite)
16410 ("r-webshot" ,r-webshot)
16411 ("r-xml2" ,r-xml2)))
16413 `(("r-knitr" ,r-knitr)))
16414 (home-page "https://haozhu233.github.io/kableExtra/")
16415 (synopsis "Construct complex tables with pipe syntax")
16417 "Build complex HTML or LaTeX tables using @code{kable()} from
16418 @code{knitr} and the piping syntax from @code{magrittr}. The function
16419 @code{kable()} is a light weight table generator coming from @code{knitr}.
16420 This package simplifies the way to manipulate the HTML or LaTeX codes
16421 generated by @code{kable()} and allows users to construct complex tables and
16422 customize styles using a readable syntax.")
16423 (license license:expat)))
16425 (define-public r-glasso
16432 (uri (cran-uri "glasso" version))
16434 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16435 (build-system r-build-system)
16436 (native-inputs `(("gfortran" ,gfortran)))
16437 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16438 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16440 "This is a package for estimation of a sparse inverse covariance matrix
16441 using a lasso (L1) penalty. Facilities are provided for estimates along a
16442 path of values for the regularization parameter.")
16443 (license license:gpl2)))
16445 (define-public r-rhpcblasctl
16447 (name "r-rhpcblasctl")
16448 (version "0.20-137")
16452 (uri (cran-uri "RhpcBLASctl" version))
16455 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16456 (properties `((upstream-name . "RhpcBLASctl")))
16457 (build-system r-build-system)
16458 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16459 (synopsis "Control the number of threads on BLAS")
16461 "This package allows you to control the number of threads the BLAS
16462 library uses. It is also possible to control the number of threads in
16464 (license license:agpl3+)))
16466 (define-public r-lda
16473 (uri (cran-uri "lda" version))
16476 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16477 (build-system r-build-system)
16478 (home-page "https://cran.r-project.org/web/packages/lda/")
16479 (synopsis "Collapsed Gibbs sampling methods for topic models")
16481 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16482 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16483 mixed-membership stochastic blockmodel. Inference for all of these models is
16484 implemented via a fast collapsed Gibbs sampler written in C. Utility
16485 functions for reading/writing data typically used in topic models, as well as
16486 tools for examining posterior distributions are also included.")
16487 ;; Any version of the LGPL
16488 (license license:lgpl3+)))
16490 (define-public r-rann-l1
16497 (uri (cran-uri "RANN.L1" version))
16500 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16501 (properties `((upstream-name . "RANN.L1")))
16502 (build-system r-build-system)
16503 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16504 (synopsis "Fast nearest neighbour search using L1 metric")
16506 "This package provides tools to find the k nearest neighbours for every
16507 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16508 library. There is support for approximate as well as exact searches, fixed
16509 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16510 computed using the L1 (Manhattan, taxicab) metric.")
16511 (license license:gpl3+)))
16513 (define-public r-leiden
16520 (uri (cran-uri "leiden" version))
16523 "0cj98s1d9771dahn2xwdb1hpkw51jsfmgvzpam34c7i57fj37hn2"))))
16524 (properties `((upstream-name . "leiden")))
16525 (build-system r-build-system)
16527 `(("r-igraph" ,r-igraph)
16528 ("r-matrix" ,r-matrix)
16529 ("r-reticulate" ,r-reticulate)))
16531 `(("r-knitr" ,r-knitr)))
16532 (home-page "https://github.com/TomKellyGenetics/leiden")
16533 (synopsis "R implementation of Leiden clustering algorithm")
16535 "This package implements the Python @code{leidenalg} module to be called
16536 in R. It enables clustering using the Leiden algorithm for partitioning a
16537 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16538 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16539 (license license:gpl3)))
16541 (define-public r-patchwork
16543 (name "r-patchwork")
16548 (uri (cran-uri "patchwork" version))
16551 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16552 (build-system r-build-system)
16554 `(("r-ggplot2" ,r-ggplot2)
16555 ("r-gtable" ,r-gtable)))
16557 `(("r-knitr" ,r-knitr)))
16558 (home-page "https://github.com/thomasp85/patchwork")
16559 (synopsis "Compose ggplot2 plots")
16561 "The @code{ggplot2} package provides a strong API for sequentially
16562 building up a plot, but does not concern itself with composition of multiple
16563 plots. Patchwork is a package that expands the API to allow for arbitrarily
16564 complex composition of plots by providing mathematical operators for combining
16566 (license license:expat)))
16568 (define-public r-liger
16575 (uri (git-reference
16576 (url "https://github.com/MacoskoLab/liger")
16577 (commit (string-append "v" version))))
16578 (file-name (git-file-name name version))
16581 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16582 (modules '((guix build utils)))
16585 (delete-file "inst/java/ModularityOptimizer.jar")
16587 (build-system r-build-system)
16590 (modify-phases %standard-phases
16591 (add-after 'unpack 'build-java-part
16592 (lambda* (#:key inputs #:allow-other-keys)
16593 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16594 (for-each (lambda (file) (invoke "javac" file))
16595 (find-files "." "\\.java$"))
16596 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16597 (find-files "." "\\.class$"))
16600 `(("r-cowplot" ,r-cowplot)
16601 ("r-dosnow" ,r-dosnow)
16602 ("r-dplyr" ,r-dplyr)
16604 ("r-foreach" ,r-foreach)
16605 ("r-ggplot2" ,r-ggplot2)
16606 ("r-ggrepel" ,r-ggrepel)
16607 ("r-hmisc" ,r-hmisc)
16609 ("r-irlba" ,r-irlba)
16610 ("r-matrix" ,r-matrix)
16611 ("r-mclust" ,r-mclust)
16612 ("r-patchwork" ,r-patchwork)
16614 ("r-rann-l1" ,r-rann-l1)
16616 ("r-rcpparmadillo" ,r-rcpparmadillo)
16617 ("r-riverplot" ,r-riverplot)
16618 ("r-rtsne" ,r-rtsne)
16619 ("r-snow" ,r-snow)))
16621 `(("jdk" ,icedtea "jdk")
16622 ;; See https://github.com/MacoskoLab/liger/issues/96
16623 ;; The optimizer is released under the Expat license.
16627 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16630 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16632 ("r-knitr" ,r-knitr))) ; for vignettes
16633 (home-page "https://github.com/MacoskoLab/liger")
16634 (synopsis "Integrate and analyze multiple single-cell datasets")
16636 "LIGER is a package for integrating and analyzing multiple single-cell
16637 datasets, developed and maintained by the Macosko lab. It relies on
16638 integrative non-negative matrix factorization to identify shared and
16639 dataset-specific factors.")
16640 (license license:gpl3)))
16642 (define-public r-harmony
16649 (uri (git-reference
16650 (url "https://github.com/immunogenomics/harmony")
16652 (file-name (git-file-name name version))
16655 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16656 (modules '((guix build utils)))
16659 (for-each delete-file '("config.status" "configure"))
16661 (build-system r-build-system)
16663 `(("r-cowplot" ,r-cowplot)
16664 ("r-dplyr" ,r-dplyr)
16665 ("r-ggplot2" ,r-ggplot2)
16666 ("r-irlba" ,r-irlba)
16667 ("r-matrix" ,r-matrix)
16669 ("r-rcpparmadillo" ,r-rcpparmadillo)
16670 ("r-rcppprogress" ,r-rcppprogress)
16671 ("r-rlang" ,r-rlang)
16672 ("r-tibble" ,r-tibble)
16673 ("r-tidyr" ,r-tidyr)))
16675 `(("autoconf" ,autoconf)))
16676 (home-page "https://github.com/immunogenomics/harmony")
16677 (synopsis "Integration of single cell sequencing data")
16679 "This package provides an implementation of the Harmony algorithm for
16680 single cell integration, described in Korsunsky et al
16681 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16682 function and interfaces to external frameworks.")
16683 (license license:gpl3)))
16685 (define-public r-covr
16692 (uri (cran-uri "covr" version))
16694 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
16695 (properties `((upstream-name . "covr")))
16696 (build-system r-build-system)
16698 `(("r-crayon" ,r-crayon)
16699 ("r-digest" ,r-digest)
16701 ("r-jsonlite" ,r-jsonlite)
16703 ("r-withr" ,r-withr)
16704 ("r-yaml" ,r-yaml)))
16706 `(("r-knitr" ,r-knitr))) ; for vignettes
16707 (home-page "https://github.com/r-lib/covr")
16708 (synopsis "Test coverage for R packages")
16710 "Thisp package enables you to track and report code coverage for your
16711 package and (optionally) upload the results to a coverage service. Code
16712 coverage is a measure of the amount of code being exercised by a set of tests.
16713 It is an indirect measure of test quality and completeness. This package is
16714 compatible with any testing methodology or framework and tracks coverage of
16715 both R code and compiled C/C++/FORTRAN code.")
16716 (license license:gpl3)))
16718 (define-public r-systemfonts
16720 (name "r-systemfonts")
16725 (uri (cran-uri "systemfonts" version))
16728 "12hdvv66kkd3b4rs82blc3c4ifz2dw1048sqpkbz6vkk1zqpc53x"))))
16729 (properties `((upstream-name . "systemfonts")))
16730 (build-system r-build-system)
16732 `(("r-cpp11" ,r-cpp11)))
16734 `(("fontconfig" ,fontconfig)
16737 `(("pkg-config" ,pkg-config)
16738 ("r-knitr" ,r-knitr)))
16739 (home-page "https://github.com/r-lib/systemfonts")
16740 (synopsis "System native font finding")
16742 "This package provides system native access to the font catalogue. As
16743 font handling varies between systems it is difficult to correctly locate
16744 installed fonts across different operating systems. The 'systemfonts' package
16745 provides bindings to the native libraries for finding font files that can then
16746 be used further by e.g. graphic devices.")
16747 (license license:expat)))
16749 (define-public r-graphlayouts
16751 (name "r-graphlayouts")
16756 (uri (cran-uri "graphlayouts" version))
16759 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
16760 (properties `((upstream-name . "graphlayouts")))
16761 (build-system r-build-system)
16763 `(("r-igraph" ,r-igraph)
16765 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16766 (home-page "https://github.com/schochastics/graphlayouts")
16767 (synopsis "Additional layout algorithms for network visualizations")
16769 "This package provides several layout algorithms to visualize networks
16770 which are not part of the igraph library. Most are based on the concept of
16771 stress majorization by Gansner et al. (2004)
16772 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16773 emphasize hidden group structures in networks or focus on specific nodes.")
16774 (license license:expat)))
16776 (define-public r-tidygraph
16778 (name "r-tidygraph")
16783 (uri (cran-uri "tidygraph" version))
16786 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16787 (properties `((upstream-name . "tidygraph")))
16788 (build-system r-build-system)
16790 `(("r-dplyr" ,r-dplyr)
16791 ("r-igraph" ,r-igraph)
16792 ("r-magrittr" ,r-magrittr)
16793 ("r-pillar" ,r-pillar)
16796 ("r-rlang" ,r-rlang)
16797 ("r-tibble" ,r-tibble)
16798 ("r-tidyr" ,r-tidyr)))
16799 (home-page "https://github.com/thomasp85/tidygraph")
16800 (synopsis "Tidy API for graph manipulation")
16802 "This package provides a graph implementation that can be thought of as
16803 two tidy data frames describing node and edge data respectively. It provides
16804 an approach to manipulate these two virtual data frames using the API defined
16805 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16806 common graph algorithms.")
16807 (license license:expat)))
16809 (define-public r-soupx
16810 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16814 (version (git-version "0.3.1" revision commit))
16818 (uri (git-reference
16819 (url "https://github.com/constantAmateur/SoupX")
16821 (file-name (git-file-name name version))
16824 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16825 (properties `((upstream-name . "SoupX")))
16826 (build-system r-build-system)
16828 `(("r-ggplot2" ,r-ggplot2)
16829 ("r-matrix" ,r-matrix)
16830 ("r-seurat" ,r-seurat)))
16831 (home-page "https://github.com/constantAmateur/SoupX")
16832 (synopsis "Single cell mRNA Soup eXterminator")
16834 "This package provides a package for quantifying, profiling and
16835 removing cell free mRNA contamination (the \"soup\") from droplet based single
16836 cell RNA-seq experiments.")
16837 (license license:gpl2))))
16839 (define-public r-assertr
16846 (uri (cran-uri "assertr" version))
16849 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16850 (build-system r-build-system)
16852 `(("r-dplyr" ,r-dplyr)
16854 ("r-rlang" ,r-rlang)))
16856 `(("r-knitr" ,r-knitr))) ; needed for vignette
16857 (home-page "https://github.com/ropensci/assertr")
16858 (synopsis "Assertive programming for R analysis pipelines")
16860 "This package provides functionality to assert conditions that have to be
16861 met so that errors in data used in analysis pipelines can fail quickly. It is
16862 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16864 (license license:expat)))
16866 (define-public r-parameters
16868 (name "r-parameters")
16873 (uri (cran-uri "parameters" version))
16876 "17jjmy1qnx25ldvasrwhmal45nl1sr8qjxprbi8fcjwra9af6cr6"))))
16877 (properties `((upstream-name . "parameters")))
16878 (build-system r-build-system)
16880 `(("r-bayestestr" ,r-bayestestr)
16881 ("r-insight" ,r-insight)))
16883 `(("r-knitr" ,r-knitr)))
16884 (home-page "https://cran.r-project.org/web/packages/parameters")
16885 (synopsis "Processing of model parameters")
16887 "This package provides utilities for processing the parameters of various
16888 statistical models. Beyond computing p values, CIs, and other indices for a
16889 wide variety of models, this package implements features like standardization
16890 or bootstrapping of parameters and models, feature reduction (feature
16891 extraction and variable selection) as well as conversion between indices of
16893 (license license:gpl3)))
16895 (define-public r-rgdal
16902 (uri (cran-uri "rgdal" version))
16904 (base32 "1pr267sh0v6cympdg12yny51cmn4r20s5sjq2hqymn4kphcpqijk"))))
16905 (properties `((upstream-name . "rgdal")))
16906 (build-system r-build-system)
16914 `(("pkg-config" ,pkg-config)
16915 ("r-knitr" ,r-knitr)))
16916 (home-page "http://rgdal.r-forge.r-project.org")
16917 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16919 "This package provides bindings to the Geospatial Data Abstraction
16920 Library (GDAL) and access to projection/transformation operations from the
16922 (license license:gpl2+)))
16924 (define-public r-insol
16931 (uri (cran-uri "insol" version))
16934 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16935 (properties `((upstream-name . "insol")))
16936 (build-system r-build-system)
16938 `(("r-raster" ,r-raster)))
16940 `(("gfortran" ,gfortran)))
16941 (home-page "https://meteoexploration.com/R/insol/index.html")
16942 (synopsis "Tools for calculating solar radiation")
16944 "This package provides functions to compute insolation on tilted
16945 surfaces, computes atmospheric transmittance and related parameters such as:
16946 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16947 time, vector in the direction of the sun, vector normal to surface, and some
16948 atmospheric physics.")
16949 (license license:gpl2+)))
16951 (define-public r-lifecycle
16953 (name "r-lifecycle")
16958 (uri (cran-uri "lifecycle" version))
16961 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16962 (properties `((upstream-name . "lifecycle")))
16963 (build-system r-build-system)
16965 `(("r-glue" ,r-glue)
16966 ("r-rlang" ,r-rlang)))
16968 `(("r-knitr" ,r-knitr))) ; for vignettes
16969 (home-page "https://github.com/r-lib/lifecycle")
16970 (synopsis "Manage the life cycle of your package functions")
16972 "Manage the life cycle of your exported functions with shared
16973 conventions, documentation badges, and non-invasive deprecation warnings. The
16974 lifecycle package defines four development stages (experimental, maturing,
16975 stable, and questioning) and three deprecation stages (soft-deprecated,
16976 deprecated, and defunct). It makes it easy to insert badges corresponding to
16977 these stages in your documentation. Usage of deprecated functions are
16978 signalled with increasing levels of non-invasive verbosity.")
16979 (license license:gpl3)))
16981 (define-public r-assertable
16983 (name "r-assertable")
16988 (uri (cran-uri "assertable" version))
16991 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16992 (build-system r-build-system)
16994 `(("r-data-table" ,r-data-table)))
16995 (home-page "https://cran.r-project.org/web/packages/assertable/")
16996 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16997 (description "This package provides simple, flexible assertions on
16998 data.frame or data.table objects with verbose output for vetting. While other
16999 assertion packages apply towards more general use-cases, @code{assertable} is
17000 tailored towards tabular data. It includes functions to check variable names
17001 and values, whether the dataset contains all combinations of a given set of
17002 unique identifiers, and whether it is a certain length. In addition,
17003 @code{assertable} includes utility functions to check the existence of target
17004 files and to efficiently import multiple tabular data files into one
17006 (license license:gpl3)))
17008 (define-public r-quadprog
17010 (name "r-quadprog")
17015 (uri (cran-uri "quadprog" version))
17017 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
17018 (build-system r-build-system)
17020 `(("gfortran" ,gfortran)))
17021 (home-page "https://cran.r-project.org/web/packages/quadprog")
17022 (synopsis "Functions to solve quadratic programming problems")
17024 "This package contains routines and documentation for solving quadratic
17025 programming problems.")
17026 (license license:gpl3+)))
17028 (define-public r-desolve
17035 (uri (cran-uri "deSolve" version))
17037 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
17038 (properties `((upstream-name . "deSolve")))
17039 (build-system r-build-system)
17041 `(("gfortran" ,gfortran)))
17042 (home-page "https://desolve.r-forge.r-project.org/")
17043 (synopsis "Solvers for initial value problems of differential equations")
17044 (description "This package provides functions that solve initial value
17045 problems of a system of first-order @dfn{ordinary differential
17046 equations} (ODE), of @dfn{partial differential equations} (PDE), of
17047 @dfn{differential algebraic equations} (DAE), and of delay differential
17048 equations. The functions provide an interface to the FORTRAN functions
17049 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
17050 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
17051 C-implementation of solvers of the Runge-Kutta family with fixed or variable
17052 time steps. The package contains routines designed for solving ODEs resulting
17053 from 1-D, 2-D and 3-D partial differential equations that have been converted
17054 to ODEs by numerical differencing.")
17055 (license license:gpl2+)))
17057 (define-public r-pracma
17063 (uri (cran-uri "pracma" version))
17065 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
17066 (build-system r-build-system)
17067 (home-page "https://cran.r-project.org/web/packages/pracma/")
17068 (synopsis "Practical numerical math functions")
17069 (description "This package provides functions for numerical analysis and
17070 linear algebra, numerical optimization, differential equations, plus some
17071 special functions. It uses Matlab function names where appropriate to simplify
17073 (license license:gpl3+)))
17075 (define-public r-subplex
17082 (uri (cran-uri "subplex" version))
17085 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
17086 (build-system r-build-system)
17088 `(("gfortran" ,gfortran)))
17089 (home-page "https://cran.r-project.org/web/packages/subplex")
17090 (synopsis "Unconstrained optimization using the subplex algorithm")
17092 "This package implements the Subplex optimization algorithm.
17093 It solves unconstrained optimization problems using a simplex method on
17094 subspaces. The method is well suited for optimizing objective functions that
17095 are noisy or are discontinuous at the solution.")
17096 (license license:gpl3+)))
17098 (define-public r-txtplot
17105 (uri (cran-uri "txtplot" version))
17108 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
17109 (build-system r-build-system)
17110 (home-page "https://cran.r-project.org/web/packages/txtplot/")
17111 (synopsis "Text-based plotting")
17112 (description "This package provides functions to produce rudimentary ASCII
17113 graphics directly in the terminal window. This package provides a basic
17114 plotting function (and equivalents of curve, density, acf and barplot) as well
17115 as a boxplot function.")
17116 (license license:lgpl3+)))
17118 (define-public r-bio3d
17125 (uri (cran-uri "bio3d" version))
17128 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
17129 (properties `((upstream-name . "bio3d")))
17130 (build-system r-build-system)
17131 (inputs `(("zlib" ,zlib)))
17132 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17133 (home-page "http://thegrantlab.org/bio3d/")
17134 (synopsis "Biological structure analysis")
17136 "This package provides utilities to process, organize and explore protein
17137 structure, sequence and dynamics data. Features include the ability to read
17138 and write structure, sequence and dynamic trajectory data, perform sequence
17139 and structure database searches, data summaries, atom selection, alignment,
17140 superposition, rigid core identification, clustering, torsion analysis,
17141 distance matrix analysis, structure and sequence conservation analysis, normal
17142 mode analysis, principal component analysis of heterogeneous structure data,
17143 and correlation network analysis from normal mode and molecular dynamics data.
17144 In addition, various utility functions are provided to enable the statistical
17145 and graphical power of the R environment to work with biological sequence and
17147 (license license:gpl2+)))
17149 (define-public r-bios2cor
17151 (name "r-bios2cor")
17156 (uri (cran-uri "Bios2cor" version))
17159 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
17160 (properties `((upstream-name . "Bios2cor")))
17161 (build-system r-build-system)
17163 `(("r-bigmemory" ,r-bigmemory)
17164 ("r-bio3d" ,r-bio3d)
17165 ("r-circular" ,r-circular)
17166 ("r-igraph" ,r-igraph)))
17167 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
17168 (synopsis "From biological sequences and simulations to correlation analysis")
17170 "This package provides utilities for computation and analysis of
17171 correlation/covariation in multiple sequence alignments and in side chain
17172 motions during molecular dynamics simulations. Features include the
17173 computation of correlation/covariation scores using a variety of scoring
17174 functions between either sequence positions in alignments or side chain
17175 dihedral angles in molecular dynamics simulations and utilities to analyze the
17176 correlation/covariation matrix through a variety of tools including network
17177 representation and principal components analysis. In addition, several
17178 utility functions are based on the R graphical environment to provide friendly
17179 tools for help in data interpretation.")
17180 (license license:gpl2+)))
17182 ;; This package includes minified JavaScript files. When upgrading please
17183 ;; check that there are no new minified JavaScript files.
17184 (define-public r-networkd3
17186 (name "r-networkd3")
17191 (uri (cran-uri "networkD3" version))
17194 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
17197 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
17199 (properties `((upstream-name . "networkD3")))
17200 (build-system r-build-system)
17202 `(#:modules ((guix build utils)
17203 (guix build r-build-system)
17207 (modify-phases %standard-phases
17208 (add-after 'unpack 'process-javascript
17209 (lambda* (#:key inputs #:allow-other-keys)
17210 (with-directory-excursion "inst/htmlwidgets/lib/"
17214 `((,(assoc-ref inputs "d3.v4.js")
17215 "d3-4.5.0/d3.min.js"))))
17216 (lambda (sources targets)
17217 (for-each (lambda (source target)
17218 (format #t "Processing ~a --> ~a~%"
17220 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17221 (call-with-output-file target
17223 (dump-port minified port)))))
17224 sources targets))))
17227 `(("uglify-js" ,uglify-js)
17228 ;; NOTE: Make sure that this version of d3 is still valid when
17229 ;; upgrading the package.
17233 (uri "https://d3js.org/d3.v4.js")
17236 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17238 `(("r-htmlwidgets" ,r-htmlwidgets)
17239 ("r-igraph" ,r-igraph)
17240 ("r-magrittr" ,r-magrittr)))
17241 (home-page "https://cran.r-project.org/package=networkD3")
17242 (synopsis "D3 JavaScript network graphs from R")
17244 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17246 (license license:gpl3+)))
17248 (define-public r-aasea
17255 (uri (cran-uri "aaSEA" version))
17258 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17259 (properties `((upstream-name . "aaSEA")))
17260 (build-system r-build-system)
17262 `(("r-bios2cor" ,r-bios2cor)
17264 ("r-hmisc" ,r-hmisc)
17265 ("r-magrittr" ,r-magrittr)
17266 ("r-networkd3" ,r-networkd3)
17267 ("r-plotly" ,r-plotly)
17268 ("r-seqinr" ,r-seqinr)
17269 ("r-shiny" ,r-shiny)
17270 ("r-shinydashboard" ,r-shinydashboard)))
17271 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17272 (synopsis "Amino acid substitution effect analyzer")
17274 "Given a protein multiple sequence alignment, it is a daunting task to
17275 assess the effects of substitutions along sequence length. The aaSEA package
17276 is intended to help researchers to rapidly analyze property changes caused by
17277 single, multiple and correlated amino acid substitutions in proteins.")
17278 (license license:gpl3)))
17280 (define-public r-abacus
17287 (uri (cran-uri "ABACUS" version))
17290 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17291 (properties `((upstream-name . "ABACUS")))
17292 (build-system r-build-system)
17294 `(("r-ggplot2" ,r-ggplot2)
17295 ("r-shiny" ,r-shiny)))
17296 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17297 (synopsis "Apps-based activities for communicating and understanding statistics")
17299 "This package provides a set of Shiny apps for effective communication
17300 and understanding in statistics. The current version includes properties of
17301 normal distribution, properties of sampling distribution, one-sample z and t
17302 tests, two samples independent (unpaired) t test and analysis of variance.")
17303 (license license:gpl3)))
17305 (define-public r-abc-rap
17312 (uri (cran-uri "ABC.RAP" version))
17315 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17316 (properties `((upstream-name . "ABC.RAP")))
17317 (build-system r-build-system)
17318 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17319 (synopsis "Array-based CpG region analysis pipeline")
17321 "This package aims to identify candidate genes that are differentially
17322 methylated between cases and controls. It applies Student's t-test and delta
17323 beta analysis to identify candidate genes containing multiple CpG sites.")
17324 (license license:gpl3)))
17326 (define-public r-abcadm
17333 (uri (cran-uri "abcADM" version))
17336 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17337 (properties `((upstream-name . "abcADM")))
17338 (build-system r-build-system)
17341 ("r-rcpp" ,r-rcpp)))
17342 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17343 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17345 "This package provides tools to estimate parameters of accumulated
17346 damage (load duration) models based on failure time data under a Bayesian
17347 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17348 long-term reliability under stochastic load profiles.")
17349 (license license:gpl3)))
17351 (define-public r-rglpk
17358 (uri (cran-uri "Rglpk" version))
17361 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17362 (properties `((upstream-name . "Rglpk")))
17363 (build-system r-build-system)
17365 `(("r-slam" ,r-slam)))
17368 (home-page "https://r-forge.r-project.org/projects/rglp/")
17369 (synopsis "R interface to the GNU Linear Programming Kit")
17371 "This package provides an R interface to the GNU Linear Programming Kit,
17372 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17373 integer linear programming} (MILP) and other related problems.")
17375 (license (list license:gpl2 license:gpl3))))
17377 (define-public r-abcdefba
17379 (name "r-abcdefba")
17384 (uri (cran-uri "abcdeFBA" version))
17387 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17388 (properties `((upstream-name . "abcdeFBA")))
17389 (build-system r-build-system)
17391 `(("r-corrplot" ,r-corrplot)
17392 ("r-lattice" ,r-lattice)
17394 ("r-rglpk" ,r-rglpk)))
17395 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17396 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17398 "This package provides functions for Constraint Based Simulation using
17399 Flux Balance Analysis and informative analysis of the data generated during
17401 (license license:gpl2)))
17403 (define-public r-abcrlda
17410 (uri (cran-uri "abcrlda" version))
17413 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17414 (properties `((upstream-name . "abcrlda")))
17415 (build-system r-build-system)
17416 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17417 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17419 "This package offers methods to perform @dfn{asymptotically
17420 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17421 cost-sensitive binary classification. The bias-correction is an estimate of
17422 the bias term added to regularized discriminant analysis that minimizes the
17424 (license license:gpl3)))
17426 (define-public r-abemus
17433 (uri (cran-uri "abemus" version))
17436 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17437 (properties `((upstream-name . "abemus")))
17438 (build-system r-build-system)
17440 `(("r-data-table" ,r-data-table)))
17441 (home-page "https://cran.r-project.org/web/packages/abemus/")
17442 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17444 "This package provides an implementation of @dfn{Adaptive Base Error
17445 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17446 platform-specific genetic knowledge and empirical signal to readily detect and
17447 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17448 cell free DNA} (cfDNA).")
17449 (license license:gpl3)))
17451 ;; This package includes minified JavaScript files. When upgrading please
17452 ;; check that there are no new minified JavaScript files.
17453 (define-public r-rintrojs
17455 (name "r-rintrojs")
17460 (uri (cran-uri "rintrojs" version))
17463 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17464 (properties `((upstream-name . "rintrojs")))
17465 (build-system r-build-system)
17467 `(#:modules ((guix build utils)
17468 (guix build r-build-system)
17472 (modify-phases %standard-phases
17473 (add-after 'unpack 'process-javascript
17474 (lambda* (#:key inputs #:allow-other-keys)
17475 (with-directory-excursion "inst/javascript/introjs/"
17479 `((,(assoc-ref inputs "intro.js")
17481 (lambda (sources targets)
17482 (for-each (lambda (source target)
17483 (format #t "Processing ~a --> ~a~%"
17485 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17486 (call-with-output-file target
17488 (dump-port minified port)))))
17489 sources targets))))
17492 `(("uglify-js" ,uglify-js)
17496 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17499 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17501 `(("r-jsonlite" ,r-jsonlite)
17502 ("r-shiny" ,r-shiny)))
17503 (home-page "https://github.com/carlganz/rintrojs")
17504 (synopsis "Wrapper for the Intro.js library")
17506 "This package provides a wrapper for the @url{http://www.introjs.com,
17507 Intro.js} library. This package makes it easy to include step-by-step
17508 introductions, and clickable hints in a Shiny application. It supports both
17509 static introductions in the UI, and programmatic introductions from the
17511 (license license:agpl3+)))
17513 (define-public r-sysfonts
17515 (name "r-sysfonts")
17520 (uri (cran-uri "sysfonts" version))
17523 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17524 (properties `((upstream-name . "sysfonts")))
17525 (build-system r-build-system)
17527 `(("freetype" ,freetype)
17531 `(("pkg-config" ,pkg-config)))
17532 (home-page "https://github.com/yixuan/sysfonts")
17533 (synopsis "Loading fonts into R")
17535 "This is a package to simplify loading of system fonts and Google Fonts
17536 into R, in order to support other packages.")
17537 (license license:gpl2)))
17539 (define-public r-showtextdb
17541 (name "r-showtextdb")
17546 (uri (cran-uri "showtextdb" version))
17549 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17550 (properties `((upstream-name . "showtextdb")))
17551 (build-system r-build-system)
17553 `(("r-sysfonts" ,r-sysfonts)))
17554 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17555 (synopsis "Font files for the 'showtext' package")
17557 "This package provides font files that can be used by the @code{showtext}
17559 (license license:asl2.0)))
17561 (define-public r-showtext
17563 (name "r-showtext")
17568 (uri (cran-uri "showtext" version))
17571 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17572 (properties `((upstream-name . "showtext")))
17573 (build-system r-build-system)
17575 `(("freetype" ,freetype)
17579 `(("r-showtextdb" ,r-showtextdb)
17580 ("r-sysfonts" ,r-sysfonts)))
17582 `(("pkg-config" ,pkg-config)
17583 ("r-knitr" ,r-knitr)))
17584 (home-page "https://github.com/yixuan/showtext")
17585 (synopsis "Using fonts more easily in R graphs")
17587 "This package aims to make it easy to use various types of
17588 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17589 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17590 will be converted into polygons or raster images, hence after the plot has
17591 been created, it no longer relies on the font files. No external software
17592 such as Ghostscript is needed to use this package.")
17593 (license license:asl2.0)))
17595 (define-public r-emojifont
17597 (name "r-emojifont")
17602 (uri (cran-uri "emojifont" version))
17605 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17606 (properties `((upstream-name . "emojifont")))
17607 (build-system r-build-system)
17609 `(("r-ggplot2" ,r-ggplot2)
17610 ("r-proto" ,r-proto)
17611 ("r-showtext" ,r-showtext)
17612 ("r-sysfonts" ,r-sysfonts)))
17613 (home-page "https://guangchuangyu.github.io/emojifont")
17614 (synopsis "Emoji and Font Awesome in R graphics")
17616 "This package enables the use of emoji and the Font Awesome glyphs in
17617 both base and ggplot2 graphics.")
17618 (license license:artistic2.0)))
17620 (define-public r-abstractr
17622 (name "r-abstractr")
17627 (uri (cran-uri "abstractr" version))
17630 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17631 (properties `((upstream-name . "abstractr")))
17632 (build-system r-build-system)
17634 `(("r-colourpicker" ,r-colourpicker)
17635 ("r-emojifont" ,r-emojifont)
17636 ("r-ggplot2" ,r-ggplot2)
17637 ("r-gridextra" ,r-gridextra)
17638 ("r-rintrojs" ,r-rintrojs)
17639 ("r-shiny" ,r-shiny)
17640 ("r-shinythemes" ,r-shinythemes)))
17641 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17642 (synopsis "R-Shiny application for creating visual abstracts")
17644 "This package provides an R Shiny application to create visual abstracts
17645 for original research. A variety of user defined options and formatting are
17647 (license license:gpl3)))
17649 (define-public r-qgam
17656 (uri (cran-uri "qgam" version))
17659 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17660 (properties `((upstream-name . "qgam")))
17661 (build-system r-build-system)
17663 `(("r-doparallel" ,r-doparallel)
17666 ("r-shiny" ,r-shiny)))
17667 (native-inputs `(("r-knitr" ,r-knitr)))
17668 (home-page "https://cran.r-project.org/web/packages/qgam/")
17669 (synopsis "Smooth additive quantile regression models")
17671 "This package provides smooth additive quantile regression models, fitted
17672 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17673 the smoothing parameters are estimated automatically by marginal loss
17674 minimization, while the regression coefficients are estimated using either
17675 PIRLS or Newton algorithm. The learning rate is determined so that the
17676 Bayesian credible intervals of the estimated effects have approximately the
17677 correct coverage. The main function is @code{qgam()} which is similar to
17678 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17679 regression models.")
17680 (license license:gpl2+)))
17682 (define-public r-abtest
17689 (uri (cran-uri "abtest" version))
17692 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17693 (properties `((upstream-name . "abtest")))
17694 (build-system r-build-system)
17696 `(("r-matrix" ,r-matrix)
17697 ("r-mvtnorm" ,r-mvtnorm)
17698 ("r-plotrix" ,r-plotrix)
17700 ("r-rcolorbrewer" ,r-rcolorbrewer)
17703 ("r-truncnorm" ,r-truncnorm)))
17704 (home-page "https://cran.r-project.org/web/packages/abtest/")
17705 (synopsis "Bayesian A/B testing")
17707 "This package provides functions for Bayesian A/B testing including prior
17708 elicitation options based on Kass and Vaidyanathan (1992)
17709 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17710 (license license:gpl2+)))
17712 (define-public r-accept
17719 (uri (cran-uri "accept" version))
17722 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17723 (properties `((upstream-name . "accept")))
17724 (build-system r-build-system)
17726 `(("r-dplyr" ,r-dplyr)
17727 ("r-extrafont" ,r-extrafont)
17729 ("r-plotly" ,r-plotly)
17730 ("r-stringr" ,r-stringr)
17731 ("r-viridis" ,r-viridis)))
17732 (home-page "https://cran.r-project.org/web/packages/accept/")
17733 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17735 "This package allows clinicians to predict the rate and severity of
17736 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17737 Disease} (COPD) patients, based on the clinical prediction model published in
17738 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17739 (license license:gpl3)))
17741 (define-public r-smpracticals
17743 (name "r-smpracticals")
17748 (uri (cran-uri "SMPracticals" version))
17751 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17752 (properties `((upstream-name . "SMPracticals")))
17753 (build-system r-build-system)
17755 `(("r-ellipse" ,r-ellipse)
17758 ("r-survival" ,r-survival)))
17759 (home-page "http://statwww.epfl.ch/davison/SM/")
17760 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17762 "This package contains the datasets and a few functions for use with the
17763 practicals outlined in Appendix A of the book Statistical Models (Davison,
17764 2003, Cambridge University Press). The practicals themselves can be found at
17765 @url{http://statwww.epfl.ch/davison/SM/}.")
17766 (license license:gpl2+)))
17768 (define-public r-fgui
17775 (uri (cran-uri "fgui" version))
17778 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17779 (properties `((upstream-name . "fgui")))
17780 (build-system r-build-system)
17782 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17783 (synopsis "Create GUI for R functions")
17785 "Rapidly create a GUI for a function you created by automatically
17786 creating widgets for arguments of the function. This package automatically
17787 parses help routines for context-sensitive help to these arguments. The
17788 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17789 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17790 incorporated into the interface for greater customization for the more
17792 ;; Any version of the GPL.
17793 (license (list license:gpl2+ license:gpl3+))))
17795 (define-public r-tcltk2
17802 (uri (cran-uri "tcltk2" version))
17805 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17806 (properties `((upstream-name . "tcltk2")))
17807 (build-system r-build-system)
17811 (home-page "https://www.sciviews.org/SciViews-R")
17812 (synopsis "Tcl/Tk additions")
17814 "This package provides a series of additional Tcl commands and Tk widgets
17815 with style and various functions to supplement the tcltk package")
17816 (license license:lgpl3)))
17818 (define-public r-accrual
17825 (uri (cran-uri "accrual" version))
17828 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17829 (properties `((upstream-name . "accrual")))
17830 (build-system r-build-system)
17832 `(("r-fgui" ,r-fgui)
17833 ("r-smpracticals" ,r-smpracticals)
17834 ("r-tcltk2" ,r-tcltk2)))
17835 (home-page "https://cran.r-project.org/web/packages/accrual/")
17836 (synopsis "Bayesian accrual prediction")
17838 "Subject recruitment for medical research is challenging. Slow patient
17839 accrual leads to delay in research. Accrual monitoring during the process of
17840 recruitment is critical. Researchers need reliable tools to manage the
17841 accrual rate. This package provides an implementation of a Bayesian method
17842 that integrates researcher's experience on previous trials and data from the
17843 current study, providing reliable prediction on accrual rate for clinical
17844 studies. It provides functions for Bayesian accrual prediction which can be
17845 easily used by statisticians and clinical researchers.")
17846 (license license:gpl2)))
17848 (define-public r-accrued
17855 (uri (cran-uri "accrued" version))
17858 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17859 (properties `((upstream-name . "accrued")))
17860 (build-system r-build-system)
17861 (home-page "https://cran.r-project.org/web/packages/accrued/")
17862 (synopsis "Data quality visualization tools for partially accruing data")
17864 "This is a package for visualizing data quality of partially accruing
17866 (license license:gpl3)))
17868 (define-public r-mda
17875 (uri (cran-uri "mda" version))
17878 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17879 (properties `((upstream-name . "mda")))
17880 (build-system r-build-system)
17881 (propagated-inputs `(("r-class" ,r-class)))
17882 (native-inputs `(("gfortran" ,gfortran)))
17883 (home-page "https://cran.r-project.org/web/packages/mda/")
17884 (synopsis "Mixture and flexible discriminant analysis")
17886 "This is a package for mixture and flexible discriminant analysis,
17887 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17888 (license license:gpl2)))
17890 (define-public r-elasticnet
17892 (name "r-elasticnet")
17897 (uri (cran-uri "elasticnet" version))
17900 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17901 (properties `((upstream-name . "elasticnet")))
17902 (build-system r-build-system)
17904 `(("r-lars" ,r-lars)))
17905 (home-page "http://users.stat.umn.edu/~zouxx019/")
17906 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17908 "This package provides functions for fitting the entire solution path of
17909 the Elastic-Net and also provides functions for estimating sparse Principal
17910 Components. The Lasso solution paths can be computed by the same function.")
17911 (license license:gpl2+)))
17913 (define-public r-sparselda
17915 (name "r-sparselda")
17920 (uri (cran-uri "sparseLDA" version))
17923 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17924 (properties `((upstream-name . "sparseLDA")))
17925 (build-system r-build-system)
17927 `(("r-elasticnet" ,r-elasticnet)
17930 (home-page "https://www.imm.dtu.dk/~lkhc/")
17931 (synopsis "Sparse discriminant analysis")
17933 "This package performs sparse linear discriminant analysis for Gaussians
17934 and mixture of Gaussian models.")
17935 (license license:gpl2+)))
17937 (define-public r-accsda
17944 (uri (cran-uri "accSDA" version))
17947 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17948 (properties `((upstream-name . "accSDA")))
17949 (build-system r-build-system)
17951 `(("r-ggplot2" ,r-ggplot2)
17952 ("r-ggthemes" ,r-ggthemes)
17953 ("r-gridextra" ,r-gridextra)
17955 ("r-rarpack" ,r-rarpack)
17956 ("r-sparselda" ,r-sparselda)))
17957 (home-page "https://github.com/gumeo/accSDA/wiki")
17958 (synopsis "Accelerated sparse discriminant analysis")
17960 "This package provides an implementation of sparse linear discriminant
17961 analysis, which is a supervised classification method for multiple classes.
17962 Various novel optimization approaches to this problem are implemented
17963 including @dfn{alternating direction method of multipliers} (ADMM),
17964 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17965 Functions for performing cross validation are also supplied along with basic
17966 prediction and plotting functions. @dfn{Sparse zero variance
17967 discriminant} (SZVD) analysis is also included in the package.")
17968 (license license:gpl2+)))
17970 (define-public r-ace2fastq
17972 (name "r-ace2fastq")
17977 (uri (cran-uri "ace2fastq" version))
17980 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17981 (properties `((upstream-name . "ace2fastq")))
17982 (build-system r-build-system)
17984 `(("r-stringr" ,r-stringr)))
17985 (home-page "https://github.com/c5sire/ace2fastq")
17986 (synopsis "ACE file to FASTQ converter")
17988 "The ACE file format is used in genomics to store contigs from sequencing
17989 machines. This tools converts it into FASTQ format. Both formats contain the
17990 sequence characters and their corresponding quality information. Unlike the
17991 FASTQ file, the ACE file stores the quality values numerically. The
17992 conversion algorithm uses the standard Sanger formula. The package
17993 facilitates insertion into pipelines, and content inspection.")
17994 (license license:gpl3)))
17996 (define-public r-rngwell
18003 (uri (cran-uri "rngWELL" version))
18006 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
18007 (properties `((upstream-name . "rngWELL")))
18008 (build-system r-build-system)
18009 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
18010 (synopsis "Toolbox for WELL random number generators")
18012 "This is a dedicated package to WELL pseudo random generators, which were
18013 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
18014 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
18015 (license license:bsd-3)))
18017 (define-public r-randtoolbox
18019 (name "r-randtoolbox")
18024 (uri (cran-uri "randtoolbox" version))
18027 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
18028 (properties `((upstream-name . "randtoolbox")))
18029 (build-system r-build-system)
18031 `(("r-rngwell" ,r-rngwell)))
18033 `(("gfortran" ,gfortran)))
18034 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
18035 (synopsis "Toolbox for pseudo and quasi random number generation")
18037 "This package provides
18040 @item pseudo random generators, such as general linear
18041 congruential generators, multiple recursive generators and generalized
18042 feedback shift register (SF-Mersenne Twister algorithm and WELL
18045 @item quasi random generators, such as the Torus algorithm, the Sobol
18046 sequence, the Halton sequence (including the Van der Corput sequence), and
18048 @item some generator tests: the gap test, the serial test, the poker test.
18051 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
18052 (license license:bsd-3)))
18054 (define-public r-lhs
18061 (uri (cran-uri "lhs" version))
18064 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
18065 (properties `((upstream-name . "lhs")))
18066 (build-system r-build-system)
18067 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18069 `(("r-knitr" ,r-knitr)))
18070 (home-page "https://github.com/bertcarnell/lhs")
18071 (synopsis "Latin Hypercube Samples")
18073 "This package provides a number of methods for creating and augmenting
18074 Latin Hypercube Samples.")
18075 (license license:gpl3)))
18077 (define-public r-acebayes
18079 (name "r-acebayes")
18084 (uri (cran-uri "acebayes" version))
18087 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
18088 (properties `((upstream-name . "acebayes")))
18089 (build-system r-build-system)
18091 `(("r-compare" ,r-compare)
18093 ("r-randtoolbox" ,r-randtoolbox)
18095 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18096 (home-page "https://cran.r-project.org/web/packages/acebayes/")
18097 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
18099 "Finding an optimal Bayesian experimental design involves maximizing an
18100 objective function given by the expectation of some appropriately chosen
18101 utility function with respect to the joint distribution of unknown
18102 quantities (including responses). This objective function is usually not
18103 available in closed form and the design space can be continuous and of high
18104 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
18105 to maximise an approximation to the expectation of the utility function.")
18106 (license license:gpl2)))
18108 (define-public r-acet
18115 (uri (cran-uri "ACEt" version))
18118 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
18119 (properties `((upstream-name . "ACEt")))
18120 (build-system r-build-system)
18125 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18126 (home-page "https://cran.r-project.org/web/packages/ACEt/")
18127 (synopsis "Estimating dynamic heritability and twin model comparison")
18129 "This package supports twin models that are able to estimate the dynamic
18130 behaviour of the variance components in the classical twin models with respect
18131 to age using B-splines and P-splines.")
18132 (license license:gpl2+)))
18134 (define-public r-acfmperiod
18136 (name "r-acfmperiod")
18141 (uri (cran-uri "acfMPeriod" version))
18144 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
18145 (properties `((upstream-name . "acfMPeriod")))
18146 (build-system r-build-system)
18148 `(("r-mass" ,r-mass)))
18149 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
18150 (synopsis "Estimation of the ACF from the M-periodogram")
18152 "This package support non-robust and robust computations of the sample
18153 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
18154 univariate and multivariate processes. The methodology consists in reversing
18155 the diagonalization procedure involving the periodogram or the
18156 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
18157 ACOVF or the ACF as discussed in Fuller (1995)
18158 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
18159 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
18160 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
18161 (license license:gpl2+)))
18163 (define-public r-gamlss-data
18165 (name "r-gamlss-data")
18170 (uri (cran-uri "gamlss.data" version))
18173 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
18174 (properties `((upstream-name . "gamlss.data")))
18175 (build-system r-build-system)
18176 (home-page "http://www.gamlss.org/")
18177 (synopsis "GAMLSS data")
18179 "This package provides data used as examples to demonstrate GAMLSS
18181 ;; Either version of the license
18182 (license (list license:gpl2 license:gpl3))))
18184 (define-public r-gamlss
18191 (uri (cran-uri "gamlss" version))
18194 "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
18195 (properties `((upstream-name . "gamlss")))
18196 (build-system r-build-system)
18198 `(("r-gamlss-data" ,r-gamlss-data)
18199 ("r-gamlss-dist" ,r-gamlss-dist)
18202 ("r-survival" ,r-survival)))
18203 (home-page "http://www.gamlss.org/")
18204 (synopsis "Generalized additive models for location scale and shape")
18206 "This package provides functions for fitting the generalized additive
18207 models for location scale and shape introduced by Rigby and
18208 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
18209 use a distributional regression approach where all the parameters of the
18210 conditional distribution of the response variable are modelled using
18211 explanatory variables.")
18212 ;; Either version of the license
18213 (license (list license:gpl2 license:gpl3))))
18215 (define-public r-acid
18222 (uri (cran-uri "acid" version))
18225 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18226 (properties `((upstream-name . "acid")))
18227 (build-system r-build-system)
18229 `(("r-gamlss" ,r-gamlss)
18230 ("r-gamlss-dist" ,r-gamlss-dist)
18231 ("r-hmisc" ,r-hmisc)))
18232 (home-page "https://cran.r-project.org/web/packages/acid/")
18233 (synopsis "Analysing conditional income distributions")
18235 "This package provides functions for the analysis of income distributions
18236 for subgroups of the population as defined by a set of variables like age,
18237 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18238 distribution as well as functions for moments, inequality measures, entropy
18239 measures and polarisation measures of income distributions. This package thus
18240 aides the analysis of income inequality by offering tools for the exploratory
18241 analysis of income distributions at the disaggregated level.")
18242 (license license:gpl3)))
18244 (define-public r-acm4r
18251 (uri (cran-uri "acm4r" version))
18254 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18255 (properties `((upstream-name . "acm4r")))
18256 (build-system r-build-system)
18257 (propagated-inputs `(("r-mass" ,r-mass)))
18258 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18259 (synopsis "Align-and-count method comparisons of RFLP data")
18261 "This is a package to compare sequence fragment lengths or molecular
18262 weights from pairs of lanes. The number of matching bands in the
18263 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18264 the align-and-count method.")
18265 ;; Any version of the GPL
18266 (license (list license:gpl2+ license:gpl3+))))
18268 (define-public r-filematrix
18270 (name "r-filematrix")
18275 (uri (cran-uri "filematrix" version))
18278 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18279 (properties `((upstream-name . "filematrix")))
18280 (build-system r-build-system)
18281 ;; These inputs are needed for vignettes
18283 `(("r-knitr" ,r-knitr)
18284 ("r-rmarkdown" ,r-rmarkdown)
18285 ("pandoc-citeproc" ,pandoc-citeproc)))
18286 (home-page "https://github.com/andreyshabalin/filematrix")
18287 (synopsis "File-backed matrix class with convenient read and write access")
18289 "This package provides an interface for working with large matrices
18290 stored in files, not in computer memory. It supports multiple non-character
18291 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18292 byte real values). Access to parts of the matrix is done by indexing, exactly
18293 as with usual R matrices. It supports very large matrices; the package has
18294 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18295 columns, ad allows for quick addition of extra columns to a filematrix.")
18296 (license license:lgpl3)))
18298 (define-public r-acmeeqtl
18300 (name "r-acmeeqtl")
18305 (uri (cran-uri "ACMEeqtl" version))
18308 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18309 (properties `((upstream-name . "ACMEeqtl")))
18310 (build-system r-build-system)
18312 `(("r-filematrix" ,r-filematrix)))
18313 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18314 (synopsis "Estimation of interpretable eQTL effect sizes")
18316 "This package provides a non-linear model, termed ACME, that reflects a
18317 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18318 With non-linear least-squares algorithm the maximum likelihood parameters can
18319 be estimated. The ACME model provides interpretable effect size estimates and
18320 p-values with well controlled Type-I error.")
18321 (license license:lgpl3)))
18323 (define-public r-acmer
18330 (uri (cran-uri "acmeR" version))
18333 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18334 (properties `((upstream-name . "acmeR")))
18335 (build-system r-build-system)
18336 (propagated-inputs `(("r-foreign" ,r-foreign)))
18337 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18338 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18340 "This package provides an implementation of the ACME estimator, described
18341 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18342 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18343 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18344 as carcasses age; variable bleed-through at successive searches; and interval
18345 mortality estimates. The package provides, based on search data, functions
18346 for estimating the mortality inflation factor in Frequentist and Bayesian
18348 (license license:expat)))
18350 (define-public r-r-huge
18357 (uri (cran-uri "R.huge" version))
18360 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18361 (properties `((upstream-name . "R.huge")))
18362 (build-system r-build-system)
18364 `(("r-r-methodss3" ,r-r-methodss3)
18366 ("r-r-utils" ,r-r-utils)))
18367 (home-page "https://github.com/HenrikBengtsson/R.huge")
18368 (synopsis "Methods for accessing huge amounts of data")
18370 "This is a deprecated package for accessing huge amounts of data.
18371 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18372 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18373 the @code{aroma.affymetrix} package.")
18374 (license license:lgpl2.1+)))
18376 (define-public r-r-filesets
18378 (name "r-r-filesets")
18383 (uri (cran-uri "R.filesets" version))
18386 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18387 (properties `((upstream-name . "R.filesets")))
18388 (build-system r-build-system)
18390 `(("r-digest" ,r-digest)
18391 ("r-r-cache" ,r-r-cache)
18392 ("r-r-methodss3" ,r-r-methodss3)
18394 ("r-r-utils" ,r-r-utils)))
18395 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18396 (synopsis "Easy handling of and access to files")
18398 "This package provides classes and methods to locate, setup, subset,
18399 navigate and iterate file sets, i.e. sets of files located in one or more
18400 directories on the file system. The API is designed such that these classes
18401 can be extended via inheritance to provide a richer API for special file
18402 formats. Moreover, a specific name format is defined such that filenames and
18403 directories can be considered to have full names which consists of a name
18404 followed by comma-separated tags. This adds additional flexibility to
18405 identify file sets and individual files.")
18406 (license license:lgpl2.1+)))
18408 (define-public r-r-devices
18410 (name "r-r-devices")
18415 (uri (cran-uri "R.devices" version))
18418 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18419 (properties `((upstream-name . "R.devices")))
18420 (build-system r-build-system)
18422 `(("r-base64enc" ,r-base64enc)
18423 ("r-r-methodss3" ,r-r-methodss3)
18425 ("r-r-utils" ,r-r-utils)))
18426 (home-page "https://github.com/HenrikBengtsson/R.devices")
18427 (synopsis "Unified handling of graphics devices")
18429 "This package provides functions for creating plots and image files in a
18430 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18431 Default device options as well as scales and aspect ratios are controlled in a
18432 uniform way across all device types. Switching output format requires minimal
18433 changes in code. This package is ideal for large-scale batch processing,
18434 because it will never leave open graphics devices or incomplete image files
18435 behind, even on errors or user interrupts.")
18436 (license license:lgpl2.1+)))
18438 (define-public r-acnr
18445 (uri (cran-uri "acnr" version))
18448 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18449 (properties `((upstream-name . "acnr")))
18450 (build-system r-build-system)
18451 (home-page "https://github.com/mpierrejean/acnr")
18452 (synopsis "Annotated copy-number regions")
18454 "This package provides SNP array data from different types of copy-number
18455 regions. These regions were identified manually by the authors of the package
18456 and may be used to generate realistic data sets with known truth.")
18457 (license license:lgpl2.1+)))
18459 (define-public r-acopula
18466 (uri (cran-uri "acopula" version))
18469 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18470 (properties `((upstream-name . "acopula")))
18471 (build-system r-build-system)
18472 (home-page "https://cran.r-project.org/web/packages/acopula/")
18473 (synopsis "Modelling dependence with multivariate Archimax copulas")
18475 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18476 package provides definitions of several parametric families of generator and
18477 dependence function, computes CDF and PDF, estimates parameters, tests for
18478 goodness of fit, generates random sample and checks copula properties for
18479 custom constructs. In the 2-dimensional case explicit formulas for density
18480 are used, contrary to higher dimensions when all derivatives are linearly
18481 approximated. Several non-archimax families (normal, FGM, Plackett) are
18482 provided as well.")
18483 (license license:gpl2)))
18485 (define-public r-tuner
18492 (uri (cran-uri "tuneR" version))
18495 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18496 (properties `((upstream-name . "tuneR")))
18497 (build-system r-build-system)
18498 (propagated-inputs `(("r-signal" ,r-signal)))
18499 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18500 (synopsis "Analysis of music and speech")
18502 "This is a package for the analysis of music and speech. Analyze music
18503 and speech, extract features like MFCCs, handle wave files and their
18504 representation in various ways, read MP3, read MIDI, perform steps of a
18505 transcription, ...")
18506 ;; Either of these versions.
18507 (license (list license:gpl2 license:gpl3))))
18509 (define-public r-seewave
18516 (uri (cran-uri "seewave" version))
18519 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18520 (properties `((upstream-name . "seewave")))
18521 (build-system r-build-system)
18523 `(("libsndfile" ,libsndfile)))
18525 `(("r-tuner" ,r-tuner)))
18526 (home-page "http://rug.mnhn.fr/seewave")
18527 (synopsis "Sound analysis and synthesis")
18529 "This package provides functions for analysing, manipulating, displaying,
18530 editing and synthesizing time waves (particularly sound). This package
18531 processes time analysis (oscillograms and envelopes), spectral content,
18532 resonance quality factor, entropy, cross correlation and autocorrelation,
18533 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18534 and 3D spectrograms and many other analyses.")
18535 (license license:gpl2+)))
18537 (define-public r-acousticndlcoder
18539 (name "r-acousticndlcoder")
18544 (uri (cran-uri "AcousticNDLCodeR" version))
18547 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18549 `((upstream-name . "AcousticNDLCodeR")))
18550 (build-system r-build-system)
18552 `(("r-seewave" ,r-seewave)
18553 ("r-tuner" ,r-tuner)
18555 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18556 (synopsis "Coding sound files for use with NDL")
18558 "Make acoustic cues to use with the R package @code{ndl}.
18559 The package implements functions used in the PLoS ONE paper \"Words from
18560 spontaneous conversational speech can be recognized with human-like accuracy
18561 by an error-driven learning algorithm that discriminates between meanings
18562 straight from smart acoustic features, bypassing the phoneme as recognition
18563 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18564 (license license:gpl2+)))
18566 (define-public r-acp
18573 (uri (cran-uri "acp" version))
18576 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18577 (properties `((upstream-name . "acp")))
18578 (build-system r-build-system)
18580 `(("r-quantmod" ,r-quantmod)
18581 ("r-tseries" ,r-tseries)))
18582 (home-page "https://cran.r-project.org/web/packages/acp/")
18583 (synopsis "Autoregressive conditional Poisson")
18585 "This package supports the analysis of count data exhibiting
18586 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18587 model (ACP(p,q)) proposed by Heinen (2003).")
18588 (license license:gpl2)))
18590 (define-public r-ada
18597 (uri (cran-uri "ada" version))
18600 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18601 (properties `((upstream-name . "ada")))
18602 (build-system r-build-system)
18603 (propagated-inputs `(("r-rpart" ,r-rpart)))
18604 (home-page "https://cran.r-project.org/web/packages/ada/")
18605 (synopsis "Stochastic boosting")
18607 "This package provides a straightforward, well-documented, and broad
18608 boosting routine for classification, ideally suited for small to
18609 moderate-sized data sets. It performs discrete, real, and gentle boost under
18610 both exponential and logistic loss on a given data set.")
18611 ;; Any version of the GPL.
18612 (license (list license:gpl2+ license:gpl3+))))
18614 (define-public r-genalg
18621 (uri (cran-uri "genalg" version))
18624 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18625 (properties `((upstream-name . "genalg")))
18626 (build-system r-build-system)
18627 (home-page "https://github.com/egonw/genalg")
18628 (synopsis "R based genetic algorithm")
18630 "This package provides an R based genetic algorithm for binary and
18631 floating point chromosomes.")
18632 (license license:gpl2)))
18634 (define-public r-kernelfactory
18636 (name "r-kernelfactory")
18641 (uri (cran-uri "kernelFactory" version))
18644 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18645 (properties `((upstream-name . "kernelFactory")))
18646 (build-system r-build-system)
18649 ("r-genalg" ,r-genalg)
18650 ("r-kernlab" ,r-kernlab)
18651 ("r-randomforest" ,r-randomforest)))
18652 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18653 (synopsis "Ensemble of kernel machines")
18655 "Kernel factory is an ensemble method where each base classifier (random
18656 forest) is fit on the kernel matrix of a subset of the training data.")
18657 (license license:gpl2+)))
18659 (define-public r-dummies
18666 (uri (cran-uri "dummies" version))
18669 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18670 (properties `((upstream-name . "dummies")))
18671 (build-system r-build-system)
18672 (home-page "https://decisionpatterns.com")
18673 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18675 "This package lets you expand factors, characters and other eligible
18676 classes into dummy/indicator variables.")
18677 (license license:gpl2+)))
18679 (define-public r-acrm
18686 (uri (cran-uri "aCRM" version))
18689 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18690 (properties `((upstream-name . "aCRM")))
18691 (build-system r-build-system)
18694 ("r-dummies" ,r-dummies)
18695 ("r-kernelfactory" ,r-kernelfactory)
18696 ("r-randomforest" ,r-randomforest)))
18697 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18698 (synopsis "Convenience functions for analytical customer relationship management")
18700 "This package provides convenience functions for data preparation and
18701 modeling often used in @dfn{analytical customer relationship
18702 management} (aCRM).")
18703 (license license:gpl2+)))
18705 (define-public r-treeclust
18707 (name "r-treeclust")
18712 (uri (cran-uri "treeClust" version))
18715 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18716 (properties `((upstream-name . "treeClust")))
18717 (build-system r-build-system)
18719 `(("r-cluster" ,r-cluster)
18720 ("r-rpart" ,r-rpart)))
18721 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18722 (synopsis "Cluster distances through trees")
18724 "This package provides tools to create a measure of inter-point
18725 dissimilarity useful for clustering mixed data, and, optionally, perform the
18727 (license license:gpl2+)))
18729 (define-public r-acrosstic
18731 (name "r-acrosstic")
18736 (uri (cran-uri "AcrossTic" version))
18739 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18740 (properties `((upstream-name . "AcrossTic")))
18741 (build-system r-build-system)
18743 `(("r-lpsolve" ,r-lpsolve)
18744 ("r-treeclust" ,r-treeclust)))
18745 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18746 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18748 "This is a package for constructing minimum-cost regular spanning
18749 subgraph as part of a non-parametric two-sample test for equality of
18751 (license license:gpl2+)))
18753 (define-public r-acrt
18760 (uri (cran-uri "acrt" version))
18763 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18764 (properties `((upstream-name . "acrt")))
18765 (build-system r-build-system)
18767 `(("r-rcpp" ,r-rcpp)
18768 ("r-rcppeigen" ,r-rcppeigen)
18769 ("r-sandwich" ,r-sandwich)))
18770 (home-page "https://cran.r-project.org/web/packages/acrt/")
18771 (synopsis "Autocorrelation robust testing")
18773 "This package provides functions for testing affine hypotheses on the
18774 regression coefficient vector in regression models with autocorrelated
18776 (license license:gpl2)))
18778 (define-public r-acs
18785 (uri (cran-uri "acs" version))
18788 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18789 (properties `((upstream-name . "acs")))
18790 (build-system r-build-system)
18792 `(("r-httr" ,r-httr)
18795 ("r-stringr" ,r-stringr)
18797 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18798 (synopsis "Work with data from the US Census")
18800 "This package provides a general toolkit for downloading, managing,
18801 analyzing, and presenting data from the
18802 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18803 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18804 American Community Survey (ACS). Confidence intervals provided with ACS data
18805 are converted to standard errors to be bundled with estimates in complex
18806 @code{acs} objects. The package provides new methods to conduct standard
18807 operations on @code{acs} objects and present/plot data in statistically
18808 appropriate ways.")
18809 (license license:gpl3)))
18811 (define-public r-acss-data
18813 (name "r-acss-data")
18818 (uri (cran-uri "acss.data" version))
18821 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18822 (properties `((upstream-name . "acss.data")))
18823 (build-system r-build-system)
18824 (home-page "http://complexitycalculator.com/methodology.html")
18825 (synopsis "Data for algorithmic complexity of short strings")
18827 "This is a data only package providing the algorithmic complexity of
18828 short strings, computed using the coding theorem method. For a given set of
18829 symbols in a string, all possible or a large number of random samples of
18830 Turing machines with a given number of states (e.g., 5) and number of symbols
18831 corresponding to the number of symbols in the strings were simulated until
18832 they reached a halting state or failed to end. This package contains data on
18833 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18834 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18835 distribution of the halting states.")
18836 (license license:gpl2+)))
18838 (define-public r-acss
18845 (uri (cran-uri "acss" version))
18848 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18849 (properties `((upstream-name . "acss")))
18850 (build-system r-build-system)
18852 `(("r-acss-data" ,r-acss-data)
18854 (home-page "http://complexitycalculator.com/methodology.html")
18855 (synopsis "Algorithmic complexity for short strings")
18857 "The main purpose of this package is to provide the algorithmic
18858 complexity for short strings, an approximation of the Kolmogorov Complexity of
18859 a short string using the coding theorem method. While the database containing
18860 the complexity is provided in the data only package @code{acss.data}, this
18861 package provides functions accessing the data such as @code{prob_random}
18862 returning the posterior probability that a given string was produced by a
18863 random process. In addition, two traditional (but problematic) measures of
18864 complexity are also provided: entropy and change complexity.")
18865 (license license:gpl2+)))
18867 (define-public r-acswr
18874 (uri (cran-uri "ACSWR" version))
18877 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18878 (properties `((upstream-name . "ACSWR")))
18879 (build-system r-build-system)
18881 `(("r-mass" ,r-mass)))
18882 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18883 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18885 "This is a companion package for the book \"A Course in Statistics with
18886 R\" (ISBN 978-1-119-15272-9.)")
18887 (license license:gpl2)))
18889 (define-public r-alabama
18892 (version "2015.3-1")
18896 (uri (cran-uri "alabama" version))
18899 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18900 (properties `((upstream-name . "alabama")))
18901 (build-system r-build-system)
18902 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18903 (home-page "https://cran.r-project.org/web/packages/alabama/")
18904 (synopsis "Constrained nonlinear optimization")
18906 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18907 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18908 constraints. Linear or nonlinear equality and inequality constraints are
18910 (license license:gpl2+)))
18912 (define-public r-gdina
18919 (uri (cran-uri "GDINA" version))
18922 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18923 (properties `((upstream-name . "GDINA")))
18924 (build-system r-build-system)
18926 `(("r-alabama" ,r-alabama)
18927 ("r-ggplot2" ,r-ggplot2)
18929 ("r-nloptr" ,r-nloptr)
18930 ("r-numderiv" ,r-numderiv)
18932 ("r-rcpparmadillo" ,r-rcpparmadillo)
18933 ("r-rsolnp" ,r-rsolnp)
18934 ("r-shiny" ,r-shiny)
18935 ("r-shinydashboard" ,r-shinydashboard)))
18937 `(("r-knitr" ,r-knitr)))
18938 (home-page "https://github.com/Wenchao-Ma/GDINA")
18939 (synopsis "Generalized DINA model framework")
18941 "This package provides a set of psychometric tools for cognitive
18942 diagnosis modeling based on the generalized deterministic inputs, noisy and
18943 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18944 and its extensions, including the sequential G-DINA model by Ma and de la
18945 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18946 polytomous G-DINA model by Chen and de la Torre
18947 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18948 distribution can be independent, saturated, higher-order, loglinear smoothed
18949 or structured. Q-matrix validation, item and model fit statistics, model
18950 comparison at test and item level and differential item functioning can also
18951 be conducted. A graphical user interface is also provided.")
18952 (license license:gpl3)))
18954 (define-public r-actcd
18961 (uri (cran-uri "ACTCD" version))
18964 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18965 (properties `((upstream-name . "ACTCD")))
18966 (build-system r-build-system)
18968 `(("r-gdina" ,r-gdina)
18969 ("r-r-methodss3" ,r-r-methodss3)))
18971 `(("gfortran" ,gfortran)))
18972 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18973 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18975 "This is a package supporting cluster analysis for cognitive diagnosis
18976 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18977 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18978 sum-scores, cluster analysis techniques can be used to classify examinees into
18979 latent classes based on their attribute patterns. In addition to the
18980 algorithms used to classify data, three labeling approaches are proposed to
18981 label clusters so that examinees' attribute profiles can be obtained.")
18982 (license license:gpl2+)))
18984 (define-public r-ineq
18991 (uri (cran-uri "ineq" version))
18994 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18995 (properties `((upstream-name . "ineq")))
18996 (build-system r-build-system)
18997 (home-page "https://cran.r-project.org/web/packages/ineq/")
18998 (synopsis "Measuring inequality, concentration, and poverty")
19000 "This package provides tools for measuring inequality, concentration, and
19001 poverty measures. It provides both empirical and theoretical Lorenz curves.")
19002 ;; Either of these two versions.
19003 (license (list license:gpl2 license:gpl3))))
19005 (define-public r-actfrag
19012 (uri (cran-uri "ActFrag" version))
19015 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
19016 (properties `((upstream-name . "ActFrag")))
19017 (build-system r-build-system)
19019 `(("r-accelerometry" ,r-accelerometry)
19020 ("r-dplyr" ,r-dplyr)
19022 ("r-survival" ,r-survival)
19023 ("r-tidyr" ,r-tidyr)))
19024 (home-page "https://github.com/junruidi/ActFrag")
19025 (synopsis "Activity fragmentation metrics extraction")
19027 "This package provides functions to extract commonly used fragmentation
19028 metrics to quantify time accumulation strategies based on minute level
19029 actigraphy-measured activity counts data.")
19030 (license license:gpl3)))
19032 (define-public r-fda
19035 (version "5.1.5.1")
19039 (uri (cran-uri "fda" version))
19042 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
19043 (properties `((upstream-name . "fda")))
19044 (build-system r-build-system)
19046 `(("r-matrix" ,r-matrix)))
19047 (home-page "https://www.functionaldata.org")
19048 (synopsis "Functional data analysis")
19050 "These functions were developed to support functional data analysis as
19051 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
19052 Analysis. The package includes data sets and script files working many
19054 (license license:gpl2+)))
19056 (define-public r-actigraphy
19058 (name "r-actigraphy")
19063 (uri (cran-uri "Actigraphy" version))
19066 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
19067 (properties `((upstream-name . "Actigraphy")))
19068 (build-system r-build-system)
19070 `(("r-fda" ,r-fda)))
19071 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
19072 (synopsis "Actigraphy data analysis")
19074 "This package provides tools for functional linear modeling and analysis
19075 of actigraphy data.")
19076 (license license:asl2.0)))
19078 (define-public r-activedriver
19080 (name "r-activedriver")
19085 (uri (cran-uri "ActiveDriver" version))
19088 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
19089 (properties `((upstream-name . "ActiveDriver")))
19090 (build-system r-build-system)
19092 `(("r-mass" ,r-mass)))
19093 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
19094 (synopsis "Tools for finding cancer driver proteins")
19096 "This package provides a mutation analysis tool that discovers cancer
19097 driver genes with frequent mutations in protein signalling sites such as
19098 post-translational modifications (phosphorylation, ubiquitination, etc). The
19099 Poisson generalized linear regression model identifies genes where cancer
19100 mutations in signalling sites are more frequent than expected from the
19101 sequence of the entire gene. Integration of mutations with signalling
19102 information helps find new driver genes and propose candidate mechanisms to
19104 (license license:gpl2+)))
19106 (define-public r-activitycounts
19108 (name "r-activitycounts")
19113 (uri (cran-uri "activityCounts" version))
19116 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
19118 `((upstream-name . "activityCounts")))
19119 (build-system r-build-system)
19121 `(("r-lubridate" ,r-lubridate)
19122 ("r-magrittr" ,r-magrittr)
19123 ("r-seewave" ,r-seewave)
19124 ("r-signal" ,r-signal)
19125 ("r-tibble" ,r-tibble)))
19126 (home-page "https://github.com/walkabillylab/activityCounts")
19127 (synopsis "Generate ActiLife counts")
19129 "ActiLife generates activity counts from data collected by Actigraph
19130 accelerometers. Actigraph is one of the most common research-grade
19131 accelerometers. There is considerable research validating and developing
19132 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
19133 counts are proprietary and difficult to implement if researchers use different
19134 accelerometer brands. The code creates ActiLife counts from raw acceleration
19135 data for different accelerometer brands.")
19136 (license license:gpl3)))
19138 (define-public r-activityindex
19140 (name "r-activityindex")
19145 (uri (cran-uri "ActivityIndex" version))
19148 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
19149 (properties `((upstream-name . "ActivityIndex")))
19150 (build-system r-build-system)
19152 `(("r-data-table" ,r-data-table)
19153 ("r-matrixstats" ,r-matrixstats)
19154 ("r-r-utils" ,r-r-utils)))
19155 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
19156 (synopsis "Activity Index calculation using raw accelerometry data")
19158 "This is a package to read raw accelerometry from GT3X+ accelerometry
19159 data and plain table data to calculate the Activity Index from Bai et
19160 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
19161 (license license:gpl3)))
19163 (define-public r-activpal
19165 (name "r-activpal")
19170 (uri (cran-uri "activPAL" version))
19173 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
19174 (properties `((upstream-name . "activPAL")))
19175 (build-system r-build-system)
19177 `(("r-devtools" ,r-devtools)
19178 ("r-dplyr" ,r-dplyr)
19179 ("r-ggplot2" ,r-ggplot2)
19180 ("r-lubridate" ,r-lubridate)
19181 ("r-magrittr" ,r-magrittr)
19182 ("r-tidyr" ,r-tidyr)))
19183 (home-page "https://cran.r-project.org/web/packages/activPAL")
19184 (synopsis "Processing and chart generation from activPAL events files")
19186 "This package contains functions to generate pre-defined summary
19187 statistics from activPAL events files. The package also contains functions to
19188 produce informative graphics that visualize physical activity behaviour and
19189 trends. This includes generating graphs that align physical activity
19190 behaviour with additional time based observations described by other data
19191 sets, such as sleep diaries and continuous glucose monitoring data.")
19192 (license license:gpl3)))
19194 (define-public r-activpalprocessing
19196 (name "r-activpalprocessing")
19201 (uri (cran-uri "activpalProcessing" version))
19204 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
19206 `((upstream-name . "activpalProcessing")))
19207 (build-system r-build-system)
19209 `(("r-chron" ,r-chron)))
19210 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
19211 (synopsis "Process activPAL events files")
19213 "This package performs estimation of physical activity and sedentary
19214 behavior variables from activPAL events files.")
19215 ;; Either version of the GPL.
19216 (license (list license:gpl2 license:gpl3))))
19218 (define-public r-actogrammr
19220 (name "r-actogrammr")
19225 (uri (cran-uri "actogrammr" version))
19228 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19229 (properties `((upstream-name . "actogrammr")))
19230 (build-system r-build-system)
19232 `(("r-dplyr" ,r-dplyr)
19233 ("r-ggplot2" ,r-ggplot2)
19234 ("r-lubridate" ,r-lubridate)
19235 ("r-readr" ,r-readr)
19236 ("r-tidyr" ,r-tidyr)))
19237 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19238 (synopsis "Read in activity data and plot actograms")
19240 "Read in activity measurements from standard file formats used by
19241 circadian rhythm researchers, currently only ClockLab format, and process and
19242 plot the data. The central type of plot is the actogram, as first described
19243 in \"Activity and distribution of certain wild mice in relation to biotic
19244 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19245 (license license:gpl3)))
19247 (define-public r-expint
19254 (uri (cran-uri "expint" version))
19257 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19258 (properties `((upstream-name . "expint")))
19259 (build-system r-build-system)
19260 (home-page "https://gitlab.com/vigou3/expint")
19261 (synopsis "Exponential integral and incomplete Gamma function")
19263 "This package provides the exponential integrals @code{E_1(x)},
19264 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19265 function @code{G(a, x)} defined for negative values of its first argument.
19266 The package also gives easy access to the underlying C routines through an
19267 API; see the package vignette for details.")
19268 (license license:gpl2+)))
19270 (define-public r-actuar
19277 (uri (cran-uri "actuar" version))
19280 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19281 (properties `((upstream-name . "actuar")))
19282 (build-system r-build-system)
19283 (propagated-inputs `(("r-expint" ,r-expint)))
19284 (home-page "https://gitlab.com/vigou3/actuar")
19285 (synopsis "Actuarial functions and heavy tailed distributions")
19287 "This package provides functions and data sets for actuarial science:
19288 modeling of loss distributions; risk theory and ruin theory; simulation of
19289 compound models, discrete mixtures and compound hierarchical models;
19290 credibility theory. It boasts support for many additional probability
19291 distributions to model insurance loss amounts and loss frequency: 19
19292 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19293 distribution; zero-truncated and zero-modified extensions of the standard
19294 discrete distributions. It also supports phase-type distributions commonly
19295 used to compute ruin probabilities.")
19296 (license license:gpl2+)))
19298 (define-public r-bmp
19305 (uri (cran-uri "bmp" version))
19308 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19309 (properties `((upstream-name . "bmp")))
19310 (build-system r-build-system)
19311 (home-page "https://cran.r-project.org/web/packages/bmp/")
19312 (synopsis "Read Bitmap (BMP) images")
19314 "This package provides pure R tools to read BMP format images. It is
19315 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19316 (license license:gpl2+)))
19318 (define-public r-readbitmap
19320 (name "r-readbitmap")
19325 (uri (cran-uri "readbitmap" version))
19328 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19329 (properties `((upstream-name . "readbitmap")))
19330 (build-system r-build-system)
19332 `(("libjpeg" ,libjpeg-turbo)
19333 ("libpng" ,libpng)))
19338 ("r-tiff" ,r-tiff)))
19339 (home-page "https://github.com/jefferis/readbitmap")
19340 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19342 "This package provides tools to identify and read BMP, JPEG, PNG, and
19343 TIFF format bitmap images. Identification defaults to the use of the magic
19344 number embedded in the file rather than the file extension.")
19345 (license license:gpl2+)))
19347 (define-public r-imager
19354 (uri (cran-uri "imager" version))
19357 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19358 (properties `((upstream-name . "imager")))
19359 (build-system r-build-system)
19362 ("libtiff" ,libtiff)
19366 `(("r-downloader" ,r-downloader)
19367 ("r-igraph" ,r-igraph)
19369 ("r-magrittr" ,r-magrittr)
19371 ("r-purrr" ,r-purrr)
19373 ("r-readbitmap" ,r-readbitmap)
19374 ("r-stringr" ,r-stringr)))
19376 `(("pkg-config" ,pkg-config)
19377 ("r-knitr" ,r-knitr)))
19378 (home-page "https://dahtah.github.io/imager/")
19379 (synopsis "Image processing library")
19381 "This is a package for fast image processing for images in up to 4
19382 dimensions (two spatial dimensions, one time/depth dimension, one color
19383 dimension). It provides most traditional image processing tools (filtering,
19384 morphology, transformations, etc.) as well as various functions for easily
19385 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19386 simple, modern C++ library for image processing.")
19387 (license license:lgpl3)))
19389 (define-public r-acuityview
19391 (name "r-acuityview")
19396 (uri (cran-uri "AcuityView" version))
19399 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19400 (properties `((upstream-name . "AcuityView")))
19401 (build-system r-build-system)
19403 `(("r-fftwtools" ,r-fftwtools)
19404 ("r-imager" ,r-imager)
19405 ("r-plotrix" ,r-plotrix)))
19406 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19407 (synopsis "Display scenes as seen by an animal with less acute vision")
19409 "This package provides a simple method for representing a visual scene as
19410 it may be seen by an animal with less acute vision.")
19411 (license license:gpl2+)))
19413 (define-public r-caret
19420 (uri (cran-uri "caret" version))
19423 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19424 (build-system r-build-system)
19426 `(("r-foreach" ,r-foreach)
19427 ("r-ggplot2" ,r-ggplot2)
19428 ("r-lattice" ,r-lattice)
19429 ("r-modelmetrics" ,r-modelmetrics)
19433 ("r-recipes" ,r-recipes)
19434 ("r-reshape2" ,r-reshape2)
19435 ("r-withr" ,r-withr)))
19437 `(("r-knitr" ,r-knitr)))
19438 (home-page "https://github.com/topepo/caret")
19439 (synopsis "Classification and regression training")
19441 "This package provides miscellaneous functions for training and plotting
19442 classification and regression models.")
19443 (license license:gpl2+)))
19445 (define-public r-adabag
19452 (uri (cran-uri "adabag" version))
19455 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19456 (properties `((upstream-name . "adabag")))
19457 (build-system r-build-system)
19459 `(("r-caret" ,r-caret)
19460 ("r-doparallel" ,r-doparallel)
19461 ("r-foreach" ,r-foreach)
19462 ("r-rpart" ,r-rpart)))
19463 (home-page "https://cran.r-project.org/web/packages/adabag/")
19464 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19466 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19467 Breiman's Bagging algorithm using classification trees as individual
19468 classifiers. Once these classifiers have been trained, they can be used to
19469 predict on new data. Also, cross validation estimation of the error can be
19471 (license license:gpl2+)))
19473 (define-public r-adagio
19480 (uri (cran-uri "adagio" version))
19483 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19484 (properties `((upstream-name . "adagio")))
19485 (build-system r-build-system)
19486 (native-inputs `(("gfortran" ,gfortran)))
19487 (home-page "https://cran.r-project.org/web/packages/adagio/")
19488 (synopsis "Discrete and global optimization routines")
19490 "This package provides methods and algorithms for discrete optimization,
19491 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19492 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19494 (license license:gpl3+)))
19496 (define-public r-univoutl
19498 (name "r-univoutl")
19503 (uri (cran-uri "univOutl" version))
19506 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19507 (properties `((upstream-name . "univOutl")))
19508 (build-system r-build-system)
19510 `(("r-hmisc" ,r-hmisc)
19511 ("r-robustbase" ,r-robustbase)))
19512 (home-page "https://github.com/marcellodo/univOutl")
19513 (synopsis "Detection of univariate outliers")
19515 "This package provides well-known outlier detection techniques in the
19516 univariate case. Methods to deal with skewed distribution are included too.
19517 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19518 historical data is implemented as well. When available, survey weights can be
19519 used in outliers detection.")
19520 (license license:gpl2+)))
19522 (define-public r-tolerance
19524 (name "r-tolerance")
19529 (uri (cran-uri "tolerance" version))
19532 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19533 (properties `((upstream-name . "tolerance")))
19534 (build-system r-build-system)
19536 `(("r-mass" ,r-mass)
19538 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19539 (synopsis "Statistical tolerance intervals and regions")
19541 "This package provides functions for estimating tolerance
19542 limits (intervals) for various univariate distributions (binomial, Cauchy,
19543 discrete Pareto, exponential, two-parameter exponential, extreme value,
19544 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19545 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19546 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19547 nonparametric tolerance intervals, tolerance bands for regression
19548 settings (linear regression, nonlinear regression, nonparametric regression,
19549 and multivariate regression), and analysis of variance tolerance intervals.
19550 Visualizations are also available for most of these settings.")
19551 (license license:gpl2+)))
19553 (define-public r-additivitytests
19555 (name "r-additivitytests")
19560 (uri (cran-uri "additivityTests" version))
19563 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19565 `((upstream-name . "additivityTests")))
19566 (build-system r-build-system)
19567 (home-page "https://github.com/simecek/additivityTests")
19568 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19570 "This package provides an implementation of the Tukey, Mandel,
19571 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19572 (license license:gpl3)))
19574 (define-public r-flexclust
19576 (name "r-flexclust")
19581 (uri (cran-uri "flexclust" version))
19584 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19585 (properties `((upstream-name . "flexclust")))
19586 (build-system r-build-system)
19588 `(("r-class" ,r-class)
19589 ("r-lattice" ,r-lattice)
19590 ("r-modeltools" ,r-modeltools)))
19591 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19592 (synopsis "Flexible cluster algorithms")
19594 "The main function @code{kcca} implements a general framework for
19595 k-centroids cluster analysis supporting arbitrary distance measures and
19596 centroid computation. Further cluster methods include hard competitive
19597 learning, neural gas, and QT clustering. There are numerous visualization
19598 methods for cluster results (neighborhood graphs, convex cluster hulls,
19599 barcharts of centroids, ...), and bootstrap methods for the analysis of
19600 cluster stability.")
19601 (license license:gpl2)))
19603 (define-public r-biclust
19610 (uri (cran-uri "biclust" version))
19613 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19614 (properties `((upstream-name . "biclust")))
19615 (build-system r-build-system)
19617 `(("r-additivitytests" ,r-additivitytests)
19618 ("r-colorspace" ,r-colorspace)
19619 ("r-flexclust" ,r-flexclust)
19620 ("r-ggplot2" ,r-ggplot2)
19621 ("r-lattice" ,r-lattice)
19623 ("r-tidyr" ,r-tidyr)))
19624 (home-page "https://cran.r-project.org/web/packages/biclust/")
19625 (synopsis "BiCluster algorithms")
19627 "The main function @code{biclust()} provides several algorithms to find
19628 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19629 In addition, the package provides methods for data
19630 preprocessing (normalization and discretization), visualization, and
19631 validation of bicluster solutions.")
19632 (license license:gpl3)))
19634 (define-public r-icge
19641 (uri (cran-uri "ICGE" version))
19644 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19645 (properties `((upstream-name . "ICGE")))
19646 (build-system r-build-system)
19648 `(("r-cluster" ,r-cluster)
19649 ("r-mass" ,r-mass)))
19650 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19651 (synopsis "Cluster estimation and identification of atypical units")
19653 "ICGE is a package that helps to estimate the number of real clusters in
19654 data as well as to identify atypical units. The underlying methods are based
19655 on distances rather than on unit x variables.")
19656 (license license:gpl2+)))
19658 (define-public r-depth
19661 (version "2.1-1.1")
19665 (uri (cran-uri "depth" version))
19668 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19669 (properties `((upstream-name . "depth")))
19670 (build-system r-build-system)
19672 `(("r-abind" ,r-abind)
19673 ("r-circular" ,r-circular)
19676 `(("gfortran" ,gfortran)))
19677 (home-page "https://cran.r-project.org/web/packages/depth/")
19678 (synopsis "Nonparametric depth functions for multivariate analysis")
19680 "This package provides tools for depth functions methodology applied to
19681 multivariate analysis. Besides allowing calculation of depth values and
19682 depth-based location estimators, the package includes functions or drawing
19683 contour plots and perspective plots of depth functions. Euclidean and
19684 spherical depths are supported.")
19685 (license license:gpl2)))
19687 (define-public r-archetypes
19689 (name "r-archetypes")
19690 (version "2.2-0.1")
19694 (uri (cran-uri "archetypes" version))
19697 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19698 (properties `((upstream-name . "archetypes")))
19699 (build-system r-build-system)
19701 `(("r-modeltools" ,r-modeltools)
19702 ("r-nnls" ,r-nnls)))
19703 (home-page "https://cran.r-project.org/web/packages/archetypes")
19704 (synopsis "Archetypal analysis")
19706 "The main function @code{archetypes} implements a framework for
19707 archetypal analysis supporting arbitrary problem solving mechanisms for the
19708 different conceptual parts of the algorithm.")
19709 (license license:gpl2+)))
19711 (define-public r-shapes
19718 (uri (cran-uri "shapes" version))
19721 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19722 (properties `((upstream-name . "shapes")))
19723 (build-system r-build-system)
19725 `(("r-mass" ,r-mass)
19726 ("r-minpack-lm" ,r-minpack-lm)
19728 ("r-scatterplot3d" ,r-scatterplot3d)))
19729 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19730 (synopsis "Statistical shape analysis")
19732 "This package provides routines for the statistical analysis of landmark
19733 shapes, including Procrustes analysis, graphical displays, principal
19734 components analysis, permutation and bootstrap tests, thin-plate spline
19735 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19736 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19737 Edition), John Wiley and Sons.")
19738 (license license:gpl2)))
19740 (define-public r-anthropometry
19742 (name "r-anthropometry")
19747 (uri (cran-uri "Anthropometry" version))
19750 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19751 (properties `((upstream-name . "Anthropometry")))
19752 (build-system r-build-system)
19754 `(("r-archetypes" ,r-archetypes)
19755 ("r-biclust" ,r-biclust)
19756 ("r-cluster" ,r-cluster)
19757 ("r-depth" ,r-depth)
19762 ("r-shapes" ,r-shapes)))
19764 `(("r-knitr" ,r-knitr)))
19765 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19766 (synopsis "Statistical methods for anthropometric data")
19768 "This package provides statistical methods especially developed to
19769 analyze anthropometric data. These methods are aimed at providing effective
19770 solutions to some commons problems related to Ergonomics and Anthropometry.
19771 They are based on clustering, the statistical concept of data depth,
19772 statistical shape analysis and archetypal analysis.")
19773 (license license:gpl2+)))
19775 (define-public r-adamethods
19777 (name "r-adamethods")
19782 (uri (cran-uri "adamethods" version))
19785 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19786 (properties `((upstream-name . "adamethods")))
19787 (build-system r-build-system)
19789 `(("r-anthropometry" ,r-anthropometry)
19790 ("r-archetypes" ,r-archetypes)
19792 ("r-foreach" ,r-foreach)
19794 ("r-tolerance" ,r-tolerance)
19795 ("r-univoutl" ,r-univoutl)))
19796 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19797 (synopsis "Archetypoid algorithms and anomaly detection")
19799 "This package is a collection of several algorithms to obtain
19800 archetypoids with small and large databases and with both classical
19801 multivariate data and functional data (univariate and multivariate). Some of
19802 these algorithms also detect anomalies (outliers).")
19803 (license license:gpl2+)))
19805 (define-public r-idpmisc
19812 (uri (cran-uri "IDPmisc" version))
19815 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19816 (properties `((upstream-name . "IDPmisc")))
19817 (build-system r-build-system)
19819 `(("r-lattice" ,r-lattice)))
19820 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19821 (synopsis "Functions for data analyses and visualization")
19823 "This package provides different high-level graphics functions for
19824 displaying large datasets, displaying circular data in a very flexible way,
19825 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19826 2D-plots, creating figures with differently colored margin and plot region.
19827 In addition, the package contains auxiliary functions for data manipulation
19828 like omitting observations with irregular values or selecting data by logical
19829 vectors, which include NAs. Other functions are especially useful in
19830 spectroscopy and analyses of environmental data: robust baseline fitting,
19831 finding peaks in spectra, converting humidity measures.")
19832 (license license:gpl3+)))
19834 (define-public r-qqman
19841 (uri (cran-uri "qqman" version))
19844 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19845 (properties `((upstream-name . "qqman")))
19846 (build-system r-build-system)
19848 `(("r-calibrate" ,r-calibrate)))
19849 (home-page "https://cran.r-project.org/web/packages/qqman/")
19850 (synopsis "Q-Q and Manhattan plots for GWAS data")
19852 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19853 from PLINK results.")
19854 (license license:gpl3)))
19856 (define-public r-ggplot-multistats
19858 (name "r-ggplot-multistats")
19863 (uri (cran-uri "ggplot.multistats" version))
19866 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19868 `((upstream-name . "ggplot.multistats")))
19869 (build-system r-build-system)
19871 `(("r-ggplot2" ,r-ggplot2)
19872 ("r-hexbin" ,r-hexbin)
19873 ("r-rlang" ,r-rlang)
19874 ("r-scales" ,r-scales)))
19875 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19876 (synopsis "Multiple summary statistics for binned stats/geometries")
19878 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19879 which functions similar to its singular form, but allows the use of multiple
19880 statistics per bin. Those statistics can be mapped to multiple bin
19882 (license license:gpl3)))
19884 (define-public r-knn-covertree
19886 (name "r-knn-covertree")
19891 (uri (cran-uri "knn.covertree" version))
19894 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19895 (properties `((upstream-name . "knn.covertree")))
19896 (build-system r-build-system)
19898 `(("r-matrix" ,r-matrix)
19900 ("r-rcppeigen" ,r-rcppeigen)))
19901 (home-page "https://github.com/flying-sheep/knn.covertree")
19902 (synopsis "Accurate kNN Implementation with multiple distance measures")
19904 "Similarly to the FNN package, this package allows calculation of the k
19905 nearest neighbors (kNN) of a data matrix. The implementation is based on
19906 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19907 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19908 (license license:agpl3+)))
19910 (define-public r-poibin
19917 (uri (cran-uri "poibin" version))
19920 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19921 (properties `((upstream-name . "poibin")))
19922 (build-system r-build-system)
19923 (home-page "https://cran.r-project.org/web/packages/poibin/")
19924 (synopsis "Poisson binomial distribution")
19926 "This package provides an implementation of both the exact and
19927 approximation methods for computing the @dfn{cumulative distribution
19928 function} (CDF) of the Poisson binomial distribution. It also provides the
19929 @dfn{probability mass function} (PMF), quantile function, and random number
19930 generation for the Poisson binomial distribution.")
19931 (license license:gpl2)))
19933 (define-public r-diagram
19940 (uri (cran-uri "diagram" version))
19943 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
19944 (properties `((upstream-name . "diagram")))
19945 (build-system r-build-system)
19947 `(("r-shape" ,r-shape)))
19948 (home-page "https://cran.r-project.org/web/packages/diagram/")
19949 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19951 "This package provides tools to visualize simple graphs (networks) based
19952 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19953 electrical networks, etc. It also includes supporting material for the book
19954 \"A practical guide to ecological modelling - using R as a simulation
19955 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19956 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19957 Francesca Mazzia (2012).")
19958 (license license:gpl2+)))
19960 (define-public r-lim
19967 (uri (cran-uri "LIM" version))
19970 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19971 (properties `((upstream-name . "LIM")))
19972 (build-system r-build-system)
19974 `(("r-diagram" ,r-diagram)
19975 ("r-limsolve" ,r-limsolve)))
19976 (home-page "https://cran.r-project.org/web/packages/LIM/")
19977 (synopsis "Linear inverse model examples and solution methods")
19979 "This package provides functions that read and solve linear inverse
19980 problems (food web problems, linear programming problems).")
19981 (license license:gpl2+)))
19983 (define-public r-shinycssloaders
19985 (name "r-shinycssloaders")
19990 (uri (cran-uri "shinycssloaders" version))
19993 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19995 `((upstream-name . "shinycssloaders")))
19996 (build-system r-build-system)
19998 `(("r-digest" ,r-digest)
20000 ("r-shiny" ,r-shiny)))
20001 (home-page "https://github.com/andrewsali/shinycssloaders")
20002 (synopsis "Add CSS loading animations to Shiny outputs")
20004 "This package provides tools to create a lightweight Shiny wrapper for
20005 the css-loaders created by Luke Hass
20006 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
20007 automatically show a loader when the output is (re)calculating.")
20008 (license license:gpl3)))
20010 (define-public r-rsvg
20017 (uri (cran-uri "rsvg" version))
20020 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
20021 (properties `((upstream-name . "rsvg")))
20022 (build-system r-build-system)
20024 `(("librsvg" ,librsvg)
20027 `(("pkg-config" ,pkg-config)
20028 ("r-knitr" ,r-knitr)))
20029 (home-page "https://github.com/jeroen/rsvg#readme")
20030 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
20032 "This package allows you to render vector-based SVG images into
20033 high-quality custom-size bitmap arrays using the librsvg2 library. The
20034 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
20035 addition, the package can convert images directly to various formats such as
20036 PDF or PostScript.")
20037 (license license:expat)))
20039 (define-public r-influencer
20041 (name "r-influencer")
20046 (uri (cran-uri "influenceR" version))
20049 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
20050 (properties `((upstream-name . "influenceR")))
20051 (build-system r-build-system)
20053 `(("r-igraph" ,r-igraph)
20054 ("r-matrix" ,r-matrix)))
20055 (home-page "https://github.com/rcc-uchicago/influenceR")
20056 (synopsis "Tools to quantify structural importance of nodes in a network")
20058 "This package provides functionality to compute various node centrality
20059 measures on networks. Included are functions to compute betweenness
20060 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
20061 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
20062 algorithm to identify key players, and Valente's bridging metric. The
20063 betweenness, Key Players, and bridging implementations are parallelized with
20065 (license license:gpl2)))
20067 (define-public r-emplik
20074 (uri (cran-uri "emplik" version))
20077 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
20078 (properties `((upstream-name . "emplik")))
20079 (build-system r-build-system)
20081 `(("r-quantreg" ,r-quantreg)))
20082 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
20083 (synopsis "Empirical likelihood ratio for censored/truncated data")
20085 "This package provides empirical likelihood ratio tests for
20086 means/quantiles/hazards from possibly censored and/or truncated data. It also
20088 (license license:gpl2+)))
20090 (define-public r-imputeyn
20092 (name "r-imputeyn")
20097 (uri (cran-uri "imputeYn" version))
20100 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
20101 (properties `((upstream-name . "imputeYn")))
20102 (build-system r-build-system)
20104 `(("r-boot" ,r-boot)
20105 ("r-emplik" ,r-emplik)
20106 ("r-mvtnorm" ,r-mvtnorm)
20107 ("r-quadprog" ,r-quadprog)
20108 ("r-survival" ,r-survival)))
20109 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
20110 (synopsis "Impute last largest censored observation under weighted least squares")
20112 "This package allows for the imputation of the last largest censored
20113 observantions. This method brings less bias and more efficient estimates for
20115 (license license:gpl2)))
20117 (define-public r-adapenetclass
20119 (name "r-adapenetclass")
20124 (uri (cran-uri "AdapEnetClass" version))
20127 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
20128 (properties `((upstream-name . "AdapEnetClass")))
20129 (build-system r-build-system)
20131 `(("r-glmnet" ,r-glmnet)
20132 ("r-imputeyn" ,r-imputeyn)
20134 ("r-quadprog" ,r-quadprog)))
20135 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
20136 (synopsis "Class of adaptive elastic net methods for censored data")
20138 "This package provides methods for variable selection for AFT models.")
20139 (license license:gpl2)))
20141 (define-public r-flock
20148 (uri (cran-uri "flock" version))
20151 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
20152 (properties `((upstream-name . "flock")))
20153 (build-system r-build-system)
20154 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
20155 (home-page "https://cran.r-project.org/web/packages/flock/")
20156 (synopsis "Process synchronization using file locks")
20158 "This package implements synchronization between R processes (spawned by
20159 using the @code{parallel} package for instance) using file locks. It supports
20160 both exclusive and shared locking.")
20161 (license license:asl2.0)))
20163 (define-public r-archivist
20165 (name "r-archivist")
20170 (uri (cran-uri "archivist" version))
20173 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
20174 (properties `((upstream-name . "archivist")))
20175 (build-system r-build-system)
20178 ("r-digest" ,r-digest)
20179 ("r-flock" ,r-flock)
20181 ("r-lubridate" ,r-lubridate)
20182 ("r-magrittr" ,r-magrittr)
20183 ("r-rcurl" ,r-rcurl)
20184 ("r-rsqlite" ,r-rsqlite)))
20185 (home-page "https://pbiecek.github.io/archivist/")
20186 (synopsis "Tools for storing, restoring and searching for R objects")
20188 "Data exploration and modelling is a process in which a lot of data
20189 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
20190 statistical models, different versions of data sets and different versions of
20191 results. Archivist helps to store and manage artifacts created in R. It
20192 allows you to store selected artifacts as binary files together with their
20193 metadata and relations. Archivist allows sharing artifacts with others. It
20194 can look for already created artifacts by using its class, name, date of the
20195 creation or other properties. It also makes it easy to restore such
20197 (license license:gpl2)))
20199 (define-public r-versions
20201 (name "r-versions")
20206 (uri (cran-uri "versions" version))
20209 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
20210 (properties `((upstream-name . "versions")))
20211 (build-system r-build-system)
20212 (home-page "https://cran.r-project.org/web/packages/versions/")
20213 (synopsis "Query and install specific versions of CRAN packages")
20215 "This package allows you to install specified versions of R packages
20216 hosted on CRAN and provides functions to list available versions and the
20217 versions of currently installed packages.")
20218 (license license:bsd-3)))
20220 (define-public r-adapr
20227 (uri (cran-uri "adapr" version))
20230 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20231 (properties `((upstream-name . "adapr")))
20232 (build-system r-build-system)
20234 `(("r-archivist" ,r-archivist)
20235 ("r-devtools" ,r-devtools)
20236 ("r-digest" ,r-digest)
20237 ("r-doparallel" ,r-doparallel)
20238 ("r-gdata" ,r-gdata)
20239 ("r-ggplot2" ,r-ggplot2)
20240 ("r-git2r" ,r-git2r)
20241 ("r-igraph" ,r-igraph)
20242 ("r-knitr" ,r-knitr)
20243 ("r-plotly" ,r-plotly)
20245 ("r-rmarkdown" ,r-rmarkdown)
20246 ("r-shiny" ,r-shiny)
20247 ("r-shinydashboard" ,r-shinydashboard)
20248 ("r-versions" ,r-versions)))
20249 (home-page "https://cran.r-project.org/web/packages/adapr/")
20250 (synopsis "Implementation of an accountable data analysis process")
20252 "This package tracks reading and writing within R scripts that are
20253 organized into a directed acyclic graph. It contains an interactive Shiny
20254 application @code{adaprApp()}. It uses Git and file hashes to track version
20255 histories of inputs and outputs.")
20256 (license license:lgpl2.0)))
20258 (define-public r-adapsamp
20260 (name "r-adapsamp")
20265 (uri (cran-uri "AdapSamp" version))
20268 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20269 (properties `((upstream-name . "AdapSamp")))
20270 (build-system r-build-system)
20271 (propagated-inputs `(("r-pracma" ,r-pracma)))
20272 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20273 (synopsis "Adaptive sampling algorithms")
20275 "For distributions whose probability density functions are log-concave,
20276 the adaptive rejection sampling algorithm can be used to build envelope
20277 functions for sampling. For others, the modified adaptive rejection sampling
20278 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20279 adaptive slice sampling algorithm can be used. This R package mainly includes
20280 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20281 @code{rASS()}. These functions can realize sampling based on the algorithms
20283 (license license:gpl2)))
20285 (define-public r-adaptalint
20287 (name "r-adaptalint")
20292 (uri (cran-uri "adaptalint" version))
20295 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20296 (properties `((upstream-name . "adaptalint")))
20297 (build-system r-build-system)
20299 `(("r-dplyr" ,r-dplyr)
20300 ("r-lintr" ,r-lintr)
20301 ("r-purrr" ,r-purrr)))
20302 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20303 (synopsis "Check R code style")
20305 "This package provides tools to infer the code style (which style rules
20306 are followed and which ones are not) from one package and use it to check
20307 another. This makes it easier to find and correct the most important problems
20309 (license license:gpl3)))
20311 (define-public r-fracdiff
20313 (name "r-fracdiff")
20318 (uri (cran-uri "fracdiff" version))
20321 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20322 (properties `((upstream-name . "fracdiff")))
20323 (build-system r-build-system)
20324 (home-page "https://github.com/mmaechler/fracdiff")
20326 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20328 "This package provides tools for the maximum likelihood estimation of the
20329 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20330 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20331 (license license:gpl2+)))
20333 (define-public r-forecast
20335 (name "r-forecast")
20340 (uri (cran-uri "forecast" version))
20343 "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
20344 (properties `((upstream-name . "forecast")))
20345 (build-system r-build-system)
20347 `(("r-colorspace" ,r-colorspace)
20348 ("r-fracdiff" ,r-fracdiff)
20349 ("r-ggplot2" ,r-ggplot2)
20350 ("r-lmtest" ,r-lmtest)
20351 ("r-magrittr" ,r-magrittr)
20354 ("r-rcpparmadillo" ,r-rcpparmadillo)
20355 ("r-timedate" ,r-timedate)
20356 ("r-tseries" ,r-tseries)
20360 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20361 (home-page "https://pkg.robjhyndman.com/forecast/")
20362 (synopsis "Forecasting functions for time series and linear models")
20364 "This package provides methods and tools for displaying and analysing
20365 univariate time series forecasts including exponential smoothing via state
20366 space models and automatic ARIMA modelling.")
20367 (license license:gpl3)))
20369 (define-public r-xmisc
20376 (uri (cran-uri "Xmisc" version))
20379 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20380 (properties `((upstream-name . "Xmisc")))
20381 (build-system r-build-system)
20382 (home-page "https://cran.r-project.org/package=Xmisc")
20384 "Xiaobei's miscellaneous classes and functions")
20386 "This package provides Xiaobei's miscellaneous classes and functions,
20387 which are useful when developing R packages for @dfn{object oriented
20388 programming} (OOP) using R Reference Class.")
20389 (license license:gpl2+)))
20391 (define-public r-proxyc
20398 (uri (cran-uri "proxyC" version))
20401 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20402 (properties `((upstream-name . "proxyC")))
20403 (build-system r-build-system)
20405 `(("r-matrix" ,r-matrix)
20407 ("r-rcpparmadillo" ,r-rcpparmadillo)
20408 ("r-rcppparallel" ,r-rcppparallel)))
20409 (home-page "https://cran.r-project.org/package=proxyC")
20410 (synopsis "Compute proximity in large sparse matrices")
20412 "This package provides efficient tools to compute the proximity between
20413 rows or columns of large matrices. Functions are optimised for large sparse
20414 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20415 similarity/distance measures, computation of correlation, cosine similarity
20416 and Euclidean distance is particularly fast.")
20417 (license license:gpl3)))
20419 (define-public r-isocodes
20421 (name "r-isocodes")
20422 (version "2020.03.16")
20426 (uri (cran-uri "ISOcodes" version))
20429 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20430 (properties `((upstream-name . "ISOcodes")))
20431 (build-system r-build-system)
20432 (home-page "https://cran.r-project.org/package=ISOcodes")
20433 (synopsis "Selected ISO codes")
20435 "This package provides ISO language, territory, currency, script and
20436 character codes. It provides ISO 639 language codes, ISO 3166 territory
20437 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20438 character codes as well as the UN M.49 area codes.")
20439 (license license:gpl2)))
20441 (define-public r-stopwords
20443 (name "r-stopwords")
20448 (uri (cran-uri "stopwords" version))
20451 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20452 (properties `((upstream-name . "stopwords")))
20453 (build-system r-build-system)
20455 `(("r-desc" ,r-desc)
20456 ("r-isocodes" ,r-isocodes)
20457 ("r-usethis" ,r-usethis)))
20458 (home-page "https://github.com/quanteda/stopwords")
20459 (synopsis "Multilingual stopword lists")
20461 "This package provides multiple sources of stopwords, for use in text
20462 analysis and natural language processing.")
20463 (license license:expat)))
20465 (define-public r-spacyr
20472 (uri (cran-uri "spacyr" version))
20475 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20476 (properties `((upstream-name . "spacyr")))
20477 (build-system r-build-system)
20479 `(("r-data-table" ,r-data-table)
20480 ("r-reticulate" ,r-reticulate)))
20481 (home-page "https://spacyr.quanteda.io")
20482 (synopsis "R wrapper for the spaCy NLP library")
20484 "This package provides an R wrapper to the Python @dfn{natural language
20485 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20486 (license license:gpl3)))
20488 (define-public r-snowballc
20490 (name "r-snowballc")
20495 (uri (cran-uri "SnowballC" version))
20498 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20499 (properties `((upstream-name . "SnowballC")))
20500 (build-system r-build-system)
20501 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20502 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20504 "This package provides an R interface to the C @code{libstemmer} library
20505 that implements Porter's word stemming algorithm for collapsing words to a
20506 common root to aid comparison of vocabulary. Currently supported languages
20507 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20508 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20509 (license license:bsd-3)))
20511 (define-public r-quanteda
20513 (name "r-quanteda")
20518 (uri (cran-uri "quanteda" version))
20521 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
20522 (properties `((upstream-name . "quanteda")))
20523 (build-system r-build-system)
20525 `(("r-data-table" ,r-data-table)
20526 ("r-digest" ,r-digest)
20527 ("r-extrafont" ,r-extrafont)
20528 ("r-fastmatch" ,r-fastmatch)
20529 ("r-ggplot2" ,r-ggplot2)
20530 ("r-ggrepel" ,r-ggrepel)
20531 ("r-jsonlite" ,r-jsonlite)
20532 ("r-magrittr" ,r-magrittr)
20533 ("r-matrix" ,r-matrix)
20534 ("r-network" ,r-network)
20535 ("r-proxyc" ,r-proxyc)
20537 ("r-rcpparmadillo" ,r-rcpparmadillo)
20538 ("r-rcppparallel" ,r-rcppparallel)
20540 ("r-snowballc" ,r-snowballc)
20541 ("r-stopwords" ,r-stopwords)
20542 ("r-stringi" ,r-stringi)
20544 ("r-yaml" ,r-yaml)))
20546 `(("r-knitr" ,r-knitr)))
20547 (home-page "https://quanteda.io")
20548 (synopsis "Quantitative analysis of textual data")
20550 "This package provides a fast, flexible, and comprehensive framework for
20551 quantitative text analysis in R. It provides functionality for corpus
20552 management, creating and manipulating tokens and ngrams, exploring keywords in
20553 context, forming and manipulating sparse matrices of documents by features and
20554 feature co-occurrences, analyzing keywords, computing feature similarities and
20555 distances, applying content dictionaries, applying supervised and unsupervised
20556 machine learning, visually representing text and text analyses, and more.")
20557 (license license:gpl3)))
20559 (define-public r-topicmodels
20561 (name "r-topicmodels")
20566 (uri (cran-uri "topicmodels" version))
20569 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20570 (properties `((upstream-name . "topicmodels")))
20571 (build-system r-build-system)
20575 `(("r-modeltools" ,r-modeltools)
20578 (home-page "https://cran.r-project.org/package=topicmodels")
20579 (synopsis "Topic models")
20581 "This package provides an interface to the C code for @dfn{Latent
20582 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20583 David M. Blei and co-authors and the C++ code for fitting LDA models using
20584 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20585 (license license:gpl2)))
20587 (define-public r-stm
20594 (uri (cran-uri "stm" version))
20597 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
20598 (properties `((upstream-name . "stm")))
20599 (build-system r-build-system)
20601 `(("r-data-table" ,r-data-table)
20602 ("r-glmnet" ,r-glmnet)
20604 ("r-matrix" ,r-matrix)
20605 ("r-matrixstats" ,r-matrixstats)
20606 ("r-quadprog" ,r-quadprog)
20607 ("r-quanteda" ,r-quanteda)
20609 ("r-rcpparmadillo" ,r-rcpparmadillo)
20611 ("r-stringr" ,r-stringr)))
20612 (home-page "http://www.structuraltopicmodel.com/")
20613 (synopsis "Estimation of the Structural Topic Model")
20615 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20616 topic models with document-level covariates. The package also includes tools
20617 for model selection, visualization, and estimation of topic-covariate
20619 (license license:expat)))
20621 (define-public r-polycor
20628 (uri (cran-uri "polycor" version))
20631 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20632 (properties `((upstream-name . "polycor")))
20633 (build-system r-build-system)
20635 `(("r-matrix" ,r-matrix)
20636 ("r-mvtnorm" ,r-mvtnorm)))
20637 (home-page "https://r-forge.r-project.org/projects/polycor/")
20638 (synopsis "Polychoric and polyserial correlations")
20640 "This package provides tools to compute polychoric and polyserial
20641 correlations by quick \"two-step\" methods or ML, optionally with standard
20642 errors; tetrachoric and biserial correlations are special cases.")
20643 (license license:gpl2+)))
20645 (define-public r-msm
20652 (uri (cran-uri "msm" version))
20655 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20656 (properties `((upstream-name . "msm")))
20657 (build-system r-build-system)
20659 `(("r-expm" ,r-expm)
20660 ("r-mvtnorm" ,r-mvtnorm)
20661 ("r-survival" ,r-survival)))
20662 (home-page "https://github.com/chjackson/msm")
20663 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20665 "This package provides functions for fitting continuous-time Markov and
20666 hidden Markov multi-state models to longitudinal data. It was designed for
20667 processes observed at arbitrary times in continuous time (panel data) but some
20668 other observation schemes are supported. Both Markov transition rates and the
20669 hidden Markov output process can be modelled in terms of covariates, which may
20670 be constant or piecewise-constant in time.")
20671 (license license:gpl2+)))
20673 (define-public r-ltm
20680 (uri (cran-uri "ltm" version))
20683 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20684 (properties `((upstream-name . "ltm")))
20685 (build-system r-build-system)
20687 `(("r-mass" ,r-mass)
20689 ("r-polycor" ,r-polycor)))
20690 (home-page "https://github.com/drizopoulos/ltm")
20691 (synopsis "Latent trait models under IRT")
20693 "This is a package supporting the analysis of multivariate dichotomous
20694 and polytomous data using latent trait models under the Item Response Theory
20695 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20696 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20698 (license license:gpl2+)))
20700 (define-public r-mi
20707 (uri (cran-uri "mi" version))
20710 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20711 (properties `((upstream-name . "mi")))
20712 (build-system r-build-system)
20715 ("r-matrix" ,r-matrix)))
20716 (home-page "http://www.stat.columbia.edu/~gelman/")
20717 (synopsis "Missing data imputation and model checking")
20719 "This package provides functions for data manipulation, imputing missing
20720 values in an approximate Bayesian framework, diagnostics of the models used to
20721 generate the imputations, confidence-building mechanisms to validate some of
20722 the assumptions of the imputation algorithm, and functions to analyze multiply
20723 imputed data sets with the appropriate degree of sampling uncertainty.")
20724 (license license:gpl2+)))
20726 (define-public r-matrixcalc
20728 (name "r-matrixcalc")
20733 (uri (cran-uri "matrixcalc" version))
20736 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20737 (properties `((upstream-name . "matrixcalc")))
20738 (build-system r-build-system)
20739 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20740 (synopsis "Collection of functions for matrix calculations")
20742 "This package provides a collection of functions to support matrix
20743 calculations for probability, econometric and numerical analysis. There are
20744 additional functions that are comparable to APL functions which are useful for
20745 actuarial models such as pension mathematics.")
20746 (license license:gpl2+)))
20748 (define-public r-sem
20755 (uri (cran-uri "sem" version))
20758 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20759 (properties `((upstream-name . "sem")))
20760 (build-system r-build-system)
20762 `(("r-boot" ,r-boot)
20764 ("r-matrixcalc" ,r-matrixcalc)
20766 (home-page "https://cran.r-project.org/package=sem")
20767 (synopsis "Structural equation models")
20769 "This package provides functions for fitting general linear structural
20770 equation models (with observed and latent variables) using the RAM approach,
20771 and for fitting structural equations in observed-variable models by two-stage
20773 (license license:gpl2+)))
20775 (define-public r-semtools
20777 (name "r-semtools")
20782 (uri (cran-uri "semTools" version))
20785 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20786 (properties `((upstream-name . "semTools")))
20787 (build-system r-build-system)
20789 `(("r-lavaan" ,r-lavaan)))
20790 (home-page "https://github.com/simsem/semTools/wiki")
20791 (synopsis "Useful tools for structural equation modeling")
20793 "This package provides useful tools for structural equation modeling.")
20794 (license license:gpl2+)))
20796 (define-public r-regsem
20803 (uri (cran-uri "regsem" version))
20806 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
20807 (properties `((upstream-name . "regsem")))
20808 (build-system r-build-system)
20810 `(("r-lavaan" ,r-lavaan)
20812 ("r-rcpparmadillo" ,r-rcpparmadillo)
20813 ("r-rsolnp" ,r-rsolnp)))
20815 `(("r-knitr" ,r-knitr)))
20816 (home-page "https://cran.r-project.org/package=regsem")
20817 (synopsis "Regularized structural equation modeling")
20819 "This package uses both ridge and lasso penalties (and extensions) to
20820 penalize specific parameters in structural equation models. The package
20821 offers additional cost functions, cross validation, and other extensions
20822 beyond traditional structural equation models. It also contains a function to
20823 perform @dfn{exploratory mediation} (XMed).")
20824 (license license:gpl2+)))
20826 (define-public r-stanheaders
20828 (name "r-stanheaders")
20829 (version "2.21.0-6")
20833 (uri (cran-uri "StanHeaders" version))
20836 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20837 (properties `((upstream-name . "StanHeaders")))
20838 (build-system r-build-system)
20839 (inputs `(("pandoc" ,pandoc)))
20841 `(("r-rcppeigen" ,r-rcppeigen)
20842 ("r-rcppparallel" ,r-rcppparallel)))
20844 `(("gfortran" ,gfortran)
20845 ("r-knitr" ,r-knitr))) ; for vignettes
20846 (home-page "https://mc-stan.org/")
20847 (synopsis "C++ header files for Stan")
20849 "The C++ header files of the Stan project are provided by this package.
20850 There is a shared object containing part of the @code{CVODES} library, but it
20851 is not accessible from R. @code{r-stanheaders} is only useful for developers
20852 who want to utilize the @code{LinkingTo} directive of their package's
20853 DESCRIPTION file to build on the Stan library without incurring unnecessary
20856 The Stan project develops a probabilistic programming language that implements
20857 full or approximate Bayesian statistical inference via Markov Chain Monte
20858 Carlo or variational methods and implements (optionally penalized) maximum
20859 likelihood estimation via optimization. The Stan library includes an advanced
20860 automatic differentiation scheme, templated statistical and linear algebra
20861 functions that can handle the automatically differentiable scalar types (and
20862 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20863 package provides user-facing R functions to parse, compile, test, estimate,
20864 and analyze Stan models.")
20865 (license license:bsd-3)))
20867 (define-public r-rpf
20874 (uri (cran-uri "rpf" version))
20877 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
20878 (properties `((upstream-name . "rpf")))
20879 (build-system r-build-system)
20881 `(("r-lifecycle" ,r-lifecycle)
20882 ("r-mvtnorm" ,r-mvtnorm)
20884 ("r-rcppeigen" ,r-rcppeigen)))
20886 `(("r-knitr" ,r-knitr)))
20887 (home-page "https://github.com/jpritikin/rpf")
20888 (synopsis "Response probability functions")
20890 "The purpose of this package is to factor out logic and math common to
20891 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20892 core support code suitable for more specialized IRT packages to build upon.
20893 Complete access to optimized C functions is made available with
20894 @code{R_RegisterCCallable()}.")
20895 (license license:gpl3+)))
20897 (define-public r-openmx
20904 (uri (cran-uri "OpenMx" version))
20907 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
20908 (properties `((upstream-name . "OpenMx")))
20909 (build-system r-build-system)
20912 ("r-digest" ,r-digest)
20913 ("r-lifecycle" ,r-lifecycle)
20915 ("r-matrix" ,r-matrix)
20917 ("r-rcppeigen" ,r-rcppeigen)
20919 ("r-stanheaders" ,r-stanheaders)))
20920 (native-inputs `(("gfortran" ,gfortran)))
20921 (home-page "http://openmx.ssri.psu.edu")
20922 (synopsis "Extended structural equation modelling")
20924 "This package allows for the estimation of a wide variety of advanced
20925 multivariate statistical models. It consists of a library of functions and
20926 optimizers that allow you to quickly and flexibly define an SEM model and
20927 estimate parameters given observed data.")
20928 (license license:asl2.0)))
20930 (define-public r-kutils
20937 (uri (cran-uri "kutils" version))
20940 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20941 (properties `((upstream-name . "kutils")))
20942 (build-system r-build-system)
20944 `(("r-foreign" ,r-foreign)
20945 ("r-openxlsx" ,r-openxlsx)
20947 ("r-runit" ,r-runit)
20948 ("r-xtable" ,r-xtable)))
20949 (home-page "https://cran.r-project.org/package=kutils")
20950 (synopsis "Project management tools")
20952 "This package provides tools for data importation, recoding, and
20953 inspection. There are functions to create new project folders, R code
20954 templates, create uniquely named output directories, and to quickly obtain a
20955 visual summary for each variable in a data frame. The main feature here is
20956 the systematic implementation of the \"variable key\" framework for data
20957 importation and recoding.")
20958 (license license:gpl2)))
20960 (define-public r-rockchalk
20962 (name "r-rockchalk")
20963 (version "1.8.144")
20967 (uri (cran-uri "rockchalk" version))
20970 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20971 (properties `((upstream-name . "rockchalk")))
20972 (build-system r-build-system)
20974 `(("r-cardata" ,r-cardata)
20975 ("r-kutils" ,r-kutils)
20977 ("r-mass" ,r-mass)))
20978 (home-page "https://cran.r-project.org/package=rockchalk")
20979 (synopsis "Regression estimation and presentation")
20981 "This package provides a collection of functions for interpretation and
20982 presentation of regression analysis. These functions are used to produce the
20983 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20984 includes regression diagnostics, regression tables, and plots of interactions
20985 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20986 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20987 fairly comprehensive overview.")
20988 (license license:gpl3+)))
20990 (define-public r-lisreltor
20992 (name "r-lisreltor")
20997 (uri (cran-uri "lisrelToR" version))
21000 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
21001 (properties `((upstream-name . "lisrelToR")))
21002 (build-system r-build-system)
21003 (home-page "https://cran.r-project.org/package=lisrelToR")
21004 (synopsis "Import output from LISREL into R")
21006 "This is an unofficial package aimed at automating the import of LISREL
21008 (license license:gpl2)))
21010 (define-public r-bdgraph
21017 (uri (cran-uri "BDgraph" version))
21020 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
21021 (properties `((upstream-name . "BDgraph")))
21022 (build-system r-build-system)
21024 `(("r-igraph" ,r-igraph)))
21025 (home-page "https://www.uva.nl/profile/a.mohammadi")
21026 (synopsis "Bayesian structure learning in graphical models")
21028 "This package provides statistical tools for Bayesian structure learning
21029 in undirected graphical models for continuous, discrete, and mixed data. It
21030 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
21031 on a continuous-time birth-death process.")
21032 (license license:gpl2+)))
21034 (define-public r-d3network
21036 (name "r-d3network")
21037 (version "0.5.2.1")
21041 (uri (cran-uri "d3Network" version))
21044 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
21045 (properties `((upstream-name . "d3Network")))
21046 (build-system r-build-system)
21048 `(("r-plyr" ,r-plyr)
21049 ("r-rjson" ,r-rjson)
21050 ("r-whisker" ,r-whisker)))
21051 (home-page "http://christophergandrud.github.io/d3Network/")
21052 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
21054 "This package is intended to make it easy to create D3 JavaScript
21055 network, tree, dendrogram, and Sankey graphs from R using data frames.")
21056 (license license:gpl3+)))
21058 (define-public r-qgraph
21065 (uri (cran-uri "qgraph" version))
21068 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
21069 (properties `((upstream-name . "qgraph")))
21070 (build-system r-build-system)
21072 `(("r-abind" ,r-abind)
21073 ("r-bdgraph" ,r-bdgraph)
21074 ("r-colorspace" ,r-colorspace)
21075 ("r-corpcor" ,r-corpcor)
21076 ("r-d3network" ,r-d3network)
21077 ("r-dplyr" ,r-dplyr)
21078 ("r-fdrtool" ,r-fdrtool)
21079 ("r-ggplot2" ,r-ggplot2)
21080 ("r-ggraph" ,r-ggraph)
21081 ("r-glasso" ,r-glasso)
21082 ("r-gtools" ,r-gtools)
21083 ("r-hmisc" ,r-hmisc)
21085 ("r-igraph" ,r-igraph)
21087 ("r-lavaan" ,r-lavaan)
21088 ("r-matrix" ,r-matrix)
21089 ("r-pbapply" ,r-pbapply)
21092 ("r-psych" ,r-psych)
21094 ("r-reshape2" ,r-reshape2)
21095 ("r-tidygraph" ,r-tidygraph)))
21096 (home-page "http://sachaepskamp.com/qgraph/")
21097 (synopsis "Weighted network visualization and analysis")
21099 "This package implements tools for weighted network visualization and
21100 analysis, as well as Gaussian graphical model computation. It contains graph
21101 plotting methods, and tools for psychometric data visualization and graphical
21102 model estimation. See Epskamp et al. (2012)
21103 @url{doi:10.18637/jss.v048.i04}.")
21104 (license license:gpl2)))
21106 (define-public r-semplot
21113 (uri (cran-uri "semPlot" version))
21116 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
21117 (properties `((upstream-name . "semPlot")))
21118 (build-system r-build-system)
21120 `(("r-colorspace" ,r-colorspace)
21121 ("r-corpcor" ,r-corpcor)
21122 ("r-igraph" ,r-igraph)
21123 ("r-lavaan" ,r-lavaan)
21124 ("r-lisreltor" ,r-lisreltor)
21125 ("r-openmx" ,r-openmx)
21127 ("r-qgraph" ,r-qgraph)
21128 ("r-regsem" ,r-regsem)
21129 ("r-rockchalk" ,r-rockchalk)
21132 (home-page "https://github.com/SachaEpskamp/semPlot")
21133 (synopsis "Unified visualizations of structural equation models")
21135 "Structural equation modeling (SEM) has a long history of representing
21136 models graphically as path diagrams. The semPlot package for R fills the gap
21137 between advanced, but time-consuming, graphical software and the limited
21138 graphics produced automatically by SEM software. In addition, semPlot offers
21139 more functionality than drawing path diagrams: it can act as a common ground
21140 for importing SEM results into R. Any result usable as input to semPlot can
21141 also be represented in any of the three popular SEM frame-works, as well as
21142 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
21143 (license license:gpl2)))
21145 (define-public r-cdm
21152 (uri (cran-uri "CDM" version))
21155 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
21156 (properties `((upstream-name . "CDM")))
21157 (build-system r-build-system)
21159 `(("r-mvtnorm" ,r-mvtnorm)
21160 ("r-polycor" ,r-polycor)
21162 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21164 "https://github.com/alexanderrobitzsch/CDM")
21165 (synopsis "Cognitive diagnosis modeling")
21167 "This package provides functions for cognitive diagnosis modeling and
21168 multidimensional item response modeling for dichotomous and polytomous item
21169 responses. It enables the estimation of the DINA and DINO model, the multiple
21170 group (polytomous) GDINA model, the multiple choice DINA model, the general
21171 diagnostic model (GDM), the structured latent class model (SLCA), and
21172 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
21173 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
21174 estimation and the package structure. For tutorials on how to use the CDM
21175 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
21176 well as Ravand and Robitzsch (2015).")
21177 (license license:gpl2+)))
21179 (define-public r-tam
21186 (uri (cran-uri "TAM" version))
21189 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
21190 (properties `((upstream-name . "TAM")))
21191 (build-system r-build-system)
21195 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21196 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
21197 (synopsis "Test analysis modules")
21199 "This package includes tools for marginal maximum likelihood estimation
21200 and joint maximum likelihood estimation for unidimensional and
21201 multidimensional item response models. The package functionality covers the
21202 Rasch model, 2PL model, 3PL model, generalized partial credit model,
21203 multi-faceted Rasch model, nominal item response model, structured latent
21204 class model, mixture distribution IRT models, and located latent class models.
21205 Latent regression models and plausible value imputation are also supported.")
21206 (license license:gpl2+)))
21208 (define-public r-erm
21215 (uri (cran-uri "eRm" version))
21218 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
21219 (properties `((upstream-name . "eRm")))
21220 (build-system r-build-system)
21222 `(("r-colorspace" ,r-colorspace)
21223 ("r-lattice" ,r-lattice)
21225 ("r-matrix" ,r-matrix)
21226 ("r-psych" ,r-psych)))
21227 (native-inputs `(("gfortran" ,gfortran)))
21228 (home-page "https://cran.r-project.org/package=eRm")
21229 (synopsis "Extended Rasch modeling")
21231 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21232 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21233 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21234 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21235 data matrix. Additional features are the ML estimation of the person
21236 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21237 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21238 infit and outfit measures, ICC and other plots, automated stepwise item
21239 elimination, and a simulation module for various binary data matrices.")
21240 (license license:gpl3)))
21242 (define-public r-irtoys
21249 (uri (cran-uri "irtoys" version))
21252 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21253 (properties `((upstream-name . "irtoys")))
21254 (build-system r-build-system)
21258 (home-page "https://cran.r-project.org/package=irtoys")
21259 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21261 "This package provides a collection of functions useful in learning and
21262 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21263 programs. It provides basic CTT analysis, a simple common interface to the
21264 estimation of item parameters in IRT models for binary responses with three
21265 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21266 EAP, WLE, plausible values), item and person fit statistics, scaling
21267 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21268 array of parametric and non-parametric (kernel) plots. It estimates and plots
21269 Haberman's interaction model when all items are dichotomously scored.")
21270 (license license:gpl2+)))
21272 (define-public r-iheatmapr
21274 (name "r-iheatmapr")
21279 (uri (cran-uri "iheatmapr" version))
21282 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
21283 (properties `((upstream-name . "iheatmapr")))
21284 (build-system r-build-system)
21286 `(("r-fastcluster" ,r-fastcluster)
21287 ("r-ggdendro" ,r-ggdendro)
21288 ("r-htmlwidgets" ,r-htmlwidgets)
21289 ("r-jsonlite" ,r-jsonlite)
21290 ("r-knitr" ,r-knitr)
21291 ("r-magrittr" ,r-magrittr)
21292 ("r-rcolorbrewer" ,r-rcolorbrewer)
21293 ("r-scales" ,r-scales)))
21295 `(("r-knitr" ,r-knitr)))
21296 (home-page "https://docs.ropensci.org/iheatmapr")
21297 (synopsis "Interactive, Complex Heatmaps")
21299 "iheatmapr is an R package for building complex, interactive heatmaps
21300 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21301 subplots along the rows or columns of the main heatmap add more information
21302 about each row or column. For example, a one column additional heatmap may
21303 indicate what group a particular row or column belongs to. Complex heatmaps
21304 may also include multiple side by side heatmaps which show different types of
21305 data for the same conditions. Interactivity can improve complex heatmaps by
21306 providing tooltips with information about each cell and enabling zooming into
21307 interesting features. iheatmapr uses the plotly library for interactivity.")
21308 (license license:expat)))
21310 (define-public r-packrat
21317 (uri (cran-uri "packrat" version))
21320 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21321 (properties `((upstream-name . "packrat")))
21322 (build-system r-build-system)
21323 (home-page "https://github.com/rstudio/packrat/")
21324 (synopsis "Dependency management R projects")
21326 "This package provides a dependency manager for R projects that allows
21327 you to manage the R packages your project depends on in an isolated, portable,
21328 and reproducible way.")
21329 (license license:gpl2)))
21331 (define-public r-rsconnect
21333 (name "r-rsconnect")
21338 (uri (cran-uri "rsconnect" version))
21341 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21342 (properties `((upstream-name . "rsconnect")))
21343 (build-system r-build-system)
21345 `(("r-curl" ,r-curl)
21346 ("r-digest" ,r-digest)
21347 ("r-jsonlite" ,r-jsonlite)
21348 ("r-openssl" ,r-openssl)
21349 ("r-packrat" ,r-packrat)
21350 ("r-rstudioapi" ,r-rstudioapi)
21351 ("r-yaml" ,r-yaml)))
21352 (home-page "https://github.com/rstudio/rsconnect")
21353 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21355 "This package provides a programmatic deployment interface for RPubs,
21356 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21357 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21358 (license license:gpl2)))
21360 ;; This package includes minified JavaScript files. When upgrading please
21361 ;; check that there are no new minified JavaScript files.
21362 (define-public r-dygraphs
21364 (name "r-dygraphs")
21365 (version "1.1.1.6")
21369 (uri (cran-uri "dygraphs" version))
21372 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21373 (properties `((upstream-name . "dygraphs")))
21374 (build-system r-build-system)
21376 `(#:modules ((guix build utils)
21377 (guix build r-build-system)
21381 (modify-phases %standard-phases
21382 (add-after 'unpack 'process-javascript
21383 (lambda* (#:key inputs #:allow-other-keys)
21384 (with-directory-excursion "inst/htmlwidgets/lib/"
21388 `(("dygraphs/dygraph-combined-dev.js"
21389 "dygraph-combined.js")
21390 (,(assoc-ref inputs "js-jquery")
21391 "jquery/jquery.min.js")
21392 (,(assoc-ref inputs "js-fquarter")
21393 "fquarter/moment-fquarter.min.js"))))
21394 (lambda (sources targets)
21395 (for-each (lambda (source target)
21396 (format #t "Processing ~a --> ~a~%"
21398 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21399 (call-with-output-file target
21401 (dump-port minified port)))))
21402 sources targets))))
21405 `(("uglify-js" ,uglify-js)
21406 ;; They actually use version 1.11.1, but this more recent version
21407 ;; should be just fine.
21411 (uri "https://code.jquery.com/jquery-1.12.4.js")
21414 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21418 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21419 "moment-fquarter/1.0.1/moment-fquarter.js"))
21422 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21424 `(("r-htmltools" ,r-htmltools)
21425 ("r-htmlwidgets" ,r-htmlwidgets)
21426 ("r-magrittr" ,r-magrittr)
21429 (home-page "https://github.com/rstudio/dygraphs")
21430 (synopsis "Interface to Dygraphs interactive time series charting library")
21432 "This package provides an R interface to the dygraphs JavaScript charting
21433 library (a copy of which is included in the package). It provides rich
21434 facilities for charting time-series data in R, including highly configurable
21435 series- and axis-display and interactive features like zoom/pan and
21436 series/point highlighting.")
21437 (license license:expat)))
21439 (define-public r-shinystan
21441 (name "r-shinystan")
21446 (uri (cran-uri "shinystan" version))
21449 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21450 (properties `((upstream-name . "shinystan")))
21451 (build-system r-build-system)
21453 `(("r-bayesplot" ,r-bayesplot)
21454 ("r-colourpicker" ,r-colourpicker)
21456 ("r-dygraphs" ,r-dygraphs)
21457 ("r-ggplot2" ,r-ggplot2)
21458 ("r-gridextra" ,r-gridextra)
21459 ("r-gtools" ,r-gtools)
21460 ("r-markdown" ,r-markdown)
21461 ("r-reshape2" ,r-reshape2)
21462 ("r-rsconnect" ,r-rsconnect)
21463 ("r-rstan" ,r-rstan)
21464 ("r-shiny" ,r-shiny)
21465 ("r-shinyjs" ,r-shinyjs)
21466 ("r-shinythemes" ,r-shinythemes)
21467 ("r-threejs" ,r-threejs)
21468 ("r-xtable" ,r-xtable)
21470 (home-page "https://mc-stan.org/")
21471 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21473 "This package provides a graphical user interface for interactive
21474 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21475 for analyzing a posterior sample. The interface is powered by the Shiny web
21476 application framework and works with the output of MCMC programs written in
21477 any programming language (and has extended functionality for Stan models fit
21478 using the @code{rstan} and @code{rstanarm} packages).")
21479 (license license:gpl3+)))
21481 (define-public r-rstantools
21483 (name "r-rstantools")
21488 (uri (cran-uri "rstantools" version))
21491 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21492 (properties `((upstream-name . "rstantools")))
21493 (build-system r-build-system)
21494 (inputs `(("pandoc" ,pandoc)))
21496 `(("r-desc" ,r-desc)
21498 ("r-rcppparallel" ,r-rcppparallel)))
21500 `(("r-knitr" ,r-knitr)))
21501 (home-page "https://mc-stan.org/rstantools/")
21502 (synopsis "Tools for developing R packages interfacing with Stan")
21504 "This package provides various tools for developers of R packages
21505 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21506 up the required package structure, S3 generics and default methods to unify
21507 function naming across Stan-based R packages, and vignettes with
21508 recommendations for developers.")
21509 (license license:gpl3+)))
21511 (define-public r-loo
21518 (uri (cran-uri "loo" version))
21520 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21521 (properties `((upstream-name . "loo")))
21522 (build-system r-build-system)
21524 `(("pandoc" ,pandoc)
21525 ("pandoc-citeproc" ,pandoc-citeproc)))
21527 `(("r-checkmate" ,r-checkmate)
21528 ("r-matrixstats" ,r-matrixstats)))
21530 `(("r-knitr" ,r-knitr)))
21531 (home-page "https://mc-stan.org/loo/")
21532 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21534 "This package provides an implementation of efficient approximate
21535 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21536 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21537 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21538 procedure for regularizing importance weights. As a byproduct of the
21539 calculations, we also obtain approximate standard errors for estimated
21540 predictive errors and for the comparison of predictive errors between models.
21541 The package also provides methods for using stacking and other model weighting
21542 techniques to average Bayesian predictive distributions.")
21543 (license license:gpl3+)))
21545 (define-public r-rstan
21552 (uri (cran-uri "rstan" version))
21555 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21556 (properties `((upstream-name . "rstan")))
21557 (build-system r-build-system)
21560 (modify-phases %standard-phases
21561 (add-before 'install 'set-timezone
21562 ;; This package is picky about timezones.
21563 (lambda* (#:key inputs #:allow-other-keys)
21564 (setenv "TZ" "UTC+1")
21566 (string-append (assoc-ref inputs "tzdata")
21567 "/share/zoneinfo"))
21570 `(("tzdata" ,tzdata-for-tests)
21572 ("r-knitr" ,r-knitr)))
21575 ("r-ggplot2" ,r-ggplot2)
21576 ("r-gridextra" ,r-gridextra)
21577 ("r-inline" ,r-inline)
21579 ("r-pkgbuild" ,r-pkgbuild)
21581 ("r-rcppeigen" ,r-rcppeigen)
21582 ("r-rcppparallel" ,r-rcppparallel)
21583 ("r-stanheaders" ,r-stanheaders)
21585 ("r-withr" ,r-withr)))
21586 (home-page "https://discourse.mc-stan.org/")
21587 (synopsis "R interface to Stan")
21589 "User-facing R functions are provided to parse, compile, test, estimate,
21590 and analyze Stan models by accessing the header-only Stan library provided by
21591 the StanHeaders package. The Stan project develops a probabilistic
21592 programming language that implements full Bayesian statistical inference via
21593 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21594 approximation, and (optionally penalized) maximum likelihood estimation via
21595 optimization. In all three cases, automatic differentiation is used to
21596 quickly and accurately evaluate gradients without burdening the user with the
21597 need to derive the partial derivatives.")
21598 (license license:gpl3+)))
21600 (define-public r-rstanarm
21602 (name "r-rstanarm")
21607 (uri (cran-uri "rstanarm" version))
21610 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21611 (properties `((upstream-name . "rstanarm")))
21612 (build-system r-build-system)
21614 `(("pandoc" ,pandoc)
21615 ("pandoc-citeproc" ,pandoc-citeproc)))
21617 `(("r-bayesplot" ,r-bayesplot)
21619 ("r-ggplot2" ,r-ggplot2)
21622 ("r-matrix" ,r-matrix)
21625 ("r-rcppeigen" ,r-rcppeigen)
21626 ("r-rcppparallel" ,r-rcppparallel)
21627 ("r-rstan" ,r-rstan)
21628 ("r-rstantools" ,r-rstantools)
21629 ("r-shinystan" ,r-shinystan)
21630 ("r-stanheaders" ,r-stanheaders)
21631 ("r-survival" ,r-survival)))
21633 `(("r-knitr" ,r-knitr)))
21634 (home-page "https://mc-stan.org/rstanarm/")
21635 (synopsis "Bayesian applied regression modeling via Stan")
21637 "This package estimates previously compiled regression models using the
21638 @code{rstan} package, which provides the R interface to the Stan C++ library
21639 for Bayesian estimation. Users specify models via the customary R syntax with
21640 a formula and @code{data.frame} plus some additional arguments for priors.")
21641 (license license:gpl3+)))
21643 (define-public r-kendall
21650 (uri (cran-uri "Kendall" version))
21653 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21654 (properties `((upstream-name . "Kendall")))
21655 (build-system r-build-system)
21657 `(("r-boot" ,r-boot)))
21659 `(("gfortran" ,gfortran)))
21660 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21661 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21663 "This package computes the Kendall rank correlation and Mann-Kendall
21665 (license license:gpl2+)))
21667 (define-public r-zyp
21670 (version "0.10-1.1")
21674 (uri (cran-uri "zyp" version))
21677 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21678 (properties `((upstream-name . "zyp")))
21679 (build-system r-build-system)
21681 `(("r-kendall" ,r-kendall)))
21682 (home-page "https://cran.r-project.org/web/packages/zyp/")
21683 (synopsis "Zhang + Yue-Pilon Trends Package")
21685 "This package contains an efficient implementation of Sen's slope
21686 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21687 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21689 (license license:lgpl2.1)))
21691 (define-public r-rlinsolve
21693 (name "r-rlinsolve")
21698 (uri (cran-uri "Rlinsolve" version))
21701 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21702 (properties `((upstream-name . "Rlinsolve")))
21703 (build-system r-build-system)
21705 `(("r-matrix" ,r-matrix)
21707 ("r-rcpparmadillo" ,r-rcpparmadillo)
21708 ("r-rdpack" ,r-rdpack)))
21709 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21710 (synopsis "Iterative solvers for (sparse) linear system of equations")
21712 "Solving a system of linear equations is one of the most fundamental
21713 computational problems for many fields of mathematical studies, such as
21714 regression problems from statistics or numerical partial differential
21715 equations. This package provides basic stationary iterative solvers such as
21716 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21717 Nonstationary, also known as Krylov subspace methods are also provided.
21718 Sparse matrix computation is also supported in that solving large and sparse
21719 linear systems can be manageable using the @code{Matrix} package along with
21720 @code{RcppArmadillo}.")
21721 (license license:gpl3+)))
21723 (define-public r-zvcv
21730 (uri (cran-uri "ZVCV" version))
21733 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21734 (properties `((upstream-name . "ZVCV")))
21735 (build-system r-build-system)
21737 `(("r-abind" ,r-abind)
21739 ("r-dplyr" ,r-dplyr)
21740 ("r-glmnet" ,r-glmnet)
21741 ("r-magrittr" ,r-magrittr)
21742 ("r-mvtnorm" ,r-mvtnorm)
21744 ("r-rcpparmadillo" ,r-rcpparmadillo)
21745 ("r-rlinsolve" ,r-rlinsolve)))
21746 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21747 (synopsis "Zero-Variance Control Variates")
21749 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21750 to reduce the variance of Monte Carlo estimators of expectations using the
21751 derivatives of the log target. Once the derivatives are available, the only
21752 additional computational effort is in solving a linear regression problem.
21753 This method has been extended to higher dimensions using regularisation. This
21754 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21755 samples, derivatives and function evaluations are available. Additional
21756 functions for applying ZV-CV to two estimators for the normalising constant of
21757 the posterior distribution in Bayesian statistics are also supplied.")
21758 (license license:gpl2+)))
21760 (define-public r-ztype
21767 (uri (cran-uri "ztype" version))
21770 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21771 (properties `((upstream-name . "ztype")))
21772 (build-system r-build-system)
21774 `(("r-assertthat" ,r-assertthat)
21775 ("r-dplyr" ,r-dplyr)
21776 ("r-ggplot2" ,r-ggplot2)
21777 ("r-lubridate" ,r-lubridate)
21778 ("r-magrittr" ,r-magrittr)
21779 ("r-rvest" ,r-rvest)
21780 ("r-stringr" ,r-stringr)))
21781 (home-page "https://cran.r-project.org/web/packages/ztype/")
21782 (synopsis "Run a Ztype game loaded with R functions")
21784 "How fast can you type R functions on your keyboard? Find out by running
21785 a @code{zty.pe} game: export R functions as instructions to type to destroy
21786 opponents' vessels.")
21787 (license license:gpl3)))
21789 (define-public r-zseq
21796 (uri (cran-uri "Zseq" version))
21799 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21800 (properties `((upstream-name . "Zseq")))
21801 (build-system r-build-system)
21803 `(("r-gmp" ,r-gmp)))
21804 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21805 (synopsis "Integer sequence generator")
21807 "This package generates well-known integer sequences. The @code{gmp}
21808 package is adopted for computing with arbitrarily large numbers. Every
21809 function has a hyperlink to its corresponding item in the @dfn{On-Line
21810 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21811 (license license:gpl3+)))
21813 (define-public r-isoband
21820 (uri (cran-uri "isoband" version))
21823 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21824 (properties `((upstream-name . "isoband")))
21825 (build-system r-build-system)
21827 `(("r-testthat" ,r-testthat)))
21829 `(("r-knitr" ,r-knitr)))
21830 (home-page "https://github.com/wilkelab/isoband")
21831 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21833 "This package provides a fast C++ implementation to generate contour
21834 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21835 containing elevation data.")
21836 (license license:expat)))
21838 (define-public r-ppcor
21845 (uri (cran-uri "ppcor" version))
21848 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21849 (properties `((upstream-name . "ppcor")))
21850 (build-system r-build-system)
21852 `(("r-mass" ,r-mass)))
21853 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21854 (synopsis "Partial and semi-partial correlation")
21856 "This package provides users not only with a function to readily
21857 calculate the higher-order partial and semi-partial correlations but also with
21858 statistics and p-values of the correlation coefficients.")
21859 (license license:gpl2)))
21861 (define-public r-hrbrthemes
21863 (name "r-hrbrthemes")
21868 (uri (cran-uri "hrbrthemes" version))
21870 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21871 (properties `((upstream-name . "hrbrthemes")))
21872 (build-system r-build-system)
21874 `(("r-extrafont" ,r-extrafont)
21875 ("r-gdtools" ,r-gdtools)
21876 ("r-ggplot2" ,r-ggplot2)
21877 ("r-htmltools" ,r-htmltools)
21878 ("r-knitr" ,r-knitr)
21879 ("r-magrittr" ,r-magrittr)
21880 ("r-rmarkdown" ,r-rmarkdown)
21881 ("r-scales" ,r-scales)))
21883 `(("r-knitr" ,r-knitr)))
21884 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21885 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21887 "This package provides a compilation of extra @code{ggplot2} themes,
21888 scales and utilities, including a spell check function for plot label fields
21889 and an overall emphasis on typography.")
21890 (license license:expat)))
21892 (define-public r-crochet
21899 (uri (cran-uri "crochet" version))
21902 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21903 (build-system r-build-system)
21905 `(("r-knitr" ,r-knitr)))
21906 (home-page "https://github.com/agrueneberg/crochet")
21907 (synopsis "Implementation Helper for Matrix-Like Types")
21909 "Functions to help implement the extraction / subsetting / indexing
21910 function @code{[} and replacement function @code{[<-} of custom matrix-like
21911 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21912 as possible (with tests to prove it).")
21913 (license license:expat)))
21915 (define-public r-boa
21918 (version "1.1.8-2")
21922 (uri (cran-uri "boa" version))
21925 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21926 (properties `((upstream-name . "boa")))
21927 (build-system r-build-system)
21928 (home-page "http://www.jstatsoft.org/v21/i11")
21929 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21931 "This package provides a menu-driven program and library of functions for
21932 carrying out convergence diagnostics and statistical and graphical analysis of
21933 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21934 (license license:gpl2+)))
21936 (define-public r-httpcode
21938 (name "r-httpcode")
21942 (uri (cran-uri "httpcode" version))
21945 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21946 (build-system r-build-system)
21947 (home-page "https://github.com/sckott/httpcode")
21948 (synopsis "HTTP status code helper")
21949 (description "@code{httpcode} provides functionality for finding and
21950 explaining the meaning of @code{HTTP} status codes. Functions are included for
21951 searching for codes by full or partial number, by message, and to get
21952 appropriate dog and cat images for many status codes.")
21953 (license license:expat)))
21955 (define-public r-latex2exp
21957 (name "r-latex2exp")
21961 (uri (cran-uri "latex2exp" version))
21964 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21965 (build-system r-build-system)
21967 `(("r-stringr" ,r-stringr)
21968 ("r-magrittr" ,r-magrittr)))
21969 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21970 (synopsis "Use LaTeX expressions in plots")
21971 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21972 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21973 rendered as text, axis labels, etc. throughout R's plotting system.")
21974 (license license:expat)))
21976 (define-public r-oai
21982 (uri (cran-uri "oai" version))
21985 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21986 (build-system r-build-system)
21988 `(("r-xml2" ,r-xml2)
21991 ("r-stringr" ,r-stringr)
21992 ("r-tibble" ,r-tibble)))
21993 (home-page "https://github.com/ropensci/oai/")
21994 (synopsis "General purpose OAI-PMH services client")
21995 (description "@code{oai} provides a general purpose client to work with
21996 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21997 service. Functions are provided to work with the OAI-PMH verbs:
21998 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21999 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
22000 (license license:expat)))
22002 (define-public r-argon2
22009 (uri (cran-uri "argon2" version))
22012 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
22013 (properties `((upstream-name . "argon2")))
22014 (build-system r-build-system)
22015 (home-page "https://github.com/wrathematics/argon2")
22016 (synopsis "Secure password hashing based on the argon2 algorithm")
22018 "This package provides utilities for secure password hashing via the
22019 argon2 algorithm.")
22020 (license license:bsd-2)))
22022 (define-public r-getpass
22029 (uri (cran-uri "getPass" version))
22032 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
22033 (properties `((upstream-name . "getPass")))
22034 (build-system r-build-system)
22036 `(("r-rstudioapi" ,r-rstudioapi)))
22037 (home-page "https://github.com/wrathematics/getPass")
22038 (synopsis "Masked user input")
22040 "This package provides a micro-package for reading \"passwords\", i.e.
22041 reading user input with masking, so that the input is not displayed as it is
22042 typed. Currently, RStudio, the command line (every OS), and any platform
22043 where tcltk is present are supported.")
22044 (license license:bsd-2)))
22046 (define-public r-remoter
22053 (uri (cran-uri "remoter" version))
22056 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
22057 (properties `((upstream-name . "remoter")))
22058 (build-system r-build-system)
22060 `(("r-argon2" ,r-argon2)
22061 ("r-getpass" ,r-getpass)
22062 ("r-pbdzmq" ,r-pbdzmq)
22064 (home-page "https://github.com/RBigData/remoter")
22065 (synopsis "Control a remote R session from a local one")
22067 "This package provides a set of utilities for client/server computing
22068 with R, controlling a remote R session (the server) from a local one (the
22070 (license license:bsd-2)))
22072 (define-public r-asd
22079 (uri (cran-uri "asd" version))
22082 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
22083 (properties `((upstream-name . "asd")))
22084 (build-system r-build-system)
22086 `(("r-mvtnorm" ,r-mvtnorm)))
22087 (home-page "https://cran.r-project.org/web/packages/asd")
22088 (synopsis "Simulations for Adaptive Seamless Designs")
22090 "This package provdes means to run simulations for adaptive seamless
22091 designs with and without early outcomes for treatment selection and
22092 subpopulation type designs.")
22093 (license license:gpl3)))
22095 (define-public r-nbconvertr
22097 (name "r-nbconvertr")
22102 (uri (cran-uri "nbconvertR" version))
22105 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
22106 (properties `((upstream-name . "nbconvertR")))
22107 (build-system r-build-system)
22109 `(("jupyter" ,python-nbconvert)
22110 ("pandoc" ,pandoc)))
22111 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
22112 (synopsis "Vignette engine wrapping Jupyter notebooks")
22114 "This package calls the Jupyter script @code{nbconvert} to create
22115 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
22116 containing rich text, code, and its output. Code cells can be edited and
22117 evaluated interactively.")
22118 (license license:gpl3)))
22120 (define-public r-bridgesampling
22122 (name "r-bridgesampling")
22127 (uri (cran-uri "bridgesampling" version))
22130 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
22132 `((upstream-name . "bridgesampling")))
22133 (build-system r-build-system)
22135 `(("r-brobdingnag" ,r-brobdingnag)
22137 ("r-matrix" ,r-matrix)
22138 ("r-mvtnorm" ,r-mvtnorm)
22139 ("r-scales" ,r-scales)
22140 ("r-stringr" ,r-stringr)))
22142 `(("r-knitr" ,r-knitr)))
22143 (home-page "https://github.com/quentingronau/bridgesampling")
22144 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
22146 "This package provides functions for estimating marginal likelihoods,
22147 Bayes factors, posterior model probabilities, and normalizing constants in
22148 general, via different versions of bridge sampling.")
22149 (license license:gpl2+)))
22151 (define-public r-tea
22158 (uri (cran-uri "tea" version))
22161 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
22163 `((upstream-name . "tea")))
22164 (build-system r-build-system)
22166 `(("r-matrix" ,r-matrix)))
22167 (home-page "https://cran.r-project.org/web/packages/tea/")
22168 (synopsis "Threshold estimation approaches")
22170 "This package provides different approaches for selecting the threshold
22171 in generalized Pareto distributions. Most of them are based on minimizing the
22172 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
22173 Others are heuristically motivated by searching for stable sample paths, i.e.
22174 a nearly constant region of the tail index estimator with respect to k, which
22175 is the number of data in the tail. The third class is motivated by graphical
22176 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
22177 is also implemented here.")
22178 (license license:gpl3)))
22180 (define-public r-awsmethods
22182 (name "r-awsmethods")
22187 (uri (cran-uri "awsMethods" version))
22190 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
22192 `((upstream-name . "awsMethods")))
22193 (build-system r-build-system)
22194 (home-page "http://www.wias-berlin.de/software/imaging/")
22195 (synopsis "Class and methods definitions")
22197 "This package defines the generic method @code{extract} and provides
22198 @code{openMP} support as needed in several packages like
22199 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
22200 (license license:gpl2+)))
22202 (define-public r-aws
22209 (uri (cran-uri "aws" version))
22212 "1mwg1q7l4a07g5aa9c6kh3fpl9lakk01pbzlk7ixbpy12yfvj9nm"))))
22214 `((upstream-name . "aws")))
22215 (build-system r-build-system)
22217 `(("r-awsmethods" ,r-awsmethods)
22220 `(("gfortran" ,gfortran)))
22221 (home-page "https://cran.r-project.org/web/packages/aws/")
22222 (synopsis "Adaptive weights smoothing")
22224 "This package provides a collection of R-functions implementing adaptive
22225 smoothing procedures in 1D, 2D and 3D. This includes the
22226 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22227 Confidence Intervals} (ICI), variational approaches, and a non-local means
22229 (license license:gpl2+)))
22231 (define-public r-sgloptim
22233 (name "r-sgloptim")
22238 (uri (cran-uri "sglOptim" version))
22241 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22243 `((upstream-name . "sglOptim")))
22244 (build-system r-build-system)
22247 ("r-doparallel" ,r-doparallel)
22248 ("r-foreach" ,r-foreach)
22249 ("r-matrix" ,r-matrix)
22251 ("r-rcpparmadillo" ,r-rcpparmadillo)
22252 ("r-rcppprogress" ,r-rcppprogress)))
22254 `(("r-knitr" ,r-knitr)))
22255 (home-page "https://github.com/nielsrhansen/sglOptim")
22256 (synopsis "Generic sparse group Lasso solver")
22258 "This package provides a fast generic solver for sparse group lasso
22259 optimization problems. The loss (objective) function must be defined in a C++
22260 module. The optimization problem is solved using a coordinate gradient
22261 descent algorithm. Convergence of the algorithm is established and the
22262 algorithm is applicable to a broad class of loss functions. Use of parallel
22263 computing for cross validation and subsampling is supported through the
22264 @code{foreach} and @code{doParallel} packages.")
22265 (license license:gpl2+)))
22267 (define-public r-grouped
22274 (uri (cran-uri "grouped" version))
22277 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22279 `((upstream-name . "grouped")))
22280 (build-system r-build-system)
22282 `(("r-mass" ,r-mass)))
22283 (home-page "https://cran.r-project.org/web/packages/grouped/")
22284 (synopsis "Regression analysis of grouped and coarse data")
22286 "This package provides regression models for grouped and coarse data,
22287 under the coarsened at random assumption.")
22288 (license license:gpl2+)))
22290 (define-public r-stam
22297 (uri (cran-uri "stam" version))
22300 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22302 `((upstream-name . "stam")))
22303 (build-system r-build-system)
22307 (home-page "https://cran.r-project.org/web/packages/stam")
22308 (synopsis "Spatio-temporal analysis and modelling")
22310 "This package provides various methods to conduct Spatio-Temporal
22311 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22312 Inferred Spatio-Temporal Modelling.")
22313 (license license:gpl2+)))
22315 (define-public r-dcv
22322 (uri (cran-uri "dcv" version))
22325 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22327 `((upstream-name . "dcv")))
22328 (build-system r-build-system)
22330 `(("r-lmtest" ,r-lmtest)))
22331 (home-page "https://cran.r-project.org/web/packages/dcv/")
22332 (synopsis "Conventional cross-validation statistics for climate-growth model")
22334 "This package performs several conventional cross-validation statistical
22335 methods for climate-growth model in the climate reconstruction from tree
22336 rings, including Sign Test statistic, Reduction of Error statistic, Product
22337 Mean Test, Durbin-Watson statistic etc.")
22338 (license license:gpl2)))
22340 (define-public r-rcdd
22347 (uri (cran-uri "rcdd" version))
22350 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22352 `((upstream-name . "rcdd")))
22353 (build-system r-build-system)
22356 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22357 (synopsis "Computational geometry")
22359 "This package converts back and forth between two representations of a
22360 convex polytope: as solution of a set of linear equalities and inequalities
22361 and as convex hull of set of points and rays. Also does linear programming
22362 and redundant generator elimination. All functions can use exact
22363 infinite-precision rational arithmetic.")
22364 (license license:gpl2)))
22366 (define-public r-rxnat
22373 (uri (cran-uri "Rxnat" version))
22376 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
22378 `((upstream-name . "Rxnat")))
22379 (build-system r-build-system)
22381 `(("r-dplyr" ,r-dplyr)
22383 ("r-rcurl" ,r-rcurl)
22384 ("r-tibble" ,r-tibble)))
22386 `(("r-knitr" ,r-knitr)))
22387 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22388 (synopsis "Queries and extracts images from neuroimaging datasets")
22390 "This package allows communication with the Extensible Neuroimaging
22391 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22393 (license license:gpl2)))
22395 (define-public r-rserve
22402 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22403 version ".tar.gz"))
22406 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22407 (build-system r-build-system)
22409 `(("r-checkmate" ,r-checkmate)
22411 ("r-jsonlite" ,r-jsonlite)
22412 ("r-knitr" ,r-knitr)
22415 ("r-uuid" ,r-uuid)))
22417 `(("openssl" ,openssl)
22419 (home-page "https://github.com/s-u/Rserve")
22421 "Server providing access to R from many languages and systems")
22423 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22424 binary requests to be sent to R. Every connection has a separate workspace
22425 and working directory. Client-side implementations are available for popular
22426 languages such as C/C++ and Java, allowing any application to use facilities
22427 of R without the need of linking to R code. Rserve supports remote
22428 connection, user authentication and file transfer. A simple R client is
22429 included in this package as well.")
22430 (license license:gpl2)))
22432 (define-public r-brms
22439 (uri (cran-uri "brms" version))
22442 "0s8dl1xm3bpivfv3hw94zv9cifjg8cgs5137yd8d755kc2v0fdmf"))))
22443 (properties `((upstream-name . "brms")))
22444 (build-system r-build-system)
22446 `(("r-abind" ,r-abind)
22447 ("r-backports" ,r-backports)
22448 ("r-bayesplot" ,r-bayesplot)
22449 ("r-bridgesampling" ,r-bridgesampling)
22451 ("r-future" ,r-future)
22452 ("r-ggplot2" ,r-ggplot2)
22455 ("r-matrix" ,r-matrix)
22456 ("r-matrixstats" ,r-matrixstats)
22458 ("r-nleqslv" ,r-nleqslv)
22461 ("r-rstan" ,r-rstan)
22462 ("r-rstantools" ,r-rstantools)
22463 ("r-shinystan" ,r-shinystan)))
22464 (native-inputs `(("r-knitr" ,r-knitr)))
22466 "https://github.com/paul-buerkner/brms")
22468 "Bayesian Regression Models using 'Stan'")
22470 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22471 using 'Stan' for full Bayesian inference. A wide range of distributions and
22472 link functions are supported, allowing users to fit -- among others -- linear,
22473 robust linear, count data, survival, response times, ordinal, zero-inflated,
22474 hurdle, and even self-defined mixture models all in a multilevel context.
22475 Further modeling options include non-linear and smooth terms, auto-correlation
22476 structures, censored data, meta-analytic standard errors, and quite a few
22477 more. In addition, all parameters of the response distribution can be
22478 predicted in order to perform distributional regression. Prior specifications
22479 are flexible and explicitly encourage users to apply prior distributions that
22480 actually reflect their beliefs. Model fit can easily be assessed and compared
22481 with posterior predictive checks and leave-one-out cross-validation.")
22482 (license license:gpl2)))
22484 (define-public r-mstate
22491 (uri (cran-uri "mstate" version))
22494 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22495 (properties `((upstream-name . "mstate")))
22496 (build-system r-build-system)
22498 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22499 ("r-survival" ,r-survival)))
22501 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22503 "Data Preparation, Estimation and Prediction in Multi-State Models")
22505 "Contains functions for data preparation, descriptives, hazard estimation
22506 and prediction with Aalen-Johansen or simulation in competing risks and
22507 multi-state models.")
22508 (license license:gpl2+)))
22510 (define-public r-scatterpie
22512 (name "r-scatterpie")
22517 (uri (cran-uri "scatterpie" version))
22520 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
22521 (properties `((upstream-name . "scatterpie")))
22522 (build-system r-build-system)
22524 `(("r-ggforce" ,r-ggforce)
22525 ("r-ggplot2" ,r-ggplot2)
22526 ("r-rlang" ,r-rlang)
22527 ("r-rvcheck" ,r-rvcheck)
22528 ("r-tidyr" ,r-tidyr)))
22530 `(("r-knitr" ,r-knitr)))
22531 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22532 (synopsis "Scatter pie plot")
22534 "This package creates scatterpie plots, especially useful for plotting
22536 (license license:artistic2.0)))
22538 (define-public r-boruta
22545 (uri (cran-uri "Boruta" version))
22548 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22549 (properties `((upstream-name . "Boruta")))
22550 (build-system r-build-system)
22551 (propagated-inputs `(("r-ranger" ,r-ranger)))
22552 (home-page "https://gitlab.com/mbq/Boruta/")
22553 (synopsis "Wrapper algorithm for all relevant feature selection")
22555 "This package provides an all relevant feature selection wrapper
22556 algorithm. It finds relevant features by comparing original attributes'
22557 importance with importance achievable at random, estimated using their
22558 permuted copies (shadows).")
22559 (license license:gpl2+)))
22561 (define-public r-directlabels
22563 (name "r-directlabels")
22564 (version "2020.6.17")
22568 (uri (cran-uri "directlabels" version))
22571 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22572 (build-system r-build-system)
22574 `(("r-quadprog" ,r-quadprog)))
22576 `(("r-knitr" ,r-knitr)))
22577 (home-page "http://directlabels.r-forge.r-project.org/")
22578 (synopsis "Direct labels for multicolor plots")
22580 "This package provides an extensible framework for automatically placing
22581 direct labels onto multicolor plots. Label positions are described using
22582 positioning methods that can be re-used across several different plots. There
22583 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22584 inferring an appropriate positioning method.")
22585 (license license:gpl3)))
22587 (define-public r-lsd
22594 (uri (cran-uri "LSD" version))
22596 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22597 (properties `((upstream-name . "LSD")))
22598 (build-system r-build-system)
22599 (home-page "https://cran.r-project.org/web/packages/LSD/")
22600 (synopsis "Lots of superior depictions tool creates colorful plots")
22602 "This package creates lots of colorful plots in a multitude of variations.
22603 Try a demo of the LSD by running @code{demotour()}.")
22605 (license (list license:gpl2 license:gpl3))))
22607 (define-public r-phylogram
22609 (name "r-phylogram")
22614 (uri (cran-uri "phylogram" version))
22616 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22617 (properties `((upstream-name . "phylogram")))
22618 (build-system r-build-system)
22619 (propagated-inputs `(("r-ape" ,r-ape)))
22620 (home-page "https://github.com/ropensci/phylogram/")
22621 (synopsis "Dendrograms for evolutionary analysis")
22623 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22624 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22625 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22626 as well as several tools for command-line tree manipulation and import/export
22627 via Newick parenthetic text. This improves accessibility to the comprehensive
22628 range of object-specific analytical and tree-visualization functions found
22629 across a wide array of bioinformatic R packages.")
22630 (license license:gpl3)))
22632 (define-public r-kmer
22639 (uri (cran-uri "kmer" version))
22641 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22642 (properties `((upstream-name . "kmer")))
22643 (build-system r-build-system)
22645 `(("r-openssl" ,r-openssl)
22646 ("r-phylogram" ,r-phylogram)
22647 ("r-rcpp" ,r-rcpp)))
22648 (home-page "https://github.com/shaunpwilkinson/kmer/")
22649 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22651 "@code{r-kmer} is an R package for rapidly computing distance matrices
22652 and clustering large sequence datasets using fast alignment-free k-mer
22653 counting and recursive k-means partitioning.")
22654 (license license:gpl3)))
22656 (define-public r-hardhat
22663 (uri (cran-uri "hardhat" version))
22666 "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
22667 (properties `((upstream-name . "hardhat")))
22668 (build-system r-build-system)
22670 `(("r-glue" ,r-glue)
22671 ("r-rlang" ,r-rlang)
22672 ("r-tibble" ,r-tibble)
22673 ("r-vctrs" ,r-vctrs)))
22675 `(("r-knitr" ,r-knitr)))
22676 (home-page "https://github.com/tidymodels/hardhat")
22677 (synopsis "Construct modeling packages")
22679 "Building modeling packages is hard. A large amount of effort generally
22680 goes into providing an implementation for a new method that is efficient,
22681 fast, and correct, but often less emphasis is put on the user interface. A
22682 good interface requires specialized knowledge about S3 methods and formulas,
22683 which the average package developer might not have. The goal of
22684 @code{hardhat} is to reduce the burden around building new modeling packages
22685 by providing functionality for preprocessing, predicting, and validating
22687 (license license:expat)))
22689 (define-public r-shapforxgboost
22691 (name "r-shapforxgboost")
22696 (uri (cran-uri "SHAPforxgboost" version))
22699 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22701 `((upstream-name . "SHAPforxgboost")))
22702 (build-system r-build-system)
22704 `(("r-bbmisc" ,r-bbmisc)
22705 ("r-data-table" ,r-data-table)
22706 ("r-ggextra" ,r-ggextra)
22707 ("r-ggforce" ,r-ggforce)
22708 ("r-ggplot2" ,r-ggplot2)
22709 ("r-ggpubr" ,r-ggpubr)
22710 ("r-rcolorbrewer" ,r-rcolorbrewer)
22711 ("r-xgboost" ,r-xgboost)))
22712 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22713 (synopsis "SHAP Plots for XGBoost")
22715 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22716 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22717 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22718 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22720 (license license:expat)))
22722 (define-public r-rismed
22729 (uri (cran-uri "RISmed" version))
22732 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
22733 (properties `((upstream-name . "RISmed")))
22734 (build-system r-build-system)
22735 (home-page "https://cran.r-project.org/web/packages/RISmed")
22736 (synopsis "Download content from NCBI databases")
22738 "This package provides a set of tools to extract bibliographic
22739 content from the National Center for Biotechnology Information (NCBI)
22740 databases, including PubMed. The name RISmed is a portmanteau of
22741 RIS (for Research Information Systems, a common tag format for
22742 bibliographic data) and PubMed.")
22743 (license license:gpl2+)))
22745 (define-public r-semver
22752 (uri (cran-uri "semver" version))
22755 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22756 (properties `((upstream-name . "semver")))
22757 (build-system r-build-system)
22759 `(("r-assertthat" ,r-assertthat)
22760 ("r-rcpp" ,r-rcpp)))
22761 (native-inputs `(("r-knitr" ,r-knitr)))
22762 (home-page "https://github.com/johndharrison/semver")
22763 (synopsis "Parser for Semantic Versioning 2.0.0")
22765 "This package provides tools and functions for parsing, rendering and
22766 operating on semantic version strings. Semantic versioning is a simple set of
22767 rules and requirements that dictate how version numbers are assigned and
22768 incremented as outlined at @url{http://semver.org}.")
22769 (license license:expat)))
22771 (define-public r-binman
22778 (uri (cran-uri "binman" version))
22781 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
22782 (properties `((upstream-name . "binman")))
22783 (build-system r-build-system)
22785 `(("r-assertthat" ,r-assertthat)
22787 ("r-jsonlite" ,r-jsonlite)
22788 ("r-rappdirs" ,r-rappdirs)
22789 ("r-semver" ,r-semver)
22791 ("r-yaml" ,r-yaml)))
22792 (native-inputs `(("r-knitr" ,r-knitr)))
22793 (home-page "https://github.com/ropensci/binman")
22794 (synopsis "Binary download manager")
22796 "This package provides tools and functions for managing the download of
22797 binary files. Binary repositories are defined in the YAML format. Defining
22798 new pre-download, download and post-download templates allow additional
22799 repositories to be added.")
22800 (license license:expat)))
22802 (define-public r-wdman
22809 (uri (cran-uri "wdman" version))
22812 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22813 (properties `((upstream-name . "wdman")))
22814 (build-system r-build-system)
22816 `(("r-assertthat" ,r-assertthat)
22817 ("r-binman" ,r-binman)
22818 ("r-processx" ,r-processx)
22819 ("r-semver" ,r-semver)
22820 ("r-yaml" ,r-yaml)))
22821 (native-inputs `(("r-knitr" ,r-knitr)))
22822 (home-page "https://docs.ropensci.org/wdman/")
22823 (synopsis "Webdriver/Selenium binary manager")
22825 "There are a number of binary files associated with the
22826 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22827 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22828 @url{https://github.com/mozilla/geckodriver},
22829 @url{http://phantomjs.org/download.html}, and
22830 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22831 more information). This package provides functions to download these binaries
22832 and to manage processes involving them.")
22833 (license license:expat)))
22835 (define-public r-rselenium
22837 (name "r-rselenium")
22842 (uri (cran-uri "RSelenium" version))
22845 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22846 (properties `((upstream-name . "RSelenium")))
22847 (build-system r-build-system)
22849 `(("r-binman" ,r-binman)
22850 ("r-catools" ,r-catools)
22852 ("r-openssl" ,r-openssl)
22853 ("r-wdman" ,r-wdman)
22855 (native-inputs `(("r-knitr" ,r-knitr)))
22856 (home-page "https://docs.ropensci.org/RSelenium/")
22857 (synopsis "R bindings for Selenium WebDriver")
22859 "This package provides a set of R bindings for the Selenium 2.0
22860 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22861 information) using the @code{JsonWireProtocol} (see
22862 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22863 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22864 a user would either locally or on a remote machine using the Selenium server
22865 it marks a leap forward in terms of web browser automation. Selenium
22866 automates web browsers (commonly referred to as browsers). Using RSelenium
22867 you can automate browsers locally or remotely.")
22868 (license license:agpl3+)))
22870 (define-public r-conquer
22877 (uri (cran-uri "conquer" version))
22880 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
22881 (properties `((upstream-name . "conquer")))
22882 (build-system r-build-system)
22884 `(("r-matrix" ,r-matrix)
22885 ("r-matrixstats" ,r-matrixstats)
22887 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22888 (home-page "https://github.com/XiaoouPan/conquer")
22889 (synopsis "Convolution-type smoothed quantile regression")
22891 "This package provides fast and accurate convolution-type smoothed
22892 quantile regression, implemented using Barzilai-Borwein gradient descent with
22893 a Huber regression warm start. Confidence intervals for regression
22894 coefficients are constructed using multiplier bootstrap.")
22895 (license license:gpl3)))
22897 (define-public r-fastshap
22899 (name "r-fastshap")
22904 (uri (cran-uri "fastshap" version))
22907 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22908 (properties `((upstream-name . "fastshap")))
22909 (build-system r-build-system)
22911 `(("r-abind" ,r-abind)
22912 ("r-ggplot2" ,r-ggplot2)
22913 ("r-gridextra" ,r-gridextra)
22914 ("r-matrixstats" ,r-matrixstats)
22917 ("r-rcpparmadillo" ,r-rcpparmadillo)
22918 ("r-tibble" ,r-tibble)))
22919 (home-page "https://github.com/bgreenwell/fastshap")
22920 (synopsis "Fast approximate Shapley values")
22922 "This package computes fast (relative to other implementations)
22923 approximate Shapley values for any supervised learning model. Shapley values
22924 help to explain the predictions from any black box model using ideas from game
22925 theory; see @url{Strumbel and Kononenko (2014),
22926 doi.org/10.1007/s10115-013-0679-x} for details.")
22927 (license license:gpl2+)))
22929 (define-public r-metrics
22936 (uri (cran-uri "Metrics" version))
22939 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22940 (properties `((upstream-name . "Metrics")))
22941 (build-system r-build-system)
22942 (home-page "https://github.com/mfrasco/Metrics")
22943 (synopsis "Evaluation metrics for machine learning")
22945 "This package provides an implementation of evaluation metrics in R that
22946 are commonly used in supervised machine learning. It implements metrics for
22947 regression, time series, binary classification, classification, and
22948 information retrieval problems. It has zero dependencies and a consistent,
22949 simple interface for all functions.")
22950 (license license:bsd-3)))
22952 (define-public r-iml
22959 (uri (cran-uri "iml" version))
22962 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22963 (properties `((upstream-name . "iml")))
22964 (build-system r-build-system)
22966 `(("r-checkmate" ,r-checkmate)
22967 ("r-data-table" ,r-data-table)
22968 ("r-formula" ,r-formula)
22969 ("r-future" ,r-future)
22970 ("r-future-apply" ,r-future-apply)
22971 ("r-ggplot2" ,r-ggplot2)
22972 ("r-gridextra" ,r-gridextra)
22973 ("r-metrics" ,r-metrics)
22974 ("r-prediction" ,r-prediction)
22976 (native-inputs `(("r-knitr" ,r-knitr)))
22977 (home-page "https://github.com/christophM/iml")
22978 (synopsis "Interpretable machine learning")
22980 "This package provides interpretability methods to analyze the behavior
22981 and predictions of any machine learning model. Implemented methods are:
22984 @item Feature importance described by Fisher et al. (2018),
22985 @item accumulated local effects plots described by Apley (2018),
22986 @item partial dependence plots described by Friedman (2001),
22987 @item individual conditional expectation ('ice') plots described by Goldstein
22988 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
22989 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
22990 @item the Shapley Value described by Strumbelj et. al (2014)
22991 @url{https://doi.org/10.1007/s10115-013-0679-x},
22992 @item feature interactions described by Friedman et. al
22993 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
22996 (license license:expat)))
22998 (define-public r-goftest
23005 (uri (cran-uri "goftest" version))
23008 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
23009 (properties `((upstream-name . "goftest")))
23010 (build-system r-build-system)
23011 (home-page "https://github.com/baddstats/goftest")
23012 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
23014 "This package provides Cramer-Von Mises and Anderson-Darling tests of
23015 goodness-of-fit for continuous univariate distributions, using efficient
23017 (license license:gpl2+)))
23019 (define-public r-tensor
23026 (uri (cran-uri "tensor" version))
23029 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
23030 (properties `((upstream-name . "tensor")))
23031 (build-system r-build-system)
23032 (home-page "https://cran.r-project.org/web/packages/tensor/")
23033 (synopsis "Tensor product of arrays")
23035 "The tensor product of two arrays is notionally an outer product of the
23036 arrays collapsed in specific extents by summing along the appropriate
23037 diagonals. This package allows you to compute the tensor product of arrays.")
23038 (license license:gpl2+)))
23040 (define-public r-spatstat-utils
23042 (name "r-spatstat-utils")
23047 (uri (cran-uri "spatstat.utils" version))
23050 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
23052 `((upstream-name . "spatstat.utils")))
23053 (build-system r-build-system)
23054 (home-page "http://www.spatstat.org")
23055 (synopsis "Utility functions for spatstat")
23057 "This package contains utility functions for the @code{spatstat} package
23058 which may also be useful for other purposes.")
23059 (license license:gpl2+)))
23061 (define-public r-spatstat-data
23063 (name "r-spatstat-data")
23068 (uri (cran-uri "spatstat.data" version))
23071 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
23072 (properties `((upstream-name . "spatstat.data")))
23073 (build-system r-build-system)
23075 `(("r-matrix" ,r-matrix)
23076 ("r-spatstat-utils" ,r-spatstat-utils)))
23077 (home-page "http://www.spatstat.org")
23078 (synopsis "Datasets for spatstat")
23080 "This package contains all the datasets for the @code{spatstat}
23082 (license license:gpl2+)))
23084 (define-public r-spatstat
23086 (name "r-spatstat")
23091 (uri (cran-uri "spatstat" version))
23094 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
23095 (properties `((upstream-name . "spatstat")))
23096 (build-system r-build-system)
23098 `(("r-abind" ,r-abind)
23099 ("r-deldir" ,r-deldir)
23100 ("r-goftest" ,r-goftest)
23101 ("r-matrix" ,r-matrix)
23104 ("r-polyclip" ,r-polyclip)
23105 ("r-rpart" ,r-rpart)
23106 ("r-spatstat-data" ,r-spatstat-data)
23107 ("r-spatstat-utils" ,r-spatstat-utils)
23108 ("r-tensor" ,r-tensor)))
23109 (home-page "http://www.spatstat.org")
23110 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
23112 "This package provides a comprehensive toolbox for analysing Spatial
23113 Point Patterns. It is focused mainly on two-dimensional point patterns,
23114 including multitype/marked points, in any spatial region. It also supports
23115 three-dimensional point patterns, space-time point patterns in any number of
23116 dimensions, point patterns on a linear network, and patterns of other
23117 geometrical objects. It supports spatial covariate data such as pixel images
23118 and contains over 2000 functions for plotting spatial data, exploratory data
23119 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
23120 formal inference.")
23121 (license license:gpl2+)))
23123 (define-public r-gaston
23130 (uri (cran-uri "gaston" version))
23133 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
23134 (properties `((upstream-name . "gaston")))
23135 (build-system r-build-system)
23136 (inputs `(("zlib" ,zlib)))
23138 `(("r-rcpp" ,r-rcpp)
23139 ("r-rcppeigen" ,r-rcppeigen)
23140 ("r-rcppparallel" ,r-rcppparallel)))
23141 (native-inputs `(("r-knitr" ,r-knitr)))
23142 (home-page "https://cran.r-project.org/web/packages/gaston/")
23143 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
23145 "This is a package for the manipulation of genetic data (SNPs).
23146 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
23147 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
23148 for linear mixed models (AIREML).")
23149 (license license:gpl3)))
23151 (define-public r-cpp11
23158 (uri (cran-uri "cpp11" version))
23161 "1avcip33bldzz0rhkl43b4sljrbb8i24684xxmr9il5bijcpyy97"))))
23162 (properties `((upstream-name . "cpp11")))
23163 (build-system r-build-system)
23164 (native-inputs `(("r-knitr" ,r-knitr)))
23165 (home-page "https://github.com/r-lib/cpp11")
23166 (synopsis "C++11 Interface for R's C Interface")
23168 "This package provides a header only, C++11 interface to R's C interface.
23169 Compared to other approaches @code{cpp11} strives to be safe against long
23170 jumps from the C API as well as C++ exceptions, conform to normal R function
23171 semantics and supports interaction with @code{ALTREP} vectors.")
23172 (license license:expat)))
23174 (define-public r-rcppziggurat
23176 (name "r-rcppziggurat")
23181 (uri (cran-uri "RcppZiggurat" version))
23184 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
23185 (properties `((upstream-name . "RcppZiggurat")))
23186 (build-system r-build-system)
23188 `(("r-rcpp" ,r-rcpp)
23189 ("r-rcppgsl" ,r-rcppgsl)))
23190 (native-inputs `(("r-knitr" ,r-knitr)))
23191 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
23192 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
23194 "The Ziggurat generator for normally distributed random numbers,
23195 originally proposed by Marsaglia and Tsang (2000,
23196 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
23197 times starting with Leong et al (2005,
23198 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
23199 aggregation for comparing different implementations in order to provide a
23200 'faster but good enough' alternative for use with R and C++ code.")
23201 (license license:gpl2+)))
23203 (define-public r-rfast
23210 (uri (cran-uri "Rfast" version))
23213 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
23214 (properties `((upstream-name . "Rfast")))
23215 (build-system r-build-system)
23217 `(("r-rcpp" ,r-rcpp)
23218 ("r-rcpparmadillo" ,r-rcpparmadillo)
23219 ("r-rcppziggurat" ,r-rcppziggurat)))
23220 (home-page "https://github.com/RfastOfficial/Rfast")
23221 (synopsis "Collection of efficient and fast R functions")
23223 "This package provides a collection of fast (utility) functions for data
23224 analysis. Column- and row- wise means, medians, variances, minimums,
23225 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23226 Poisson), are some of the many fast functions.")
23227 (license license:gpl2+)))
23229 (define-public r-clusterr
23231 (name "r-clusterr")
23236 (uri (cran-uri "ClusterR" version))
23239 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23240 (properties `((upstream-name . "ClusterR")))
23241 (build-system r-build-system)
23243 `(("r-ggplot2" ,r-ggplot2)
23245 ("r-gtools" ,r-gtools)
23247 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23248 (native-inputs `(("r-knitr" ,r-knitr)))
23249 (home-page "https://github.com/mlampros/ClusterR")
23250 (synopsis "Clustering")
23252 "This package provides Gaussian mixture models, k-means,
23253 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23254 option to plot, validate, predict (new data) and estimate the optimal number
23255 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23256 the computationally intensive parts of the functions. For more information,
23260 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23261 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23262 @url{https://doi.org/10.18637/jss.v001.i04};
23263 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23264 Library, @url{https://doi.org/10.1145/1772690.1772862};
23265 @item \"Armadillo: a template-based C++ library
23266 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23267 Software, @url{https://doi.org/10.21105/joss.00026};
23268 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23269 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23270 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23273 (license license:gpl3)))
23275 (define-public r-spectrum
23277 (name "r-spectrum")
23282 (uri (cran-uri "Spectrum" version))
23285 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23286 (properties `((upstream-name . "Spectrum")))
23287 (build-system r-build-system)
23289 `(("r-clusterr" ,r-clusterr)
23290 ("r-diptest" ,r-diptest)
23291 ("r-ggplot2" ,r-ggplot2)
23292 ("r-rfast" ,r-rfast)))
23293 (native-inputs `(("r-knitr" ,r-knitr)))
23294 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23295 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23297 "This package provides a self-tuning spectral clustering method for
23298 single or multi-view data. Spectrum uses a new type of adaptive density aware
23299 kernel that strengthens connections in the graph based on common nearest
23300 neighbours. It uses a tensor product graph data integration and diffusion
23301 procedure to integrate different data sources and reduce noise. Spectrum uses
23302 either the eigengap or multimodality gap heuristics to determine the number of
23303 clusters. The method is sufficiently flexible so that a wide range of
23304 Gaussian and non-Gaussian structures can be clustered with automatic selection
23306 (license license:agpl3+)))
23308 (define-public r-nabor
23315 (uri (cran-uri "nabor" version))
23318 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23319 (properties `((upstream-name . "nabor")))
23320 (build-system r-build-system)
23324 ("r-rcppeigen" ,r-rcppeigen)))
23325 (home-page "https://cran.r-project.org/web/packages/nabor/")
23326 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23328 "This package provides an R wrapper for libnabo, an exact or approximate
23329 k nearest neighbour library which is optimised for low dimensional
23330 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23331 designed as a drop-in replacement for the RANN function @code{nn2}. In
23332 addition, objects which include the k-d tree search structure can be returned
23333 to speed up repeated queries of the same set of target points.")
23334 (license license:bsd-3)))
23336 (define-public r-muhaz
23339 (version "1.2.6.1")
23343 (uri (cran-uri "muhaz" version))
23346 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
23347 (properties `((upstream-name . "muhaz")))
23348 (build-system r-build-system)
23350 `(("r-survival" ,r-survival)))
23352 `(("gfortran" ,gfortran)))
23353 (home-page "https://cran.r-project.org/web/packages/muhaz/")
23354 (synopsis "Hazard function estimation in survival analysis")
23356 "This package produces a smooth estimate of the hazard function for
23358 ;; Any version of the GPL.
23359 (license license:gpl3+)))
23361 (define-public r-flexsurv
23363 (name "r-flexsurv")
23368 (uri (cran-uri "flexsurv" version))
23371 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
23372 (properties `((upstream-name . "flexsurv")))
23373 (build-system r-build-system)
23375 `(("r-desolve" ,r-desolve)
23376 ("r-mstate" ,r-mstate)
23377 ("r-muhaz" ,r-muhaz)
23378 ("r-mvtnorm" ,r-mvtnorm)
23379 ("r-quadprog" ,r-quadprog)
23381 ("r-survival" ,r-survival)
23382 ("r-tibble" ,r-tibble)
23383 ("r-tidyr" ,r-tidyr)))
23385 `(("r-knitr" ,r-knitr)))
23386 (home-page "https://github.com/chjackson/flexsurv-dev")
23387 (synopsis "Flexible parametric survival and multi-state models")
23389 "This package provides flexible parametric models for time-to-event data,
23390 including the Royston-Parmar spline model, generalized gamma and generalized F
23391 distributions. Any user-defined parametric distribution can be fitted, given
23392 at least an R function defining the probability density or hazard. There are
23393 also tools for fitting and predicting from fully parametric multi-state
23395 (license license:gpl2+)))
23397 (define-public r-transphylo
23399 (name "r-transphylo")
23404 (uri (cran-uri "TransPhylo" version))
23407 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
23408 (properties `((upstream-name . "TransPhylo")))
23409 (build-system r-build-system)
23412 ("r-rcpp" ,r-rcpp)))
23414 `(("r-knitr" ,r-knitr)))
23415 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
23416 (synopsis "Inference of transmission tree from a dated phylogeny")
23418 "This is a package to infer transmission trees from a dated phylogeny.
23419 It includes methods to simulate and analyze outbreaks. The methodology is
23420 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
23421 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
23422 (license license:gpl2+)))
23424 (define-public r-km-ci
23431 (uri (cran-uri "km.ci" version))
23434 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
23435 (properties `((upstream-name . "km.ci")))
23436 (build-system r-build-system)
23438 `(("r-survival" ,r-survival)))
23439 (home-page "https://cran.r-project.org/web/packages/km.ci/")
23440 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
23442 "This package computes various @dfn{confidence intervals} (CI) for the
23443 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
23444 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
23445 Nair and Hall and Wellner.")
23446 (license license:gpl2+)))
23448 (define-public r-kmsurv
23455 (uri (cran-uri "KMsurv" version))
23458 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
23459 (properties `((upstream-name . "KMsurv")))
23460 (build-system r-build-system)
23461 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
23462 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
23464 "This package provides data sets and functions for Klein and Moeschberger
23465 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
23467 (license license:gpl3+)))
23469 (define-public r-survmisc
23471 (name "r-survmisc")
23476 (uri (cran-uri "survMisc" version))
23479 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
23480 (properties `((upstream-name . "survMisc")))
23481 (build-system r-build-system)
23483 `(("r-data-table" ,r-data-table)
23484 ("r-ggplot2" ,r-ggplot2)
23485 ("r-gridextra" ,r-gridextra)
23486 ("r-km-ci" ,r-km-ci)
23487 ("r-kmsurv" ,r-kmsurv)
23488 ("r-knitr" ,r-knitr)
23489 ("r-survival" ,r-survival)
23490 ("r-xtable" ,r-xtable)
23493 `(("r-knitr" ,r-knitr)))
23494 (home-page "https://cran.r-project.org/web/packages/survMisc/")
23495 (synopsis "Miscellaneous functions for survival data")
23497 "This package provides a collection of functions to help in the analysis
23498 of right-censored survival data. These extend the methods available in
23499 the @code{survival} package.")
23500 (license license:gpl2)))
23502 (define-public r-exactranktests
23504 (name "r-exactranktests")
23509 (uri (cran-uri "exactRankTests" version))
23512 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
23514 `((upstream-name . "exactRankTests")))
23515 (build-system r-build-system)
23516 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
23517 (synopsis "Exact distributions for rank and permutation tests")
23519 "This package computes exact conditional p-values and quantiles using an
23520 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
23521 (license license:gpl2+)))
23523 (define-public r-maxstat
23530 (uri (cran-uri "maxstat" version))
23533 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
23534 (properties `((upstream-name . "maxstat")))
23535 (build-system r-build-system)
23537 `(("r-exactranktests" ,r-exactranktests)
23538 ("r-mvtnorm" ,r-mvtnorm)))
23539 (home-page "https://cran.r-project.org/web/packages/maxstat/")
23540 (synopsis "Maximally selected rank statistics")
23542 "This package provides maximally selected rank statistics with several
23543 p-value approximations.")
23544 (license license:gpl2+)))
23546 (define-public r-survminer
23548 (name "r-survminer")
23553 (uri (cran-uri "survminer" version))
23556 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
23557 (properties `((upstream-name . "survminer")))
23558 (build-system r-build-system)
23560 `(("r-broom" ,r-broom)
23561 ("r-dplyr" ,r-dplyr)
23562 ("r-ggplot2" ,r-ggplot2)
23563 ("r-ggpubr" ,r-ggpubr)
23564 ("r-gridextra" ,r-gridextra)
23565 ("r-magrittr" ,r-magrittr)
23566 ("r-maxstat" ,r-maxstat)
23567 ("r-purrr" ,r-purrr)
23568 ("r-rlang" ,r-rlang)
23569 ("r-scales" ,r-scales)
23570 ("r-survival" ,r-survival)
23571 ("r-survmisc" ,r-survmisc)
23572 ("r-tibble" ,r-tibble)
23573 ("r-tidyr" ,r-tidyr)))
23575 `(("r-knitr" ,r-knitr)))
23576 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
23577 (synopsis "Drawing survival curves using ggplot2")
23579 "This package contains the function @code{ggsurvplot()} for easily
23580 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
23581 risk' table and 'censoring count plot'. Other functions are also available to
23582 plot adjusted curves for Cox model and to visually examine Cox model
23584 (license license:gpl2)))
23586 (define-public r-forge
23593 (uri (cran-uri "forge" version))
23596 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
23597 (properties `((upstream-name . "forge")))
23598 (build-system r-build-system)
23600 `(("r-magrittr" ,r-magrittr)
23601 ("r-rlang" ,r-rlang)))
23602 (home-page "https://cran.r-project.org/web/packages/forge/")
23603 (synopsis "Cast values into shape")
23605 "This package provides helper functions with a consistent interface to
23606 coerce and verify the types and shapes of values for input checking.")
23607 (license license:asl2.0)))
23609 (define-public r-config
23616 (uri (cran-uri "config" version))
23619 "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
23620 (properties `((upstream-name . "config")))
23621 (build-system r-build-system)
23623 `(("r-yaml" ,r-yaml)))
23625 `(("r-knitr" ,r-knitr)))
23626 (home-page "https://github.com/rstudio/config")
23627 (synopsis "Manage environment specific configuration values")
23629 "This package lets you manage configuration values across multiple
23630 environments (e.g. development, test, production). It reads values using a
23631 function that determines the current environment and returns the appropriate
23633 (license license:gpl3)))
23635 (define-public r-adaptivesparsity
23637 (name "r-adaptivesparsity")
23641 (uri (cran-uri "AdaptiveSparsity" version))
23644 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
23646 `((upstream-name . "AdaptiveSparsity")))
23647 (build-system r-build-system)
23650 (modify-phases %standard-phases
23651 (add-after 'unpack 'link-against-armadillo
23653 (substitute* "src/Makevars"
23654 (("PKG_LIBS=" prefix)
23655 (string-append prefix "-larmadillo")))
23658 `(("r-mass" ,r-mass)
23659 ("r-matrix" ,r-matrix)
23661 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23663 `(("armadillo" ,armadillo)))
23664 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
23665 (synopsis "Adaptive sparsity models")
23667 "This package implements the Figueiredo machine learning algorithm for
23668 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
23669 geometric models.")
23670 (license license:lgpl3+)))
23672 (define-public r-diffusionmap
23674 (name "r-diffusionmap")
23679 (uri (cran-uri "diffusionMap" version))
23682 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
23683 (properties `((upstream-name . "diffusionMap")))
23684 (build-system r-build-system)
23686 `(("r-igraph" ,r-igraph)
23687 ("r-matrix" ,r-matrix)
23688 ("r-scatterplot3d" ,r-scatterplot3d)))
23689 (home-page "https://www.r-project.org")
23690 (synopsis "Diffusion map")
23691 (description "This package implements the diffusion map method of data
23692 parametrization, including creation and visualization of diffusion maps,
23693 clustering with diffusion K-means and regression using the adaptive regression
23695 (license license:gpl2)))
23697 (define-public r-igraph
23704 (uri (cran-uri "igraph" version))
23707 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
23708 (build-system r-build-system)
23710 `(("gfortran" ,gfortran)))
23714 ("libxml2" ,libxml2)
23717 `(("r-magrittr" ,r-magrittr)
23718 ("r-matrix" ,r-matrix)
23719 ("r-pkgconfig" ,r-pkgconfig)))
23720 (home-page "https://igraph.org")
23721 (synopsis "Network analysis and visualization")
23723 "This package provides routines for simple graphs and network analysis.
23724 It can handle large graphs very well and provides functions for generating
23725 random and regular graphs, graph visualization, centrality methods and much
23727 (license license:gpl2+)))
23729 (define-public r-workflows
23731 (name "r-workflows")
23736 (uri (cran-uri "workflows" version))
23739 "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9"))))
23740 (properties `((upstream-name . "workflows")))
23741 (build-system r-build-system)
23744 ("r-ellipsis" ,r-ellipsis)
23745 ("r-generics" ,r-generics)
23747 ("r-hardhat" ,r-hardhat)
23748 ("r-parsnip" ,r-parsnip)
23749 ("r-rlang" ,r-rlang)
23750 ("r-tidyselect" ,r-tidyselect)))
23752 `(("r-knitr" ,r-knitr)))
23753 (home-page "https://github.com/tidymodels/workflows")
23754 (synopsis "Modeling workflows")
23756 "A workflow is an object that can bundle together your pre-processing,
23757 modeling, and post-processing requests. For example, if you have a
23758 @code{recipe} and @code{parsnip} model, these can be combined into a
23759 workflow. The advantages are:
23762 @item You don’t have to keep track of separate objects in your workspace.
23763 @item The recipe prepping and model fitting can be executed using a single
23764 call to @code{fit()}.
23765 @item If you have custom tuning parameter settings, these can be defined using
23766 a simpler interface when combined with @code{tune}.
23767 @item In the future, workflows will be able to add post-processing operations,
23768 such as modifying the probability cutoff for two-class models.
23771 (license license:expat)))
23773 (define-public r-gpfit
23780 (uri (cran-uri "GPfit" version))
23783 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
23784 (properties `((upstream-name . "GPfit")))
23785 (build-system r-build-system)
23787 `(("r-lattice" ,r-lattice)
23789 (home-page "https://cran.r-project.org/web/packages/GPfit/")
23790 (synopsis "Gaussian Processes modeling")
23792 "This package provides a computationally stable approach of fitting a
23793 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
23794 (license license:gpl2)))
23796 (define-public r-yardstick
23798 (name "r-yardstick")
23803 (uri (cran-uri "yardstick" version))
23806 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
23807 (properties `((upstream-name . "yardstick")))
23808 (build-system r-build-system)
23810 `(("r-dplyr" ,r-dplyr)
23811 ("r-generics" ,r-generics)
23813 ("r-rlang" ,r-rlang)
23814 ("r-tidyselect" ,r-tidyselect)))
23816 `(("r-knitr" ,r-knitr)))
23817 (home-page "https://github.com/tidymodels/yardstick")
23818 (synopsis "Tidy characterizations of model performance")
23820 "This package provides tidy tools for quantifying how well a model fits
23821 to a data set such as confusion matrices, class probability curve summaries,
23822 and regression metrics (e.g., RMSE).")
23823 (license license:gpl2)))
23825 (define-public r-warp
23832 (uri (cran-uri "warp" version))
23835 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
23836 (properties `((upstream-name . "warp")))
23837 (build-system r-build-system)
23838 (native-inputs `(("r-knitr" ,r-knitr)))
23839 (home-page "https://github.com/DavisVaughan/warp")
23840 (synopsis "Group dates")
23842 "This package provides tooling to group dates by a variety of periods
23843 including: yearly, monthly, by second, by week of the month, and more. The
23844 groups are defined in such a way that they also represent the distance between
23845 dates in terms of the period. This extracts valuable information that can be
23846 used in further calculations that rely on a specific temporal spacing between
23848 (license license:expat)))
23850 (define-public r-slider
23857 (uri (cran-uri "slider" version))
23860 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
23861 (properties `((upstream-name . "slider")))
23862 (build-system r-build-system)
23864 `(("r-glue" ,r-glue)
23865 ("r-rlang" ,r-rlang)
23866 ("r-vctrs" ,r-vctrs)
23867 ("r-warp" ,r-warp)))
23868 (native-inputs `(("r-knitr" ,r-knitr)))
23869 (home-page "https://github.com/DavisVaughan/slider")
23870 (synopsis "Sliding window functions")
23872 "This package provides type-stable rolling window functions over any R
23873 data type. Cumulative and expanding windows are also supported. For more
23874 advanced usage, an index can be used as a secondary vector that defines how
23875 sliding windows are to be created.")
23876 (license license:expat)))
23878 (define-public r-rsample
23885 (uri (cran-uri "rsample" version))
23888 "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i"))))
23889 (properties `((upstream-name . "rsample")))
23890 (build-system r-build-system)
23892 `(("r-dplyr" ,r-dplyr)
23893 ("r-ellipsis" ,r-ellipsis)
23894 ("r-furrr" ,r-furrr)
23895 ("r-generics" ,r-generics)
23896 ("r-modeldata" ,r-modeldata)
23897 ("r-purrr" ,r-purrr)
23898 ("r-rlang" ,r-rlang)
23899 ("r-slider" ,r-slider)
23900 ("r-tibble" ,r-tibble)
23901 ("r-tidyr" ,r-tidyr)
23902 ("r-tidyselect" ,r-tidyselect)
23903 ("r-vctrs" ,r-vctrs)))
23905 `(("r-knitr" ,r-knitr)))
23906 (home-page "https://rsample.tidymodels.org")
23907 (synopsis "General resampling infrastructure")
23909 "This package provides classes and functions to create and summarize
23910 different types of resampling objects (e.g. bootstrap, cross-validation).")
23911 (license license:gpl2)))
23913 (define-public r-dicedesign
23915 (name "r-dicedesign")
23920 (uri (cran-uri "DiceDesign" version))
23923 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
23924 (properties `((upstream-name . "DiceDesign")))
23925 (build-system r-build-system)
23926 (home-page "http://dice.emse.fr/")
23927 (synopsis "Designs of computer experiments")
23929 "This package provides tools to create some specific @code{Space-Filling
23930 Design} (SFD) and to test their quality.")
23931 (license license:gpl3)))
23933 (define-public r-dials
23940 (uri (cran-uri "dials" version))
23943 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
23944 (properties `((upstream-name . "dials")))
23945 (build-system r-build-system)
23947 `(("r-dicedesign" ,r-dicedesign)
23948 ("r-dplyr" ,r-dplyr)
23950 ("r-purrr" ,r-purrr)
23951 ("r-rlang" ,r-rlang)
23952 ("r-scales" ,r-scales)
23953 ("r-tibble" ,r-tibble)
23954 ("r-vctrs" ,r-vctrs)
23955 ("r-withr" ,r-withr)))
23956 (native-inputs `(("r-knitr" ,r-knitr)))
23957 (home-page "https://dials.tidymodels.org/")
23958 (synopsis "Tools for creating tuning parameter values")
23960 "Many models contain tuning parameters (i.e. parameters that cannot be
23961 directly estimated from the data). These tools can be used to define objects
23962 for creating, simulating, or validating values for such parameters.")
23963 (license license:gpl2)))
23965 (define-public r-tune
23972 (uri (cran-uri "tune" version))
23975 "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
23976 (properties `((upstream-name . "tune")))
23977 (build-system r-build-system)
23980 ("r-crayon" ,r-crayon)
23981 ("r-dials" ,r-dials)
23982 ("r-dplyr" ,r-dplyr)
23983 ("r-foreach" ,r-foreach)
23984 ("r-ggplot2" ,r-ggplot2)
23986 ("r-gpfit" ,r-gpfit)
23987 ("r-hardhat" ,r-hardhat)
23988 ("r-lifecycle" ,r-lifecycle)
23989 ("r-parsnip" ,r-parsnip)
23990 ("r-purrr" ,r-purrr)
23991 ("r-recipes" ,r-recipes)
23992 ("r-rlang" ,r-rlang)
23993 ("r-rsample" ,r-rsample)
23994 ("r-tibble" ,r-tibble)
23995 ("r-tidyr" ,r-tidyr)
23996 ("r-vctrs" ,r-vctrs)
23997 ("r-workflows" ,r-workflows)
23998 ("r-yardstick" ,r-yardstick)))
23999 (home-page "https://github.com/tidymodels/tune")
24000 (synopsis "Tidy tuning tools")
24002 "The ability to tune models is important. @code{tune} contains functions
24003 and classes to be used in conjunction with other @code{tidymodels} packages
24004 for finding reasonable values of hyper-parameters in models, pre-processing
24005 methods, and post-processing steps.")
24006 (license license:expat)))
24008 (define-public r-tidyposterior
24010 (name "r-tidyposterior")
24015 (uri (cran-uri "tidyposterior" version))
24018 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
24019 (properties `((upstream-name . "tidyposterior")))
24020 (build-system r-build-system)
24022 `(("r-dplyr" ,r-dplyr)
24023 ("r-generics" ,r-generics)
24024 ("r-ggplot2" ,r-ggplot2)
24025 ("r-lifecycle" ,r-lifecycle)
24026 ("r-purrr" ,r-purrr)
24027 ("r-rlang" ,r-rlang)
24028 ("r-rsample" ,r-rsample)
24029 ("r-rstanarm" ,r-rstanarm)
24030 ("r-tibble" ,r-tibble)
24031 ("r-tidyr" ,r-tidyr)
24032 ("r-vctrs" ,r-vctrs)))
24034 `(("r-knitr" ,r-knitr)))
24035 (home-page "https://tidyposterior.tidymodels.org")
24036 (synopsis "Bayesian analysis to compare models using resampling statistics")
24038 "This package can be used to conduct post hoc analyses of resampling
24039 results generated by models. For example, if two models are evaluated with
24040 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
24041 are 10 paired statistics. These can be used to make comparisons between
24042 models without involving a test set.")
24043 (license license:gpl2)))
24045 (define-public r-tidypredict
24047 (name "r-tidypredict")
24052 (uri (cran-uri "tidypredict" version))
24055 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
24056 (properties `((upstream-name . "tidypredict")))
24057 (build-system r-build-system)
24059 `(("r-dplyr" ,r-dplyr)
24060 ("r-generics" ,r-generics)
24061 ("r-knitr" ,r-knitr)
24062 ("r-purrr" ,r-purrr)
24063 ("r-rlang" ,r-rlang)
24064 ("r-stringr" ,r-stringr)
24065 ("r-tibble" ,r-tibble)
24066 ("r-tidyr" ,r-tidyr)))
24068 `(("r-knitr" ,r-knitr)))
24069 (home-page "https://tidypredict.tidymodels.org")
24070 (synopsis "Run predictions inside the database")
24072 "This package parses a fitted R model object, and returns a formula in
24073 Tidy Eval code that calculates the predictions. It works with several
24074 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
24075 final SQL translation of the algorithm. It currently supports @code{lm()},
24076 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
24077 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
24078 (license license:gpl3)))
24080 (define-public r-janeaustenr
24082 (name "r-janeaustenr")
24087 (uri (cran-uri "janeaustenr" version))
24090 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
24091 (properties `((upstream-name . "janeaustenr")))
24092 (build-system r-build-system)
24093 (home-page "https://github.com/juliasilge/janeaustenr")
24094 (synopsis "Jane Austen's complete novels")
24096 "This package provides the full texts for Jane Austen's six completed
24097 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
24098 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
24099 and \"Persuasion\".")
24100 (license license:expat)))
24102 (define-public r-tokenizers
24104 (name "r-tokenizers")
24109 (uri (cran-uri "tokenizers" version))
24112 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
24113 (properties `((upstream-name . "tokenizers")))
24114 (build-system r-build-system)
24116 `(("r-rcpp" ,r-rcpp)
24117 ("r-snowballc" ,r-snowballc)
24118 ("r-stringi" ,r-stringi)))
24120 `(("r-knitr" ,r-knitr)))
24121 (home-page "https://lincolnmullen.com/software/tokenizers/")
24122 (synopsis "Fast, consistent tokenization of natural language text")
24124 "This is a package for converting natural language text into tokens.
24125 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
24126 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
24127 Treebank, regular expressions, as well as functions for counting characters,
24128 words, and sentences, and a function for splitting longer texts into separate
24129 documents, each with the same number of words. The tokenizers have a
24130 consistent interface, and the package is built on the @code{stringi} and
24131 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
24132 (license license:expat)))
24134 (define-public r-hunspell
24136 (name "r-hunspell")
24141 (uri (cran-uri "hunspell" version))
24144 "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
24145 (properties `((upstream-name . "hunspell")))
24146 (build-system r-build-system)
24148 `(("r-digest" ,r-digest)
24149 ("r-rcpp" ,r-rcpp)))
24151 `(("r-knitr" ,r-knitr)))
24152 (home-page "https://github.com/ropensci/hunspell#readme")
24153 (synopsis "High-performance stemmer, tokenizer, and spell checker")
24155 "This package provides a low-level spell checker and morphological
24156 analyzer based on the famous @code{hunspell} library. The package can analyze
24157 or check individual words as well as parse text, LaTeX, HTML or XML documents.
24158 For a more user-friendly interface use the @code{spelling} package which
24159 builds on this package to automate checking of files, documentation and
24160 vignettes in all common formats.")
24161 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
24162 ;; MPL; in addition to these licenses the rest of the R wrapper is also
24163 ;; available under the Expat license.
24164 (license (list license:gpl2
24169 (define-public r-tidytext
24171 (name "r-tidytext")
24176 (uri (cran-uri "tidytext" version))
24179 "0xmjkab7p13ncfglf3a9hvndf8fh96mmxw3l7hcpbnaq9qkiwk29"))))
24180 (properties `((upstream-name . "tidytext")))
24181 (build-system r-build-system)
24183 `(("r-dplyr" ,r-dplyr)
24184 ("r-generics" ,r-generics)
24185 ("r-hunspell" ,r-hunspell)
24186 ("r-janeaustenr" ,r-janeaustenr)
24187 ("r-matrix" ,r-matrix)
24188 ("r-purrr" ,r-purrr)
24189 ("r-rlang" ,r-rlang)
24190 ("r-stringr" ,r-stringr)
24191 ("r-tibble" ,r-tibble)
24192 ("r-tokenizers" ,r-tokenizers)))
24194 `(("r-knitr" ,r-knitr)))
24195 (home-page "https://github.com/juliasilge/tidytext")
24196 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
24198 "This is a package for text mining for word processing and sentiment
24199 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
24200 (license license:expat)))
24202 (define-public r-parsnip
24209 (uri (cran-uri "parsnip" version))
24212 "1134840xisvkkrbkh5kvx24vxp7sx06124svy573a9m4h8c492sr"))))
24213 (properties `((upstream-name . "parsnip")))
24214 (build-system r-build-system)
24216 `(("r-dplyr" ,r-dplyr)
24217 ("r-generics" ,r-generics)
24218 ("r-globals" ,r-globals)
24220 ("r-magrittr" ,r-magrittr)
24221 ("r-prettyunits" ,r-prettyunits)
24222 ("r-purrr" ,r-purrr)
24223 ("r-rlang" ,r-rlang)
24224 ("r-tibble" ,r-tibble)
24225 ("r-tidyr" ,r-tidyr)
24226 ("r-vctrs" ,r-vctrs)))
24228 `(("r-knitr" ,r-knitr)))
24229 (home-page "https://parsnip.tidymodels.org")
24230 (synopsis "Common API to modeling and analysis functions")
24232 "This package provides a common interface to allow users to specify a
24233 model without having to remember the different argument names across different
24234 functions or computational engines (e.g. R, Spark, Stan, etc).")
24235 (license license:gpl2)))
24237 (define-public r-infer
24244 (uri (cran-uri "infer" version))
24247 "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
24248 (properties `((upstream-name . "infer")))
24249 (build-system r-build-system)
24251 `(("r-dplyr" ,r-dplyr)
24252 ("r-ggplot2" ,r-ggplot2)
24254 ("r-magrittr" ,r-magrittr)
24255 ("r-purrr" ,r-purrr)
24256 ("r-rlang" ,r-rlang)
24257 ("r-tibble" ,r-tibble)))
24259 `(("r-knitr" ,r-knitr)))
24260 (home-page "https://github.com/tidymodels/infer")
24261 (synopsis "Tidy statistical inference")
24263 "The objective of this package is to perform inference using an
24264 expressive statistical grammar that coheres with the Tidy design framework.")
24265 (license license:cc0)))
24267 (define-public r-modeldata
24269 (name "r-modeldata")
24274 (uri (cran-uri "modeldata" version))
24277 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
24278 (properties `((upstream-name . "modeldata")))
24279 (build-system r-build-system)
24280 (home-page "https://modeldata.tidymodels.org")
24281 (synopsis "Data sets useful for modeling packages")
24283 "This package provides data sets used for demonstrating or testing
24284 model-related packages.")
24285 (license license:expat)))
24287 (define-public r-tidymodels
24289 (name "r-tidymodels")
24294 (uri (cran-uri "tidymodels" version))
24297 "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
24298 (properties `((upstream-name . "tidymodels")))
24299 (build-system r-build-system)
24301 `(("r-broom" ,r-broom)
24303 ("r-crayon" ,r-crayon)
24304 ("r-dials" ,r-dials)
24305 ("r-dplyr" ,r-dplyr)
24306 ("r-ggplot2" ,r-ggplot2)
24307 ("r-infer" ,r-infer)
24308 ("r-magrittr" ,r-magrittr)
24309 ("r-modeldata" ,r-modeldata)
24310 ("r-parsnip" ,r-parsnip)
24311 ("r-purrr" ,r-purrr)
24312 ("r-recipes" ,r-recipes)
24313 ("r-rlang" ,r-rlang)
24314 ("r-rsample" ,r-rsample)
24315 ("r-rstudioapi" ,r-rstudioapi)
24316 ("r-tibble" ,r-tibble)
24317 ("r-tidyr" ,r-tidyr)
24319 ("r-workflows" ,r-workflows)
24320 ("r-yardstick" ,r-yardstick)))
24322 `(("r-knitr" ,r-knitr)
24323 ("r-rmarkdown" ,r-rmarkdown)
24325 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
24326 (home-page "https://github.com/tidymodels/tidymodels")
24327 (synopsis "Tidy collection for modeling and statistical analysis")
24329 "The tidy modeling \"verse\" is a collection of packages for modeling and
24330 statistical analysis that share the underlying design philosophy, grammar, and
24331 data structures of the tidyverse.")
24332 (license license:gpl3)))
24334 (define-public r-mlecens
24341 (uri (cran-uri "MLEcens" version))
24344 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
24345 (properties `((upstream-name . "MLEcens")))
24346 (build-system r-build-system)
24347 (home-page "http://stat.ethz.ch/~maathuis/")
24348 (synopsis "Computation of the MLE for bivariate (interval) censored data")
24350 "This package contains functions to compute the nonparametric
24351 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
24352 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
24353 To be more precise, we consider the situation where we observe a set of
24354 rectangles that are known to contain the unobservable realizations of (X,Y).
24355 We compute the MLE based on such a set of rectangles. The methods can also be
24356 used for univariate censored data (see data set @code{cosmesis}), and for
24357 censored data with competing risks (see data set @code{menopause}). The
24358 package also provides functions to visualize the observed data and the MLE.")
24359 (license license:gpl2+)))
24361 (define-public r-perm
24364 (version "1.0-0.0")
24368 (uri (cran-uri "perm" version))
24371 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
24372 (properties `((upstream-name . "perm")))
24373 (build-system r-build-system)
24374 (home-page "https://cran.r-project.org/web/packages/perm/")
24375 (synopsis "Exact or asymptotic permutation tests")
24377 "This package provides several methods for performing permutation tests.
24378 It has three main functions, to perform linear permutation tests. These tests
24379 are tests where the test statistic is the sum of the product of a
24380 covariate (usually group indicator) and the scores.")
24381 ;; Any version of the GPL
24382 (license license:gpl2+)))
24384 (define-public r-qtl
24391 (uri (cran-uri "qtl" version))
24394 "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
24395 (build-system r-build-system)
24396 (home-page "https://rqtl.org/")
24397 (synopsis "R package for analyzing QTL experiments in genetics")
24398 (description "R/qtl is an extension library for the R statistics system.
24399 It is used to analyze experimental crosses for identifying genes contributing
24400 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
24402 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
24403 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
24405 (license license:gpl3)))
24407 (define-public r-qtl2
24410 (version "0.22-11")
24413 (uri (cran-uri "qtl2" version))
24415 (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
24416 (build-system r-build-system)
24418 `(("r-data-table" ,r-data-table)
24419 ("r-jsonlite" ,r-jsonlite)
24421 ("r-rcppeigen" ,r-rcppeigen)
24422 ("r-rsqlite" ,r-rsqlite)
24423 ("r-yaml" ,r-yaml)))
24424 (home-page "https://kbroman.org/qtl2/")
24425 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
24427 "This package provides a set of tools to perform @dfn{Quantitative Trait
24428 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
24429 @code{R/qtl} package to better handle high-dimensional data and complex cross
24430 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
24431 (license license:gpl3)))
24433 (define-public r-seqminer
24435 (name "r-seqminer")
24440 (uri (cran-uri "seqminer" version))
24443 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
24444 (build-system r-build-system)
24447 (home-page "http://seqminer.genomic.codes")
24448 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
24450 "This package provides tools to integrate nucleotide sequencing
24451 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
24452 ;; Any version of the GPL is acceptable
24453 (license (list license:gpl2+ license:gpl3+))))
24455 (define-public r-maldiquant
24457 (name "r-maldiquant")
24462 (uri (cran-uri "MALDIquant" version))
24465 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
24466 (properties `((upstream-name . "MALDIquant")))
24467 (build-system r-build-system)
24468 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
24469 (synopsis "Quantitative analysis of mass spectrometry data")
24471 "This package provides a complete analysis pipeline for matrix-assisted
24472 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
24473 two-dimensional mass spectrometry data. In addition to commonly used plotting
24474 and processing methods it includes distinctive features, namely baseline
24475 subtraction methods such as morphological filters (TopHat) or the
24476 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
24477 alignment using warping functions, handling of replicated measurements as well
24478 as allowing spectra with different resolutions.")
24479 (license license:gpl3+)))
24481 (define-public r-seurat
24487 (uri (cran-uri "Seurat" version))
24490 "048vnj0c3mrwhr6yq3jqhgnkg68w99nj1ccsmgnd8rl694w26spj"))))
24491 (properties `((upstream-name . "Seurat")))
24492 (build-system r-build-system)
24494 `(("r-cluster" ,r-cluster)
24495 ("r-cowplot" ,r-cowplot)
24496 ("r-fitdistrplus" ,r-fitdistrplus)
24497 ("r-future" ,r-future)
24498 ("r-future-apply" ,r-future-apply)
24499 ("r-ggplot2" ,r-ggplot2)
24500 ("r-ggrepel" ,r-ggrepel)
24501 ("r-ggridges" ,r-ggridges)
24504 ("r-igraph" ,r-igraph)
24505 ("r-irlba" ,r-irlba)
24506 ("r-jsonlite" ,r-jsonlite)
24507 ("r-kernsmooth" ,r-kernsmooth)
24508 ("r-leiden" ,r-leiden)
24509 ("r-lmtest" ,r-lmtest)
24511 ("r-matrix" ,r-matrix)
24512 ("r-matrixstats" ,r-matrixstats)
24513 ("r-miniui" ,r-miniui)
24514 ("r-patchwork" ,r-patchwork)
24515 ("r-pbapply" ,r-pbapply)
24516 ("r-plotly" ,r-plotly)
24519 ("r-rcolorbrewer" ,r-rcolorbrewer)
24521 ("r-rcppannoy" ,r-rcppannoy)
24522 ("r-rcppeigen" ,r-rcppeigen)
24523 ("r-rcppprogress" ,r-rcppprogress)
24524 ("r-reticulate" ,r-reticulate)
24525 ("r-rlang" ,r-rlang)
24528 ("r-rtsne" ,r-rtsne)
24529 ("r-scales" ,r-scales)
24530 ("r-sctransform" ,r-sctransform)
24531 ("r-shiny" ,r-shiny)
24532 ("r-spatstat" ,r-spatstat)
24533 ("r-tibble" ,r-tibble)
24534 ("r-uwot" ,r-uwot)))
24535 (home-page "http://www.satijalab.org/seurat")
24536 (synopsis "Seurat is an R toolkit for single cell genomics")
24538 "This package is an R package designed for QC, analysis, and
24539 exploration of single cell RNA-seq data. It easily enables widely-used
24540 analytical techniques, including the identification of highly variable genes,
24541 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
24542 algorithms; density clustering, hierarchical clustering, k-means, and the
24543 discovery of differentially expressed genes and markers.")
24544 (license license:gpl3)))
24546 (define-public r-phangorn
24548 (name "r-phangorn")
24553 (uri (cran-uri "phangorn" version))
24556 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
24557 (build-system r-build-system)
24560 ("r-fastmatch" ,r-fastmatch)
24561 ("r-igraph" ,r-igraph)
24562 ("r-magrittr" ,r-magrittr)
24563 ("r-matrix" ,r-matrix)
24564 ("r-quadprog" ,r-quadprog)
24565 ("r-rcpp" ,r-rcpp)))
24566 (home-page "https://github.com/KlausVigo/phangorn")
24567 (synopsis "Phylogenetic analysis in R")
24569 "Phangorn is a package for phylogenetic analysis in R. It supports
24570 estimation of phylogenetic trees and networks using Maximum Likelihood,
24571 Maximum Parsimony, distance methods and Hadamard conjugation.")
24572 (license license:gpl2+)))
24574 (define-public r-diversitree
24576 (name "r-diversitree")
24581 (uri (cran-uri "diversitree" version))
24584 "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
24585 (build-system r-build-system)
24587 `(("gfortran" ,gfortran)))
24588 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
24591 ("r-desolve" ,r-desolve)
24593 ("r-subplex" ,r-subplex)))
24594 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
24595 (synopsis "Comparative 'phylogenetic' analyses of diversification")
24596 (description "This package contains a number of comparative \"phylogenetic\"
24597 methods, mostly focusing on analysing diversification and character evolution.
24598 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
24599 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
24600 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
24601 include Markov models of discrete and continuous trait evolution and constant
24602 rate speciation and extinction.")
24603 (license license:gpl2+)))
24605 (define-public r-absfiltergsea
24607 (name "r-absfiltergsea")
24612 (uri (cran-uri "AbsFilterGSEA" version))
24614 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
24615 (properties `((upstream-name . "AbsFilterGSEA")))
24616 (build-system r-build-system)
24618 `(("r-biobase" ,r-biobase)
24619 ("r-deseq" ,r-deseq)
24620 ("r-limma" ,r-limma)
24622 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24623 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
24624 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
24626 "This package provides a function that performs gene-permuting of a gene-set
24627 enrichment analysis (GSEA) calculation with or without the absolute filtering.
24628 Without filtering, users can perform (original) two-tailed or one-tailed
24630 (license license:gpl2)))
24632 (define-public r-calculus
24634 (name "r-calculus")
24639 (uri (cran-uri "calculus" version))
24642 "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp"))))
24643 (properties `((upstream-name . "calculus")))
24644 (build-system r-build-system)
24646 `(("r-rcpp" ,r-rcpp)))
24647 (home-page "https://github.com/eguidotti/calculus")
24648 (synopsis "High dimensional numerical and symbolic calculus")
24650 "Efficient C++ optimized functions for numerical and symbolic calculus.
24651 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
24652 convention, fast computation of the Levi-Civita symbol and generalized
24653 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
24654 accurate high-order derivatives, differential operators (Gradient, Jacobian,
24655 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
24656 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
24657 parabolic or user defined by custom scale factors.")
24658 (license license:gpl3)))