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 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>
33 ;;; This file is part of GNU Guix.
35 ;;; GNU Guix is free software; you can redistribute it and/or modify it
36 ;;; under the terms of the GNU General Public License as published by
37 ;;; the Free Software Foundation; either version 3 of the License, or (at
38 ;;; your option) any later version.
40 ;;; GNU Guix is distributed in the hope that it will be useful, but
41 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
42 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
43 ;;; GNU General Public License for more details.
45 ;;; You should have received a copy of the GNU General Public License
46 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
48 (define-module (gnu packages cran)
49 #:use-module ((guix licenses) #:prefix license:)
50 #:use-module (guix packages)
51 #:use-module (guix download)
52 #:use-module (guix git-download)
53 #:use-module (guix utils)
54 #:use-module (guix build-system r)
55 #:use-module (gnu packages)
56 #:use-module (gnu packages algebra)
57 #:use-module (gnu packages autotools)
58 #:use-module (gnu packages base)
59 #:use-module (gnu packages bioinformatics)
60 #:use-module (gnu packages c)
61 #:use-module (gnu packages compression)
62 #:use-module (gnu packages curl)
63 #:use-module (gnu packages databases)
64 #:use-module (gnu packages fontutils)
65 #:use-module (gnu packages gcc)
66 #:use-module (gnu packages geo)
67 #:use-module (gnu packages ghostscript)
68 #:use-module (gnu packages gl)
69 #:use-module (gnu packages gnome)
70 #:use-module (gnu packages graph)
71 #:use-module (gnu packages gtk)
72 #:use-module (gnu packages haskell-xyz)
73 #:use-module (gnu packages icu4c)
74 #:use-module (gnu packages image)
75 #:use-module (gnu packages imagemagick)
76 #:use-module (gnu packages java)
77 #:use-module (gnu packages javascript)
78 #:use-module (gnu packages libevent)
79 #:use-module (gnu packages lisp-xyz)
80 #:use-module (gnu packages machine-learning)
81 #:use-module (gnu packages maths)
82 #:use-module (gnu packages mpi)
83 #:use-module (gnu packages multiprecision)
84 #:use-module (gnu packages networking)
85 #:use-module (gnu packages node)
86 #:use-module (gnu packages pcre)
87 #:use-module (gnu packages perl)
88 #:use-module (gnu packages pkg-config)
89 #:use-module (gnu packages pulseaudio) ;libsndfile
90 #:use-module (gnu packages python)
91 #:use-module (gnu packages python-xyz)
92 #:use-module (gnu packages statistics)
93 #:use-module (gnu packages tcl)
94 #:use-module (gnu packages tls)
95 #:use-module (gnu packages web)
96 #:use-module (gnu packages xml)
97 #:use-module (gnu packages xorg))
99 (define-public r-rticles
106 (uri (cran-uri "rticles" version))
109 "0svh2bcqnlqdxdpw5afz1b980i2q13k8cxpq6flfqbi3dlwf3h8l"))))
110 (properties `((upstream-name . "rticles")))
111 (build-system r-build-system)
113 `(("r-knitr" ,r-knitr)
114 ("r-rmarkdown" ,r-rmarkdown)
115 ("r-tinytex" ,r-tinytex)
118 (home-page "https://github.com/rstudio/rticles")
119 (synopsis "Article formats for R Markdown")
121 "This package provides a suite of custom R Markdown formats and templates
122 for authoring journal articles and conference submissions.")
123 (license license:gpl3)))
125 (define-public r-bezier
131 (uri (cran-uri "bezier" version))
134 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
135 (build-system r-build-system)
136 (home-page "https://cran.r-project.org/web/packages/bezier/")
137 (synopsis "Bezier curve and spline toolkit")
139 "This package is a toolkit for working with Bezier curves and splines.
140 The package provides functions for point generation, arc length estimation,
141 degree elevation and curve fitting.")
142 (license license:gpl2+)))
151 (uri (cran-uri "V8" version))
154 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
155 (properties `((upstream-name . "V8")))
156 (build-system r-build-system)
159 (modify-phases %standard-phases
160 (add-after 'unpack 'find-v8
161 (lambda* (#:key inputs #:allow-other-keys)
162 (substitute* "configure"
164 (string-append "PKG_LIBS="
165 (assoc-ref inputs "node")
166 "/lib/libnode.so.64\n")))
167 (setenv "INCLUDE_DIR"
169 (assoc-ref inputs "node")
173 (assoc-ref inputs "node") "/lib"))
176 `(("node" ,libnode)))
179 ("r-jsonlite" ,r-jsonlite)
182 `(("r-knitr" ,r-knitr)))
183 (home-page "https://jeroen.cran.dev/V8")
184 (synopsis "Embedded JavaScript and WebAssembly engine for R")
186 "This package provides an R interface to V8: Google's JavaScript and
187 WebAssembly engine.")
188 (license license:expat)))
197 (uri (cran-uri "DOT" version))
200 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
201 (properties `((upstream-name . "DOT")))
202 (build-system r-build-system)
205 (home-page "http://haghish.com/dot")
206 (synopsis "Render and Export DOT Graphs in R")
208 "This package provides tools to render DOT diagram markup language in R
209 and also provides the possibility to export the graphs in PostScript and
210 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
211 programming packages such as @code{knitr} and @code{rmarkdown}.")
212 (license license:expat)))
214 (define-public r-clipr
221 (uri (cran-uri "clipr" version))
224 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
225 (build-system r-build-system)
226 (home-page "https://github.com/mdlincoln/clipr")
227 (synopsis "Read and write from the system clipboard")
229 "This package provides simple utility functions to read from and write to
230 the system clipboards.")
231 (license license:gpl3)))
239 (uri (cran-uri "zoo" version))
242 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
243 (build-system r-build-system)
245 `(("r-lattice" ,r-lattice)))
246 (home-page "http://zoo.R-Forge.R-project.org/")
247 (synopsis "S3 infrastructure for regular and irregular time series")
248 (description "This package contains an S3 class with methods for totally
249 ordered indexed observations. It is particularly aimed at irregular time
250 series of numeric vectors/matrices and factors.")
251 (license license:gpl2+)))
253 (define-public r-ggpmisc
259 (uri (cran-uri "ggpmisc" version))
262 "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
263 (build-system r-build-system)
265 `(("r-broom" ,r-broom)
268 ("r-ggplot2" ,r-ggplot2)
269 ("r-gridextra" ,r-gridextra)
270 ("r-lubridate" ,r-lubridate)
271 ("r-magrittr" ,r-magrittr)
274 ("r-polynom" ,r-polynom)
276 ("r-scales" ,r-scales)
277 ("r-splus2r" ,r-splus2r)
278 ("r-stringr" ,r-stringr)
279 ("r-tibble" ,r-tibble)
283 `(("r-knitr" ,r-knitr)))
284 (home-page "https://www.r4photobiology.info/")
285 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
286 (description "This package provides extensions to @code{ggplot2},
287 respecting the grammar of its graphics paradigm.")
288 (license license:gpl2+)))
290 (define-public r-gprofiler
297 (uri (cran-uri "gProfileR" version))
300 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
301 (properties `((upstream-name . "gProfileR")))
302 (build-system r-build-system)
305 ("r-rcurl" ,r-rcurl)))
306 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
307 (synopsis "Interface to the g:Profiler toolkit")
309 "This package provides tools for functional enrichment analysis,
310 gene identifier conversion and mapping homologous genes across related
311 organisms via the @code{g:Profiler} toolkit.")
312 (license license:gpl2+)))
314 (define-public r-gprofiler2
316 (name "r-gprofiler2")
321 (uri (cran-uri "gprofiler2" version))
324 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
325 (properties `((upstream-name . "gprofiler2")))
326 (build-system r-build-system)
328 `(("r-crosstalk" ,r-crosstalk)
330 ("r-ggplot2" ,r-ggplot2)
331 ("r-gridextra" ,r-gridextra)
332 ("r-jsonlite" ,r-jsonlite)
333 ("r-plotly" ,r-plotly)
336 ("r-viridislite" ,r-viridislite)))
337 (native-inputs `(("r-knitr" ,r-knitr)))
338 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
339 (synopsis "Interface to the g:Profiler toolset")
341 "This package provides a toolset for functional enrichment analysis and
342 visualization, gene/protein/SNP identifier conversion and mapping orthologous
343 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
347 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
349 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
351 @item @code{g:Orth}, orthology search across species;
352 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
353 genes and variant effects.
356 This package is an R interface corresponding to the 2019 update of
357 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
359 (license license:gpl2+)))
361 (define-public r-oenb
368 (uri (cran-uri "oenb" version))
371 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
372 (properties `((upstream-name . "oenb")))
373 (build-system r-build-system)
375 `(("r-dplyr" ,r-dplyr)
377 (native-inputs `(("r-knitr" ,r-knitr)))
378 (home-page "https://github.com/franzmohr/oenb")
379 (synopsis "Tools for the OeNB Data Web Service")
381 "Tools to access data from the data web service of the
382 @acronym{OeNB, Oesterreichische Nationalbank},
383 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
384 (license license:gpl2+)))
386 (define-public r-scales
393 (uri (cran-uri "scales" version))
395 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
396 (build-system r-build-system)
398 `(("r-farver" ,r-farver)
399 ("r-labeling" ,r-labeling)
400 ("r-lifecycle" ,r-lifecycle)
401 ("r-munsell" ,r-munsell)
402 ("r-rcolorbrewer" ,r-rcolorbrewer)
404 ("r-viridislite" ,r-viridislite)))
405 (home-page "https://github.com/hadley/scales")
406 (synopsis "Scale functions for visualization")
408 "This package provides graphical scales that map data to aesthetics, and
409 provides methods for automatically determining breaks and labels for axes and
411 (license license:expat)))
413 (define-public r-pheatmap
420 (uri (cran-uri "pheatmap" version))
423 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
424 (build-system r-build-system)
426 `(("r-gtable" ,r-gtable)
427 ("r-rcolorbrewer" ,r-rcolorbrewer)
428 ("r-scales" ,r-scales)))
429 (home-page "https://cran.r-project.org/web/packages/pheatmap")
430 (synopsis "Pretty heatmaps")
432 "This package provides an implementation of heatmaps that offers more
433 control over dimensions and appearance.")
434 (license license:gpl2+)))
442 (uri (cran-uri "ecp" version))
445 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
446 (build-system r-build-system)
448 `(("r-rcpp" ,r-rcpp)))
449 (home-page "https://cran.r-project.org/web/packages/ecp/")
450 (synopsis "Multiple change-point analysis of multivariate data")
452 "This package implements various procedures for finding multiple
453 change-points. Two methods make use of dynamic programming and pruning, with
454 no distributional assumptions other than the existence of certain absolute
455 moments in one method. Hierarchical and exact search methods are included.
456 All methods return the set of estimated change-points as well as other summary
458 (license license:gpl2+)))
460 (define-public r-ellipsis
467 (uri (cran-uri "ellipsis" version))
470 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
471 (build-system r-build-system)
473 `(("r-rlang" ,r-rlang)))
474 (home-page "https://github.com/hadley/ellipsis")
475 (synopsis "Tools for working with additional arguments")
477 "In S3 generics, it's useful to take @code{...} so that methods can have
478 additional arguments. But this flexibility comes at a cost: misspelled
479 arguments will be silently ignored. The @code{ellipsis} package is an
480 experiment that allows a generic to warn if any arguments passed in @code{...}
482 (license license:gpl3)))
491 (uri (cran-uri "grr" version))
494 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
495 (build-system r-build-system)
496 (home-page "https://cran.r-project.org/web/packages/grr")
497 (synopsis "Alternative implementations of base R functions")
499 "This package provides alternative implementations of some base R
500 functions, including @code{sort}, @code{order}, and @code{match}. The
501 functions are simplified but can be faster or have other advantages.")
502 (license license:gpl3)))
504 (define-public r-matrix-utils
506 (name "r-matrix-utils")
511 (uri (cran-uri "Matrix.utils" version))
514 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
515 (properties `((upstream-name . "Matrix.utils")))
516 (build-system r-build-system)
519 ("r-matrix" ,r-matrix)))
520 (home-page "https://github.com/cvarrichio/Matrix.utils")
522 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
524 "This package implements data manipulation methods such as @code{cast},
525 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
527 (license license:gpl3)))
529 (define-public r-mboost
535 (uri (cran-uri "mboost" version))
538 "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf"))))
539 (build-system r-build-system)
541 `(("r-lattice" ,r-lattice)
542 ("r-matrix" ,r-matrix)
544 ("r-partykit" ,r-partykit)
545 ("r-quadprog" ,r-quadprog)
547 ("r-survival" ,r-survival)))
548 (home-page "https://github.com/boost-R/mboost")
549 (synopsis "Model-based boosting")
551 "This package provides a functional gradient descent algorithm (boosting)
552 for optimizing general risk functions utilizing component-wise (penalised)
553 least squares estimates or regression trees as base-learners for fitting
554 generalized linear, additive and interaction models to potentially
555 high-dimensional data.")
556 (license license:gpl2)))
565 (uri (cran-uri "sys" version))
568 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
569 (build-system r-build-system)
570 (home-page "https://github.com/jeroen/sys")
571 (synopsis "Powerful and reliable tools for running system commands in R")
573 "This package provides drop-in replacements for the base @code{system2()}
574 function with fine control and consistent behavior across platforms. It
575 supports clean interruption, timeout, background tasks, and streaming STDIN /
576 STDOUT / STDERR over binary or text connections. The package also provides
577 functions for evaluating expressions inside a temporary fork. Such
578 evaluations have no side effects on the main R process, and support reliable
579 interrupts and timeouts. This provides the basis for a sandboxing
581 (license license:expat)))
583 (define-public r-askpass
590 (uri (cran-uri "askpass" version))
593 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
594 (build-system r-build-system)
595 (propagated-inputs `(("r-sys" ,r-sys)))
596 (home-page "https://github.com/jeroen/askpass")
597 (synopsis "Safe password entry for R")
599 "This package provides cross-platform utilities for prompting the user
600 for credentials or a passphrase, for example to authenticate with a server or
601 read a protected key.")
602 (license license:expat)))
604 (define-public r-vegan
611 (uri (cran-uri "vegan" version))
614 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
615 (build-system r-build-system)
617 `(("gfortran" ,gfortran)))
619 `(("r-cluster" ,r-cluster)
620 ("r-knitr" ,r-knitr) ; needed for vignettes
621 ("r-lattice" ,r-lattice)
624 ("r-permute" ,r-permute)))
625 (home-page "https://cran.r-project.org/web/packages/vegan")
626 (synopsis "Functions for community ecology")
628 "The vegan package provides tools for descriptive community ecology. It
629 has most basic functions of diversity analysis, community ordination and
630 dissimilarity analysis. Most of its multivariate tools can be used for other
631 data types as well.")
632 (license license:gpl2+)))
634 (define-public r-tidyverse
641 (uri (cran-uri "tidyverse" version))
644 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
645 (build-system r-build-system)
647 `(("r-broom" ,r-broom)
649 ("r-crayon" ,r-crayon)
650 ("r-dbplyr" ,r-dbplyr)
652 ("r-forcats" ,r-forcats)
653 ("r-ggplot2" ,r-ggplot2)
657 ("r-jsonlite" ,r-jsonlite)
658 ("r-lubridate" ,r-lubridate)
659 ("r-magrittr" ,r-magrittr)
660 ("r-modelr" ,r-modelr)
661 ("r-pillar" ,r-pillar)
664 ("r-readxl" ,r-readxl)
665 ("r-reprex" ,r-reprex)
667 ("r-rstudioapi" ,r-rstudioapi)
669 ("r-stringr" ,r-stringr)
670 ("r-tibble" ,r-tibble)
673 (home-page "https://tidyverse.tidyverse.org")
674 (synopsis "Install and load packages from the \"Tidyverse\"")
676 "The @code{tidyverse} is a set of packages that work in harmony because
677 they share common data representations and API design. This package is
678 designed to make it easy to install and load multiple tidyverse packages in a
680 (license license:gpl3)))
682 (define-public r-rvest
689 (uri (cran-uri "rvest" version))
691 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
692 (build-system r-build-system)
695 ("r-magrittr" ,r-magrittr)
696 ("r-selectr" ,r-selectr)
699 `(("r-knitr" ,r-knitr)))
700 (home-page "https://github.com/hadley/rvest")
701 (synopsis "Simple web scraping for R")
703 "@code{r-rvest} helps you scrape information from web pages. It is
704 designed to work with @code{magrittr} to make it easy to express common web
705 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
706 (license license:gpl3)))
708 (define-public r-selectr
715 (uri (cran-uri "selectr" version))
717 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
718 (build-system r-build-system)
720 `(("r-stringr" ,r-stringr)
722 (home-page "https://sjp.co.nz/projects/selectr/")
723 (synopsis "Translate CSS selectors to XPath expressions")
725 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
726 expression. This allows you to use CSS selectors when working with the XML
727 package as it can only evaluate XPath expressions. Also provided are
728 convenience functions useful for using CSS selectors on XML nodes. This
729 package is a port of the Python package @code{cssselect}.")
730 (license license:bsd-3)))
732 (define-public r-reprex
739 (uri (cran-uri "reprex" version))
742 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
743 (build-system r-build-system)
745 `(("r-callr" ,r-callr)
749 ("r-rmarkdown" ,r-rmarkdown)
750 ("r-whisker" ,r-whisker)
751 ("r-withr" ,r-withr)))
752 (home-page "https://github.com/tidyverse/reprex")
753 (synopsis "Prepare reproducible R code examples for sharing")
755 "This package provides a convenience wrapper that uses the
756 @code{rmarkdown} package to render small snippets of code to target formats
757 that include both code and output. The goal is to encourage the sharing of
758 small, reproducible, and runnable examples on code-oriented websites or email.
759 @code{reprex} also extracts clean, runnable R code from various common formats,
760 such as copy/paste from an R session.")
761 (license license:expat)))
763 (define-public r-reordercluster
765 (name "r-reordercluster")
769 (uri (cran-uri "ReorderCluster" version))
772 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
773 (build-system r-build-system)
775 `(("r-gplots" ,r-gplots)
777 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
778 (synopsis "Reordering the dendrogram according to the class labels")
779 (description "This package provides tools for performing the leaf reordering
780 for the dendrogram that preserves the hierarchical clustering result and at the
781 same time tries to group instances from the same class together.")
782 (license license:gpl3+)))
784 (define-public r-callr
791 (uri (cran-uri "callr" version))
794 "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642"))))
795 (build-system r-build-system)
798 ("r-processx" ,r-processx)))
799 (home-page "https://github.com/r-lib/callr#readme")
800 (synopsis "Call R from R")
802 "It is sometimes useful to perform a computation in a separate R process,
803 without affecting the current R process at all. This package does exactly
805 (license license:expat)))
807 (define-public r-readxl
814 (uri (cran-uri "readxl" version))
817 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
818 (build-system r-build-system)
820 `(("r-cellranger" ,r-cellranger)
821 ("r-progress" ,r-progress)
823 ("r-tibble" ,r-tibble)))
824 (home-page "https://readxl.tidyverse.org")
825 (synopsis "Read Excel files")
827 "This package lets you import Excel files into R. It supports
828 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
829 the embedded @code{RapidXML} C++ library.")
830 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
831 ;; 'rapidxml' which is Boost.
832 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
834 (define-public r-modelr
841 (uri (cran-uri "modelr" version))
844 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
845 (build-system r-build-system)
847 `(("r-broom" ,r-broom)
848 ("r-magrittr" ,r-magrittr)
851 ("r-tibble" ,r-tibble)
853 ("r-tidyselect" ,r-tidyselect)
854 ("r-vctrs" ,r-vctrs)))
855 (home-page "https://github.com/tidyverse/modelr")
856 (synopsis "Helper functions for modelling in pipelines")
858 "Functions for modelling that help you seamlessly integrate modelling
859 into a pipeline of data manipulation and visualisation.")
860 (license license:gpl3)))
862 (define-public r-httpuv
868 (uri (cran-uri "httpuv" version))
871 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))
872 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
873 ;; only contains fixes for building on Solaris.
874 (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch"))
875 (modules '((guix build utils)
880 (delete-file-recursively "src/libuv")
881 ;; Cannot unbundle http-parser, because it contains local
884 (build-system r-build-system)
887 (modify-phases %standard-phases
888 (add-after 'unpack 'unbundle-libuv
889 (lambda* (#:key outputs #:allow-other-keys)
890 (substitute* (find-files "src" "\\.cpp$|\\.h$")
891 (("\"libuv/include/uv\\.h\"")
893 ;; Fix https://github.com/rstudio/httpuv/issues/282
894 (substitute* "src/http.cpp"
895 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
896 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
903 ("r-promises" ,r-promises)
906 (home-page "https://github.com/rstudio/httpuv")
907 (synopsis "HTTP and WebSocket server library for R")
909 "The httpuv package provides low-level socket and protocol support for
910 handling HTTP and WebSocket requests directly from within R. It is primarily
911 intended as a building block for other packages, rather than making it
912 particularly easy to create complete web applications using httpuv alone.")
913 ;; This package includes third-party code that was originally released
914 ;; under various non-copyleft licenses. Full licensing information can be
915 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
916 (license license:gpl3+)))
918 (define-public r-jsonlite
924 (uri (cran-uri "jsonlite" version))
927 "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
928 (build-system r-build-system)
930 `(("r-knitr" ,r-knitr)))
931 (home-page "https://arxiv.org/abs/1403.2805")
932 (synopsis "Robust, high performance JSON parser and generator for R")
934 "The jsonlite package provides a fast JSON parser and generator optimized
935 for statistical data and the web. It offers flexible, robust, high
936 performance tools for working with JSON in R and is particularly powerful for
937 building pipelines and interacting with a web API. In addition to converting
938 JSON data from/to R objects, jsonlite contains functions to stream, validate,
939 and prettify JSON data. The unit tests included with the package verify that
940 all edge cases are encoded and decoded consistently for use with dynamic data
941 in systems and applications.")
942 (license license:expat)))
944 (define-public r-servr
950 (uri (cran-uri "servr" version))
953 "0xfbf1a1w34hbsx4jrdr4rqf22v7gf1p37ngknglv1dyxih7ipja"))))
954 (build-system r-build-system)
956 `(("r-httpuv" ,r-httpuv)
957 ("r-jsonlite" ,r-jsonlite)
960 (home-page "https://github.com/yihui/servr")
961 (synopsis "Simple HTTP server to serve static files or dynamic documents")
963 "Servr provides an HTTP server in R to serve static files, or dynamic
964 documents that can be converted to HTML files (e.g., R Markdown) under a given
966 (license license:expat)))
968 (define-public r-htmltools
974 (uri (cran-uri "htmltools" version))
977 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
978 (build-system r-build-system)
980 `(("r-base64enc" ,r-base64enc)
981 ("r-digest" ,r-digest)
982 ("r-rlang" ,r-rlang)))
983 (home-page "https://cran.r-project.org/web/packages/htmltools")
984 (synopsis "R tools for HTML")
986 "This package provides tools for HTML generation and output in R.")
987 (license license:expat)))
989 (define-public r-htmlwidgets
991 (name "r-htmlwidgets")
995 (uri (cran-uri "htmlwidgets" version))
998 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
999 (build-system r-build-system)
1001 `(("r-htmltools" ,r-htmltools)
1002 ("r-jsonlite" ,r-jsonlite)
1003 ("r-yaml" ,r-yaml)))
1004 (home-page "https://github.com/ramnathv/htmlwidgets")
1005 (synopsis "HTML Widgets for R")
1007 "HTML widgets is a framework for creating HTML widgets that render in
1008 various contexts including the R console, R Markdown documents, and Shiny web
1010 (license license:expat)))
1012 (define-public r-htmltable
1014 (name "r-htmltable")
1019 (uri (cran-uri "htmlTable" version))
1021 (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6"))))
1022 (properties `((upstream-name . "htmlTable")))
1023 (build-system r-build-system)
1025 `(("r-checkmate" ,r-checkmate)
1026 ("r-htmltools" ,r-htmltools)
1027 ("r-htmlwidgets" ,r-htmlwidgets)
1028 ("r-knitr" ,r-knitr)
1029 ("r-magrittr" ,r-magrittr)
1030 ("r-rstudioapi" ,r-rstudioapi)
1031 ("r-stringr" ,r-stringr)))
1033 `(("r-knitr" ,r-knitr)))
1034 (home-page "http://gforge.se/packages/")
1035 (synopsis "Advanced tables for Markdown/HTML")
1037 "This package provides functions to build tables with advanced layout
1038 elements such as row spanners, column spanners, table spanners, zebra
1039 striping, and more. While allowing advanced layout, the underlying
1040 CSS-structure is simple in order to maximize compatibility with word
1041 processors such as LibreOffice. The package also contains a few text
1042 formatting functions that help outputting text compatible with HTML or
1044 (license license:gpl3+)))
1046 (define-public r-curl
1052 (uri (cran-uri "curl" version))
1055 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1056 (build-system r-build-system)
1059 (modify-phases %standard-phases
1060 ;; The environment variable CURL_CA_BUNDLE is only respected when
1061 ;; running Windows, so we disable the platform checks.
1062 ;; This can be removed once the libcurl has been patched.
1063 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1065 (substitute* "R/onload.R"
1066 (("if \\(!grepl\\(\"mingw\".*")
1068 (substitute* "src/handle.c"
1069 (("/\\* Only set" m)
1071 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1072 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1079 `(("pkg-config" ,pkg-config)))
1080 (home-page "https://github.com/jeroenooms/curl")
1081 (synopsis "HTTP client for R")
1083 "The @code{curl()} and @code{curl_download()} functions provide highly
1084 configurable drop-in replacements for base @code{url()} and
1085 @code{download.file()} with better performance, support for encryption, gzip
1086 compression, authentication, and other @code{libcurl} goodies. The core of
1087 the package implements a framework for performing fully customized requests
1088 where data can be processed either in memory, on disk, or streaming via the
1089 callback or connection interfaces.")
1090 (license license:expat)))
1092 (define-public r-hwriter
1099 (uri (cran-uri "hwriter" version))
1102 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1103 (build-system r-build-system)
1104 (home-page "https://cran.r-project.org/web/packages/hwriter")
1105 (synopsis "Output R objects in HTML format")
1107 "This package provides easy-to-use and versatile functions to output R
1108 objects in HTML format.")
1109 (license license:lgpl2.1+)))
1111 (define-public r-rjson
1118 (uri (cran-uri "rjson" version))
1121 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1122 (build-system r-build-system)
1123 (home-page "https://cran.r-project.org/web/packages/rjson")
1124 (synopsis "JSON library for R")
1126 "This package provides functions to convert R objects into JSON objects
1128 (license license:gpl2+)))
1130 (define-public r-fastmap
1137 (uri (cran-uri "fastmap" version))
1140 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1141 (properties `((upstream-name . "fastmap")))
1142 (build-system r-build-system)
1143 (home-page "https://r-lib.github.io/fastmap/")
1144 (synopsis "Fast implementation of a key-value store")
1146 "This package provides a fast implementation of a key-value store.
1147 Environments are commonly used as key-value stores, but every time a new key
1148 is used, it is added to R's global symbol table, causing a small amount of
1149 memory leakage. This can be problematic in cases where many different keys
1150 are used. Fastmap avoids this memory leak issue by implementing the map using
1151 data structures in C++.")
1152 (license license:expat)))
1154 (define-public r-shiny
1162 (url "https://github.com/rstudio/shiny")
1163 (commit (string-append "v" version))))
1164 (file-name (git-file-name name version))
1167 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1168 (build-system r-build-system)
1170 `(#:modules ((guix build r-build-system)
1171 (guix build minify-build-system)
1174 #:imported-modules (,@%r-build-system-modules
1175 (guix build minify-build-system))
1177 (modify-phases (@ (guix build r-build-system) %standard-phases)
1178 (add-after 'unpack 'replace-bundled-minified-JavaScript
1179 (lambda* (#:key inputs #:allow-other-keys)
1180 (let ((replace-file (lambda (old new)
1181 (format #t "replacing ~a with ~a\n" old new)
1183 (symlink new old))))
1184 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1185 ;; contain just data. They are not minified code, so we don't
1187 (with-directory-excursion "inst/www/shared"
1188 (replace-file "bootstrap/shim/respond.min.js"
1189 (string-append (assoc-ref inputs "js-respond")
1190 "/share/javascript/respond.min.js"))
1191 (replace-file "bootstrap/shim/html5shiv.min.js"
1192 (string-append (assoc-ref inputs "js-html5shiv")
1193 "/share/javascript/html5shiv.min.js"))
1194 (replace-file "json2-min.js"
1195 (string-append (assoc-ref inputs "js-json2")
1196 "/share/javascript/json2-min.js"))
1197 (replace-file "strftime/strftime-min.js"
1198 (string-append (assoc-ref inputs "js-strftime")
1199 "/share/javascript/strftime.min.js"))
1200 (replace-file "highlight/highlight.pack.js"
1201 (string-append (assoc-ref inputs "js-highlight")
1202 "/share/javascript/highlight.min.js"))
1203 (replace-file "datatables/js/jquery.dataTables.min.js"
1204 (string-append (assoc-ref inputs "js-datatables")
1205 "/share/javascript/jquery.dataTables.min.js"))
1206 (replace-file "selectize/js/selectize.min.js"
1207 (string-append (assoc-ref inputs "js-selectize")
1208 "/share/javascript/selectize.min.js"))
1209 (replace-file "selectize/js/es5-shim.min.js"
1210 (string-append (assoc-ref inputs "js-es5-shim")
1211 "/share/javascript/es5-shim.min.js"))
1212 (for-each (match-lambda
1214 (delete-file target)
1215 (minify source #:target target)))
1216 '(("jqueryui/jquery-ui.js" .
1217 "jqueryui/jquery-ui.min.js")
1218 ("datepicker/js/bootstrap-datepicker.js" .
1219 "datepicker/js/bootstrap-datepicker.min.js")
1220 ("ionrangeslider/js/ion.rangeSlider.js" .
1221 "ionrangeslider/js/ion.rangeSlider.min.js")
1222 ("bootstrap/js/bootstrap.js" .
1223 "bootstrap/js/bootstrap.min.js")
1228 ("legacy/jquery.js" .
1229 "legacy/jquery.min.js")
1230 ("showdown/src/showdown.js" .
1231 "showdown/compressed/showdown.js")))))
1234 `(("r-crayon" ,r-crayon)
1235 ("r-digest" ,r-digest)
1236 ("r-fastmap" ,r-fastmap)
1237 ("r-htmltools" ,r-htmltools)
1238 ("r-httpuv" ,r-httpuv)
1239 ("r-jsonlite" ,r-jsonlite)
1240 ("r-later" ,r-later)
1242 ("r-promises" ,r-promises)
1244 ("r-rlang" ,r-rlang)
1245 ("r-sourcetools" ,r-sourcetools)
1246 ("r-withr" ,r-withr)
1247 ("r-xtable" ,r-xtable)))
1249 `(("js-datatables" ,js-datatables)
1250 ("js-html5shiv" ,js-html5shiv)
1251 ("js-json2" ,js-json2)
1252 ("js-respond" ,js-respond)
1253 ("js-selectize" ,js-selectize)
1254 ("js-strftime" ,js-strftime)
1255 ("js-highlight" ,js-highlight)
1256 ("js-es5-shim" ,js-es5-shim)))
1258 `(("uglify-js" ,uglify-js)
1259 ("gfortran" ,gfortran)))
1260 (home-page "http://shiny.rstudio.com")
1261 (synopsis "Easy interactive web applications with R")
1263 "Makes it incredibly easy to build interactive web applications
1264 with R. Automatic \"reactive\" binding between inputs and outputs and
1265 extensive prebuilt widgets make it possible to build beautiful,
1266 responsive, and powerful applications with minimal effort.")
1267 (license license:artistic2.0)))
1269 ;; This package includes minified JavaScript files. When upgrading please
1270 ;; check that there are no new minified JavaScript files.
1271 (define-public r-shinytree
1273 (name "r-shinytree")
1278 (uri (cran-uri "shinyTree" version))
1281 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1282 (modules '((guix build utils)))
1285 ;; Delete minified JavaScript
1286 (for-each delete-file
1287 '("inst/www/jsTree-3.3.7/libs/require.js"
1288 "inst/www/jsTree-3.3.7/libs/jquery.js"
1289 "inst/www/jsTree-3.3.7/jstree.min.js"))
1291 (properties `((upstream-name . "shinyTree")))
1292 (build-system r-build-system)
1294 `(#:modules ((guix build utils)
1295 (guix build r-build-system)
1299 (modify-phases %standard-phases
1300 (add-after 'unpack 'replace-minified-javascript
1301 (lambda* (#:key inputs #:allow-other-keys)
1302 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1303 (symlink (string-append (assoc-ref inputs "js-requirejs")
1304 "/share/javascript/require.min.js")
1309 `((,(assoc-ref inputs "js-jquery")
1313 (lambda (sources targets)
1314 (for-each (lambda (source target)
1315 (format #t "Processing ~a --> ~a~%"
1317 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1318 (call-with-output-file target
1320 (dump-port minified port)))))
1324 `(("r-htmlwidgets" ,r-htmlwidgets)
1325 ("r-jsonlite" ,r-jsonlite)
1326 ("r-promises" ,r-promises)
1327 ("r-shiny" ,r-shiny)
1328 ("r-stringr" ,r-stringr)))
1330 `(("js-requirejs" ,js-requirejs)))
1332 `(("uglify-js" ,uglify-js)
1336 (uri "https://code.jquery.com/jquery-3.3.1.js")
1339 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1340 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1341 (synopsis "jsTree bindings for Shiny")
1343 "This package exposes R bindings to jsTree, a JavaScript library that
1344 supports interactive trees, to enable rich, editable trees in Shiny.")
1345 (license license:expat)))
1347 (define-public r-shinydashboard
1349 (name "r-shinydashboard")
1353 (uri (cran-uri "shinydashboard" version))
1356 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1357 (build-system r-build-system)
1358 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1359 ;; Regenerate it from the included sources.
1361 `(#:modules ((guix build utils)
1362 (guix build r-build-system)
1365 (modify-phases %standard-phases
1366 (add-after 'unpack 'generate-minified-javascript
1368 (with-directory-excursion "inst/AdminLTE"
1369 (delete-file "app.min.js")
1370 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1371 (call-with-output-file "app.min.js"
1373 (dump-port minified port))))))))))
1375 `(("r-htmltools" ,r-htmltools)
1376 ("r-promises" ,r-promises)
1377 ("r-shiny" ,r-shiny)))
1379 `(("uglify-js" ,uglify-js)))
1380 (home-page "https://rstudio.github.io/shinydashboard/")
1381 (synopsis "Create dashboards with shiny")
1382 (description "This package provides an extension to the Shiny web
1383 application framework for R, making it easy to create attractive dashboards.")
1384 ;; This package includes software that was released under the Expat
1385 ;; license, but the whole package is released under GPL version 2 or
1387 (license license:gpl2+)))
1389 (define-public r-shinyfiles
1391 (name "r-shinyfiles")
1396 (uri (cran-uri "shinyFiles" version))
1398 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1399 (properties `((upstream-name . "shinyFiles")))
1400 (build-system r-build-system)
1403 ("r-htmltools" ,r-htmltools)
1404 ("r-jsonlite" ,r-jsonlite)
1405 ("r-shiny" ,r-shiny)
1406 ("r-tibble" ,r-tibble)))
1407 (home-page "https://github.com/thomasp85/shinyFiles")
1408 (synopsis "Server-side file system viewer for Shiny")
1410 "This package provides functionality for client-side navigation of the
1411 server side file system in shiny apps. In case the app is running locally
1412 this gives the user direct access to the file system without the need to
1413 \"download\" files to a temporary location. Both file and folder selection as
1414 well as file saving is available.")
1415 (license license:gpl2+)))
1417 (define-public r-shinythemes
1419 (name "r-shinythemes")
1424 (uri (cran-uri "shinythemes" version))
1427 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1428 (properties `((upstream-name . "shinythemes")))
1429 (build-system r-build-system)
1430 (propagated-inputs `(("r-shiny" ,r-shiny)))
1431 (home-page "https://rstudio.github.io/shinythemes/")
1432 (synopsis "Themes for Shiny")
1434 "This package provides themes for use with Shiny. It includes several
1435 Bootstrap themes, which are packaged for use with Shiny applications.")
1436 ;; The package is released under version 3 of the GPL, but it includes
1437 ;; source files that are covered by the Expat license. It also includes
1438 ;; fonts under SIL or the ASL.
1439 (license (list license:gpl3 license:expat
1440 license:silofl1.1 license:asl2.0))))
1442 ;; The package sources include minified variants of d3.js and non-minified
1443 ;; source code of d3-jetpack.
1444 (define-public r-d3r
1451 (uri (cran-uri "d3r" version))
1454 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1455 (build-system r-build-system)
1457 `(#:modules ((guix build utils)
1458 (guix build r-build-system)
1462 (modify-phases %standard-phases
1463 (add-after 'unpack 'process-javascript
1464 (lambda* (#:key inputs #:allow-other-keys)
1465 (with-directory-excursion "inst/www/d3/"
1469 `((,(assoc-ref inputs "d3.v3.js")
1470 "v3/dist/d3.min.js")
1471 (,(assoc-ref inputs "d3.v4.js")
1472 "v4/dist/d3.min.js")
1473 (,(assoc-ref inputs "d3.v5.js")
1474 "v5/dist/d3.min.js"))))
1475 (lambda (sources targets)
1476 (for-each (lambda (source target)
1477 (format #t "Processing ~a --> ~a~%"
1479 (delete-file target)
1480 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1481 (call-with-output-file target
1483 (dump-port minified port)))))
1487 `(("r-dplyr" ,r-dplyr)
1488 ("r-htmltools" ,r-htmltools)
1489 ("r-rlang" ,r-rlang)
1490 ("r-tidyr" ,r-tidyr)))
1492 `(("uglify-js" ,uglify-js)
1496 (uri "https://d3js.org/d3.v3.js")
1499 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1503 (uri "https://d3js.org/d3.v4.js")
1506 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1510 (uri "https://d3js.org/d3.v5.js")
1513 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1514 (home-page "https://github.com/timelyportfolio/d3r")
1515 (synopsis "d3.js utilities for R")
1517 "This package provides a suite of functions to help ease the use of the
1518 d3.js visualization library in R. These helpers include
1519 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1520 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1521 R objects into the JSON format that the d3.js library expects.")
1522 (license license:bsd-3)))
1524 ;; We use the latest commit here because the last release was in 2016 while
1525 ;; the latest commit was in 2018.
1526 (define-public r-sankeyd3
1527 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1531 (version (git-version "0.3.2" revision commit))
1536 (url "https://github.com/fbreitwieser/sankeyD3")
1538 (file-name (git-file-name name version))
1541 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1542 (build-system r-build-system)
1545 ("r-htmlwidgets" ,r-htmlwidgets)
1546 ("r-shiny" ,r-shiny)
1547 ("r-magrittr" ,r-magrittr)))
1548 (home-page "https://github.com/fbreitwieser/sankeyD3")
1549 (synopsis "Sankey network graphs from R")
1551 "This package provides an R library to generate Sankey network graphs
1552 in R and Shiny via the D3 visualization library.")
1553 ;; The R code is licensed under GPLv3+. It includes the non-minified
1554 ;; JavaScript source code of d3-sankey, which is released under the
1555 ;; 3-clause BSD license.
1556 (license (list license:gpl3+ license:bsd-3)))))
1558 (define-public r-crosstalk
1560 (name "r-crosstalk")
1565 (uri (cran-uri "crosstalk" version))
1568 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1569 (build-system r-build-system)
1571 `(("r-htmltools" ,r-htmltools)
1572 ("r-jsonlite" ,r-jsonlite)
1573 ("r-lazyeval" ,r-lazyeval)
1575 (home-page "https://rstudio.github.io/crosstalk/")
1576 (synopsis "Inter-widget interactivity for HTML widgets")
1578 "This package provides building blocks for allowing HTML widgets to
1579 communicate with each other, with Shiny or without (i.e. static @code{.html}
1580 files). It currently supports linked brushing and filtering.")
1581 (license license:expat)))
1583 (define-public r-rook
1590 (uri (cran-uri "Rook" version))
1593 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1594 (properties `((upstream-name . "Rook")))
1595 (build-system r-build-system)
1596 (propagated-inputs `(("r-brew" ,r-brew)))
1597 (home-page "https://cran.r-project.org/web/packages/Rook")
1598 (synopsis "Web server interface for R")
1600 "This package contains the Rook specification and convenience software
1601 for building and running Rook applications. A Rook application is an R
1602 reference class object that implements a @code{call} method or an R closure
1603 that takes exactly one argument, an environment, and returns a list with three
1604 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1605 (license license:gpl2)))
1607 (define-public r-miniui
1614 (uri (cran-uri "miniUI" version))
1617 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1618 (properties `((upstream-name . "miniUI")))
1619 (build-system r-build-system)
1621 `(("r-htmltools" ,r-htmltools)
1622 ("r-shiny" ,r-shiny)))
1623 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1624 (synopsis "Shiny UI widgets for small screens")
1626 "This package provides UI widget and layout functions for writing Shiny apps that
1627 work well on small screens.")
1628 (license license:gpl3)))
1630 (define-public r-feather
1637 (uri (cran-uri "feather" version))
1640 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1641 (build-system r-build-system)
1645 ("r-tibble" ,r-tibble)))
1646 (home-page "https://github.com/wesm/feather")
1647 (synopsis "R Bindings to the Feather API")
1648 (description "Read and write feather files, a lightweight binary columnar
1649 data store designed for maximum speed.")
1650 (license license:asl2.0)))
1652 (define-public r-maps
1659 (uri (cran-uri "maps" version))
1662 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1663 (build-system r-build-system)
1664 (home-page "https://cran.r-project.org/web/packages/maps")
1665 (synopsis "Draw geographical maps")
1666 (description "This package provides an R module for display of maps.
1667 Projection code and larger maps are in separate packages (@code{mapproj} and
1669 (license license:gpl2)))
1671 (define-public r-mapproj
1678 (uri (cran-uri "mapproj" version))
1681 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1682 (build-system r-build-system)
1683 (propagated-inputs `(("r-maps" ,r-maps)))
1684 (home-page "https://cran.r-project.org/web/packages/mapproj")
1685 (synopsis "Map projection in R")
1686 (description "This package converts latitude/longitude into projected
1688 (license (list license:gpl2 ; The R interface
1689 (license:non-copyleft ; The C code
1690 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1691 "Lucent Public License Version 1.02")))))
1693 (define-public r-rgooglemaps
1695 (name "r-rgooglemaps")
1700 (uri (cran-uri "RgoogleMaps" version))
1703 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1704 (properties `((upstream-name . "RgoogleMaps")))
1705 (build-system r-build-system)
1709 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1710 (synopsis "Use Google Maps in R")
1711 (description "This package serves two purposes:
1713 @item Provide a comfortable R interface to query the Google server for static
1715 @item Use the map as a background image to overlay plots within R. This
1716 requires proper coordinate scaling.
1718 (license license:gpl2+)))
1720 (define-public r-geosphere
1722 (name "r-geosphere")
1727 (uri (cran-uri "geosphere" version))
1730 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1731 (build-system r-build-system)
1732 (propagated-inputs `(("r-sp" ,r-sp)))
1733 (home-page "https://cran.r-project.org/web/packages/geosphere")
1734 (synopsis "Spherical trigonometry")
1735 (description "This package computes spherical trigonometry for geographic
1736 applications. That is, compute distances and related measures for angular
1737 (longitude/latitude) locations.")
1738 (license license:gpl3+)))
1740 (define-public r-jpeg
1747 (uri (cran-uri "jpeg" version))
1750 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1751 (build-system r-build-system)
1752 (inputs `(("libjpeg" ,libjpeg-turbo)))
1753 (home-page "https://www.rforge.net/jpeg/")
1754 (synopsis "Read and write JPEG images with R")
1755 (description "This package provides a way to read, write and display
1756 bitmap images stored in the JPEG format with R. It can read and write both
1757 files and in-memory raw vectors.")
1758 (license license:gpl2+)))
1760 (define-public r-ggmap
1767 (uri (cran-uri "ggmap" version))
1770 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1771 (build-system r-build-system)
1773 `(("r-bitops" ,r-bitops)
1774 ("r-digest" ,r-digest)
1775 ("r-dplyr" ,r-dplyr)
1776 ("r-ggplot2" ,r-ggplot2)
1780 ("r-magrittr" ,r-magrittr)
1783 ("r-purrr" ,r-purrr)
1784 ("r-rgooglemaps" ,r-rgooglemaps)
1785 ("r-rjson" ,r-rjson)
1786 ("r-scales" ,r-scales)
1787 ("r-stringr" ,r-stringr)
1788 ("r-tibble" ,r-tibble)
1789 ("r-tidyr" ,r-tidyr)))
1790 (home-page "https://github.com/dkahle/ggmap")
1791 (synopsis "Spatial visualization with ggplot2")
1792 (description "This package provides a collection of functions to visualize
1793 spatial data and models on top of static maps from various online sources (e.g
1794 Google Maps and Stamen Maps). It includes tools common to those tasks,
1795 including functions for geolocation and routing.")
1796 (license license:gpl2)))
1798 (define-public r-haven
1805 (uri (cran-uri "haven" version))
1808 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1809 (build-system r-build-system)
1813 `(("r-knitr" ,r-knitr)))
1815 `(("r-forcats" ,r-forcats)
1818 ("r-rlang" ,r-rlang)
1819 ("r-readr" ,r-readr)
1820 ("r-tibble" ,r-tibble)
1821 ("r-tidyselect" ,r-tidyselect)
1822 ("r-vctrs" ,r-vctrs)))
1823 (home-page "https://haven.tidyverse.org")
1824 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1826 "This package lets you mport foreign statistical formats into R via the
1827 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1828 (license license:expat)))
1830 (define-public r-amap
1836 (uri (cran-uri "amap" version))
1839 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1840 (build-system r-build-system)
1842 `(("gfortran" ,gfortran)))
1843 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1844 (synopsis "Another multidimensional analysis package")
1845 (description "This package provides tools for clustering and principal
1846 component analysis (with robust methods, and parallelized functions).")
1847 (license license:gpl2+)))
1849 (define-public r-ape
1856 (uri (cran-uri "ape" version))
1859 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
1860 (build-system r-build-system)
1862 `(("r-lattice" ,r-lattice)
1864 ("r-rcpp" ,r-rcpp)))
1865 (home-page "http://ape-package.ird.fr/")
1866 (synopsis "Analyses of phylogenetics and evolution")
1868 "This package provides functions for reading, writing, plotting, and
1869 manipulating phylogenetic trees, analyses of comparative data in a
1870 phylogenetic framework, ancestral character analyses, analyses of
1871 diversification and macroevolution, computing distances from DNA sequences,
1872 and several other tools.")
1873 (license license:gpl2+)))
1875 (define-public r-abbyyr
1882 (uri (cran-uri "abbyyR" version))
1885 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1886 (properties `((upstream-name . "abbyyR")))
1887 (build-system r-build-system)
1889 `(("r-curl" ,r-curl)
1892 ("r-progress" ,r-progress)
1893 ("r-readr" ,r-readr)
1895 (home-page "https://github.com/soodoku/abbyyR")
1896 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1898 "This package provides tools to get text from images of text using Abbyy
1899 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1900 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1901 passports and get the results in a variety of formats including plain text and
1902 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1903 (license license:expat)))
1905 (define-public r-colorspace
1907 (name "r-colorspace")
1912 (uri (cran-uri "colorspace" version))
1914 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1915 (build-system r-build-system)
1916 (home-page "https://cran.r-project.org/web/packages/colorspace")
1917 (synopsis "Color space manipulation")
1919 "This package carries out a mapping between assorted color spaces
1920 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1921 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1922 colors are provided.")
1923 (license license:bsd-3)))
1925 (define-public r-glue
1932 (uri (cran-uri "glue" version))
1935 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
1936 (build-system r-build-system)
1937 ;; knitr depends on glue, so we can't add knitr here to build the
1941 `(("r-knitr" ,r-knitr)))
1942 (home-page "https://github.com/tidyverse/glue")
1943 (synopsis "Interpreted string literals")
1945 "This package provides an implementation of interpreted string literals,
1946 inspired by Python's Literal String Interpolation (PEP-0498) and
1947 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1948 (license license:expat)))
1950 (define-public r-pastecs
1956 (uri (cran-uri "pastecs" version))
1959 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1960 (build-system r-build-system)
1962 `(("r-boot" ,r-boot)))
1963 (home-page "http://www.sciviews.org/pastecs")
1964 (synopsis "Analysis of space-time ecological series")
1966 "This package provides functions for regulation, decomposition and analysis
1967 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1968 initiative to bring PASSTEC 2000 functionalities to R.")
1969 (license license:gpl2+)))
1971 (define-public r-partykit
1977 (uri (cran-uri "partykit" version))
1980 "18nc6vvj1cy8ly2hqixg544sbg8vbpzwsr1cdlzrqfykd0pzgkvf"))))
1981 (build-system r-build-system)
1983 `(("r-formula" ,r-formula)
1985 ("r-libcoin" ,r-libcoin)
1986 ("r-mvtnorm" ,r-mvtnorm)
1987 ("r-rpart" ,r-rpart)
1988 ("r-survival" ,r-survival)))
1989 (home-page "http://partykit.R-Forge.R-project.org/partykit")
1990 (synopsis "Toolkit for recursive partytioning")
1992 "This package provides a toolkit with infrastructure for representing,
1993 summarizing, and visualizing tree-structured regression and classification
1995 (license license:gpl2+)))
1997 (define-public r-plogr
2004 (uri (cran-uri "plogr" version))
2007 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2008 (build-system r-build-system)
2009 (home-page "https://github.com/krlmlr/plogr")
2010 (synopsis "R bindings for the plog C++ logging library")
2012 "This package provides the header files for a stripped-down version of
2013 the plog header-only C++ logging library, and a method to log to R's standard
2015 (license license:expat)))
2017 (define-public r-pls
2024 (uri (cran-uri "pls" version))
2026 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2027 (build-system r-build-system)
2028 (home-page "https://mevik.net/work/software/pls.html")
2029 (synopsis "Partial Least Squares and Principal Component Regression")
2031 "The pls package implements multivariate regression methods: Partial Least
2032 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2033 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2036 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2037 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2038 @item multi-response models (or @dfn{PLS2})
2039 @item flexible cross-validation
2040 @item Jackknife variance estimates of regression coefficients
2041 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2042 (R)MSEP, R², and correlation loadings
2043 @item formula interface, modelled after @code{lm()}, with methods for predict,
2044 print, summary, plot, update, etc.
2045 @item extraction functions for coefficients, scores, and loadings
2046 @item MSEP, RMSEP, and R² estimates
2047 @item multiplicative scatter correction (@dfn{MSC})
2049 (license license:gpl2)))
2058 (uri (cran-uri "ps" version))
2060 (base32 "1cxfhnff22fbsr9vynhql0rhhrqfxvkb6kv11h2m740r9scwcs44"))))
2061 (build-system r-build-system)
2062 (home-page "https://ps.r-lib.org")
2063 (synopsis "List, query, and manipulate system processes")
2065 "The ps package implements an API to list, query, and manipulate system
2066 processes. Most of its code is based on the @code{psutil} Python package.")
2067 (license license:bsd-3)))
2069 (define-public r-pkgbuild
2076 (uri (cran-uri "pkgbuild" version))
2078 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk"))))
2079 (build-system r-build-system)
2081 `(("r-callr" ,r-callr)
2083 ("r-crayon" ,r-crayon)
2085 ("r-prettyunits" ,r-prettyunits)
2087 ("r-rprojroot" ,r-rprojroot)
2088 ("r-withr" ,r-withr)))
2089 (home-page "https://github.com/r-pkgs/pkgbuild")
2090 (synopsis "Find tools needed to build R packages")
2092 "This package provides functions used to build R packages. It locates
2093 compilers needed to build R packages on various platforms and ensures the PATH
2094 is configured appropriately so R can use them.")
2095 (license license:gpl3)))
2097 (define-public r-pkgload
2104 (uri (cran-uri "pkgload" version))
2107 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2108 (build-system r-build-system)
2111 ("r-crayon" ,r-crayon)
2113 ("r-pkgbuild" ,r-pkgbuild)
2114 ("r-rlang" ,r-rlang)
2115 ("r-rprojroot" ,r-rprojroot)
2116 ("r-rstudioapi" ,r-rstudioapi)
2117 ("r-withr" ,r-withr)))
2118 (home-page "https://github.com/r-lib/pkgload")
2119 (synopsis "Simulate package installation and attach")
2121 "This package simulates the process of installing a package and then
2122 attaching it. This is a key part of the @code{devtools} package as it allows
2123 you to rapidly iterate while developing a package.")
2124 (license license:gpl3)))
2126 (define-public r-rcpp
2133 (uri (cran-uri "Rcpp" version))
2135 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2136 (build-system r-build-system)
2137 (home-page "http://www.rcpp.org")
2138 (synopsis "Seamless R and C++ integration")
2140 "The Rcpp package provides R functions as well as C++ classes which offer
2141 a seamless integration of R and C++. Many R data types and objects can be
2142 mapped back and forth to C++ equivalents which facilitates both writing of new
2143 code as well as easier integration of third-party libraries. Documentation
2144 about Rcpp is provided by several vignettes included in this package, via the
2145 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2146 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2147 @code{citation(\"Rcpp\")} for details on these last two.")
2148 (license license:gpl2+)))
2150 (define-public r-bindr
2157 (uri (cran-uri "bindr" version))
2160 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2161 (build-system r-build-system)
2162 (home-page "https://github.com/krlmlr/bindr")
2163 (synopsis "Parametrized active bindings")
2165 "This package provides a simple interface for creating active bindings
2166 where the bound function accepts additional arguments.")
2167 (license license:expat)))
2169 (define-public r-bindrcpp
2176 (uri (cran-uri "bindrcpp" version))
2179 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2180 (build-system r-build-system)
2182 `(("r-bindr" ,r-bindr)
2183 ("r-plogr" ,r-plogr)
2184 ("r-rcpp" ,r-rcpp)))
2185 (home-page "https://github.com/krlmlr/bindrcpp")
2186 (synopsis "Rcpp interface to active bindings")
2188 "This package provides an easy way to fill an environment with active
2189 bindings that call a C++ function.")
2190 (license license:expat)))
2192 (define-public r-bisquerna
2194 (name "r-bisquerna")
2198 (uri (cran-uri "BisqueRNA" version))
2201 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2202 (properties `((upstream-name . "BisqueRNA")))
2203 (build-system r-build-system)
2205 `(("r-biobase" ,r-biobase)
2206 ("r-limsolve" ,r-limsolve)))
2207 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2208 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2209 (description "This package provides tools to accurately estimate cell type
2210 abundances from heterogeneous bulk expression. A reference-based method
2211 utilizes single-cell information to generate a signature matrix and
2212 transformation of bulk expression for accurate regression based estimates.
2213 A marker-based method utilizes known cell-specific marker genes to measure
2214 relative abundances across samples.")
2215 (license license:gpl3)))
2217 (define-public r-auc
2224 (uri (cran-uri "AUC" version))
2227 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2228 (properties `((upstream-name . "AUC")))
2229 (build-system r-build-system)
2230 (home-page "https://cran.r-project.org/web/packages/AUC")
2231 (synopsis "Compute the area under the curve of selected measures")
2233 "This package includes functions to compute the area under the curve of
2234 selected measures: the area under the sensitivity curve (AUSEC), the area
2235 under the specificity curve (AUSPC), the area under the accuracy
2236 curve (AUACC), and the area under the receiver operating characteristic
2237 curve (AUROC). The curves can also be visualized. Support for partial areas
2239 (license license:gpl2+)))
2241 (define-public r-calibrate
2243 (name "r-calibrate")
2248 (uri (cran-uri "calibrate" version))
2250 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2251 (build-system r-build-system)
2253 `(("r-mass" ,r-mass)))
2254 (home-page "https://cran.r-project.org/web/packages/calibrate")
2255 (synopsis "Calibration of scatterplot and biplot axes")
2257 "This is a package for drawing calibrated scales with tick marks
2258 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2259 (license license:gpl2)))
2261 (define-public r-shape
2268 (uri (cran-uri "shape" version))
2271 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2272 (build-system r-build-system)
2273 (home-page "https://cran.r-project.org/web/packages/shape")
2274 (synopsis "Functions for plotting graphical shapes")
2276 "This package provides functions for plotting graphical shapes such as
2277 ellipses, circles, cylinders, arrows, ...")
2278 (license license:gpl3+)))
2280 (define-public r-globaloptions
2282 (name "r-globaloptions")
2287 (uri (cran-uri "GlobalOptions" version))
2289 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2290 (properties `((upstream-name . "GlobalOptions")))
2291 (build-system r-build-system)
2293 `(("r-knitr" ,r-knitr)))
2294 (home-page "https://github.com/jokergoo/GlobalOptions")
2295 (synopsis "Generate functions to get or set global options")
2297 "This package provides more controls on the option values such as
2298 validation and filtering on the values, making options invisible or private.")
2299 (license license:gpl2+)))
2301 (define-public r-circlize
2308 (uri (cran-uri "circlize" version))
2311 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2312 (build-system r-build-system)
2314 `(("r-colorspace" ,r-colorspace)
2315 ("r-globaloptions" ,r-globaloptions)
2316 ("r-shape" ,r-shape)))
2318 `(("r-knitr" ,r-knitr)))
2319 (home-page "https://github.com/jokergoo/circlize")
2320 (synopsis "Circular visualization")
2322 "Circular layout is an efficient way to visualise huge amounts of
2323 information. This package provides an implementation of circular layout
2324 generation in R as well as an enhancement of available software. Its
2325 flexibility is based on the usage of low-level graphics functions such that
2326 self-defined high-level graphics can be easily implemented by users for
2327 specific purposes. Together with the seamless connection between the powerful
2328 computational and visual environment in R, it gives users more convenience and
2329 freedom to design figures for better understanding complex patterns behind
2330 multi-dimensional data.")
2331 (license license:gpl2+)))
2333 (define-public r-powerlaw
2340 (uri (cran-uri "poweRlaw" version))
2342 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2343 (properties `((upstream-name . "poweRlaw")))
2344 (build-system r-build-system)
2346 `(("r-pracma" ,r-pracma)))
2348 `(("r-knitr" ,r-knitr)))
2349 (home-page "https://github.com/csgillespie/poweRlaw")
2350 (synopsis "Tools for the analysis of heavy tailed distributions")
2352 "This package provides an implementation of maximum likelihood estimators
2353 for a variety of heavy tailed distributions, including both the discrete and
2354 continuous power law distributions. Additionally, a goodness-of-fit based
2355 approach is used to estimate the lower cut-off for the scaling region.")
2356 ;; Any of these GPL versions.
2357 (license (list license:gpl2 license:gpl3))))
2359 (define-public r-compare
2366 (uri (cran-uri "compare" version))
2369 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2370 (build-system r-build-system)
2371 (home-page "https://cran.r-project.org/web/packages/compare")
2372 (synopsis "Comparing objects for differences")
2374 "This package provides functions to compare a model object to a
2375 comparison object. If the objects are not identical, the functions can be
2376 instructed to explore various modifications of the objects (e.g., sorting
2377 rows, dropping names) to see if the modified versions are identical.")
2378 (license license:gpl2+)))
2380 (define-public r-dendextend
2382 (name "r-dendextend")
2387 (uri (cran-uri "dendextend" version))
2390 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2391 (build-system r-build-system)
2393 `(("r-ggplot2" ,r-ggplot2)
2394 ("r-magrittr" ,r-magrittr)
2395 ("r-viridis" ,r-viridis)))
2397 `(("r-knitr" ,r-knitr)))
2398 (home-page "https://cran.r-project.org/web/packages/dendextend")
2399 (synopsis "Extending 'dendrogram' functionality in R")
2401 "This package offers a set of functions for extending @code{dendrogram}
2402 objects in R, letting you visualize and compare trees of hierarchical
2403 clusterings. You can adjust a tree's graphical parameters (the color, size,
2404 type, etc of its branches, nodes and labels) and visually and statistically
2405 compare different dendrograms to one another.")
2406 ;; Any of these versions
2407 (license (list license:gpl2 license:gpl3))))
2409 (define-public r-getoptlong
2411 (name "r-getoptlong")
2416 (uri (cran-uri "GetoptLong" version))
2419 "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
2420 (properties `((upstream-name . "GetoptLong")))
2421 (build-system r-build-system)
2425 `(("r-crayon" ,r-crayon)
2426 ("r-globaloptions" ,r-globaloptions)
2427 ("r-rjson" ,r-rjson)))
2429 `(("r-knitr" ,r-knitr)))
2430 (home-page "https://github.com/jokergoo/GetoptLong")
2431 (synopsis "Parsing command-line arguments and variable interpolation")
2433 "This is yet another command-line argument parser which wraps the
2434 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2435 use in R. It also provides a simple way for variable interpolation in R.")
2436 (license license:gpl2+)))
2438 (define-public r-fastmatch
2440 (name "r-fastmatch")
2445 (uri (cran-uri "fastmatch" version))
2448 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2449 (build-system r-build-system)
2450 (home-page "https://www.rforge.net/fastmatch")
2451 (synopsis "Fast match function")
2453 "This package provides a fast @code{match} replacement for cases that
2454 require repeated look-ups. It is slightly faster that R's built-in
2455 @code{match} function on first match against a table, but extremely fast on
2456 any subsequent lookup as it keeps the hash table in memory.")
2457 (license license:gpl2)))
2466 (uri (cran-uri "ff" version))
2469 "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0"))))
2470 (build-system r-build-system)
2471 (propagated-inputs `(("r-bit" ,r-bit)))
2472 (home-page "http://ff.r-forge.r-project.org/")
2473 (synopsis "Memory-efficient storage of large data on disk and access functions")
2475 "This package provides data structures that are stored on disk but
2476 behave (almost) as if they were in RAM by transparently mapping only a section
2478 ;; error Architecture not supported.
2479 (supported-systems (delete "aarch64-linux" %supported-systems))
2480 (license license:gpl2)))
2482 (define-public r-ffbase
2489 (uri (cran-uri "ffbase" version))
2492 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2493 (build-system r-build-system)
2496 ("r-fastmatch" ,r-fastmatch)
2498 (home-page "https://github.com/edwindj/ffbase")
2499 (synopsis "Basic statistical functions for package 'ff'")
2501 "This package extends the out of memory vectors of @code{ff} with
2502 statistical functions and other utilities to ease their usage.")
2503 (license license:gpl3)))
2505 (define-public r-prettyunits
2507 (name "r-prettyunits")
2512 (uri (cran-uri "prettyunits" version))
2515 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2516 (build-system r-build-system)
2517 (home-page "https://github.com/gaborcsardi/prettyunits")
2518 (synopsis "Pretty, human readable formatting of quantities")
2520 "This package provides tools for pretty, human readable formatting of
2522 (license license:expat)))
2524 (define-public r-reshape
2531 (uri (cran-uri "reshape" version))
2534 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2535 (build-system r-build-system)
2537 `(("r-plyr" ,r-plyr)
2538 ("r-rcpp" ,r-rcpp)))
2539 (home-page "http://had.co.nz/reshape")
2540 (synopsis "Flexibly reshape data")
2542 "Flexibly restructure and aggregate data using just two functions:
2543 @code{melt} and @code{cast}. This package provides them.")
2544 (license license:expat)))
2546 (define-public r-progress
2553 (uri (cran-uri "progress" version))
2556 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2557 (build-system r-build-system)
2559 `(("r-crayon" ,r-crayon)
2561 ("r-prettyunits" ,r-prettyunits)
2563 (home-page "https://github.com/gaborcsardi/progress")
2564 (synopsis "Terminal progress bars")
2566 "This package provides configurable progress bars. They may include
2567 percentage, elapsed time, and/or the estimated completion time. They work in
2568 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2569 package also provides a C++ API, that works with or without Rcpp.")
2570 (license license:expat)))
2572 (define-public r-ggally
2579 (uri (cran-uri "GGally" version))
2582 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2583 (properties `((upstream-name . "GGally")))
2584 (build-system r-build-system)
2586 `(("libressl" ,libressl)))
2588 `(("r-ggplot2" ,r-ggplot2)
2589 ("r-gtable" ,r-gtable)
2590 ("r-lifecycle" ,r-lifecycle)
2592 ("r-progress" ,r-progress)
2593 ("r-rcolorbrewer" ,r-rcolorbrewer)
2594 ("r-reshape" ,r-reshape)
2595 ("r-rlang" ,r-rlang)
2596 ("r-scales" ,r-scales)))
2597 (home-page "https://ggobi.github.io/ggally")
2598 (synopsis "Extension to ggplot2")
2600 "The R package ggplot2 is a plotting system based on the grammar of
2601 graphics. GGally extends ggplot2 by adding several functions to reduce the
2602 complexity of combining geometric objects with transformed data. Some of
2603 these functions include a pairwise plot matrix, a two group pairwise plot
2604 matrix, a parallel coordinates plot, a survival plot, and several functions to
2606 (license license:gpl2+)))
2608 (define-public r-proxy
2615 (uri (cran-uri "proxy" version))
2618 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2619 (build-system r-build-system)
2620 (home-page "https://cran.r-project.org/web/packages/proxy")
2621 (synopsis "Distance and similarity measures")
2623 "This package provides an extensible framework for the efficient
2624 calculation of auto- and cross-proximities, along with implementations of the
2625 most popular ones.")
2626 (license license:gpl2)))
2635 (uri (cran-uri "sp" version))
2637 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2638 (build-system r-build-system)
2640 `(("r-lattice" ,r-lattice)))
2641 (home-page "https://cran.r-project.org/web/packages/sp")
2642 (synopsis "Classes and methods for spatial data")
2644 "This package provides classes and methods for spatial data; the classes
2645 document where the spatial location information resides, for 2D or 3D data.
2646 Utility functions are provided, e.g. for plotting data as maps, spatial
2647 selection, as well as methods for retrieving coordinates, for subsetting,
2648 print, summary, etc.")
2649 (license license:gpl2+)))
2651 (define-public r-laplacesdemon
2653 (name "r-laplacesdemon")
2658 (uri (cran-uri "LaplacesDemon" version))
2660 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
2661 (properties `((upstream-name . "LaplacesDemon")))
2662 (build-system r-build-system)
2663 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
2664 (synopsis "Complete environment for Bayesian inference")
2666 "This package provides a complete environment for Bayesian inference using
2667 a variety of different samplers.")
2668 (license license:expat)))
2670 (define-public r-rmtstat
2677 (uri (cran-uri "RMTstat" version))
2680 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2681 (properties `((upstream-name . "RMTstat")))
2682 (build-system r-build-system)
2683 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2684 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2686 "This package provides functions for working with the Tracy-Widom laws
2687 and other distributions related to the eigenvalues of large Wishart
2689 (license license:bsd-3)))
2691 (define-public r-rmpi
2697 (uri (cran-uri "Rmpi" version))
2700 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2701 (properties `((upstream-name . "Rmpi")))
2702 (build-system r-build-system)
2704 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2705 #:phases (modify-phases %standard-phases
2706 (add-before 'install 'mpi-setup
2709 `(("openmpi" ,openmpi)))
2711 `(("pkg-config" ,pkg-config)))
2712 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2713 (synopsis "R interface to message-passing interface (MPI)")
2715 "This package provides an interface (wrapper) to MPI APIs. It also
2716 provides an interactive R manager and worker environment.")
2717 (license license:gpl2+)))
2719 (define-public r-lmoments
2726 (uri (cran-uri "Lmoments" version))
2729 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2730 (properties `((upstream-name . "Lmoments")))
2731 (build-system r-build-system)
2733 `(("r-rcpp" ,r-rcpp)
2734 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2735 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2736 (synopsis "L-moments and quantile mixtures")
2738 "This package contains functions to estimate L-moments and trimmed
2739 L-moments from the data. It also contains functions to estimate the
2740 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2741 quantile mixture from L-moments and trimmed L-moments.")
2742 (license license:gpl2)))
2744 (define-public r-distillery
2746 (name "r-distillery")
2751 (uri (cran-uri "distillery" version))
2754 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
2755 (build-system r-build-system)
2756 (home-page "https://ral.ucar.edu/staff/ericg/")
2757 (synopsis "Functions for confidence intervals and object information")
2759 "This package provides some very simple method functions for confidence
2760 interval calculation and to distill pertinent information from a potentially
2761 complex object; primarily used in common with the packages extRemes and
2763 (license license:gpl2+)))
2765 (define-public r-extremes
2772 (uri (cran-uri "extRemes" version))
2775 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2776 (properties `((upstream-name . "extRemes")))
2777 (build-system r-build-system)
2779 `(("r-distillery" ,r-distillery)
2780 ("r-lmoments" ,r-lmoments)))
2781 (home-page "https://www.assessment.ucar.edu/toolkit/")
2782 (synopsis "Extreme value analysis")
2784 "ExtRemes is a suite of functions for carrying out analyses on the
2785 extreme values of a process of interest; be they block maxima over long blocks
2786 or excesses over a high threshold.")
2787 (license license:gpl2+)))
2789 (define-public r-lmtest
2796 (uri (cran-uri "lmtest" version))
2799 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
2800 (build-system r-build-system)
2802 `(("r-zoo" ,r-zoo)))
2804 `(("gfortran" ,gfortran)))
2805 (home-page "https://cran.r-project.org/web/packages/lmtest")
2806 (synopsis "Testing linear regression models")
2808 "This package provides a collection of tests, data sets, and examples for
2809 diagnostic checking in linear regression models. Furthermore, some generic
2810 tools for inference in parametric models are provided.")
2811 ;; Either version is okay
2812 (license (list license:gpl2 license:gpl3))))
2814 (define-public r-idr
2820 (uri (cran-uri "idr" version))
2823 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2824 (build-system r-build-system)
2825 (home-page "https://cran.r-project.org/web/packages/idr/")
2826 (synopsis "Irreproducible discovery rate")
2828 "This is a package for estimating the copula mixture model and plotting
2829 correspondence curves in \"Measuring reproducibility of high-throughput
2830 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2831 by Li, Brown, Huang, and Bickel")
2832 (license license:gpl2+)))
2834 (define-public r-inline
2840 (uri (cran-uri "inline" version))
2843 "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj"))))
2844 (build-system r-build-system)
2845 (home-page "https://cran.r-project.org/web/packages/inline")
2846 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2848 "This package provides functionality to dynamically define R functions
2849 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2850 @code{.Call} calling conventions.")
2851 ;; Any version of the LGPL.
2852 (license license:lgpl3+)))
2854 (define-public r-inum
2860 (uri (cran-uri "inum" version))
2863 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2864 (build-system r-build-system)
2866 `(("r-libcoin" ,r-libcoin)))
2867 (home-page "https://cran.r-project.org/web/packages/inum/")
2868 (synopsis "Interval and enum-type representation of vectors")
2870 "This package provides an enum-type representation of vectors and
2871 representation of intervals, including a method of coercing variables
2873 (license license:gpl2)))
2875 (define-public r-bdsmatrix
2877 (name "r-bdsmatrix")
2882 (uri (cran-uri "bdsmatrix" version))
2885 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2886 (properties `((upstream-name . "bdsmatrix")))
2887 (build-system r-build-system)
2888 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2889 (synopsis "Routines for block diagonal symmetric matrices")
2891 "This package provides procedures to work with block diagonal symmetric
2892 matrices, a special case of sparse matrices.")
2893 (license license:lgpl2.0)))
2895 (define-public r-bbmle
2898 (version "1.0.23.1")
2902 (uri (cran-uri "bbmle" version))
2905 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2906 (build-system r-build-system)
2908 `(("r-bdsmatrix" ,r-bdsmatrix)
2909 ("r-lattice" ,r-lattice)
2911 ("r-matrix" ,r-matrix)
2912 ("r-mvtnorm" ,r-mvtnorm)
2913 ("r-numderiv" ,r-numderiv)))
2914 (home-page "https://cran.r-project.org/web/packages/bbmle")
2915 (synopsis "Tools for General Maximum Likelihood Estimation")
2917 "This package provides methods and functions for fitting maximum
2918 likelihood models in R. This package modifies and extends the @code{mle}
2919 classes in the @code{stats4} package.")
2920 ;; Any version of the GPL
2921 (license license:gpl2+)))
2923 (define-public r-emdbook
2930 (uri (cran-uri "emdbook" version))
2933 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2934 (build-system r-build-system)
2936 `(("r-bbmle" ,r-bbmle)
2938 ("r-lattice" ,r-lattice)
2940 ("r-plyr" ,r-plyr)))
2941 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2942 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2944 "This package provides auxiliary functions and data sets for \"Ecological
2945 Models and Data\", a book presenting maximum likelihood estimation and related
2946 topics for ecologists (ISBN 978-0-691-12522-0).")
2948 (license (list license:gpl2 license:gpl3))))
2950 (define-public r-lpsolve
2957 (uri (cran-uri "lpSolve" version))
2960 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2961 (properties `((upstream-name . "lpSolve")))
2962 (build-system r-build-system)
2963 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2964 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2966 "Lp_solve is software for solving linear, integer and mixed integer
2967 programs. This implementation supplies a \"wrapper\" function in C and some R
2968 functions that solve general linear/integer problems, assignment problems, and
2969 transportation problems.")
2970 (license license:lgpl2.0)))
2972 (define-public r-limsolve
2979 (uri (cran-uri "limSolve" version))
2982 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2983 (properties `((upstream-name . "limSolve")))
2984 (build-system r-build-system)
2986 `(("r-lpsolve" ,r-lpsolve)
2988 ("r-quadprog" ,r-quadprog)))
2989 (native-inputs `(("gfortran" ,gfortran)))
2990 (home-page "https://cran.r-project.org/web/packages/limSolve")
2991 (synopsis "Solving linear inverse models")
2993 "This package provides functions that:
2996 @item find the minimum/maximum of a linear or quadratic function,
2997 @item sample an underdetermined or overdetermined system,
2998 @item solve a linear system Ax=B for the unknown x.
3001 It includes banded and tridiagonal linear systems. The package calls Fortran
3002 functions from LINPACK.")
3004 (license (list license:gpl2+ license:gpl3+))))
3006 (define-public r-fitdistrplus
3008 (name "r-fitdistrplus")
3013 (uri (cran-uri "fitdistrplus" version))
3016 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
3017 (build-system r-build-system)
3019 `(("r-mass" ,r-mass)
3020 ("r-survival" ,r-survival)))
3022 `(("r-knitr" ,r-knitr)))
3023 (home-page "http://riskassessment.r-forge.r-project.org")
3024 (synopsis "Fitting a parametric distribution from data")
3026 "This package extends the @code{fitdistr} function of the MASS package
3027 with several functions to help the fit of a parametric distribution to
3028 non-censored or censored data. Censored data may contain left-censored,
3029 right-censored and interval-censored values, with several lower and upper
3030 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3031 provides moment matching (MME), quantile matching (QME) and maximum
3032 goodness-of-fit estimation (MGE) methods (available only for non-censored
3033 data). Weighted versions of MLE, MME and QME are available.")
3034 (license license:gpl2+)))
3036 (define-public r-energy
3043 (uri (cran-uri "energy" version))
3046 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3047 (build-system r-build-system)
3049 `(("r-boot" ,r-boot)
3050 ("r-rcpp" ,r-rcpp)))
3051 (home-page "https://cran.r-project.org/web/packages/energy")
3052 (synopsis "Multivariate inference via the energy of data")
3054 "This package provides e-statistics (energy) tests and statistics for
3055 multivariate and univariate inference, including distance correlation,
3056 one-sample, two-sample, and multi-sample tests for comparing multivariate
3057 distributions, are implemented. Measuring and testing multivariate
3058 independence based on distance correlation, partial distance correlation,
3059 multivariate goodness-of-fit tests, clustering based on energy distance,
3060 testing for multivariate normality, distance components (disco) for
3061 non-parametric analysis of structured data, and other energy
3062 statistics/methods are implemented.")
3063 (license license:gpl2+)))
3065 (define-public r-suppdists
3067 (name "r-suppdists")
3072 (uri (cran-uri "SuppDists" version))
3075 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3076 (properties `((upstream-name . "SuppDists")))
3077 (build-system r-build-system)
3078 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3079 (synopsis "Supplementary distributions")
3081 "This package provides ten distributions supplementing those built into
3082 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3083 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3084 coefficient, Johnson distributions, normal scores and generalized
3085 hypergeometric distributions. In addition two random number generators of
3086 George Marsaglia are included.")
3087 (license license:gpl2+)))
3089 (define-public r-ksamples
3096 (uri (cran-uri "kSamples" version))
3099 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3100 (properties `((upstream-name . "kSamples")))
3101 (build-system r-build-system)
3103 `(("r-suppdists" ,r-suppdists)))
3104 (home-page "https://cran.r-project.org/web/packages/kSamples")
3105 (synopsis "K-Sample rank tests and their combinations")
3107 "This package provides tools to compares k samples using the
3108 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3109 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3110 test. It computes asymptotic, simulated or (limited) exact P-values, all
3111 valid under randomization, with or without ties, or conditionally under random
3112 sampling from populations, given the observed tie pattern. Except for Steel's
3113 test and the JT test it also combines these tests across several blocks of
3115 (license license:gpl2+)))
3117 (define-public r-cvst
3124 (uri (cran-uri "CVST" version))
3127 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3128 (properties `((upstream-name . "CVST")))
3129 (build-system r-build-system)
3131 `(("r-kernlab" ,r-kernlab)
3132 ("r-matrix" ,r-matrix)))
3133 (home-page "https://cran.r-project.org/web/packages/CVST")
3134 (synopsis "Fast cross-validation via sequential testing")
3136 "This package implements the fast cross-validation via sequential
3137 testing (CVST) procedure. CVST is an improved cross-validation procedure
3138 which uses non-parametric testing coupled with sequential analysis to
3139 determine the best parameter set on linearly increasing subsets of the data.
3140 Additionally to the CVST the package contains an implementation of the
3141 ordinary k-fold cross-validation with a flexible and powerful set of helper
3142 objects and methods to handle the overall model selection process. The
3143 implementations of the Cochran's Q test with permutations and the sequential
3144 testing framework of Wald are generic and can therefore also be used in other
3146 (license license:gpl2+)))
3148 (define-public r-squarem
3155 (uri (cran-uri "SQUAREM" version))
3158 "1r2yxfiqbpwy5ccg94r7f6sz7lh5aq0xjpf632s42wgmml1dvlzb"))))
3159 (properties `((upstream-name . "SQUAREM")))
3160 (build-system r-build-system)
3161 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3162 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3164 "This package provides algorithms for accelerating the convergence of
3165 slow, monotone sequences from smooth, contraction mapping such as the EM
3166 algorithm. It can be used to accelerate any smooth, linearly convergent
3167 acceleration scheme. A tutorial style introduction to this package is
3168 available in a vignette.")
3169 (license license:gpl2+)))
3171 (define-public r-lava
3178 (uri (cran-uri "lava" version))
3181 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3182 (build-system r-build-system)
3184 `(("r-numderiv" ,r-numderiv)
3185 ("r-squarem" ,r-squarem)
3186 ("r-survival" ,r-survival)))
3187 (home-page "https://github.com/kkholst/lava")
3188 (synopsis "Latent variable models")
3190 "This package provides tools for the estimation and simulation of latent
3192 (license license:gpl3)))
3194 (define-public r-drr
3201 (uri (cran-uri "DRR" version))
3204 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3205 (properties `((upstream-name . "DRR")))
3206 (build-system r-build-system)
3208 `(("r-cvst" ,r-cvst)
3209 ("r-kernlab" ,r-kernlab)
3210 ("r-matrix" ,r-matrix)))
3211 (home-page "https://cran.r-project.org/web/packages/DRR")
3212 (synopsis "Dimensionality reduction via regression")
3214 "This package provides an implementation of dimensionality reduction via
3215 regression using Kernel Ridge Regression.")
3216 (license license:gpl3)))
3218 (define-public r-prodlim
3221 (version "2019.11.13")
3225 (uri (cran-uri "prodlim" version))
3228 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3229 (build-system r-build-system)
3231 `(("r-kernsmooth" ,r-kernsmooth)
3234 ("r-survival" ,r-survival)))
3235 (home-page "https://cran.r-project.org/web/packages/prodlim")
3236 (synopsis "Product-limit estimation for censored event history analysis")
3238 "This package provides a fast and user-friendly implementation of
3239 nonparametric estimators for censored event history (survival) analysis with
3240 the Kaplan-Meier and Aalen-Johansen methods.")
3241 (license license:gpl2+)))
3243 (define-public r-dimred
3250 (uri (cran-uri "dimRed" version))
3253 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3254 (properties `((upstream-name . "dimRed")))
3255 (build-system r-build-system)
3258 ("r-magrittr" ,r-magrittr)))
3259 (home-page "https://github.com/gdkrmr/dimRed")
3260 (synopsis "Framework for dimensionality reduction")
3262 "This package provides a collection of dimensionality reduction
3263 techniques from R packages and provides a common interface for calling the
3265 (license license:gpl3)))
3267 (define-public r-timedate
3270 (version "3043.102")
3274 (uri (cran-uri "timeDate" version))
3277 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3278 (properties `((upstream-name . "timeDate")))
3279 (build-system r-build-system)
3280 (home-page "https://www.rmetrics.org")
3281 (synopsis "Chronological and calendar objects")
3283 "This package provides an environment for teaching \"Financial
3284 Engineering and Computational Finance\" and for managing chronological and
3286 (license license:gpl2+)))
3288 (define-public r-magic
3295 (uri (cran-uri "magic" version))
3298 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3299 (build-system r-build-system)
3301 `(("r-abind" ,r-abind)))
3302 (home-page "https://github.com/RobinHankin/magic.git")
3303 (synopsis "Create and investigate magic squares")
3305 "This package provides a collection of efficient, vectorized algorithms
3306 for the creation and investigation of magic squares and hypercubes, including
3307 a variety of functions for the manipulation and analysis of arbitrarily
3308 dimensioned arrays.")
3309 (license license:gpl2)))
3311 (define-public r-rmysql
3318 (uri (cran-uri "RMySQL" version))
3321 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3322 (properties `((upstream-name . "RMySQL")))
3323 (build-system r-build-system)
3325 `(("mariadb" ,mariadb "lib")
3326 ("mariadb-dev" ,mariadb "dev")
3329 `(("r-dbi" ,r-dbi)))
3330 (home-page "https://github.com/r-dbi/RMySQL")
3331 (synopsis "Database interface and MySQL driver for R")
3333 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3334 package contains an old implementation based on legacy code from S-PLUS which
3335 is being phased out. A modern MySQL client based on Rcpp is available from
3336 the RMariaDB package.")
3337 (license license:gpl2)))
3339 (define-public r-rpostgresql
3341 (name "r-rpostgresql")
3346 (uri (cran-uri "RPostgreSQL" version))
3349 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3350 (properties `((upstream-name . "RPostgreSQL")))
3351 (build-system r-build-system)
3353 `(("postgresql" ,postgresql)))
3355 `(("r-dbi" ,r-dbi)))
3356 (home-page "https://github.com/tomoakin/RPostgreSQL")
3357 (synopsis "R interface to the PostgreSQL database system")
3359 "This package provides a Database Interface (DBI) compliant driver for R
3360 to access PostgreSQL database systems.")
3361 ;; The whole package is released under GPL version 2. It includes code
3362 ;; under the PostgreSQL license.
3363 (license license:gpl2)))
3365 (define-public r-linprog
3372 (uri (cran-uri "linprog" version))
3375 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3376 (build-system r-build-system)
3377 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3378 (home-page "http://linprog.r-forge.r-project.org/")
3379 (synopsis "Linear programming and optimization")
3381 "This package can be used to solve Linear Programming / Linear
3382 Optimization problems by using the simplex algorithm.")
3383 (license license:gpl2+)))
3385 (define-public r-geometry
3392 (uri (cran-uri "geometry" version))
3395 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3396 (build-system r-build-system)
3398 `(("r-magic" ,r-magic)
3399 ("r-linprog" ,r-linprog)
3400 ("r-lpsolve" ,r-lpsolve)
3402 ("r-rcppprogress" ,r-rcppprogress)))
3403 (home-page "http://geometry.r-forge.r-project.org/")
3404 (synopsis "Mesh generation and surface tesselation")
3406 "This package makes the qhull library available in R, in a similar manner
3407 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3408 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3409 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3410 and higher dimensions. It implements the Quickhull algorithm for computing
3411 the convex hull. Qhull does not support constrained Delaunay triangulations,
3412 or mesh generation of non-convex objects, but the package does include some R
3413 functions that allow for this. Currently the package only gives access to
3414 Delaunay triangulation and convex hull computation.")
3415 ;; The Qhull sources are included and are distributed under a custom
3416 ;; non-copyleft license. The R sources are released under GPL version 2.
3417 (license (list license:gpl2
3418 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3420 (define-public r-ddalpha
3427 (uri (cran-uri "ddalpha" version))
3430 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3431 (build-system r-build-system)
3434 ("r-class" ,r-class)
3435 ("r-geometry" ,r-geometry)
3438 ("r-robustbase" ,r-robustbase)
3439 ("r-sfsmisc" ,r-sfsmisc)))
3441 `(("gfortran" ,gfortran)))
3442 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3443 (synopsis "Depth-Based classification and calculation of data depth")
3445 "This package contains procedures for depth-based supervised learning,
3446 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3447 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3448 statistical depth function to a compact low-dimensional space, where the final
3449 classification is done. It also offers an extension to functional data and
3450 routines for calculating certain notions of statistical depth functions. 50
3451 multivariate and 5 functional classification problems are included.")
3452 (license license:gpl2)))
3454 (define-public r-gower
3461 (uri (cran-uri "gower" version))
3464 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3465 (build-system r-build-system)
3466 (home-page "https://github.com/markvanderloo/gower")
3467 (synopsis "Gower's distance")
3469 "This package provides tools to compute Gower's distance (or similarity)
3470 coefficient between records, and to compute the top-n matches between records.
3471 Core algorithms are executed in parallel on systems supporting OpenMP.")
3472 (license license:gpl3)))
3474 (define-public r-rcpproll
3481 (uri (cran-uri "RcppRoll" version))
3484 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3485 (properties `((upstream-name . "RcppRoll")))
3486 (build-system r-build-system)
3488 `(("r-rcpp" ,r-rcpp)))
3489 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3490 (synopsis "Efficient rolling and windowed operations")
3492 "This package provides fast and efficient routines for common rolling /
3493 windowed operations. Routines for the efficient computation of windowed mean,
3494 median, sum, product, minimum, maximum, standard deviation and variance are
3496 (license license:gpl2+)))
3498 (define-public r-ipred
3505 (uri (cran-uri "ipred" version))
3508 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3509 (build-system r-build-system)
3511 `(("r-class" ,r-class)
3514 ("r-prodlim" ,r-prodlim)
3515 ("r-rpart" ,r-rpart)
3516 ("r-survival" ,r-survival)))
3517 (home-page "https://cran.r-project.org/web/packages/ipred")
3518 (synopsis "Improved predictors")
3520 "This package provides improved predictive models by indirect
3521 classification and bagging for classification, regression and survival
3522 problems as well as resampling based estimators of prediction error.")
3523 (license license:gpl2+)))
3525 (define-public r-psych
3532 (uri (cran-uri "psych" version))
3535 "0ymds7ql2dv994m73h68dnhbsws8bl09p2rqvl6xsq6c6xr0yryg"))))
3536 (build-system r-build-system)
3538 `(("r-lattice" ,r-lattice)
3539 ("r-mnormt" ,r-mnormt)
3540 ("r-nlme" ,r-nlme)))
3541 (home-page "https://cran.r-project.org/web/packages/psych/")
3542 (synopsis "Procedures for psychological, psychometric, and personality research")
3544 "This package provides a general purpose toolbox for personality,
3545 psychometric theory and experimental psychology. Functions are primarily for
3546 multivariate analysis and scale construction using factor analysis, principal
3547 component analysis, cluster analysis and reliability analysis, although others
3548 provide basic descriptive statistics. Item Response Theory is done using
3549 factor analysis of tetrachoric and polychoric correlations. Functions for
3550 analyzing data at multiple levels include within and between group statistics,
3551 including correlations and factor analysis. Functions for simulating and
3552 testing particular item and test structures are included. Several functions
3553 serve as a useful front end for structural equation modeling. Graphical
3554 displays of path diagrams, factor analysis and structural equation models are
3555 created using basic graphics.")
3556 (license license:gpl2+)))
3558 (define-public r-generics
3565 (uri (cran-uri "generics" version))
3568 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3569 (build-system r-build-system)
3570 (home-page "https://github.com/r-lib/generics")
3571 (synopsis "Common S3 generics not provided by base R methods")
3573 "In order to reduce potential package dependencies and conflicts,
3574 generics provides a number of commonly used S3 generics that are not provided
3575 by base R methods related to model fitting.")
3576 (license license:gpl2)))
3578 (define-public r-broom
3585 (uri (cran-uri "broom" version))
3588 "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
3589 (build-system r-build-system)
3591 `(("r-backports" ,r-backports)
3592 ("r-dplyr" ,r-dplyr)
3593 ("r-ellipsis" ,r-ellipsis)
3594 ("r-generics" ,r-generics)
3596 ("r-purrr" ,r-purrr)
3597 ("r-rlang" ,r-rlang)
3598 ("r-stringr" ,r-stringr)
3599 ("r-tibble" ,r-tibble)
3600 ("r-tidyr" ,r-tidyr)))
3602 `(("r-knitr" ,r-knitr)))
3603 (home-page "https://github.com/tidyverse/broom")
3604 (synopsis "Convert statistical analysis objects into tidy data frames")
3606 "This package provides tools to convert statistical analysis objects from
3607 R into tidy data frames, so that they can more easily be combined, reshaped
3608 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3609 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3610 summarizes a model's statistical findings such as coefficients of a
3611 regression; @code{augment}, which adds columns to the original data such as
3612 predictions, residuals and cluster assignments; and @code{glance}, which
3613 provides a one-row summary of model-level statistics.")
3614 (license license:expat)))
3616 (define-public r-recipes
3623 (uri (cran-uri "recipes" version))
3626 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3627 (build-system r-build-system)
3629 `(("r-dplyr" ,r-dplyr)
3630 ("r-generics" ,r-generics)
3632 ("r-gower" ,r-gower)
3633 ("r-ipred" ,r-ipred)
3634 ("r-lifecycle" ,r-lifecycle)
3635 ("r-lubridate" ,r-lubridate)
3636 ("r-magrittr" ,r-magrittr)
3637 ("r-matrix" ,r-matrix)
3638 ("r-purrr" ,r-purrr)
3639 ("r-rlang" ,r-rlang)
3640 ("r-tibble" ,r-tibble)
3641 ("r-tidyr" ,r-tidyr)
3642 ("r-tidyselect" ,r-tidyselect)
3643 ("r-timedate" ,r-timedate)
3644 ("r-withr" ,r-withr)))
3646 `(("r-knitr" ,r-knitr)))
3647 (home-page "https://github.com/topepo/recipes")
3648 (synopsis "Preprocessing tools to create design matrices")
3650 "Recipes is an extensible framework to create and preprocess design
3651 matrices. Recipes consist of one or more data manipulation and analysis
3652 \"steps\". Statistical parameters for the steps can be estimated from an
3653 initial data set and then applied to other data sets. The resulting design
3654 matrices can then be used as inputs into statistical or machine learning
3656 (license license:gpl2)))
3658 (define-public r-pdist
3665 (uri (cran-uri "pdist" version))
3668 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3669 (build-system r-build-system)
3670 (home-page "https://github.com/jeffwong/pdist")
3671 (synopsis "Partitioned distance function")
3673 "Pdist computes the euclidean distance between rows of a matrix X and
3674 rows of another matrix Y. Previously, this could be done by binding the two
3675 matrices together and calling @code{dist}, but this creates unnecessary
3676 computation by computing the distances between a row of X and another row of
3677 X, and likewise for Y. Pdist strictly computes distances across the two
3678 matrices, not within the same matrix, making computations significantly faster
3679 for certain use cases.")
3680 (license license:gpl3+)))
3682 (define-public r-ggrepel
3689 (uri (cran-uri "ggrepel" version))
3692 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3693 (build-system r-build-system)
3695 `(("r-ggplot2" ,r-ggplot2)
3697 ("r-scales" ,r-scales)))
3699 `(("r-knitr" ,r-knitr))) ; for vignettes
3700 (home-page "https://github.com/slowkow/ggrepel")
3701 (synopsis "Repulsive text and label geometries for ggplot2")
3703 "This package provides text and label geometries for ggplot2 that help to
3704 avoid overlapping text labels. Labels repel away from each other and away
3705 from the data points.")
3706 (license license:gpl3)))
3708 (define-public r-corrplot
3715 (uri (cran-uri "corrplot" version))
3718 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3719 (build-system r-build-system)
3720 (home-page "https://github.com/taiyun/corrplot")
3721 (synopsis "Visualization of a correlation matrix")
3723 "This package provides a graphical display of a correlation matrix or
3724 general matrix. It also contains some algorithms to do matrix reordering. In
3725 addition, corrplot is good at details, including choosing color, text labels,
3726 color labels, layout, etc.")
3727 ;; Any version of the GPL
3728 (license license:gpl2+)))
3730 (define-public r-stringdist
3732 (name "r-stringdist")
3737 (uri (cran-uri "stringdist" version))
3739 (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb"))))
3740 (build-system r-build-system)
3741 (home-page "https://github.com/markvanderloo/stringdist")
3742 (synopsis "Approximate string matching and string distance functions")
3744 "This package implements an approximate string matching version of R's
3745 native @code{match} function. It can calculate various string distances based
3746 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3747 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3748 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3749 can be computed between character vectors while taking proper care of encoding
3750 or between integer vectors representing generic sequences.")
3751 (license license:gpl3+)))
3753 (define-public r-ucminf
3760 (uri (cran-uri "ucminf" version))
3763 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3764 (build-system r-build-system)
3765 (native-inputs `(("gfortran" ,gfortran)))
3766 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3767 (synopsis "General-purpose unconstrained non-linear optimization")
3769 "This package provides an implementation of an algorithm for
3770 general-purpose unconstrained non-linear optimization. The algorithm is of
3771 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3772 search with a trust region type monitoring of the input to the line search
3773 algorithm. The interface of @code{ucminf} is designed for easy interchange
3774 with the package @code{optim}.")
3775 (license license:gpl2+)))
3777 (define-public r-useful
3783 (uri (cran-uri "useful" version))
3786 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
3787 (properties `((upstream-name . "useful")))
3788 (build-system r-build-system)
3790 `(("r-assertthat" ,r-assertthat)
3791 ("r-dplyr" ,r-dplyr)
3792 ("r-ggplot2" ,r-ggplot2)
3793 ("r-magrittr" ,r-magrittr)
3794 ("r-matrix" ,r-matrix)
3796 ("r-purrr" ,r-purrr)
3797 ("r-scales" ,r-scales)))
3798 (home-page "https://github.com/jaredlander/useful")
3799 (synopsis "Collection of handy, useful functions")
3800 (description "This package provides a set of little functions that have been
3801 found useful to do little odds and ends such as plotting the results of K-means
3802 clustering, substituting special text characters, viewing parts of a
3803 @code{data.frame}, constructing formulas from text and building design and
3804 response matrices.")
3805 (license license:bsd-3)))
3807 (define-public r-ordinal
3810 (version "2019.12-10")
3814 (uri (cran-uri "ordinal" version))
3817 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3818 (build-system r-build-system)
3820 `(("r-mass" ,r-mass)
3821 ("r-matrix" ,r-matrix)
3822 ("r-numderiv" ,r-numderiv)
3823 ("r-ucminf" ,r-ucminf)))
3824 (home-page "https://github.com/runehaubo/ordinal")
3825 (synopsis "Regression models for ordinal data")
3827 "This package provides an implementation of cumulative link (mixed)
3828 models also known as ordered regression models, proportional odds models,
3829 proportional hazards models for grouped survival times and ordered models.
3830 Estimation is via maximum likelihood and mixed models are fitted with the
3831 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3832 (license license:gpl2+)))
3834 (define-public r-jomo
3841 (uri (cran-uri "jomo" version))
3844 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
3845 (build-system r-build-system)
3847 `(("r-lme4" ,r-lme4)
3849 ("r-ordinal" ,r-ordinal)
3850 ("r-survival" ,r-survival)))
3851 (home-page "https://cran.r-project.org/web/packages/jomo/")
3852 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3854 "Similarly to Schafer's package pan, jomo is a package for multilevel
3855 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3856 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3857 possibility of handling binary and categorical data through latent normal
3858 variables, the option to use cluster-specific covariance matrices and to
3859 impute compatibly with the substantive model.")
3860 (license license:gpl2)))
3862 (define-public r-pan
3869 (uri (cran-uri "pan" version))
3872 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3873 (build-system r-build-system)
3874 (native-inputs `(("gfortran" ,gfortran)))
3875 (home-page "https://cran.r-project.org/web/packages/pan/")
3876 (synopsis "Multiple imputation for multivariate panel or clustered data")
3878 "This package implements multiple imputation for multivariate panel or
3880 (license license:gpl3)))
3882 (define-public r-mitml
3889 (uri (cran-uri "mitml" version))
3892 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3893 (build-system r-build-system)
3895 `(("r-haven" ,r-haven)
3898 (home-page "https://cran.r-project.org/web/packages/mitml/")
3899 (synopsis "Tools for multiple imputation in multilevel modeling")
3901 "This package provides tools for multiple imputation of missing data in
3902 multilevel modeling. It includes a user-friendly interface to the packages
3903 pan and jomo, and several functions for visualization, data management and the
3904 analysis of multiply imputed data sets.")
3905 (license license:gpl2+)))
3907 (define-public r-mice
3914 (uri (cran-uri "mice" version))
3917 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
3918 (build-system r-build-system)
3920 `(("r-broom" ,r-broom)
3921 ("r-dplyr" ,r-dplyr)
3922 ("r-generics" ,r-generics)
3923 ("r-lattice" ,r-lattice)
3925 ("r-tidyr" ,r-tidyr)))
3926 (home-page "https://cran.r-project.org/web/packages/mice/")
3927 (synopsis "Multivariate imputation by chained equations")
3929 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3930 implemented by the MICE algorithm as described in @url{Van Buuren and
3931 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3932 variable has its own imputation model. Built-in imputation models are
3933 provided for continuous data (predictive mean matching, normal), binary
3934 data (logistic regression), unordered categorical data (polytomous logistic
3935 regression) and ordered categorical data (proportional odds). MICE can also
3936 impute continuous two-level data (normal model, pan, second-level variables).
3937 Passive imputation can be used to maintain consistency between variables.
3938 Various diagnostic plots are available to inspect the quality of the
3940 ;; Any of these two versions.
3941 (license (list license:gpl2 license:gpl3))))
3943 (define-public r-truncnorm
3945 (name "r-truncnorm")
3950 (uri (cran-uri "truncnorm" version))
3953 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3954 (build-system r-build-system)
3955 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3956 (synopsis "Truncated normal distribution")
3957 (description "This package provides functions for the truncated normal
3958 distribution with mean equal to @code{mean} and standard deviation equal to
3959 @code{sd}. It includes density, distribution, quantile, and expected value
3960 functions, as well as a random generation function.")
3961 (license license:gpl2)))
3963 (define-public r-rsolnp
3970 (uri (cran-uri "Rsolnp" version))
3973 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3974 (properties `((upstream-name . "Rsolnp")))
3975 (build-system r-build-system)
3977 `(("r-truncnorm" ,r-truncnorm)))
3978 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3979 (synopsis "General non-linear optimization")
3980 (description "The Rsolnp package implements a general non-linear augmented
3981 Lagrange multiplier method solver, a @dfn{sequential quadratic
3982 programming} (SQP) based solver).")
3983 ;; Any version of the GPL.
3984 (license license:gpl2+)))
3986 (define-public r-hardyweinberg
3988 (name "r-hardyweinberg")
3993 (uri (cran-uri "HardyWeinberg" version))
3996 "1qn1bbzfk4w3mqrzisshw5xx7x249sgmj6qdi39lkqb58a4mf4kh"))))
3997 (properties `((upstream-name . "HardyWeinberg")))
3998 (build-system r-build-system)
4000 `(("r-mice" ,r-mice)
4002 ("r-rsolnp" ,r-rsolnp)))
4003 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4004 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4006 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4007 diallelic genetic marker data. All classical tests (chi-square, exact,
4008 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4009 included in the package, as well as functions for power computation and for
4010 the simulation of marker data under equilibrium and disequilibrium. Routines
4011 for dealing with markers on the X-chromosome are included. Functions for
4012 testing equilibrium in the presence of missing data by using multiple
4013 imputation are also provided. Implements several graphics for exploring the
4014 equilibrium status of a large set of diallelic markers: ternary plots with
4015 acceptance regions, log-ratio plots and Q-Q plots.")
4016 (license license:gpl2+)))
4025 (uri (cran-uri "sm" version))
4028 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4029 (build-system r-build-system)
4030 (native-inputs `(("gfortran" ,gfortran)))
4031 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4032 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4034 "This is software accompanying the book 'Applied Smoothing Techniques for
4035 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4036 University Press. It provides smoothing methods for nonparametric regression
4037 and density estimation")
4038 (license license:gpl2+)))
4040 (define-public r-venndiagram
4042 (name "r-venndiagram")
4046 (uri (cran-uri "VennDiagram" version))
4049 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4050 (properties `((upstream-name . "VennDiagram")))
4051 (build-system r-build-system)
4053 `(("r-futile-logger" ,r-futile-logger)))
4054 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4055 (synopsis "Generate High-Resolution Venn and Euler Plots")
4057 "This package provides a set of functions to generate high-resolution
4058 Venn and Euler plots. It includes handling for several special cases,
4059 including two-case scaling, and extensive customization of plot shape and
4061 (license license:gpl2+)))
4063 (define-public r-vioplot
4070 (uri (cran-uri "vioplot" version))
4073 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4074 (build-system r-build-system)
4079 `(("r-knitr" ,r-knitr)))
4080 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4081 (synopsis "Violin plot")
4083 "This package provides a violin plot, which is a combination of a box
4084 plot and a kernel density plot.")
4085 (license license:bsd-3)))
4087 (define-public r-rsofia
4093 ;; This package has been removed from CRAN, so we can
4094 ;; only fetch it from the archives.
4095 (uri (string-append "https://cran.r-project.org/src/"
4096 "contrib/Archive/RSofia/RSofia_"
4100 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4101 (properties `((upstream-name . "RSofia")))
4102 (build-system r-build-system)
4104 `(("r-rcpp" ,r-rcpp)))
4105 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4106 (synopsis "Port of sofia-ml to R")
4107 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4108 suite of fast incremental algorithms for machine learning that can be used for
4109 training models for classification or ranking.")
4110 (license license:asl2.0)))
4112 (define-public r-xts
4119 (uri (cran-uri "xts" version))
4122 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4123 (build-system r-build-system)
4124 (propagated-inputs `(("r-zoo" ,r-zoo)))
4125 (home-page "https://github.com/joshuaulrich/xts")
4126 (synopsis "Extensible time series")
4128 "This package provides for uniform handling of R's different time-based
4129 data classes by extending @code{zoo}, maximizing native format information
4130 preservation and allowing for user-level customization and extension, while
4131 simplifying cross-class interoperability.")
4132 (license license:gpl2+)))
4134 (define-public r-performanceanalytics
4136 (name "r-performanceanalytics")
4141 (uri (cran-uri "PerformanceAnalytics" version))
4144 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4146 `((upstream-name . "PerformanceAnalytics")))
4147 (build-system r-build-system)
4149 `(("r-quadprog" ,r-quadprog)
4152 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4153 (synopsis "Econometric tools for performance and risk analysis")
4154 (description "This is a collection of econometric functions for
4155 performance and risk analysis. This package aims to aid practitioners and
4156 researchers in utilizing the latest research in analysis of non-normal return
4157 streams. In general, it is most tested on return (rather than price) data on
4158 a regular scale, but most functions will work with irregular return data as
4159 well, and increasing numbers of functions will work with P&L or price data
4161 ;; Either version may be picked.
4162 (license (list license:gpl2 license:gpl3))))
4164 (define-public r-laeken
4171 (uri (cran-uri "laeken" version))
4174 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4175 (build-system r-build-system)
4177 `(("r-boot" ,r-boot)
4178 ("r-mass" ,r-mass)))
4179 (home-page "https://cran.r-project.org/web/packages/laeken/")
4180 (synopsis "Estimation of indicators on social exclusion and poverty")
4181 (description "This package provides tools for the estimation of indicators
4182 on social exclusion and poverty, as well as an implementation of Pareto tail
4183 modeling for empirical income distributions.")
4184 (license license:gpl2+)))
4186 (define-public r-vcd
4193 (uri (cran-uri "vcd" version))
4196 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
4197 (build-system r-build-system)
4199 `(("r-colorspace" ,r-colorspace)
4200 ("r-lmtest" ,r-lmtest)
4201 ("r-mass" ,r-mass)))
4202 (home-page "https://cran.r-project.org/web/packages/vcd/")
4203 (synopsis "Visualizing categorical data")
4204 (description "This package provides visualization techniques, data sets,
4205 summary and inference procedures aimed particularly at categorical data.
4206 Special emphasis is given to highly extensible grid graphics. The package was
4207 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4208 Friendly and is now the main support package for a new book, \"Discrete Data
4209 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4210 (license license:gpl2)))
4212 (define-public r-ica
4219 (uri (cran-uri "ica" version))
4222 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4223 (build-system r-build-system)
4224 (home-page "https://cran.r-project.org/web/packages/ica/")
4225 (synopsis "Independent component analysis")
4226 (description "This package provides tools for @dfn{Independent Component
4227 Analysis} (ICA) using various algorithms: FastICA,
4228 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4229 of Eigenmatrices} (JADE).")
4230 (license license:gpl2+)))
4232 (define-public r-dtw
4239 (uri (cran-uri "dtw" version))
4242 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4243 (build-system r-build-system)
4244 (propagated-inputs `(("r-proxy" ,r-proxy)))
4245 (home-page "http://dtw.r-forge.r-project.org/")
4246 (synopsis "Dynamic Time Warping Algorithms")
4247 (description "This package provides a comprehensive implementation of
4248 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4249 optimal (least cumulative distance) alignment between points of two time
4250 series. Common DTW variants covered include local (slope) and global (window)
4251 constraints, subsequence matches, arbitrary distance definitions,
4252 normalizations, minimum variance matching, and so on.")
4253 (license license:gpl2+)))
4255 (define-public r-sdmtools
4258 (version "1.1-221.2")
4262 (uri (cran-uri "SDMTools" version))
4265 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4266 (properties `((upstream-name . "SDMTools")))
4267 (build-system r-build-system)
4268 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4269 (home-page "https://www.rforge.net/SDMTools/")
4270 (synopsis "Species distribution modelling tools")
4271 (description "This package provides a set of tools for post processing
4272 the outcomes of species distribution modeling exercises. It includes novel
4273 methods for comparing models and tracking changes in distributions through
4274 time. It further includes methods for visualizing outcomes, selecting
4275 thresholds, calculating measures of accuracy and landscape fragmentation
4277 (license license:gpl3+)))
4279 (define-public r-scatterplot3d
4281 (name "r-scatterplot3d")
4286 (uri (cran-uri "scatterplot3d" version))
4289 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4290 (build-system r-build-system)
4291 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4292 (synopsis "3D scatter plot")
4293 (description "This package provides an implementation of scatter plots for
4294 plotting. a three dimensional point cloud.")
4295 (license license:gpl2)))
4297 (define-public r-ggridges
4304 (uri (cran-uri "ggridges" version))
4307 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4308 (build-system r-build-system)
4310 `(("r-ggplot2" ,r-ggplot2)
4312 ("r-scales" ,r-scales)
4313 ("r-withr" ,r-withr)))
4314 (home-page "https://github.com/clauswilke/ggridges")
4315 (synopsis "Ridgeline plots in ggplot2")
4317 "Ridgeline plots provide a convenient way of visualizing changes in
4318 distributions over time or space. This package enables the creation of such
4319 plots in @code{ggplot2}.")
4320 (license license:gpl2)))
4322 (define-public r-ggjoy
4329 (uri (cran-uri "ggjoy" version))
4332 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4333 (build-system r-build-system)
4335 `(("r-ggplot2" ,r-ggplot2)
4336 ("r-ggridges" ,r-ggridges)))
4337 (home-page "https://github.com/clauswilke/ggjoy")
4338 (synopsis "Joyplots in ggplot2")
4339 (description "Joyplots provide a convenient way of visualizing changes in
4340 distributions over time or space. This package enables the creation of such
4341 plots in @code{ggplot2}.")
4342 (license license:gpl2)))
4344 (define-public r-cli
4351 (uri (cran-uri "cli" version))
4354 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4355 (build-system r-build-system)
4357 `(("r-assertthat" ,r-assertthat)
4358 ("r-crayon" ,r-crayon)
4359 ("r-fansi" ,r-fansi)
4360 ("r-glue" ,r-glue)))
4361 (home-page "https://github.com/r-lib/cli#readme")
4362 (synopsis "Helpers for developing command line interfaces")
4363 (description "This package provides a suite of tools designed to build
4364 attractive command line interfaces (CLIs). It includes tools for drawing
4365 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4366 (license license:expat)))
4368 (define-public r-argparser
4370 (name "r-argparser")
4375 (uri (cran-uri "argparser" version))
4378 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4379 (build-system r-build-system)
4380 (home-page "https://bitbucket.org/djhshih/argparser")
4381 (synopsis "Command-line argument parser")
4383 "This package provides a cross-platform command-line argument parser
4384 written purely in R with no external dependencies. It is useful with the
4385 Rscript front-end and facilitates turning an R script into an executable
4387 (license license:gpl3+)))
4389 (define-public r-debugme
4396 (uri (cran-uri "debugme" version))
4399 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4400 (build-system r-build-system)
4401 (propagated-inputs `(("r-crayon" ,r-crayon)))
4402 (home-page "https://github.com/r-lib/debugme#readme")
4403 (synopsis "Debug R packages")
4405 "This package allows the user to specify debug messages as special string
4406 constants, and control debugging of packages via environment variables.")
4407 (license license:expat)))
4409 (define-public r-processx
4416 (uri (cran-uri "processx" version))
4418 (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a"))))
4419 (build-system r-build-system)
4423 (home-page "https://github.com/r-lib/processx3")
4424 (synopsis "Execute and control system processes")
4426 "This package provides portable tools to run system processes in the
4427 background. It can check if a background process is running; wait on a
4428 background process to finish; get the exit status of finished processes; kill
4429 background processes and their children; restart processes. It can read the
4430 standard output and error of the processes, using non-blocking connections.
4431 @code{processx} can poll a process for standard output or error, with a
4432 timeout. It can also poll several processes at once.")
4433 (license license:expat)))
4435 (define-public r-tsp
4442 (uri (cran-uri "TSP" version))
4445 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4446 (properties `((upstream-name . "TSP")))
4447 (build-system r-build-system)
4448 (propagated-inputs `(("r-foreach" ,r-foreach)))
4449 (home-page "https://cran.r-project.org/web/packages/TSP/")
4450 (synopsis "Traveling salesperson problem (TSP)")
4451 (description "This package provides basic infrastructure and some
4452 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4453 traveling salesman problem).")
4454 (license license:gpl3)))
4456 (define-public r-qap
4463 (uri (cran-uri "qap" version))
4466 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4467 (build-system r-build-system)
4468 (native-inputs `(("gfortran" ,gfortran)))
4469 (home-page "https://cran.r-project.org/web/packages/qap/")
4470 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4471 (description "This package implements heuristics for the @dfn{quadratic
4472 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4474 (license license:gpl3)))
4476 (define-public r-gclus
4483 (uri (cran-uri "gclus" version))
4486 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4487 (build-system r-build-system)
4488 (propagated-inputs `(("r-cluster" ,r-cluster)))
4489 (home-page "https://cran.r-project.org/web/packages/gclus/")
4490 (synopsis "Clustering graphics")
4491 (description "This package orders panels in scatterplot matrices and
4492 parallel coordinate displays by some merit index. It contains various indices
4493 of merit, ordering functions, and enhanced versions of @code{pairs} and
4494 @code{parcoord} which color panels according to their merit level.")
4495 (license license:gpl2+)))
4497 (define-public r-webshot
4504 (uri (cran-uri "webshot" version))
4507 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4508 (build-system r-build-system)
4510 `(("r-callr" ,r-callr)
4511 ("r-jsonlite" ,r-jsonlite)
4512 ("r-magrittr" ,r-magrittr)))
4513 (home-page "https://github.com/wch/webshot/")
4514 (synopsis "Take screenshots of web pages")
4516 "Webshot makes it easy to take screenshots of web pages from within R.
4517 It can also run Shiny applications locally and take screenshots of the
4518 application; and it can render and screenshot static as well as interactive R
4519 Markdown documents.")
4520 (license license:gpl2)))
4522 (define-public r-seriation
4524 (name "r-seriation")
4529 (uri (cran-uri "seriation" version))
4532 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4533 (build-system r-build-system)
4535 `(("r-cluster" ,r-cluster)
4536 ("r-colorspace" ,r-colorspace)
4537 ("r-dendextend" ,r-dendextend)
4538 ("r-gclus" ,r-gclus)
4539 ("r-gplots" ,r-gplots)
4542 ("r-registry" ,r-registry)
4544 (native-inputs `(("gfortran" ,gfortran)))
4545 (home-page "https://s2.smu.edu/IDA/seriation/")
4546 (synopsis "Infrastructure for ordering objects using seriation")
4548 "This package provides infrastructure for seriation with an
4549 implementation of several seriation/sequencing techniques to reorder matrices,
4550 dissimilarity matrices, and dendrograms. It also provides (optimally)
4551 reordered heatmaps, color images and clustering visualizations like
4552 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4554 (license license:gpl3)))
4556 (define-public r-xfun
4563 (uri (cran-uri "xfun" version))
4565 (base32 "1zd5qi1rrz3b1lpisapa2yscanz39ghaamf28g7aq3z9ai2a2ymj"))))
4566 (build-system r-build-system)
4567 ;; knitr itself depends on xfun
4570 `(("r-knitr" ,r-knitr)))
4571 (home-page "https://github.com/yihui/xfun")
4572 (synopsis "Miscellaneous functions")
4574 "This package provides miscellaneous functions commonly used in other
4575 packages maintained by Yihui Xie.")
4576 (license license:expat)))
4578 (define-public r-utf8
4585 (uri (cran-uri "utf8" version))
4588 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4589 (build-system r-build-system)
4590 (home-page "https://github.com/patperry/r-utf8")
4591 (synopsis "Unicode text processing")
4593 "This package provides tools to process and print UTF-8 encoded
4594 international text (Unicode). Input, validate, normalize, encode, format, and
4596 (license license:asl2.0)))
4598 (define-public r-zeallot
4605 (uri (cran-uri "zeallot" version))
4608 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4609 (build-system r-build-system)
4610 (home-page "https://github.com/nteetor/zeallot")
4611 (synopsis "Multiple, unpacking, and destructuring assignment")
4613 "This package provides a @code{%<-%} operator to perform multiple,
4614 unpacking, and destructuring assignment in R. The operator unpacks the
4615 right-hand side of an assignment into multiple values and assigns these values
4616 to variables on the left-hand side of the assignment.")
4617 (license license:expat)))
4619 (define-public r-vctrs
4626 (uri (cran-uri "vctrs" version))
4629 "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
4630 (build-system r-build-system)
4632 `(("r-digest" ,r-digest)
4633 ("r-ellipsis" ,r-ellipsis)
4635 ("r-rlang" ,r-rlang)))
4637 `(("r-knitr" ,r-knitr)))
4638 (home-page "https://github.com/r-lib/vctrs")
4639 (synopsis "Vector helpers")
4641 "There are three main goals to the @code{vctrs} package:
4644 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4645 @code{length()} and @code{class()}. These definitions are paired with a
4646 framework for type-coercion and size-recycling.
4647 @item To define type- and size-stability as desirable function properties, use
4648 them to analyse existing base function, and to propose better alternatives.
4649 This work has been particularly motivated by thinking about the ideal
4650 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4651 @item To provide a new @code{vctr} base class that makes it easy to create new
4652 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4653 a few new @code{vctrs} generics, making implementation considerably simpler
4656 (license license:gpl3)))
4658 (define-public r-pillar
4665 (uri (cran-uri "pillar" version))
4668 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4669 (build-system r-build-system)
4672 ("r-crayon" ,r-crayon)
4673 ("r-ellipsis" ,r-ellipsis)
4674 ("r-fansi" ,r-fansi)
4675 ("r-lifecycle" ,r-lifecycle)
4676 ("r-rlang" ,r-rlang)
4678 ("r-vctrs" ,r-vctrs)))
4679 (home-page "https://github.com/r-lib/pillar")
4680 (synopsis "Coloured formatting for columns")
4682 "This package provides a @code{pillar} generic designed for formatting
4683 columns of data using the full range of colours provided by modern
4685 (license license:gpl3)))
4687 (define-public r-uuid
4694 (uri (cran-uri "uuid" version))
4697 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4698 (build-system r-build-system)
4699 (home-page "https://www.rforge.net/uuid")
4700 (synopsis "Tools for generating and handling of UUIDs")
4702 "This package provides tools for generating and handling of
4703 @dfn{Universally Unique Identifiers} (UUIDs).")
4704 (license license:expat)))
4706 (define-public r-tinytex
4713 (uri (cran-uri "tinytex" version))
4716 "0zbhzxxjlkdj9byxyab477p7cnws5y87nyg989lkzarxdc7dglza"))))
4717 (build-system r-build-system)
4719 `(("r-xfun" ,r-xfun)))
4720 (home-page "https://github.com/yihui/tinytex")
4721 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4723 "This package provides helper functions to install and maintain the LaTeX
4724 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4725 easy-to-maintain version of TeX Live. This package also contains helper
4726 functions to compile LaTeX documents, and install missing LaTeX packages
4728 (license license:expat)))
4730 (define-public r-network
4737 (uri (cran-uri "network" version))
4740 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4741 (build-system r-build-system)
4743 `(("r-magrittr" ,r-magrittr)
4744 ("r-tibble" ,r-tibble)))
4745 (home-page "https://statnet.org/")
4746 (synopsis "Classes for relational data")
4748 "This package provides tools to create and modify network objects. The
4749 @code{network} class can represent a range of relational data types, and
4750 supports arbitrary vertex/edge/graph attributes.")
4751 (license license:gpl2+)))
4753 (define-public r-stabs
4760 (uri (cran-uri "stabs" version))
4763 "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
4764 (build-system r-build-system)
4765 (home-page "https://github.com/hofnerb/stabs")
4766 (synopsis "Stability selection with error control")
4768 "This package provides resampling procedures to assess the stability of
4769 selected variables with additional finite sample error control for
4770 high-dimensional variable selection procedures such as Lasso or boosting.
4771 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
4772 complementary pairs stability selection with improved error bounds
4773 (Shah & Samworth, 2013) are implemented. The package can be combined with
4774 arbitrary user specified variable selection approaches.")
4775 (license license:gpl2)))
4777 (define-public r-statnet-common
4779 (name "r-statnet-common")
4784 (uri (cran-uri "statnet.common" version))
4787 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4789 `((upstream-name . "statnet.common")))
4790 (build-system r-build-system)
4792 `(("r-coda" ,r-coda)))
4793 (home-page "https://statnet.org")
4794 (synopsis "R scripts and utilities used by the Statnet software")
4795 (description "This package provides non-statistical utilities used by the
4796 software developed by the Statnet Project.")
4797 (license license:gpl3)))
4799 (define-public r-statcheck
4801 (name "r-statcheck")
4806 (uri (cran-uri "statcheck" version))
4809 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4810 (build-system r-build-system)
4812 `(("r-ggplot2" ,r-ggplot2)
4814 ("r-rmarkdown" ,r-rmarkdown)))
4815 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4816 (synopsis "Extract statistics from articles and recompute p-values")
4817 (description "This package can automatically extract statistical
4818 null-hypothesis significant testing (NHST) results from articles and recompute
4819 the p-values based on the reported test statistic and degrees of freedom to
4820 detect possible inconsistencies.")
4821 (license license:gpl2)))
4823 (define-public r-sna
4830 (uri (cran-uri "sna" version))
4833 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4834 (build-system r-build-system)
4836 `(("r-network" ,r-network)
4837 ("r-statnet-common" ,r-statnet-common)))
4838 (home-page "https://statnet.org")
4839 (synopsis "Tools for social network analysis")
4841 "This package provides a range of tools for social network analysis,
4842 including node and graph-level indices, structural distance and covariance
4843 methods, structural equivalence detection, network regression, random graph
4844 generation, and 2D/3D network visualization.")
4845 (license license:gpl2+)))
4847 (define-public r-tfisher
4854 (uri (cran-uri "TFisher" version))
4857 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4858 (properties `((upstream-name . "TFisher")))
4859 (build-system r-build-system)
4861 `(("r-matrix" ,r-matrix)
4862 ("r-mvtnorm" ,r-mvtnorm)
4864 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4865 (synopsis "Optimal thresholding Fisher's p-value combination method")
4867 "This package provides the @dfn{cumulative distribution function} (CDF),
4868 quantile, and statistical power calculator for a collection of thresholding
4869 Fisher's p-value combination methods, including Fisher's p-value combination
4870 method, truncated product method and, in particular, soft-thresholding
4871 Fisher's p-value combination method which is proven to be optimal in some
4872 context of signal detection. The p-value calculator for the omnibus version
4873 of these tests are also included.")
4874 (license license:gpl2)))
4876 (define-public r-ttr
4883 (uri (cran-uri "TTR" version))
4886 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
4887 (properties `((upstream-name . "TTR")))
4888 (build-system r-build-system)
4890 `(("r-curl" ,r-curl)
4893 (home-page "https://github.com/joshuaulrich/TTR")
4894 (synopsis "Technical trading rules")
4896 "This package provides functions and data to construct technical trading
4898 (license license:gpl2)))
4900 (define-public r-leaps
4907 (uri (cran-uri "leaps" version))
4910 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4911 (build-system r-build-system)
4912 (native-inputs `(("gfortran" ,gfortran)))
4913 (home-page "https://cran.r-project.org/web/packages/leaps/")
4914 (synopsis "Regression subset selection")
4916 "This package provides tools for regression subset selection, including
4917 exhaustive search.")
4918 (license license:gpl2+)))
4920 (define-public r-splus2r
4927 (uri (cran-uri "splus2R" version))
4930 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4931 (properties `((upstream-name . "splus2R")))
4932 (build-system r-build-system)
4933 (native-inputs `(("gfortran" ,gfortran)))
4934 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4935 (synopsis "Supplemental S-PLUS functionality in R")
4937 "Currently there are many functions in S-PLUS that are missing in R. To
4938 facilitate the conversion of S-PLUS packages to R packages, this package
4939 provides some missing S-PLUS functionality in R.")
4940 (license license:gpl2)))
4942 (define-public r-ifultools
4944 (name "r-ifultools")
4949 (uri (cran-uri "ifultools" version))
4952 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4953 (build-system r-build-system)
4955 `(("r-mass" ,r-mass)
4956 ("r-splus2r" ,r-splus2r)))
4957 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4958 (synopsis "Insightful research tools")
4959 (description "This package provides C code used by the wmtsa, fractal, and
4961 (license license:gpl2)))
4963 (define-public r-sapa
4970 (uri (cran-uri "sapa" version))
4973 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4974 (build-system r-build-system)
4976 `(("r-ifultools" ,r-ifultools)
4977 ("r-splus2r" ,r-splus2r)))
4978 (home-page "https://cran.r-project.org/web/packages/sapa/")
4979 (synopsis "Spectral analysis for physical applications")
4980 (description "This package provides software for the book Spectral
4981 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4982 Cambridge University Press, 1993.")
4983 (license license:gpl2)))
4985 (define-public r-aggregation
4987 (name "r-aggregation")
4992 (uri (cran-uri "aggregation" version))
4995 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4996 (build-system r-build-system)
4997 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4998 (synopsis "Methods for p-value aggregation")
5000 "This package contains functionality for performing the following methods
5001 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5002 Fisher's method), and Sidak correction.")
5003 (license license:gpl3)))
5005 (define-public r-quantmod
5012 (uri (cran-uri "quantmod" version))
5015 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
5016 (build-system r-build-system)
5018 `(("r-curl" ,r-curl)
5022 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5023 (synopsis "Quantitative financial modelling framework")
5024 (description "This package provides a quantitative financial modelling
5025 framework to allow users to specify, build, trade, and analyse quantitative
5026 financial trading strategies.")
5027 (license license:gpl3)))
5029 (define-public r-tseries
5036 (uri (cran-uri "tseries" version))
5039 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
5040 (build-system r-build-system)
5042 `(("r-quadprog" ,r-quadprog)
5043 ("r-quantmod" ,r-quantmod)
5046 `(("gfortran" ,gfortran)))
5047 (home-page "https://cran.r-project.org/web/packages/tseries/")
5048 (synopsis "Time series analysis and computational finance")
5050 "This package provides functions relating to time series analysis and
5051 computational finance.")
5052 (license license:gpl2)))
5054 (define-public r-wmtsa
5061 (uri (cran-uri "wmtsa" version))
5064 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5065 (build-system r-build-system)
5067 `(("r-ifultools" ,r-ifultools)
5069 ("r-splus2r" ,r-splus2r)))
5070 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5071 (synopsis "Wavelet methods for time series analysis")
5073 "This package provides software to accompany the book \"Wavelet Methods
5074 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5075 University Press, 2000.")
5076 (license license:gpl2)))
5078 (define-public r-tsa
5085 (uri (cran-uri "TSA" version))
5088 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5089 (properties `((upstream-name . "TSA")))
5090 (build-system r-build-system)
5092 `(("r-leaps" ,r-leaps)
5093 ("r-locfit" ,r-locfit)
5095 ("r-tseries" ,r-tseries)))
5096 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5097 (synopsis "Time series analysis")
5099 "This package contains R functions and datasets detailed in the book
5100 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5101 Cryer and Kung-Sik Chan.")
5102 (license license:gpl2+)))
5104 (define-public r-extradistr
5106 (name "r-extradistr")
5111 (uri (cran-uri "extraDistr" version))
5114 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5115 (properties `((upstream-name . "extraDistr")))
5116 (build-system r-build-system)
5118 `(("r-rcpp" ,r-rcpp)))
5119 (home-page "https://github.com/twolodzko/extraDistr")
5120 (synopsis "Additional univariate and multivariate distributions")
5122 "This package implements density, distribution functions, quantile
5123 functions and random generation functions for a large number of univariate and
5124 multivariate distributions.")
5125 (license license:gpl2)))
5127 (define-public r-fractal
5134 (uri (cran-uri "fractal" version))
5137 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5138 (build-system r-build-system)
5140 `(("r-ifultools" ,r-ifultools)
5143 ("r-scatterplot3d" ,r-scatterplot3d)
5144 ("r-splus2r" ,r-splus2r)
5145 ("r-wmtsa" ,r-wmtsa)))
5146 (home-page "https://cran.r-project.org/web/packages/fractal/")
5147 (synopsis "Fractal time series modeling and analysis")
5149 "This package provides tools for stochastic fractal and deterministic
5150 chaotic time series analysis.")
5151 (license license:gpl2)))
5153 (define-public r-urca
5160 (uri (cran-uri "urca" version))
5163 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5164 (build-system r-build-system)
5165 (propagated-inputs `(("r-nlme" ,r-nlme)))
5166 (native-inputs `(("gfortran" ,gfortran)))
5167 (home-page "https://cran.r-project.org/web/packages/urca/")
5168 (synopsis "Unit root and cointegration tests for time series data")
5170 "This package provides unit root and cointegration tests encountered in
5171 applied econometric analysis.")
5172 (license license:gpl2+)))
5174 (define-public r-cubature
5181 (uri (cran-uri "cubature" version))
5184 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5185 (build-system r-build-system)
5187 `(("r-rcpp" ,r-rcpp)))
5189 `(("r-knitr" ,r-knitr)))
5190 (home-page "https://github.com/bnaras/cubature")
5191 (synopsis "Adaptive multivariate integration over hypercubes")
5193 "This package is an R wrapper around the cubature C library for adaptive
5194 multivariate integration over hypercubes. This version provides both
5195 @code{hcubature} and @code{pcubature} routines in addition to a vector
5197 ;; The included cubature C library is released under GPLv2+, but the
5198 ;; wrapper declares the license to be GPLv3+.
5199 (license (list license:gpl2+ license:gpl3+))))
5201 (define-public r-trend
5208 (uri (cran-uri "trend" version))
5211 "0bj40acr1sc7vfxdcsdja3g28xsmrclmgb3n94p89gfjcgp8nv1d"))))
5212 (build-system r-build-system)
5214 `(("r-extradistr" ,r-extradistr)))
5216 `(("gfortran" ,gfortran)))
5217 (home-page "https://cran.r-project.org/web/packages/trend/")
5218 (synopsis "Non-parametric trend tests and change-point detection")
5220 "The analysis of environmental data often requires the detection of
5221 trends and change-points. This package includes tests for trend
5222 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5223 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5224 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5225 correlation trend test), change-point detection (Lanzante's test procedures,
5226 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5227 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5228 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5229 sample Robust Rank-Order Distributional Test.")
5230 (license license:gpl3)))
5232 (define-public r-expm
5239 (uri (cran-uri "expm" version))
5242 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5243 (build-system r-build-system)
5244 (propagated-inputs `(("r-matrix" ,r-matrix)))
5245 (native-inputs `(("gfortran" ,gfortran)))
5246 (home-page "https://r-forge.r-project.org/projects/expm/")
5247 (synopsis "Tools for matrix exponentials and related quantities")
5249 "This package provides tools for the computation of the matrix
5250 exponential, logarithm, square root, and related quantities.")
5251 (license license:gpl2+)))
5253 (define-public r-complexplus
5255 (name "r-complexplus")
5260 (uri (cran-uri "complexplus" version))
5263 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5264 (build-system r-build-system)
5266 `(("r-expm" ,r-expm)
5267 ("r-matrix" ,r-matrix)))
5268 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5269 (synopsis "Functions of complex or real variables")
5271 "This package extends several functions to the complex domain, including
5272 the matrix exponential and logarithm, and the determinant.")
5273 (license license:gpl2)))
5275 (define-public r-phontools
5277 (name "r-phontools")
5282 (uri (cran-uri "phonTools" version))
5285 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5286 (properties `((upstream-name . "phonTools")))
5287 (build-system r-build-system)
5288 (home-page "http://www.santiagobarreda.com/rscripts.html")
5289 (synopsis "Tools for phonetic and acoustic analyses")
5291 "This package contains tools for the organization, display, and analysis
5292 of the sorts of data frequently encountered in phonetics research and
5293 experimentation, including the easy creation of IPA vowel plots, and the
5294 creation and manipulation of WAVE audio files.")
5295 (license license:bsd-2)))
5304 (uri (cran-uri "np" version))
5307 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5308 (build-system r-build-system)
5310 `(("r-boot" ,r-boot)
5311 ("r-cubature" ,r-cubature)
5312 ("r-quadprog" ,r-quadprog)
5313 ("r-quantreg" ,r-quantreg)))
5314 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5315 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5316 (description "This package provides non-parametric (and semi-parametric)
5317 kernel methods that seamlessly handle a mix of continuous, unordered, and
5318 ordered factor data types.")
5319 ;; Any version of the GPL.
5320 (license license:gpl3+)))
5322 (define-public r-powerplus
5324 (name "r-powerplus")
5329 (uri (cran-uri "powerplus" version))
5332 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5333 (build-system r-build-system)
5335 `(("r-complexplus" ,r-complexplus)
5338 ("r-matrix" ,r-matrix)
5339 ("r-phontools" ,r-phontools)))
5340 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5341 (synopsis "Exponentiation operations")
5343 "This package provides tools for the computation of matrix and scalar
5345 (license license:gpl2)))
5347 (define-public r-egg
5354 (uri (cran-uri "egg" version))
5357 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5358 (properties `((upstream-name . "egg")))
5359 (build-system r-build-system)
5361 `(("r-ggplot2" ,r-ggplot2)
5362 ("r-gridextra" ,r-gridextra)
5363 ("r-gtable" ,r-gtable)))
5364 (home-page "https://cran.r-project.org/web/packages/egg")
5365 (synopsis "Extensions for ggplot2")
5367 "This package provides miscellaneous functions to help customize ggplot2
5368 objects. High-level functions are provided to post-process ggplot2 layouts
5369 and allow alignment between plot panels, as well as setting panel sizes to
5370 fixed values. Other functions include a custom @code{geom}, and helper
5371 functions to enforce symmetric scales or add tags to facetted plots.")
5372 (license license:gpl3)))
5374 (define-public r-heatmaply
5376 (name "r-heatmaply")
5381 (uri (cran-uri "heatmaply" version))
5384 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
5385 (build-system r-build-system)
5387 `(("r-assertthat" ,r-assertthat)
5388 ("r-colorspace" ,r-colorspace)
5389 ("r-dendextend" ,r-dendextend)
5391 ("r-ggplot2" ,r-ggplot2)
5392 ("r-htmlwidgets" ,r-htmlwidgets)
5393 ("r-magrittr" ,r-magrittr)
5394 ("r-plotly" ,r-plotly)
5395 ("r-rcolorbrewer" ,r-rcolorbrewer)
5396 ("r-reshape2" ,r-reshape2)
5397 ("r-scales" ,r-scales)
5398 ("r-seriation" ,r-seriation)
5399 ("r-viridis" ,r-viridis)
5400 ("r-webshot" ,r-webshot)))
5402 `(("r-knitr" ,r-knitr)))
5403 (home-page "https://cran.r-project.org/package=heatmaply")
5404 (synopsis "Interactive cluster heat maps using plotly")
5406 "This package enables you to create interactive cluster heatmaps that can
5407 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5408 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5409 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5410 a popular graphical method for visualizing high-dimensional data, in which a
5411 table of numbers is encoded as a grid of colored cells. The rows and columns
5412 of the matrix are ordered to highlight patterns and are often accompanied by
5414 ;; Either version of the license.
5415 (license (list license:gpl2 license:gpl3))))
5424 (uri (cran-uri "h5" version))
5427 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5428 (build-system r-build-system)
5433 `(("which" ,which)))
5435 `(("r-rcpp" ,r-rcpp)))
5436 (home-page "https://github.com/mannau/h5")
5437 (synopsis "Interface to the HDF5 Library")
5439 "This package provides an S4 interface to the HDF5 library supporting
5440 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5441 binary files in a language independent format. The HDF5 format can therefore
5442 be used as an alternative to R's save/load mechanism. Since h5 is able to
5443 access only subsets of stored data it can also handle data sets which do not
5445 (license license:bsd-2)))
5447 (define-public r-cgdsr
5454 (uri (cran-uri "cgdsr" version))
5457 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5458 (build-system r-build-system)
5460 `(("r-httr" ,r-httr)
5461 ("r-r-methodss3" ,r-r-methodss3)
5462 ("r-r-oo" ,r-r-oo)))
5463 (home-page "https://github.com/cBioPortal/cgdsr")
5464 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5466 "This package provides a basic set of R functions for querying the Cancer
5467 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5468 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5469 (license license:lgpl3)))
5471 (define-public r-import
5478 (uri (cran-uri "import" version))
5481 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5482 (build-system r-build-system)
5483 (home-page "https://github.com/smbache/import")
5484 (synopsis "Import mechanism for R")
5486 "This is an alternative mechanism for importing objects from packages.
5487 The syntax allows for importing multiple objects from a package with a single
5488 command in an expressive way. The import package bridges some of the gap
5489 between using @code{library} (or @code{require}) and direct (single-object)
5490 imports. Furthermore the imported objects are not placed in the current
5491 environment. It is also possible to import objects from stand-alone @code{.R}
5493 (license license:expat)))
5495 (define-public r-shinyace
5502 (uri (cran-uri "shinyAce" version))
5505 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5506 (properties `((upstream-name . "shinyAce")))
5507 (build-system r-build-system)
5509 `(("r-shiny" ,r-shiny)
5510 ("r-jsonlite" ,r-jsonlite)))
5511 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5512 (synopsis "Ace editor bindings for Shiny")
5514 "This package provides Ace editor bindings to enable a rich text editing
5515 environment within Shiny.")
5516 (license license:expat)))
5518 (define-public r-randomizr
5520 (name "r-randomizr")
5525 (uri (cran-uri "randomizr" version))
5528 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5529 (properties `((upstream-name . "randomizr")))
5530 (build-system r-build-system)
5532 `(("r-knitr" ,r-knitr)))
5533 (home-page "https://declaredesign.org/r/randomizr/")
5534 (synopsis "Tools for common forms of random assignment and sampling")
5536 "This package provides tools for generating random assignments for common
5537 experimental designs and random samples for common sampling designs.")
5538 (license license:expat)))
5540 (define-public r-base64url
5542 (name "r-base64url")
5547 (uri (cran-uri "base64url" version))
5550 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5551 (build-system r-build-system)
5553 `(("r-backports" ,r-backports)))
5554 (home-page "https://github.com/mllg/base64url")
5555 (synopsis "Fast and URL-safe base64 encoder and decoder")
5557 "This package provides a URL-safe base64 encoder and decoder. In
5558 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5559 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5560 encoder does not fill the string with trailing @code{=}. The resulting
5561 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5562 and thus are safe to use in URLs or for file names. The package also comes
5563 with a simple base32 encoder/decoder suited for case insensitive file
5565 (license license:gpl3)))
5567 (define-public r-radiant-data
5569 (name "r-radiant-data")
5574 (uri (cran-uri "radiant.data" version))
5577 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
5578 (modules '((guix build utils)))
5581 ;; Delete files that are under CC-NC-SA.
5582 (delete-file-recursively "inst/app/tools/help")
5584 (properties `((upstream-name . "radiant.data")))
5585 (build-system r-build-system)
5587 `(("r-base64enc" ,r-base64enc)
5588 ("r-broom" ,r-broom)
5591 ("r-dplyr" ,r-dplyr)
5594 ("r-ggplot2" ,r-ggplot2)
5595 ("r-import" ,r-import)
5596 ("r-jsonlite" ,r-jsonlite)
5597 ("r-knitr" ,r-knitr)
5598 ("r-lubridate" ,r-lubridate)
5599 ("r-magrittr" ,r-magrittr)
5600 ("r-markdown" ,r-markdown)
5602 ("r-patchwork" ,r-patchwork)
5603 ("r-plotly" ,r-plotly)
5604 ("r-psych" ,r-psych)
5605 ("r-randomizr" ,r-randomizr)
5606 ("r-readr" ,r-readr)
5607 ("r-readxl" ,r-readxl)
5608 ("r-rlang" ,r-rlang)
5609 ("r-rmarkdown" ,r-rmarkdown)
5610 ("r-rstudioapi" ,r-rstudioapi)
5611 ("r-scales" ,r-scales)
5612 ("r-shiny" ,r-shiny)
5613 ("r-shinyfiles" ,r-shinyfiles)
5614 ("r-shinyace" ,r-shinyace)
5615 ("r-stringi" ,r-stringi)
5616 ("r-tibble" ,r-tibble)
5617 ("r-tidyr" ,r-tidyr)
5618 ("r-writexl" ,r-writexl)))
5619 (home-page "https://github.com/radiant-rstats/radiant.data")
5620 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5622 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5623 visualizing, summarizing, transforming, and combining data. It also contains
5624 functionality to generate reproducible reports of the analyses conducted in
5626 (license license:agpl3)))
5628 (define-public r-algdesign
5630 (name "r-algdesign")
5635 (uri (cran-uri "AlgDesign" version))
5637 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5638 (properties `((upstream-name . "AlgDesign")))
5639 (build-system r-build-system)
5640 (home-page "https://github.com/jvbraun/AlgDesign")
5641 (synopsis "Algorithmic experimental design")
5643 "This package provides tools to calculate exact and approximate theory
5644 experimental designs for D, A, and I criteria. Very large designs may be
5645 created. Experimental designs may be blocked or blocked designs created from
5646 a candidate list, using several criteria. The blocking can be done when whole
5647 and within plot factors interact.")
5648 (license license:gpl2+)))
5650 (define-public r-signal
5657 (uri (cran-uri "signal" version))
5660 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5661 (build-system r-build-system)
5662 (propagated-inputs `(("r-mass" ,r-mass)))
5663 (native-inputs `(("gfortran" ,gfortran)))
5664 (home-page "https://cran.r-project.org/web/packages/signal/")
5665 (synopsis "Signal processing")
5667 "This package provides a set of signal processing functions originally
5668 written for Matlab and GNU Octave. It includes filter generation utilities,
5669 filtering functions, resampling routines, and visualization of filter models.
5670 It also includes interpolation functions.")
5671 (license license:gpl2)))
5673 (define-public r-gsubfn
5680 (uri (cran-uri "gsubfn" version))
5683 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5684 (build-system r-build-system)
5685 (propagated-inputs `(("r-proto" ,r-proto)))
5686 (home-page "https://code.google.com/archive/p/gsubfn/")
5687 (synopsis "Utilities for strings and function arguments.")
5689 "This package provides @code{gsubfn} which is like @code{gsub} but can
5690 take a replacement function or certain other objects instead of the
5691 replacement string. Matches and back references are input to the replacement
5692 function and replaced by the function output. @code{gsubfn} can be used to
5693 split strings based on content rather than delimiters and for quasi-perl-style
5694 string interpolation. The package also has facilities for translating
5695 formulas to functions and allowing such formulas in function calls instead of
5697 (license license:gpl2+)))
5699 (define-public r-sqldf
5706 (uri (cran-uri "sqldf" version))
5709 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5710 (build-system r-build-system)
5712 `(("r-chron" ,r-chron)
5714 ("r-gsubfn" ,r-gsubfn)
5715 ("r-proto" ,r-proto)
5716 ("r-rsqlite" ,r-rsqlite)))
5717 (home-page "https://github.com/ggrothendieck/sqldf")
5718 (synopsis "Manipulate R data frames using SQL")
5720 "The @code{sqldf} function is typically passed a single argument which is
5721 an SQL select statement where the table names are ordinary R data frame names.
5722 @code{sqldf} transparently sets up a database, imports the data frames into
5723 that database, performs the SQL statement and returns the result using a
5724 heuristic to determine which class to assign to each column of the returned
5725 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5726 used to read filtered files into R even if the original files are larger than
5727 R itself can handle.")
5728 (license license:gpl2)))
5730 (define-public r-abind
5737 (uri (cran-uri "abind" version))
5740 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5741 (build-system r-build-system)
5742 (home-page "https://cran.r-project.org/web/packages/abind/")
5743 (synopsis "Combine multidimensional arrays")
5745 "This package provides tools to combine multidimensional arrays into a
5746 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5747 works with vectors, matrices, and higher-dimensional arrays. It also provides
5748 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5749 extracting and replacing data in arrays.")
5750 (license license:lgpl2.0+)))
5752 (define-public r-prroc
5759 (uri (cran-uri "PRROC" version))
5762 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5763 (properties `((upstream-name . "PRROC")))
5764 (build-system r-build-system)
5765 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5766 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5768 "This package computes the areas under the @dfn{precision-recall} (PR)
5769 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5770 contrast to other implementations, the interpolation between points of the PR
5771 curve is done by a non-linear piecewise function. In addition to the areas
5772 under the curves, the curves themselves can also be computed and plotted by a
5773 specific S3-method.")
5774 (license license:gpl3)))
5776 (define-public r-vim
5783 (uri (cran-uri "VIM" version))
5786 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5787 (properties `((upstream-name . "VIM")))
5788 (build-system r-build-system)
5791 ("r-colorspace" ,r-colorspace)
5792 ("r-data-table" ,r-data-table)
5793 ("r-e1071" ,r-e1071)
5794 ("r-laeken" ,r-laeken)
5795 ("r-magrittr" ,r-magrittr)
5798 ("r-ranger" ,r-ranger)
5800 ("r-robustbase" ,r-robustbase)
5804 `(("r-knitr" ,r-knitr)))
5805 (home-page "https://github.com/alexkowa/VIM")
5806 (synopsis "Visualization and imputation of missing values")
5808 "This package provides tools for the visualization of missing and/or
5809 imputed values are introduced, which can be used for exploring the data and
5810 the structure of the missing and/or imputed values. Depending on this
5811 structure of the missing values, the corresponding methods may help to
5812 identify the mechanism generating the missing values and allows to explore the
5813 data including missing values. In addition, the quality of imputation can be
5814 visually explored using various univariate, bivariate, multiple and
5815 multivariate plot methods.")
5816 (license license:gpl2+)))
5818 (define-public r-fnn
5825 (uri (cran-uri "FNN" version))
5828 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5829 (properties `((upstream-name . "FNN")))
5830 (build-system r-build-system)
5831 (home-page "https://cran.r-project.org/web/packages/FNN")
5832 (synopsis "Fast nearest neighbor search algorithms and applications")
5834 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5835 search algorithms. Related applications including KNN classification,
5836 regression and information measures are implemented.")
5837 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5838 ;; later can be used.
5839 (license license:gpl2+)))
5841 (define-public r-smoother
5848 (uri (cran-uri "smoother" version))
5851 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5852 (build-system r-build-system)
5854 `(("r-ttr" ,r-ttr)))
5855 (home-page "https://cran.r-project.org/web/packages/smoother")
5856 (synopsis "Functions relating to the smoothing of numerical data")
5858 "This package provides a collection of methods for smoothing numerical
5859 data, commencing with a port of the Matlab gaussian window smoothing function.
5860 In addition, several functions typically used in smoothing of financial data
5862 (license license:gpl2)))
5864 (define-public r-riverplot
5866 (name "r-riverplot")
5871 (uri (cran-uri "riverplot" version))
5874 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5875 (build-system r-build-system)
5876 (home-page "https://logfc.wordpress.com")
5877 (synopsis "Sankey or ribbon plots")
5879 "Sankey plots are a type of diagram that is convenient to illustrate how
5880 flow of information, resources etc. separates and joins, much like observing
5881 how rivers split and merge. For example, they can be used to compare
5882 different clusterings. This package provides an implementation of Sankey
5884 (license license:gpl2+)))
5886 (define-public r-dyn
5893 (uri (cran-uri "dyn" version))
5896 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5897 (build-system r-build-system)
5899 `(("r-zoo" ,r-zoo)))
5900 (home-page "https://cran.r-project.org/web/packages/dyn")
5901 (synopsis "Time series regression")
5903 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5904 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5905 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5906 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5907 @code{randomForest::randomForest()} and other regression functions, allowing
5908 those functions to be used with time series including specifications that may
5909 contain lags, diffs and missing values.")
5911 (license license:gpl2+)))
5913 (define-public r-catdap
5920 (uri (cran-uri "catdap" version))
5923 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5924 (build-system r-build-system)
5926 `(("gfortran" ,gfortran)))
5927 (home-page "https://cran.r-project.org/web/packages/catdap/")
5928 (synopsis "Tools for categorical data analysis")
5930 "This package provides functions for analyzing multivariate data.
5931 Dependencies of the distribution of the specified variable (response
5932 variable) to other variables (explanatory variables) are derived and
5933 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5934 (license license:gpl2+)))
5936 (define-public r-arules
5943 (uri (cran-uri "arules" version))
5946 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5947 (build-system r-build-system)
5949 `(("r-matrix" ,r-matrix)))
5950 (home-page "https://github.com/mhahsler/arules")
5951 (synopsis "Mining association rules and frequent itemsets")
5953 "This package provides an infrastructure for representing, manipulating
5954 and analyzing transaction data and patterns (frequent itemsets and association rules).
5955 It also provides C implementations of the association mining algorithms Apriori
5957 (license license:gpl3)))
5959 (define-public r-parsedate
5961 (name "r-parsedate")
5966 (uri (cran-uri "parsedate" version))
5969 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5970 (build-system r-build-system)
5972 `(("r-rematch2" ,r-rematch2)))
5973 (home-page "https://github.com/gaborcsardi/parsedate")
5975 "Recognize and parse dates in various formats")
5977 "This package provides three functions for dealing with dates:
5978 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5979 time formats, @code{parse_date} parses dates in unspecified formats,
5980 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5981 (license license:gpl2)))
5983 (define-public r-abc-data
5990 (uri (cran-uri "abc.data" version))
5993 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5994 (properties `((upstream-name . "abc.data")))
5995 (build-system r-build-system)
5996 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5997 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5999 "This package contains data which are used by functions of the abc
6000 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6001 algorithms for performing parameter estimation, model selection, and
6003 (license license:gpl3+)))
6005 (define-public r-abc
6012 (uri (cran-uri "abc" version))
6015 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6016 (build-system r-build-system)
6018 `(("r-abc-data" ,r-abc-data)
6019 ("r-locfit" ,r-locfit)
6022 ("r-quantreg" ,r-quantreg)))
6023 (home-page "https://cran.r-project.org/web/packages/abc/")
6024 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6026 "This package implements several @dfn{Approximate Bayesian
6027 Computation} (ABC) algorithms for performing parameter estimation, model
6028 selection, and goodness-of-fit. Cross-validation tools are also available for
6029 measuring the accuracy of ABC estimates, and to calculate the
6030 misclassification probabilities of different models.")
6031 (license license:gpl3+)))
6033 (define-public r-zip
6040 (uri (cran-uri "zip" version))
6043 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6044 (build-system r-build-system)
6045 (home-page "https://github.com/gaborcsardi/zip")
6046 (synopsis "Cross-platform Zip compression")
6048 "This package provides a cross-platform Zip compression library for R.
6049 It is a replacement for the @code{zip} function, that does not require any
6050 additional external tools on any platform.")
6051 (license license:cc0)))
6053 (define-public r-openxlsx
6060 (uri (cran-uri "openxlsx" version))
6063 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
6064 (build-system r-build-system)
6066 `(("r-rcpp" ,r-rcpp)
6067 ("r-stringi" ,r-stringi)
6070 `(("r-knitr" ,r-knitr)))
6071 (home-page "https://github.com/awalker89/openxlsx")
6072 (synopsis "Read, write and edit XLSX files")
6074 "This package simplifies the creation of Excel @code{.xlsx} files by
6075 providing a high level interface to writing, styling and editing worksheets.
6076 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6077 and @code{XLConnect} packages with the added benefit of removing the
6078 dependency on Java.")
6079 (license license:gpl3)))
6081 (define-public r-rio
6088 (uri (cran-uri "rio" version))
6091 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6092 (build-system r-build-system)
6094 `(("r-curl" ,r-curl)
6095 ("r-data-table" ,r-data-table)
6096 ("r-foreign" ,r-foreign)
6097 ("r-haven" ,r-haven)
6098 ("r-openxlsx" ,r-openxlsx)
6099 ("r-readxl" ,r-readxl)
6100 ("r-tibble" ,r-tibble)))
6101 (home-page "https://github.com/leeper/rio")
6102 (synopsis "Swiss-army knife for data I/O")
6104 "This package provides streamlined data import and export infrastructure
6105 by making assumptions that the user is probably willing to make: @code{import}
6106 and @code{export} determine the data structure from the file extension,
6107 reasonable defaults are used for data import and export (e.g.,
6108 @code{stringsAsFactors=FALSE}), web-based import is natively
6109 supported (including from SSL/HTTPS), compressed files can be read directly
6110 without explicit decompression, and fast import packages are used where
6111 appropriate. An additional convenience function, @code{convert}, provides a
6112 simple method for converting between file types.")
6113 (license license:gpl2)))
6115 (define-public r-maptools
6122 (uri (cran-uri "maptools" version))
6125 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6126 (build-system r-build-system)
6128 `(("r-foreign" ,r-foreign)
6129 ("r-lattice" ,r-lattice)
6131 (home-page "https://r-forge.r-project.org/projects/maptools/")
6132 (synopsis "Tools for reading and handling spatial objects")
6134 "This package provides a set of tools for manipulating and reading
6135 geographic data, in particular ESRI Shapefiles. It includes binary access to
6136 GSHHG shoreline files. The package also provides interface wrappers for
6137 exchanging spatial objects with other R packages.")
6138 ;; The C source files from shapelib are released under the Expat license.
6139 ;; The R code is released under GPL version 2 or later.
6140 (license (list license:gpl2+
6143 (define-public r-later
6150 (uri (cran-uri "later" version))
6153 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6154 (build-system r-build-system)
6158 ("r-rlang" ,r-rlang)))
6160 `(("r-knitr" ,r-knitr)))
6161 (home-page "https://github.com/r-lib/later")
6162 (synopsis "Utilities for delaying function execution")
6164 "This package provides tools to execute arbitrary R or C functions some
6165 time after the current time, after the R execution stack has emptied.")
6166 (license license:gpl2+)))
6168 (define-public r-promises
6175 (uri (cran-uri "promises" version))
6178 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6179 (build-system r-build-system)
6181 `(("r-later" ,r-later)
6182 ("r-magrittr" ,r-magrittr)
6185 ("r-rlang" ,r-rlang)))
6187 `(("r-knitr" ,r-knitr)))
6188 (home-page "https://rstudio.github.io/promises")
6189 (synopsis "Abstractions for promise-based asynchronous programming")
6191 "This package provides fundamental abstractions for doing asynchronous
6192 programming in R using promises. Asynchronous programming is useful for
6193 allowing a single R process to orchestrate multiple tasks in the background
6194 while also attending to something else. Semantics are similar to JavaScript
6195 promises, but with a syntax that is idiomatic R.")
6196 (license license:expat)))
6198 (define-public r-dosnow
6205 (uri (cran-uri "doSNOW" version))
6208 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
6209 (properties `((upstream-name . "doSNOW")))
6210 (build-system r-build-system)
6212 `(("r-foreach" ,r-foreach)
6213 ("r-iterators" ,r-iterators)
6214 ("r-snow" ,r-snow)))
6215 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6216 (synopsis "Foreach parallel adaptor for the snow package")
6218 "This package provides a parallel backend for the @code{%dopar%} function
6219 using the @code{snow} package.")
6220 (license license:gpl2)))
6222 (define-public r-snowfall
6225 (version "1.84-6.1")
6228 (uri (cran-uri "snowfall" version))
6230 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6231 (build-system r-build-system)
6233 `(("r-snow" ,r-snow)))
6234 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6235 (synopsis "Easier cluster computing")
6236 (description "This package is a usability wrapper around snow for easier
6237 development of parallel R programs. This package offers e.g. extended error
6238 checks, and additional functions. All functions work in sequential mode, too,
6239 if no cluster is present or wished. The package is also designed as connector
6240 to the cluster management tool @code{sfCluster}, but can also used without
6242 (license license:gpl2+)))
6244 (define-public r-rappdirs
6251 (uri (cran-uri "rappdirs" version))
6254 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6255 (build-system r-build-system)
6256 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6257 (synopsis "Determine where to save data, caches, and logs")
6259 "This package provides an easy way to determine which directories on the
6260 user's computer should be used to save data, caches and logs. It is a port of
6261 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6262 (license license:expat)))
6264 (define-public r-renv
6271 (uri (cran-uri "renv" version))
6274 "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
6275 (properties `((upstream-name . "renv")))
6276 (build-system r-build-system)
6278 `(("r-knitr" ,r-knitr)))
6279 (home-page "https://rstudio.github.io/renv")
6280 (synopsis "Project environments")
6282 "This package provides a dependency management toolkit for R. Using
6283 renv, you can create and manage project-local R libraries, save the state of
6284 these libraries to a lockfile, and later restore your library as required.
6285 Together, these tools can help make your projects more isolated, portable, and
6287 (license license:expat)))
6289 (define-public r-learnr
6296 (uri (cran-uri "learnr" version))
6299 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6300 (build-system r-build-system)
6302 `(("r-checkmate" ,r-checkmate)
6303 ("r-ellipsis" ,r-ellipsis)
6304 ("r-evaluate" ,r-evaluate)
6305 ("r-htmltools" ,r-htmltools)
6306 ("r-htmlwidgets" ,r-htmlwidgets)
6307 ("r-jsonlite" ,r-jsonlite)
6308 ("r-knitr" ,r-knitr)
6309 ("r-markdown" ,r-markdown)
6310 ("r-rappdirs" ,r-rappdirs)
6312 ("r-rmarkdown" ,r-rmarkdown)
6313 ("r-rprojroot" ,r-rprojroot)
6314 ("r-shiny" ,r-shiny)
6315 ("r-withr" ,r-withr)))
6316 (home-page "https://rstudio.github.io/learnr/")
6317 (synopsis "Interactive tutorials for R")
6319 "This package provides tools to create interactive tutorials using R
6320 Markdown. Use a combination of narrative, figures, videos, exercises, and
6321 quizzes to create self-paced tutorials for learning about R and R packages.")
6322 (license license:asl2.0)))
6324 (define-public r-analytics
6326 (name "r-analytics")
6331 (uri (cran-uri "analytics" version))
6334 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6335 (build-system r-build-system)
6338 ("r-cluster" ,r-cluster)
6339 ("r-fractal" ,r-fractal)
6340 ("r-lmtest" ,r-lmtest)
6343 ("r-powerplus" ,r-powerplus)
6344 ("r-robust" ,r-robust)
6345 ("r-trend" ,r-trend)
6349 (home-page "https://cran.r-project.org/web/packages/analytics/")
6350 (synopsis "Collection of data analysis tools")
6352 "This package is a collection of data analysis tools. It includes tools
6353 for regression outlier detection in a fitted linear model, stationary
6354 bootstrap using a truncated geometric distribution, a comprehensive test for
6355 weak stationarity, column means by group, weighted biplots, and a heuristic to
6356 obtain a better initial configuration in non-metric MDS.")
6357 (license license:gpl2)))
6359 (define-public r-reticulate
6361 (name "r-reticulate")
6366 (uri (cran-uri "reticulate" version))
6369 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6370 (build-system r-build-system)
6371 (inputs `(("python" ,python)))
6373 `(("r-rappdirs" ,r-rappdirs)
6374 ("r-jsonlite" ,r-jsonlite)
6375 ("r-matrix" ,r-matrix)
6376 ("r-rcpp" ,r-rcpp)))
6378 `(("r-knitr" ,r-knitr)))
6379 (home-page "https://github.com/rstudio/reticulate")
6380 (synopsis "R interface to Python")
6382 "This package provides an interface from R to Python modules, classes,
6383 and functions. When calling into Python, R data types are automatically
6384 converted to their equivalent Python types. When values are returned from
6385 Python to R they are converted back to R types.")
6386 (license license:asl2.0)))
6388 (define-public r-bibtex
6395 (uri (cran-uri "bibtex" version))
6398 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6399 (build-system r-build-system)
6400 (propagated-inputs `(("r-stringr" ,r-stringr)))
6401 (home-page "https://github.com/romainfrancois/bibtex")
6402 (synopsis "Bibtex parser")
6403 (description "This package provides a utility for R to parse a bibtex
6405 (license license:gpl2+)))
6407 (define-public r-ggseqlogo
6409 (name "r-ggseqlogo")
6414 (uri (cran-uri "ggseqlogo" version))
6417 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6418 (build-system r-build-system)
6419 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6420 (home-page "https://github.com/omarwagih/ggseqlogo")
6421 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6423 "The range of functions provided by this package makes it possible to
6424 draw highly versatile genomic sequence logos. Features include, but are not
6425 limited to, modifying colour schemes and fonts used to draw the logo,
6426 generating multiple logo plots, and aiding the visualisation with annotations.
6427 Sequence logos can easily be combined with other ggplot2 plots.")
6428 ;; Unspecified version of the LGPL.
6429 (license license:lgpl3+)))
6431 (define-public r-ggsci
6438 (uri (cran-uri "ggsci" version))
6441 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6442 (build-system r-build-system)
6444 `(("r-ggplot2" ,r-ggplot2)
6445 ("r-scales" ,r-scales)))
6446 (home-page "https://nanx.me/ggsci/")
6447 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6449 "This package provides a collection of ggplot2 color palettes inspired by
6450 plots in scientific journals, data visualization libraries, science fiction
6451 movies, and TV shows.")
6452 (license license:gpl3)))
6454 (define-public r-ggsignif
6461 (uri (cran-uri "ggsignif" version))
6464 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6465 (build-system r-build-system)
6467 `(("r-knitr" ,r-knitr)))
6469 `(("r-ggplot2" ,r-ggplot2)))
6470 (home-page "https://github.com/const-ae/ggsignif")
6471 (synopsis "Significance brackets for ggplot2")
6473 "Enrich your ggplots with group-wise comparisons. This package provides
6474 an easy way to indicate if two groups are significantly different. Commonly
6475 this is shown by a bracket on top connecting the groups of interest which
6476 itself is annotated with the level of significance. The package provides a
6477 single layer that takes the groups for comparison and the test as arguments
6478 and adds the annotation to the plot.")
6479 (license license:gpl3)))
6481 (define-public r-rstatix
6488 (uri (cran-uri "rstatix" version))
6491 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6492 (properties `((upstream-name . "rstatix")))
6493 (build-system r-build-system)
6495 `(("r-broom" ,r-broom)
6497 ("r-corrplot" ,r-corrplot)
6498 ("r-dplyr" ,r-dplyr)
6499 ("r-generics" ,r-generics)
6500 ("r-magrittr" ,r-magrittr)
6501 ("r-purrr" ,r-purrr)
6502 ("r-rlang" ,r-rlang)
6503 ("r-tibble" ,r-tibble)
6504 ("r-tidyr" ,r-tidyr)
6505 ("r-tidyselect" ,r-tidyselect)))
6506 (home-page "https://rpkgs.datanovia.com/rstatix/")
6507 (synopsis "Pipe-friendly framework for basic statistical tests")
6509 "This package provides a simple and intuitive pipe-friendly framework,
6510 coherent with the @code{tidyverse} design philosophy, for performing basic
6511 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6512 correlation analyses. The output of each test is automatically transformed
6513 into a tidy data frame to facilitate visualization. Additional functions are
6514 available for reshaping, reordering, manipulating and visualizing correlation
6516 (license license:gpl2)))
6518 (define-public r-ggpubr
6525 (uri (cran-uri "ggpubr" version))
6528 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6529 (build-system r-build-system)
6531 `(("r-cowplot" ,r-cowplot)
6532 ("r-dplyr" ,r-dplyr)
6533 ("r-ggplot2" ,r-ggplot2)
6534 ("r-ggrepel" ,r-ggrepel)
6535 ("r-ggsci" ,r-ggsci)
6536 ("r-ggsignif" ,r-ggsignif)
6538 ("r-gridextra" ,r-gridextra)
6539 ("r-magrittr" ,r-magrittr)
6540 ("r-polynom" ,r-polynom)
6541 ("r-purrr" ,r-purrr)
6542 ("r-rlang" ,r-rlang)
6543 ("r-scales" ,r-scales)
6544 ("r-rstatix" ,r-rstatix)
6545 ("r-tibble" ,r-tibble)
6546 ("r-tidyr" ,r-tidyr)))
6547 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6548 (synopsis "ggplot2-based publication-ready plots")
6550 "The ggplot2 package is an excellent and flexible package for elegant
6551 data visualization in R. However the default generated plots require some
6552 formatting before we can send them for publication. The ggpubr package
6553 provides some easy-to-use functions for creating and customizing ggplot2-based
6554 publication-ready plots.")
6555 (license license:gpl2)))
6557 (define-public r-ellipse
6564 (uri (cran-uri "ellipse" version))
6567 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6568 (build-system r-build-system)
6569 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6570 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6572 "This package contains various routines for drawing ellipses and
6573 ellipse-like confidence regions, implementing the plots described in Murdoch
6574 and Chow (1996), A graphical display of large correlation matrices, The
6575 American Statistician 50, 178-180. There are also routines implementing the
6576 profile plots described in Bates and Watts (1988), Nonlinear Regression
6577 Analysis and its Applications.")
6578 (license license:gpl2+)))
6580 (define-public r-flashclust
6582 (name "r-flashclust")
6587 (uri (cran-uri "flashClust" version))
6590 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6591 (properties `((upstream-name . "flashClust")))
6592 (build-system r-build-system)
6593 (native-inputs `(("gfortran" ,gfortran)))
6594 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6595 (synopsis "Implementation of optimal hierarchical clustering")
6597 "This package provides a fast implementation of hierarchical
6599 (license license:gpl2+)))
6601 (define-public r-factominer
6603 (name "r-factominer")
6608 (uri (cran-uri "FactoMineR" version))
6611 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6612 (properties `((upstream-name . "FactoMineR")))
6613 (build-system r-build-system)
6616 ("r-cluster" ,r-cluster)
6617 ("r-ellipse" ,r-ellipse)
6618 ("r-flashclust" ,r-flashclust)
6619 ("r-ggplot2" ,r-ggplot2)
6620 ("r-ggrepel" ,r-ggrepel)
6621 ("r-lattice" ,r-lattice)
6622 ("r-leaps" ,r-leaps)
6624 ("r-scatterplot3d" ,r-scatterplot3d)))
6625 (home-page "http://factominer.free.fr")
6626 (synopsis "Multivariate exploratory data analysis and data mining")
6628 "This package provides exploratory data analysis methods to summarize,
6629 visualize and describe datasets. The main principal component methods are
6630 available, those with the largest potential in terms of applications:
6631 principal component analysis (PCA) when variables are quantitative,
6632 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6633 variables are categorical, Multiple Factor Analysis when variables are
6634 structured in groups, etc. and hierarchical cluster analysis.")
6635 (license license:gpl2+)))
6637 (define-public r-factoextra
6639 (name "r-factoextra")
6644 (uri (cran-uri "factoextra" version))
6647 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6648 (build-system r-build-system)
6650 `(("r-abind" ,r-abind)
6651 ("r-cluster" ,r-cluster)
6652 ("r-dendextend" ,r-dendextend)
6653 ("r-factominer" ,r-factominer)
6654 ("r-ggplot2" ,r-ggplot2)
6655 ("r-ggpubr" ,r-ggpubr)
6656 ("r-ggrepel" ,r-ggrepel)
6657 ("r-reshape2" ,r-reshape2)
6658 ("r-tidyr" ,r-tidyr)))
6659 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6660 (synopsis "Extract and visualize the results of multivariate data analyses")
6662 "This package provides some easy-to-use functions to extract and
6663 visualize the output of multivariate data analyses, including
6664 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6665 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6666 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6667 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6668 packages. It contains also functions for simplifying some clustering analysis
6669 steps and provides ggplot2-based elegant data visualization.")
6670 (license license:gpl2)))
6672 (define-public r-fansi
6679 (uri (cran-uri "fansi" version))
6682 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6683 (build-system r-build-system)
6685 `(("r-knitr" ,r-knitr))) ; for vignettes
6686 (home-page "https://github.com/brodieG/fansi")
6687 (synopsis "ANSI control sequence aware string functions")
6689 "This package provides counterparts to R string manipulation functions
6690 that account for the effects of ANSI text formatting control sequences.")
6691 (license license:gpl2+)))
6693 (define-public r-nbclust
6700 (uri (cran-uri "NbClust" version))
6703 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6704 (properties `((upstream-name . "NbClust")))
6705 (build-system r-build-system)
6706 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6707 (synopsis "Determine the best number of clusters in a data set")
6709 "NbClust provides 30 indexes for determining the optimal number of
6710 clusters in a data set and offers the best clustering scheme from different
6711 results to the user.")
6712 (license license:gpl2)))
6714 (define-public r-hdf5r
6721 (uri (cran-uri "hdf5r" version))
6724 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6725 (build-system r-build-system)
6730 `(("r-bit64" ,r-bit64)
6733 `(("r-knitr" ,r-knitr)))
6734 (home-page "https://hhoeflin.github.io/hdf5r")
6735 (synopsis "Interface to the HDF5 binary data format")
6737 "HDF5 is a data model, library and file format for storing and managing
6738 large amounts of data. This package provides a nearly feature complete,
6739 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6740 functionality is added so that HDF5 objects behave very similar to their
6741 corresponding R counterparts.")
6742 (license license:asl2.0)))
6744 (define-public r-itertools
6746 (name "r-itertools")
6751 (uri (cran-uri "itertools" version))
6754 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6755 (build-system r-build-system)
6757 `(("r-iterators" ,r-iterators)))
6758 (home-page "https://cran.r-project.org/web/packages/itertools/")
6759 (synopsis "Iterator tools")
6761 "This package provides various tools for creating iterators, many
6762 patterned after functions in the Python @code{itertools} module, and others
6763 patterned after functions in the snow package.")
6764 (license license:gpl2)))
6766 (define-public r-polynom
6773 (uri (cran-uri "polynom" version))
6776 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6777 (build-system r-build-system)
6778 (home-page "https://cran.r-project.org/web/packages/polynom/")
6779 (synopsis "Functions for univariate polynomial manipulations")
6781 "This package provides a collection of functions to implement a class for
6782 univariate polynomial manipulations.")
6783 (license license:gpl2)))
6785 (define-public r-gbrd
6792 (uri (cran-uri "gbRd" version))
6795 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6796 (properties `((upstream-name . "gbRd")))
6797 (build-system r-build-system)
6798 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6799 (synopsis "Utilities for processing Rd objects and files")
6801 "This package provides utilities for processing Rd objects and files.
6802 Extract argument descriptions and other parts of the help pages of
6804 (license license:gpl2+)))
6806 (define-public r-rjags
6813 (uri (cran-uri "rjags" version))
6816 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6817 (build-system r-build-system)
6819 `(("r-coda" ,r-coda)))
6823 `(("pkg-config" ,pkg-config)))
6824 (home-page "http://mcmc-jags.sourceforge.net")
6825 (synopsis "Bayesian graphical models using MCMC")
6827 "This package provides an R interface to the JAGS MCMC library. JAGS is
6828 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6829 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6830 (license license:gpl2)))
6832 (define-public r-rdpack
6839 (uri (cran-uri "Rdpack" version))
6842 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6843 (properties `((upstream-name . "Rdpack")))
6844 (build-system r-build-system)
6846 `(("r-bibtex" ,r-bibtex)
6847 ("r-gbrd" ,r-gbrd)))
6848 (home-page "https://github.com/GeoBosh/Rdpack")
6849 (synopsis "Update and manipulate Rd documentation objects")
6851 "This package provides functions for manipulation of R documentation
6852 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6853 updating Rd documentation for functions, methods and classes; it also includes
6854 Rd macros for citations and import of references from bibtex files for use in
6855 Rd files and roxygen2 comments, as well as many functions for manipulation of
6856 references and Rd files.")
6857 (license license:gpl2+)))
6859 (define-public r-officer
6866 (uri (cran-uri "officer" version))
6869 "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h"))))
6870 (build-system r-build-system)
6872 `(("r-magrittr" ,r-magrittr)
6878 `(("r-knitr" ,r-knitr)))
6879 (home-page "https://davidgohel.github.io/officer")
6880 (synopsis "Manipulation of Word and PowerPoint documents")
6882 "This package provides tools to access and manipulate Word and PowerPoint
6883 documents from R. The package focuses on tabular and graphical reporting from
6884 R; it also provides two functions that let users get document content into
6885 data objects. A set of functions lets add and remove images, tables and
6886 paragraphs of text in new or existing documents. When working with PowerPoint
6887 presentations, slides can be added or removed; shapes inside slides can also
6888 be added or removed. When working with Word documents, a cursor can be used
6889 to help insert or delete content at a specific location in the document.")
6890 (license license:gpl3)))
6892 (define-public r-profilemodel
6894 (name "r-profilemodel")
6899 (uri (cran-uri "profileModel" version))
6902 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6903 (properties `((upstream-name . "profileModel")))
6904 (build-system r-build-system)
6905 (home-page "https://github.com/ikosmidis/profileModel")
6906 (synopsis "Profiling inference functions for various model classes")
6908 "This package provides tools that can be used to calculate, evaluate,
6909 plot and use for inference the profiles of *arbitrary* inference functions for
6910 arbitrary @code{glm}-like fitted models with linear predictors. More information
6911 on the methods that are implemented can be found in Kosmidis (2008)
6912 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6913 (license license:gpl2+)))
6915 (define-public r-brglm
6922 (uri (cran-uri "brglm" version))
6925 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6926 (properties `((upstream-name . "brglm")))
6927 (build-system r-build-system)
6929 `(("r-profilemodel" ,r-profilemodel)))
6930 (home-page "https://github.com/ikosmidis/brglm")
6931 (synopsis "Bias reduction in binomial-response generalized linear models")
6933 "Fit generalized linear models with binomial responses using either an
6934 adjusted-score approach to bias reduction or maximum penalized likelihood
6935 where penalization is by Jeffreys invariant prior. These procedures return
6936 estimates with improved frequentist properties (bias, mean squared error) that
6937 are always finite even in cases where the maximum likelihood estimates are
6938 infinite (data separation). Fitting takes place by fitting generalized linear
6939 models on iteratively updated pseudo-data. The interface is essentially the
6940 same as @code{glm}. More flexibility is provided by the fact that custom
6941 pseudo-data representations can be specified and used for model fitting.
6942 Functions are provided for the construction of confidence intervals for the
6943 reduced-bias estimates.")
6944 (license license:gpl2+)))
6946 (define-public r-entropy
6953 (uri (cran-uri "entropy" version))
6956 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6957 (properties `((upstream-name . "entropy")))
6958 (build-system r-build-system)
6959 (home-page "https://www.strimmerlab.org/software/entropy/")
6960 (synopsis "Estimation of entropy, mutual information and related quantities")
6962 "This package implements various estimators of entropy, such as the
6963 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6964 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6965 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6966 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6967 mutual information, and chi-squared statistic of independence. In addition
6968 there are functions for discretizing continuous random variables.")
6969 (license license:gpl3+)))
6971 (define-public r-abn
6978 (uri (cran-uri "abn" version))
6981 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6982 (build-system r-build-system)
6986 `(("r-boot" ,r-boot)
6987 ("r-brglm" ,r-brglm)
6988 ("r-entropy" ,r-entropy)
6991 ("r-moments" ,r-moments)
6994 ("r-rcpparmadillo" ,r-rcpparmadillo)
6995 ("r-rjags" ,r-rjags)))
6996 (home-page "https://r-bayesian-networks.org/")
6997 (synopsis "Modelling multivariate data with additive bayesian networks")
6999 "Bayesian network analysis is a form of probabilistic graphical models
7000 which derives from empirical data a directed acyclic graph, DAG, describing
7001 the dependency structure between random variables. An additive Bayesian
7002 network model consists of a form of a DAG where each node comprises a
7003 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
7004 equivalent to Bayesian multivariate regression using graphical modelling, they
7005 generalises the usual multivariable regression, GLM, to multiple dependent
7006 variables. This package provides routines to help determine optimal Bayesian
7007 network models for a given data set, where these models are used to identify
7008 statistical dependencies in messy, complex data.")
7009 (license license:gpl2+)))
7011 (define-public r-acd
7018 (uri (cran-uri "ACD" version))
7021 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
7022 (properties `((upstream-name . "ACD")))
7023 (build-system r-build-system)
7024 (home-page "https://cran.r-project.org/web/packages/ACD/")
7025 (synopsis "Categorical data analysis with complete or missing responses")
7027 "This package provides tools for categorical data analysis with complete
7028 or missing responses.")
7029 (license license:gpl2+)))
7031 (define-public r-acdm
7038 (uri (cran-uri "ACDm" version))
7041 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
7042 (properties `((upstream-name . "ACDm")))
7043 (build-system r-build-system)
7045 `(("r-dplyr" ,r-dplyr)
7046 ("r-ggplot2" ,r-ggplot2)
7048 ("r-rsolnp" ,r-rsolnp)
7050 (home-page "https://cran.r-project.org/web/packages/ACDm/")
7051 (synopsis "Tools for Autoregressive Conditional Duration Models")
7053 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
7054 and Russell, 1998) models. It creates trade, price or volume durations from
7055 transactions (tic) data, performs diurnal adjustments, fits various ACD models
7057 (license license:gpl2+)))
7059 (define-public r-overlap
7066 (uri (cran-uri "overlap" version))
7069 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
7070 (build-system r-build-system)
7071 (home-page "https://cran.r-project.org/web/packages/overlap/")
7072 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
7074 "This package provides functions to fit kernel density functions to data
7075 on temporal activity patterns of animals; estimate coefficients of overlapping
7076 of densities for two species; and calculate bootstrap estimates of confidence
7078 (license license:gpl3+)))
7080 (define-public r-snakecase
7082 (name "r-snakecase")
7087 (uri (cran-uri "snakecase" version))
7090 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
7091 (build-system r-build-system)
7093 `(("r-stringi" ,r-stringi)
7094 ("r-stringr" ,r-stringr)))
7095 (home-page "https://github.com/Tazinho/snakecase")
7096 (synopsis "Convert strings into any case")
7098 "This package provides a consistent, flexible and easy to use tool to
7099 parse and convert strings into cases like snake or camel among others.")
7100 (license license:gpl3)))
7102 (define-public r-prediction
7104 (name "r-prediction")
7109 (uri (cran-uri "prediction" version))
7112 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
7113 (build-system r-build-system)
7115 `(("r-data-table" ,r-data-table)))
7116 (home-page "https://github.com/leeper/prediction")
7117 (synopsis "Tidy, type-safe prediction methods")
7119 "This package provides the @code{prediction()} function, a type-safe
7120 alternative to @code{predict()} that always returns a data frame. The package
7121 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
7122 from the @code{stats} package, as well as numerous other model classes from
7123 other add-on packages.")
7124 (license license:expat)))
7126 (define-public r-insight
7133 (uri (cran-uri "insight" version))
7136 "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
7137 (build-system r-build-system)
7139 `(("r-knitr" ,r-knitr)))
7140 (home-page "https://easystats.github.io/insight/")
7141 (synopsis "Easy access to model information for various model objects")
7143 "This package provides a tool to provide an easy, intuitive and
7144 consistent access to information contained in various R models, like model
7145 formulas, model terms, information about random effects, data that was used to
7146 fit the model or data from response variables. The package mainly revolves
7147 around two types of functions: Functions that find (the names of) information,
7148 starting with @code{find_}, and functions that get the underlying data,
7149 starting with @code{get_}. The package has a consistent syntax and works with
7150 many different model objects, where otherwise functions to access these
7151 information are missing.")
7152 (license license:gpl3)))
7154 (define-public r-sjlabelled
7156 (name "r-sjlabelled")
7161 (uri (cran-uri "sjlabelled" version))
7164 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
7165 (build-system r-build-system)
7167 `(("r-insight" ,r-insight)))
7169 `(("r-knitr" ,r-knitr)))
7170 (home-page "https://github.com/strengejacke/sjlabelled")
7171 (synopsis "Labelled data utility functions")
7173 "This package provides a collection of functions dealing with labelled
7174 data, like reading and writing data between R and other statistical software
7175 packages. This includes easy ways to get, set or change value and variable
7176 label attributes, to convert labelled vectors into factors or numeric (and
7177 vice versa), or to deal with multiple declared missing values.")
7178 (license license:gpl3)))
7180 (define-public r-sjmisc
7187 (uri (cran-uri "sjmisc" version))
7190 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
7191 (build-system r-build-system)
7193 `(("r-dplyr" ,r-dplyr)
7194 ("r-insight" ,r-insight)
7195 ("r-magrittr" ,r-magrittr)
7196 ("r-purrr" ,r-purrr)
7197 ("r-rlang" ,r-rlang)
7198 ("r-sjlabelled" ,r-sjlabelled)
7199 ("r-tidyselect" ,r-tidyselect)))
7201 `(("r-knitr" ,r-knitr)))
7202 (home-page "https://github.com/strengejacke/sjmisc")
7203 (synopsis "Data and variable transformation functions")
7205 "This package is a collection of miscellaneous utility functions,
7206 supporting data transformation tasks like recoding, dichotomizing or grouping
7207 variables, setting and replacing missing values. The data transformation
7208 functions also support labelled data, and all integrate seamlessly into a
7209 tidyverse workflow.")
7210 (license license:gpl3)))
7212 (define-public r-nortest
7219 (uri (cran-uri "nortest" version))
7222 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7223 (build-system r-build-system)
7224 (home-page "https://cran.r-project.org/web/packages/nortest/")
7225 (synopsis "Tests for normality")
7227 "This package provides five omnibus tests for testing the composite
7228 hypothesis of normality.")
7229 (license license:gpl2+)))
7231 (define-public r-moonbook
7238 (uri (cran-uri "moonBook" version))
7241 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7242 (properties `((upstream-name . "moonBook")))
7243 (build-system r-build-system)
7245 `(("r-magrittr" ,r-magrittr)
7246 ("r-nortest" ,r-nortest)
7247 ("r-purrr" ,r-purrr)
7248 ("r-sjmisc" ,r-sjmisc)
7249 ("r-stringr" ,r-stringr)
7250 ("r-survival" ,r-survival)))
7251 (home-page "https://github.com/cardiomoon/moonBook")
7252 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7254 "This package provides several analysis-related functions for the book
7255 entitled \"R statistics and graph for medical articles\" (written in Korean),
7256 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7258 (license license:gpl2)))
7260 (define-public r-flextable
7262 (name "r-flextable")
7267 (uri (cran-uri "flextable" version))
7270 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7271 (build-system r-build-system)
7273 `(("r-base64enc" ,r-base64enc)
7274 ("r-data-table" ,r-data-table)
7275 ("r-gdtools" ,r-gdtools)
7276 ("r-htmltools" ,r-htmltools)
7277 ("r-knitr" ,r-knitr)
7278 ("r-officer" ,r-officer)
7279 ("r-rlang" ,r-rlang)
7280 ("r-rmarkdown" ,r-rmarkdown)
7282 ("r-xml2" ,r-xml2)))
7283 (home-page "https://davidgohel.github.io/flextable")
7284 (synopsis "Functions for tabular reporting")
7286 "This package provides tools to create pretty tables for HTML documents
7287 and other formats. Functions are provided to let users create tables, modify
7288 and format their content. It extends the @code{officer} package and can be
7289 used within R markdown documents when rendering to HTML and to Word
7291 (license license:gpl3)))
7293 (define-public r-writexl
7300 (uri (cran-uri "writexl" version))
7303 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
7304 (build-system r-build-system)
7305 (inputs `(("zlib" ,zlib)))
7306 (home-page "https://github.com/ropensci/writexl")
7307 (synopsis "Export data frames to xlsx format")
7309 "This package provides a data frame to xlsx exporter based on
7311 (license license:bsd-2)))
7313 (define-public r-biasedurn
7315 (name "r-biasedurn")
7320 (uri (cran-uri "BiasedUrn" version))
7323 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7324 (properties `((upstream-name . "BiasedUrn")))
7325 (build-system r-build-system)
7326 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7327 (synopsis "Biased Urn model distributions")
7329 "This package provides statistical models of biased sampling in the form
7330 of univariate and multivariate noncentral hypergeometric distributions,
7331 including Wallenius' noncentral hypergeometric distribution and Fisher's
7332 noncentral hypergeometric distribution (also called extended hypergeometric
7334 (license license:gpl3)))
7336 (define-public r-goplot
7343 (uri (cran-uri "GOplot" version))
7346 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7347 (properties `((upstream-name . "GOplot")))
7348 (build-system r-build-system)
7350 `(("r-ggdendro" ,r-ggdendro)
7351 ("r-ggplot2" ,r-ggplot2)
7352 ("r-gridextra" ,r-gridextra)
7353 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7354 (home-page "https://github.com/wencke/wencke.github.io")
7355 (synopsis "Visualization of functional analysis data")
7357 "This package provides an implementation of multilayered visualizations
7358 for enhanced graphical representation of functional analysis data. It
7359 combines and integrates omics data derived from expression and functional
7360 annotation enrichment analyses. Its plotting functions have been developed
7361 with an hierarchical structure in mind: starting from a general overview to
7362 identify the most enriched categories (modified bar plot, bubble plot) to a
7363 more detailed one displaying different types of relevant information for the
7364 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7365 Venn diagram, heatmap).")
7366 (license license:gpl2)))
7368 (define-public r-getopt
7375 (uri (cran-uri "getopt" version))
7378 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7379 (build-system r-build-system)
7380 (home-page "https://github.com/trevorld/getopt")
7381 (synopsis "Command-line option processor for R")
7383 "This package is designed to be used with Rscript to write shebang
7384 scripts that accept short and long options. Many users will prefer to
7385 use the packages @code{optparse} or @code{argparse} which add extra
7386 features like automatically generated help options and usage texts,
7387 support for default values, positional argument support, etc.")
7388 (license license:gpl2+)))
7390 (define-public r-findpython
7392 (name "r-findpython")
7397 (uri (cran-uri "findpython" version))
7400 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7401 (build-system r-build-system)
7402 (home-page "https://github.com/trevorld/findpython")
7403 (synopsis "Functions to find an acceptable Python binary")
7405 "This package was designed to find an acceptable Python binary that
7406 matches version and feature constraints.")
7407 (license license:expat)))
7409 ;; This in not the same as "r-argparser"
7410 (define-public r-argparse
7417 (uri (cran-uri "argparse" version))
7420 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7421 (build-system r-build-system)
7422 (inputs `(("python" ,python)))
7424 `(("r-findpython" ,r-findpython)
7425 ("r-jsonlite" ,r-jsonlite)
7427 (home-page "https://github.com/trevorld/argparse")
7428 (synopsis "Command line optional and positional argument parser")
7430 "This package provides a command line parser to be used with Rscript to
7431 write shebang scripts that gracefully accept positional and optional arguments
7432 and automatically generate usage notices.")
7433 (license license:gpl2+)))
7435 (define-public r-hash
7442 (uri (cran-uri "hash" version))
7445 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7446 (build-system r-build-system)
7447 (home-page "https://cran.r-project.org/web/packages/hash/")
7448 (synopsis "Implementation of hash/associated arrays/dictionaries")
7450 "This package implements a data structure similar to hashes in Perl and
7451 dictionaries in Python but with a purposefully R flavor. For objects of
7452 appreciable size, access using hashes outperforms native named lists and
7454 (license license:gpl2+)))
7456 (define-public r-orddom
7463 (uri (cran-uri "orddom" version))
7466 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7467 (build-system r-build-system)
7468 (propagated-inputs `(("r-psych" ,r-psych)))
7469 (home-page "https://cran.r-project.org/web/packages/orddom/")
7470 (synopsis "Ordinal dominance statistics")
7472 "This package provides tools to compute ordinal, statistics and effect
7473 sizes as an alternative to mean comparison: Cliff's delta or success rate
7474 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7475 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7476 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7477 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7478 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7479 Group (Non-)Overlap considerations.")
7480 (license license:gpl2)))
7482 (define-public r-deriv
7489 (uri (cran-uri "Deriv" version))
7492 "16rq65x1xhxvqwn4p427divay3b9fgam2lxccxb8529adnrxmw6p"))))
7493 (properties `((upstream-name . "Deriv")))
7494 (build-system r-build-system)
7495 (home-page "https://cran.r-project.org/web/packages/Deriv")
7496 (synopsis "Symbolic differentiation")
7498 "This package provides an R-based solution for symbolic differentiation.
7499 It admits user-defined functions as well as function substitution in arguments
7500 of functions to be differentiated. Some symbolic simplification is part of
7502 (license license:gpl3+)))
7504 (define-public r-doby
7511 (uri (cran-uri "doBy" version))
7514 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7515 (properties `((upstream-name . "doBy")))
7516 (build-system r-build-system)
7518 `(("r-broom" ,r-broom)
7519 ("r-deriv" ,r-deriv)
7520 ("r-dplyr" ,r-dplyr)
7521 ("r-ggplot2" ,r-ggplot2)
7522 ("r-magrittr" ,r-magrittr)
7524 ("r-matrix" ,r-matrix)
7525 ("r-pbkrtest" ,r-pbkrtest)
7526 ("r-tibble" ,r-tibble)))
7528 `(("r-knitr" ,r-knitr)))
7529 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7530 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7532 "This package contains:
7535 @item facilities for working with grouped data: @code{do}
7536 something to data stratified @code{by} some variables.
7537 @item implementations of least-squares means, general linear contrasts, and
7538 @item miscellaneous other utilities.
7540 (license license:gpl2+)))
7542 (define-public r-refgenome
7544 (name "r-refgenome")
7549 (uri (cran-uri "refGenome" version))
7552 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7553 (properties `((upstream-name . "refGenome")))
7554 (build-system r-build-system)
7558 ("r-rsqlite" ,r-rsqlite)))
7559 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7561 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7563 "This package contains functionality for importing and managing of
7564 downloaded genome annotation data from the Ensembl genome browser (European
7565 Bioinformatics Institute) and from the UCSC genome browser (University of
7566 California, Santa Cruz) and annotation routines for genomic positions and
7567 splice site positions.")
7568 (license license:gpl2)))
7570 (define-public r-basix
7577 (uri (cran-uri "BASIX" version))
7580 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7581 (properties `((upstream-name . "BASIX")))
7582 (build-system r-build-system)
7583 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7584 (synopsis "Efficient C/C++ toolset for R")
7586 "BASIX provides some efficient C/C++ implementations of native R
7587 procedures to speed up calculations in R.")
7588 (license license:gpl2)))
7590 (define-public r-blockfest
7592 (name "r-blockfest")
7597 (uri (cran-uri "BlockFeST" version))
7600 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7601 (properties `((upstream-name . "BlockFeST")))
7602 (build-system r-build-system)
7603 (propagated-inputs `(("r-basix" ,r-basix)))
7604 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7605 (synopsis "Bayesian calculation of region-specific fixation index")
7607 "This package provides an R implementation of an extension of the
7608 BayeScan software for codominant markers, adding the option to group
7609 individual SNPs into pre-defined blocks. A typical application of this new
7610 approach is the identification of genomic regions, genes, or gene sets
7611 containing one or more SNPs that evolved under directional selection.")
7612 (license license:gpl2)))
7614 (define-public r-proc
7621 (uri (cran-uri "pROC" version))
7624 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7625 (properties `((upstream-name . "pROC")))
7626 (build-system r-build-system)
7628 `(("r-plyr" ,r-plyr)
7629 ("r-rcpp" ,r-rcpp)))
7630 (home-page "https://web.expasy.org/pROC/")
7631 (synopsis "Display and analyze ROC curves")
7633 "This package provides tools for visualizing, smoothing and comparing
7634 receiver operating characteristic (ROC curves). The area under the
7635 curve (AUC) can be compared with statistical tests based on U-statistics or
7636 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7637 (license license:gpl3+)))
7639 (define-public r-rootsolve
7641 (name "r-rootsolve")
7646 (uri (cran-uri "rootSolve" version))
7649 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7650 (properties `((upstream-name . "rootSolve")))
7651 (build-system r-build-system)
7652 (native-inputs `(("gfortran" ,gfortran)))
7653 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7654 (synopsis "Tools for the analysis of ordinary differential equations")
7656 "This package provides routines to find the root of nonlinear functions,
7657 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7658 differential equations} (ODE). It includes routines that:
7661 @item generate gradient and jacobian matrices (full and banded),
7662 @item find roots of non-linear equations by the Newton-Raphson method,
7663 @item estimate steady-state conditions of a system of (differential) equations
7664 in full, banded or sparse form, using the Newton-Raphson method, or by
7665 dynamically running,
7666 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7667 and 3-D partial differential equations, that have been converted to ordinary
7668 differential equations by numerical differencing (using the method-of-lines
7671 (license license:gpl2+)))
7673 (define-public r-abcanalysis
7675 (name "r-abcanalysis")
7680 (uri (cran-uri "ABCanalysis" version))
7682 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7683 (properties `((upstream-name . "ABCanalysis")))
7684 (build-system r-build-system)
7685 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7686 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7687 (synopsis "Computed ABC Analysis")
7689 "Multivariate data sets often differ in several factors or derived statistical
7690 parameters, which have to be selected for a valid interpretation. Basing this
7691 selection on traditional statistical limits leads occasionally to the perception
7692 of losing information from a data set. This package provides tools to calculate
7693 these limits on the basis of the mathematical properties of the distribution of
7694 the analyzed items.")
7695 (license license:gpl3)))
7697 (define-public r-slam
7704 (uri (cran-uri "slam" version))
7706 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7707 (build-system r-build-system)
7708 (home-page "https://cran.r-project.org/web/packages/slam/")
7709 (synopsis "Sparse lightweight arrays and matrices")
7711 "This package contains data structures and algorithms for sparse arrays and matrices,
7712 based on index arrays and simple triplet representations, respectively.")
7713 (license license:gpl2)))
7715 (define-public r-manipulatewidget
7717 (name "r-manipulatewidget")
7722 (uri (cran-uri "manipulateWidget" version))
7724 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7726 `((upstream-name . "manipulateWidget")))
7727 (build-system r-build-system)
7729 `(("r-base64enc" ,r-base64enc)
7730 ("r-codetools" ,r-codetools)
7731 ("r-htmltools" ,r-htmltools)
7732 ("r-htmlwidgets" ,r-htmlwidgets)
7733 ("r-knitr" ,r-knitr)
7734 ("r-miniui" ,r-miniui)
7735 ("r-shiny" ,r-shiny)
7736 ("r-webshot" ,r-webshot)))
7737 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7738 (synopsis "Add even more interactivity to interactive charts")
7740 "This package lets you create in just a few lines of R code a nice user interface to
7741 modify the data or the graphical parameters of one or multiple interactive
7742 charts. It is useful to quickly explore visually some data or for package
7743 developers to generate user interfaces easy to maintain.")
7744 (license license:gpl2+)))
7753 (uri (cran-uri "A3" version))
7755 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7756 (properties `((upstream-name . "A3")))
7757 (build-system r-build-system)
7759 `(("r-pbapply" ,r-pbapply)
7760 ("r-xtable" ,r-xtable)))
7761 (home-page "https://cran.r-project.org/web/packages/A3/")
7762 (synopsis "Error metrics for predictive models")
7764 "This package supplies tools for tabulating and analyzing the results of predictive
7765 models. The methods employed are applicable to virtually any predictive model
7766 and make comparisons between different methodologies straightforward.")
7767 (license license:gpl2+)))
7769 (define-public r-infotheo
7776 (uri (cran-uri "infotheo" version))
7779 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7780 (build-system r-build-system)
7781 (home-page "http://homepage.meyerp.com/software")
7782 (synopsis "Information-theoretic measures")
7784 "This package implements various measures of information theory based on
7785 several entropy estimators.")
7786 (license license:gpl3+)))
7788 (define-public r-abcoptim
7795 (uri (cran-uri "ABCoptim" version))
7797 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7798 (properties `((upstream-name . "ABCoptim")))
7799 (build-system r-build-system)
7800 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7801 (home-page "https://github.com/gvegayon/ABCoptim/")
7802 (synopsis "Optimization of Artificial Bee Colony algorithm")
7804 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7805 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7806 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7807 algorithms, and uses only common control parameters such as colony size and
7808 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7809 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7810 This version is a work-in-progress and is written in R code.")
7811 (license license:expat)))
7813 (define-public r-abcp2
7820 (uri (cran-uri "ABCp2" version))
7822 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7823 (properties `((upstream-name . "ABCp2")))
7824 (build-system r-build-system)
7825 (propagated-inputs `(("r-mass" ,r-mass)))
7826 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7827 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7829 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7830 Poisson, and Gamma distribution and estimates the proportional paternity of the
7831 second male (P2) based on the best fit distribution.")
7832 (license license:gpl2)))
7834 (define-public r-abcrf
7841 (uri (cran-uri "abcrf" version))
7843 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7844 (build-system r-build-system)
7846 `(("r-doparallel" ,r-doparallel)
7847 ("r-foreach" ,r-foreach)
7849 ("r-matrixstats" ,r-matrixstats)
7850 ("r-ranger" ,r-ranger)
7852 ("r-rcpparmadillo" ,r-rcpparmadillo)
7853 ("r-readr" ,r-readr)
7854 ("r-stringr" ,r-stringr)))
7855 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7856 (synopsis "Approximate bayesian computation via random forests")
7858 "This package performs approximate bayesian computation (ABC) model choice and
7859 parameter inference via random forests. This machine learning tool named random
7860 forests (RF) can conduct selection among the highly complex models covered by
7862 (license license:gpl2+)))
7864 (define-public r-abctools
7871 (uri (cran-uri "abctools" version))
7873 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7874 (build-system r-build-system)
7877 ("r-abind" ,r-abind)
7878 ("r-hmisc" ,r-hmisc)
7879 ("r-plyr" ,r-plyr)))
7880 (home-page "https://github.com/dennisprangle/abctools/")
7881 (synopsis "Tools for ABC analyses")
7883 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7884 including summary statistic selection and assessing coverage. This includes
7885 recent dimension reduction algorithms to tune the choice of summary statistics,
7886 and coverage methods to tune the choice of threshold.")
7887 (license license:gpl2+)))
7889 (define-public r-ggstance
7896 (uri (cran-uri "ggstance" version))
7898 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7899 (build-system r-build-system)
7901 `(("r-ggplot2" ,r-ggplot2)
7903 ("r-rlang" ,r-rlang)
7904 ("r-withr" ,r-withr)))
7905 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7906 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7908 "This package is a @code{r-ggplot2} extension that provides flipped components:
7910 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7911 @item vertical versions of @code{r-ggplot2} positions.
7913 (license license:gpl3)))
7915 (define-public r-mosaiccore
7917 (name "r-mosaiccore")
7922 (uri (cran-uri "mosaicCore" version))
7924 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7925 (properties `((upstream-name . "mosaicCore")))
7926 (build-system r-build-system)
7928 `(("r-dplyr" ,r-dplyr)
7929 ("r-lazyeval" ,r-lazyeval)
7931 ("r-rlang" ,r-rlang)
7932 ("r-tidyr" ,r-tidyr)))
7933 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7934 (synopsis "Common utilities for mosaic family packages")
7936 "Common utilities used in other Mosaic family packages are collected here.")
7937 (license license:gpl2+)))
7939 (define-public r-ggformula
7941 (name "r-ggformula")
7946 (uri (cran-uri "ggformula" version))
7948 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7949 (build-system r-build-system)
7951 `(("r-ggforce" ,r-ggforce)
7952 ("r-ggplot2" ,r-ggplot2)
7953 ("r-ggstance" ,r-ggstance)
7954 ("r-magrittr" ,r-magrittr)
7955 ("r-mosaiccore" ,r-mosaiccore)
7956 ("r-rlang" ,r-rlang)
7957 ("r-stringr" ,r-stringr)
7958 ("r-tibble" ,r-tibble)))
7959 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7960 (synopsis "Formula interface for the @code{r-ggplot2}")
7962 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7963 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7964 and extends the excellent simplicity of the lattice-graphics formula interface,
7965 while providing the intuitive capabilities of @code{r-ggplot2}.")
7966 (license license:expat)))
7968 (define-public r-mosaicdata
7970 (name "r-mosaicdata")
7975 (uri (cran-uri "mosaicData" version))
7977 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7978 (properties `((upstream-name . "mosaicData")))
7979 (build-system r-build-system)
7980 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7981 (synopsis "Data sets for project Mosaic")
7983 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7984 used to teach mathematics, statistics, computation and modeling.")
7985 (license license:gpl2+)))
7987 (define-public r-raster
7994 (uri (cran-uri "raster" version))
7997 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
7998 (build-system r-build-system)
8000 `(("r-rcpp" ,r-rcpp)
8002 (home-page "https://www.rspatial.org/")
8003 (synopsis "Geographic data analysis and modeling")
8005 "The package implements basic and high-level functions for reading,
8006 writing, manipulating, analyzing and modeling of gridded spatial data.
8007 Processing of very large files is supported.")
8008 (license license:gpl3+)))
8010 (define-public r-mosaic
8017 (uri (cran-uri "mosaic" version))
8019 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8020 (build-system r-build-system)
8022 `(("r-broom" ,r-broom)
8023 ("r-dplyr" ,r-dplyr)
8024 ("r-ggdendro" ,r-ggdendro)
8025 ("r-ggformula" ,r-ggformula)
8026 ("r-ggplot2" ,r-ggplot2)
8027 ("r-ggrepel" ,r-ggrepel)
8029 ("r-gridextra" ,r-gridextra)
8030 ("r-lattice" ,r-lattice)
8031 ("r-latticeextra" ,r-latticeextra)
8032 ("r-lazyeval" ,r-lazyeval)
8034 ("r-matrix" ,r-matrix)
8035 ("r-mosaiccore" ,r-mosaiccore)
8036 ("r-mosaicdata" ,r-mosaicdata)
8037 ("r-readr" ,r-readr)
8038 ("r-tidyr" ,r-tidyr)))
8040 `(("r-knitr" ,r-knitr)))
8041 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8042 (synopsis "Mathematics, statistics, and computation teaching utilities")
8044 "This package contain data sets and utilities from
8045 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8046 statistics, computation and modeling. Project MOSAIC is a community of
8047 educators working to tie together aspects of quantitative work that students
8048 in science, technology, engineering and mathematics will need in their
8049 professional lives, but which are usually taught in isolation, if at all.")
8050 (license license:gpl2+)))
8052 (define-public r-abd
8059 (uri (cran-uri "abd" version))
8061 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8062 (build-system r-build-system)
8064 `(("r-lattice" ,r-lattice)
8065 ("r-mosaic" ,r-mosaic)
8066 ("r-nlme" ,r-nlme)))
8067 (home-page "https://cran.r-project.org/web/packages/abd/")
8068 (synopsis "Analysis of biological data")
8070 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8071 biological data by Michael Whitlock and Dolph Schluter.")
8072 (license license:gpl2)))
8074 (define-public r-svgui
8081 (uri (cran-uri "svGUI" version))
8083 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8084 (properties `((upstream-name . "svGUI")))
8085 (build-system r-build-system)
8086 (home-page "https://github.com/SciViews/svGUI/")
8087 (synopsis "Functions for managing GUI clients in R")
8089 "The SciViews @code{svGUI} package eases the management of Graphical User
8090 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8091 centralizes info about GUI elements currently used, and it dispatches GUI
8092 calls to the particular toolkits in use in function of the context.")
8093 (license license:gpl2)))
8095 (define-public r-svdialogs
8097 (name "r-svdialogs")
8102 (uri (cran-uri "svDialogs" version))
8104 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8105 (properties `((upstream-name . "svDialogs")))
8106 (build-system r-build-system)
8109 ("zenity" ,zenity)))
8111 `(("r-rstudioapi" ,r-rstudioapi)
8112 ("r-svgui" ,r-svgui)))
8113 (home-page "https://github.com/SciViews/svDialogs/")
8114 (synopsis "Portable dialog boxes")
8116 "This package helps to construct standard dialog boxes for your GUI, including
8117 message boxes, input boxes, list, file or directory selection, and others. In
8118 case R cannot display GUI dialog boxes, a simpler command line version of these
8119 interactive elements is also provided as a fallback solution.")
8120 (license license:gpl2)))
8122 (define-public r-abe
8129 (uri (cran-uri "abe" version))
8132 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8133 (build-system r-build-system)
8134 (home-page "https://cran.r-project.org/web/packages/abe/")
8135 (synopsis "Augmented backward elimination")
8137 "This package performs augmented backward elimination and checks the
8138 stability of the obtained model. Augmented backward elimination combines
8139 significance or information based criteria with the change in estimate to
8140 either select the optimal model for prediction purposes or to serve as a tool
8141 to obtain a practically sound, highly interpretable model.")
8142 (license license:gpl2+)))
8144 (define-public r-abf2
8151 (uri (cran-uri "abf2" version))
8153 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8154 (build-system r-build-system)
8155 (home-page "https://cran.r-project.org/web/packages/abf2/")
8156 (synopsis "Load gap-free axon @code{r-abf2} files")
8158 "This package loads electrophysiology data from ABF2 files, as created by
8159 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8160 mode are currently supported.")
8161 (license license:artistic2.0)))
8163 (define-public r-abhgenotyper
8165 (name "r-abhgenotyper")
8170 (uri (cran-uri "ABHgenotypeR" version))
8172 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8173 (properties `((upstream-name . "ABHgenotypeR")))
8174 (build-system r-build-system)
8176 `(("r-ggplot2" ,r-ggplot2)
8177 ("r-reshape2" ,r-reshape2)))
8178 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8179 (synopsis "Visualize and manipulate ABH genotypes")
8181 "The @code{r-abhgenotyper} package provides simple imputation,
8182 error-correction and plotting capacities for genotype data. The package is
8183 supposed to serve as an intermediate but independent analysis tool between the
8184 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8185 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8186 genotypes as \"graphical genotypes\".")
8187 (license license:gpl3)))
8189 (define-public r-furrr
8196 (uri (cran-uri "furrr" version))
8199 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8200 (build-system r-build-system)
8202 `(("r-future" ,r-future)
8203 ("r-globals" ,r-globals)
8204 ("r-purrr" ,r-purrr)
8205 ("r-rlang" ,r-rlang)))
8206 (home-page "https://github.com/DavisVaughan/furrr")
8207 (synopsis "Apply mapping functions in parallel using futures")
8209 "This package provides implementations of the family of @code{map()}
8210 functions from the @code{purrr} package that can be resolved using any
8211 @code{future}-supported backend, e.g. parallel on the local machine or
8212 distributed on a compute cluster.")
8213 (license license:lgpl2.1+)))
8215 (define-public r-abjutils
8222 (uri (cran-uri "abjutils" version))
8224 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8225 (build-system r-build-system)
8227 `(("r-dplyr" ,r-dplyr)
8228 ("r-magrittr" ,r-magrittr)
8229 ("r-purrr" ,r-purrr)
8230 ("r-rlang" ,r-rlang)
8231 ("r-rstudioapi" ,r-rstudioapi)
8232 ("r-stringi" ,r-stringi)
8233 ("r-stringr" ,r-stringr)
8234 ("r-tidyr" ,r-tidyr)))
8235 (home-page "https://github.com/abjur/abjutils/")
8236 (synopsis "Collection of tools for jurimetrical analysis")
8238 "This package implements general purpose tools, such as functions for
8239 sampling and basic manipulation of Brazilian lawsuits identification number.
8240 It also implements functions for text cleaning, such as accentuation
8242 (license license:expat)))
8244 (define-public r-abnormality
8246 (name "r-abnormality")
8251 (uri (cran-uri "abnormality" version))
8253 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8254 (build-system r-build-system)
8256 `(("r-mass" ,r-mass)
8257 ("r-matrix" ,r-matrix)))
8258 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8259 (synopsis "Measure a subject's abnormality with respect to a reference population")
8261 "This package contains functions to implement the methodology and
8262 considerations laid out by Marks et al. in the article \"Measuring abnormality
8263 in high dimensional spaces: applications in biomechanical gait analysis\".
8264 Using high-dimensional datasets to measure a subject's overall level of
8265 abnormality as compared to a reference population is often needed in outcomes
8267 (license license:expat)))
8269 (define-public r-abodoutlier
8271 (name "r-abodoutlier")
8276 (uri (cran-uri "abodOutlier" version))
8278 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8279 (properties `((upstream-name . "abodOutlier")))
8280 (build-system r-build-system)
8282 `(("r-cluster" ,r-cluster)))
8283 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8284 (synopsis "Angle-based outlier detection")
8286 "This package performs angle-based outlier detection on a given data
8287 frame. It offers three methods to process data:
8289 @item full but slow implementation using all the data that has cubic
8291 @item a fully randomized method;
8292 @item a method using k-nearest neighbours.
8294 These algorithms are well suited for high dimensional data outlier
8296 (license license:expat)))
8298 (define-public r-abps
8305 (uri (cran-uri "ABPS" version))
8307 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8308 (properties `((upstream-name . "ABPS")))
8309 (build-system r-build-system)
8310 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8311 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8312 (synopsis "Abnormal blood profile score to detect blood doping")
8314 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8315 The ABPS is a part of the Athlete biological passport program of the World
8316 anti-doping agency, which combines several blood parameters into a single
8317 score in order to detect blood doping. The package also contains functions to
8318 calculate other scores used in anti-doping programs, such as the ratio of
8319 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8320 (license license:gpl2+)))
8322 (define-public r-parmigene
8324 (name "r-parmigene")
8329 (uri (cran-uri "parmigene" version))
8332 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8333 (build-system r-build-system)
8334 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8335 (synopsis "Mutual information estimation for gene network reconstruction")
8337 "This package provides a parallel estimation of the mutual information
8338 based on entropy estimates from k-nearest neighbors distances and algorithms
8339 for the reconstruction of gene regulatory networks.")
8340 (license license:agpl3+)))
8342 (define-public r-pscl
8349 (uri (cran-uri "pscl" version))
8351 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8352 (build-system r-build-system)
8354 `(("r-mass" ,r-mass)))
8355 (home-page "https://github.com/atahk/pscl/")
8356 (synopsis "Political science computational laboratory")
8358 "The @code{pscl} is an R package providing classes and methods for:
8360 @item Bayesian analysis of roll call data (item-response models);
8361 @item elementary Bayesian statistics;
8362 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8364 @item utility functions.
8366 (license license:gpl2)))
8368 (define-public r-accelmissing
8370 (name "r-accelmissing")
8375 (uri (cran-uri "accelmissing" version))
8377 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8378 (build-system r-build-system)
8380 `(("r-mice" ,r-mice)
8381 ("r-pscl" ,r-pscl)))
8382 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8383 (synopsis "Missing value imputation for accelerometer data")
8385 "This package provides a statistical method to impute the missing values in
8386 accelerometer data. The methodology includes both parametric and
8387 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8388 model. It also provides multiple functions to preprocess the accelerometer data
8389 previous to the missing data imputation. These include detecting the wearing
8390 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8391 (license license:gpl2+)))
8393 (define-public r-mhsmm
8400 (uri (cran-uri "mhsmm" version))
8402 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8403 (build-system r-build-system)
8404 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8405 (home-page "https://github.com/jaredo/mhsmm/")
8406 (synopsis "Inference for hidden Markov and semi-Markov models")
8408 "The @code{r-mhsmm} package implements estimation and prediction methods for
8409 hidden Markov and semi-Markov models for multiple observation sequences. Such
8410 techniques are of interest when observed data is thought to be dependent on some
8411 unobserved (or hidden) state. Also, this package is suitable for equidistant
8412 time series data, with multivariate and/or missing data. Allows user defined
8413 emission distributions.")
8414 (license license:gpl2+)))
8416 (define-public r-nleqslv
8423 (uri (cran-uri "nleqslv" version))
8425 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8426 (build-system r-build-system)
8427 (native-inputs `(("gfortran" ,gfortran)))
8428 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8429 (synopsis "Solve systems of nonlinear equations")
8431 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8432 Broyden or a Newton method with a choice of global strategies such as line
8433 search and trust region. There are options for using a numerical or user
8434 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8435 singular or ill-conditioned Jacobian.")
8436 (license license:gpl2+)))
8438 (define-public r-physicalactivity
8440 (name "r-physicalactivity")
8445 (uri (cran-uri "PhysicalActivity" version))
8447 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8449 `((upstream-name . "PhysicalActivity")))
8450 (build-system r-build-system)
8451 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8452 (synopsis "Procesing accelerometer data for physical activity measurement")
8454 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8455 for classification of monitor wear and nonwear time intervals in accelerometer
8456 data collected to assess physical activity. The package also contains functions
8457 for making plots of accelerometer data and obtaining the summary of various
8458 information including daily monitor wear time and the mean monitor wear time
8459 during valid days. The revised package version 0.2-1 improved the functions
8460 regarding speed, robustness and add better support for time zones and daylight
8461 saving. In addition, several functions were added:
8463 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8464 @item the @code{markPAI} can categorize physical activity intensity level based
8465 on user-defined cut-points of accelerometer counts.
8467 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8468 @code{queryActigraph} functions.")
8469 (license license:gpl3+)))
8471 (define-public r-acc
8478 (uri (cran-uri "acc" version))
8480 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8481 (build-system r-build-system)
8483 `(("r-circlize" ,r-circlize)
8485 ("r-ggplot2" ,r-ggplot2)
8486 ("r-iterators" ,r-iterators)
8487 ("r-mhsmm" ,r-mhsmm)
8488 ("r-nleqslv" ,r-nleqslv)
8489 ("r-physicalactivity" ,r-physicalactivity)
8491 ("r-r-utils" ,r-r-utils)
8493 ("r-rcpparmadillo" ,r-rcpparmadillo)
8494 ("r-rsqlite" ,r-rsqlite)
8496 (home-page "https://cran.r-project.org/web/packages/acc/")
8497 (synopsis "Exploring accelerometer data")
8499 "This package processes accelerometer data from uni-axial and tri-axial devices
8500 and generates data summaries. Also, includes functions to plot, analyze, and
8501 simulate accelerometer data.")
8502 (license license:gpl2+)))
8504 (define-public r-rbenchmark
8506 (name "r-rbenchmark")
8511 (uri (cran-uri "rbenchmark" version))
8513 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8514 (build-system r-build-system)
8515 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8516 (synopsis "Benchmarking routine for R")
8518 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8519 and is intended to facilitate benchmarking of arbitrary R code. The library
8520 consists of just one function, benchmark, which is a simple wrapper around
8521 system.time. Given a specification of the benchmarking process (counts of
8522 replications, evaluation environment) and an arbitrary number of expressions,
8523 benchmark evaluates each of the expressions in the specified environment,
8524 replicating the evaluation as many times as specified, and returning the results
8525 conveniently wrapped into a data frame.")
8526 (license license:gpl2+)))
8528 (define-public r-mitools
8535 (uri (cran-uri "mitools" version))
8538 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8539 (build-system r-build-system)
8540 (propagated-inputs `(("r-dbi" ,r-dbi)))
8541 (home-page "https://cran.r-project.org/web/packages/mitools/")
8542 (synopsis "Tools for multiple imputation of missing data")
8544 "This package provides tools to perform analyses and combine results from
8545 multiple-imputation datasets.")
8546 (license license:gpl2)))
8548 (define-public r-magick
8555 (uri (cran-uri "magick" version))
8558 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8559 (build-system r-build-system)
8561 `(("imagemagick" ,imagemagick)
8564 `(("r-curl" ,r-curl)
8565 ("r-magrittr" ,r-magrittr)
8566 ("r-rcpp" ,r-rcpp)))
8568 `(("pkg-config" ,pkg-config)
8569 ("r-knitr" ,r-knitr)))
8570 (home-page "https://github.com/ropensci/magick")
8571 (synopsis "Advanced graphics and image-processing in R")
8573 "This package provides bindings to ImageMagick, a comprehensive image
8574 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8575 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8576 operations are vectorized via the Magick++ STL meaning they operate either on
8577 a single frame or a series of frames for working with layers, collages, or
8578 animation. In RStudio, images are automatically previewed when printed to the
8579 console, resulting in an interactive editing environment.")
8580 (license license:expat)))
8582 (define-public r-survey
8589 (uri (cran-uri "survey" version))
8592 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8593 (build-system r-build-system)
8595 `(("r-lattice" ,r-lattice)
8596 ("r-matrix" ,r-matrix)
8597 ("r-minqa" ,r-minqa)
8598 ("r-mitools" ,r-mitools)
8599 ("r-numderiv" ,r-numderiv)
8600 ("r-survival" ,r-survival)))
8601 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8602 (synopsis "Analysis of complex survey samples")
8604 "This package provides tools for the analysis of complex survey samples.
8605 The provided features include: summary statistics, two-sample tests, rank
8606 tests, generalised linear models, cumulative link models, Cox models,
8607 loglinear models, and general maximum pseudolikelihood estimation for
8608 multistage stratified, cluster-sampled, unequally weighted survey samples;
8609 variances by Taylor series linearisation or replicate weights;
8610 post-stratification, calibration, and raking; two-phase subsampling designs;
8611 graphics; PPS sampling without replacement; principal components, and factor
8613 ;; Either version of the GPL.
8614 (license (list license:gpl2 license:gpl3))))
8616 (define-public r-gee
8623 (uri (cran-uri "gee" version))
8626 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8627 (properties `((upstream-name . "gee")))
8628 (build-system r-build-system)
8630 `(("gfortran" ,gfortran)))
8631 (home-page "https://cran.r-project.org/web/packages/gee/")
8632 (synopsis "Generalized estimation equation solver")
8634 "This package provides a solver for generalized estimation equations.")
8635 (license license:gpl2)))
8637 (define-public r-tab
8644 (uri (cran-uri "tab" version))
8647 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8648 (properties `((upstream-name . "tab")))
8649 (build-system r-build-system)
8651 `(("r-dplyr" ,r-dplyr)
8653 ("r-knitr" ,r-knitr)
8655 ("r-survey" ,r-survey)
8656 ("r-survival" ,r-survival)
8657 ("r-xtable" ,r-xtable)))
8658 (home-page "https://cran.r-project.org/web/packages/tab/")
8659 (synopsis "Create summary tables for statistical reports")
8661 "This package contains functions for creating various types of summary
8662 tables, e.g. comparing characteristics across levels of a categorical variable
8663 and summarizing fitted generalized linear models, generalized estimating
8664 equations, and Cox proportional hazards models. Functions are available to
8665 handle data from simple random samples as well as complex surveys.")
8666 (license license:gpl3+)))
8668 (define-public r-dvmisc
8675 (uri (cran-uri "dvmisc" version))
8677 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8678 (build-system r-build-system)
8680 `(("r-cubature" ,r-cubature)
8681 ("r-data-table" ,r-data-table)
8682 ("r-dplyr" ,r-dplyr)
8683 ("r-ggplot2" ,r-ggplot2)
8685 ("r-mvtnorm" ,r-mvtnorm)
8686 ("r-pracma" ,r-pracma)
8687 ("r-rbenchmark" ,r-rbenchmark)
8689 ("r-survey" ,r-survey)
8691 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8692 (synopsis "Faster computation of common statistics and miscellaneous functions")
8694 "This package implements faster versions of base R functions (e.g. mean, standard
8695 deviation, covariance, weighted mean), mostly written in C++, along with
8696 miscellaneous functions for various purposes (e.g. create the histogram with
8697 fitted probability density function or probability mass function curve, create
8698 the body mass index groups, assess the linearity assumption in logistic
8700 (license license:gpl2)))
8702 (define-public r-accelerometry
8704 (name "r-accelerometry")
8709 (uri (cran-uri "accelerometry" version))
8711 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8712 (build-system r-build-system)
8714 `(("r-dvmisc" ,r-dvmisc)
8715 ("r-rcpp" ,r-rcpp)))
8716 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8717 (synopsis "Functions for processing accelerometer data")
8719 "This package provides a collection of functions that perform operations on
8720 time-series accelerometer data, such as identify the non-wear time, flag minutes
8721 that are part of an activity bout, and find the maximum 10-minute average count
8722 value. The functions are generally very flexible, allowing for a variety of
8723 algorithms to be implemented.")
8724 (license license:gpl3)))
8726 (define-public r-absim
8733 (uri (cran-uri "AbSim" version))
8735 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8736 (properties `((upstream-name . "AbSim")))
8737 (build-system r-build-system)
8740 ("r-powerlaw" ,r-powerlaw)))
8741 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8742 (synopsis "Time resolved simulations of antibody repertoires")
8744 "This package provides simulation methods for the evolution of antibody repertoires.
8745 The heavy and light chain variable region of both human and C57BL/6 mice can
8746 be simulated in a time-dependent fashion. Both single lineages using one set of
8747 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8748 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8749 Upon completion, the main loop of the algorithm begins, with each iteration
8750 representing one simulated time step. Various mutation events are possible at
8751 each time step, contributing to a diverse final repertoire.")
8752 (license license:gpl2)))
8754 (define-public r-quic
8761 (uri (cran-uri "QUIC" version))
8763 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8764 (properties `((upstream-name . "QUIC")))
8765 (build-system r-build-system)
8766 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8767 (synopsis "Regularized sparse inverse covariance matrix estimation")
8769 "This package implements the regularized Gaussian maximum likelihood
8770 estimation of the inverse of a covariance matrix. It uses Newton's method and
8771 coordinate descent to solve the regularized inverse covariance matrix
8772 estimation problem.")
8773 ;; The project home page states that the release is under GPLv3 or later.
8774 ;; The CRAN page only says GPL-3.
8775 (license license:gpl3+)))
8777 (define-public r-abundant
8784 (uri (cran-uri "abundant" version))
8786 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8787 (build-system r-build-system)
8789 `(("r-quic" ,r-quic)))
8790 (home-page "https://cran.r-project.org/web/packages/abundant/")
8791 (synopsis "Abundant regression and high-dimensional principal fitted components")
8793 "This package provides tools to fit and predict with the high-dimensional
8794 principal fitted components model. This model is described by Cook, Forzani,
8795 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8796 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8797 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8798 (license license:gpl2+)))
8800 (define-public r-ac3net
8807 (uri (cran-uri "Ac3net" version))
8809 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8810 (properties `((upstream-name . "Ac3net")))
8811 (build-system r-build-system)
8813 `(("r-data-table" ,r-data-table)))
8814 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8815 (synopsis "Inferring directional conservative causal core gene networks")
8816 (description "This package infers directional Conservative causal core
8817 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8818 directional network.")
8819 (license license:gpl3+)))
8821 (define-public r-aca
8828 (uri (cran-uri "ACA" version))
8830 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8831 (properties `((upstream-name . "ACA")))
8832 (build-system r-build-system)
8833 (home-page "https://cran.r-project.org/web/packages/ACA/")
8834 (synopsis "Abrupt change-point or aberration detection in point series")
8836 "This package offers an interactive function for the detection of breakpoints in
8838 ;; Any version of the GPL
8839 (license (list license:gpl2+ license:gpl3+))))
8841 (define-public r-acceptancesampling
8843 (name "r-acceptancesampling")
8848 (uri (cran-uri "AcceptanceSampling" version))
8850 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8852 `((upstream-name . "AcceptanceSampling")))
8853 (build-system r-build-system)
8854 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8855 (synopsis "Creation and evaluation of acceptance sampling plans")
8857 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8858 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8859 in quality control and improvement. International standards of acceptance
8860 sampling provide sampling plans for specific circumstances. The aim of this
8861 package is to provide an easy-to-use interface to visualize single, double or
8862 multiple sampling plans. In addition, methods have been provided to enable the
8863 user to assess sampling plans against pre-specified levels of performance, as
8864 measured by the probability of acceptance for a given level of quality in the
8866 (license license:gpl3+)))
8868 (define-public r-acclma
8875 (uri (cran-uri "ACCLMA" version))
8877 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8878 (properties `((upstream-name . "ACCLMA")))
8879 (build-system r-build-system)
8880 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8881 (synopsis "ACC & LMA graph plotting")
8883 "This package contains a function that imports data from a @acronym{CSV,
8884 Comma-Separated Values} file, or uses manually entered data from the format (x,
8885 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8886 Curve} vs @acronym{LOI, Line of Independence} graph and
8887 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8888 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8889 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8890 string) was passed, a manual data entry window is opened. The header parameter
8891 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8892 a header row or not. The dataset should contain only one independent variable
8893 (x) and one dependent variable (y) and can contain a weight for each
8895 (license license:gpl2)))
8897 (define-public r-aspi
8904 (uri (cran-uri "aspi" version))
8906 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8907 (build-system r-build-system)
8909 "https://cran.r-project.org/web/packages/aspi/")
8911 "Analysis of symmetry of parasitic infections")
8913 "This package provides tools for the analysis and visualization of bilateral
8914 asymmetry in parasitic infections.")
8915 (license license:gpl3+)))
8917 (define-public r-sandwich
8924 (uri (cran-uri "sandwich" version))
8927 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8928 (build-system r-build-system)
8930 `(("r-zoo" ,r-zoo)))
8931 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8932 (synopsis "Robust Covariance Matrix Estimators")
8934 "This package provides model-robust standard error estimators for
8935 cross-sectional, time series, clustered, panel, and longitudinal data.")
8936 ;; Either version of the license.
8937 (license (list license:gpl2 license:gpl3))))
8939 (define-public r-th-data
8946 (uri (cran-uri "TH.data" version))
8949 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8950 (properties `((upstream-name . "TH.data")))
8951 (build-system r-build-system)
8953 `(("r-mass" ,r-mass)
8954 ("r-survival" ,r-survival)))
8955 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8956 (synopsis "Shared data sets")
8958 "This package contains supporting data sets that are used in other
8959 packages maintained by Torsten Hothorn.")
8960 (license license:gpl3)))
8962 (define-public r-multcomp
8969 (uri (cran-uri "multcomp" version))
8972 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8973 (build-system r-build-system)
8975 `(("r-codetools" ,r-codetools)
8976 ("r-mvtnorm" ,r-mvtnorm)
8977 ("r-sandwich" ,r-sandwich)
8978 ("r-survival" ,r-survival)
8979 ("r-th-data" ,r-th-data)))
8980 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8981 (synopsis "Simultaneous inference in general parametric models")
8983 "Simultaneous tests and confidence intervals for general linear
8984 hypotheses in parametric models, including linear, generalized linear, linear
8985 mixed effects, and survival models. The package includes demos reproducing
8986 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8987 Hothorn, Westfall, 2010, CRC Press).")
8988 (license license:gpl2)))
8990 (define-public r-emmeans
8997 (uri (cran-uri "emmeans" version))
9000 "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k"))))
9001 (build-system r-build-system)
9003 `(("r-estimability" ,r-estimability)
9004 ("r-mvtnorm" ,r-mvtnorm)
9005 ("r-numderiv" ,r-numderiv)
9007 ("r-xtable" ,r-xtable)))
9009 `(("r-knitr" ,r-knitr)))
9010 (home-page "https://github.com/rvlenth/emmeans")
9011 (synopsis "Estimated marginal means, aka least-squares means")
9013 "This package provides tools to obtain @dfn{estimated marginal
9014 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9015 be used to compute contrasts or linear functions of EMMs, trends, and
9016 comparisons of slopes.")
9017 ;; Either version of the license.
9018 (license (list license:gpl2 license:gpl3))))
9020 (define-public r-pwr
9027 (uri (cran-uri "pwr" version))
9030 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9031 (build-system r-build-system)
9033 `(("r-knitr" ,r-knitr)))
9034 (home-page "https://github.com/heliosdrm/pwr")
9035 (synopsis "Basic functions for power analysis")
9037 "This package provides power analysis functions along the lines of
9039 (license license:gpl3+)))
9041 (define-public r-libcoin
9048 (uri (cran-uri "libcoin" version))
9050 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
9051 (build-system r-build-system)
9052 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9053 (home-page "https://cran.r-project.org/web/packages/libcoin")
9054 (synopsis "Linear test statistics for permutation inference")
9056 "This package provides basic infrastructure for linear test statistics
9057 and permutation inference in the framework of Strasser and Weber (1999).")
9058 (license license:gpl2)))
9060 (define-public r-coin
9067 (uri (cran-uri "coin" version))
9070 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
9071 (build-system r-build-system)
9073 `(("r-libcoin" ,r-libcoin)
9074 ("r-matrixstats" ,r-matrixstats)
9075 ("r-modeltools" ,r-modeltools)
9076 ("r-multcomp" ,r-multcomp)
9077 ("r-mvtnorm" ,r-mvtnorm)
9078 ("r-survival" ,r-survival)))
9079 (home-page "http://coin.r-forge.r-project.org")
9080 (synopsis "Conditional inference procedures in a permutation test framework")
9082 "This package provides conditional inference procedures for the general
9083 independence problem including two-sample, K-sample (non-parametric ANOVA),
9084 correlation, censored, ordered and multivariate problems.")
9085 (license license:gpl2)))
9087 (define-public r-bayesplot
9089 (name "r-bayesplot")
9094 (uri (cran-uri "bayesplot" version))
9097 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
9098 (build-system r-build-system)
9100 `(("pandoc" ,pandoc)
9101 ("pandoc-citeproc" ,pandoc-citeproc)))
9103 `(("r-knitr" ,r-knitr)))
9105 `(("r-dplyr" ,r-dplyr)
9106 ("r-ggplot2" ,r-ggplot2)
9107 ("r-ggridges" ,r-ggridges)
9109 ("r-reshape2" ,r-reshape2)
9110 ("r-rlang" ,r-rlang)
9111 ("r-tibble" ,r-tibble)
9112 ("r-tidyselect" ,r-tidyselect)))
9113 (home-page "https://mc-stan.org/bayesplot")
9114 (synopsis "Plotting for Bayesian models")
9116 "This package provides plotting functions for posterior analysis, model
9117 checking, and MCMC diagnostics. The package is designed not only to provide
9118 convenient functionality for users, but also a common set of functions that
9119 can be easily used by developers working on a variety of R packages for
9120 Bayesian modeling.")
9121 (license license:gpl3+)))
9123 (define-public r-tmb
9130 (uri (cran-uri "TMB" version))
9133 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
9134 (properties `((upstream-name . "TMB")))
9135 (build-system r-build-system)
9137 `(("r-matrix" ,r-matrix)
9138 ("r-rcppeigen" ,r-rcppeigen)))
9139 (home-page "http://tmb-project.org")
9140 (synopsis "Template model builder: a general random effect tool")
9142 "With this tool, a user should be able to quickly implement complex
9143 random effect models through simple C++ templates. The package combines
9144 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9145 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9146 from R) to obtain an efficient implementation of the applied Laplace
9147 approximation with exact derivatives. Key features are: Automatic sparseness
9148 detection, parallelism through BLAS and parallel user templates.")
9149 (license license:gpl2)))
9151 (define-public r-sjstats
9158 (uri (cran-uri "sjstats" version))
9160 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
9161 (build-system r-build-system)
9163 `(("r-bayestestr" ,r-bayestestr)
9164 ("r-broom" ,r-broom)
9165 ("r-dplyr" ,r-dplyr)
9166 ("r-effectsize" ,r-effectsize)
9167 ("r-emmeans" ,r-emmeans)
9168 ("r-insight" ,r-insight)
9170 ("r-magrittr" ,r-magrittr)
9172 ("r-modelr" ,r-modelr)
9173 ("r-parameters" ,r-parameters)
9174 ("r-performance" ,r-performance)
9175 ("r-purrr" ,r-purrr)
9176 ("r-rlang" ,r-rlang)
9177 ("r-sjlabelled" ,r-sjlabelled)
9178 ("r-sjmisc" ,r-sjmisc)
9179 ("r-tidyr" ,r-tidyr)))
9180 (home-page "https://github.com/strengejacke/sjstats")
9181 (synopsis "Functions for common statistical computations")
9183 "This package provides a collection of convenient functions for common
9184 statistical computations, which are not directly provided by R's @code{base}
9185 or @code{stats} packages. This package aims at providing, first, shortcuts
9186 for statistical measures, which otherwise could only be calculated with
9187 additional effort. Second, these shortcut functions are generic, and can be
9188 applied not only to vectors, but also to other objects as well. The focus of
9189 most functions lies on summary statistics or fit measures for regression
9190 models, including generalized linear models, mixed effects models and Bayesian
9192 (license license:gpl3)))
9194 (define-public r-glmmtmb
9201 (uri (cran-uri "glmmTMB" version))
9204 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9205 (properties `((upstream-name . "glmmTMB")))
9206 (build-system r-build-system)
9208 `(("r-lme4" ,r-lme4)
9209 ("r-matrix" ,r-matrix)
9211 ("r-rcppeigen" ,r-rcppeigen)
9214 `(("r-knitr" ,r-knitr))) ; for vignettes
9215 (home-page "https://github.com/glmmTMB")
9216 (synopsis "Generalized linear mixed models")
9218 "Fit linear and generalized linear mixed models with various extensions,
9219 including zero-inflation. The models are fitted using maximum likelihood
9220 estimation via the Template Model Builder. Random effects are assumed to be
9221 Gaussian on the scale of the linear predictor and are integrated out using the
9222 Laplace approximation. Gradients are calculated using automatic
9224 (license license:agpl3+)))
9226 (define-public r-bayestestr
9228 (name "r-bayestestr")
9233 (uri (cran-uri "bayestestR" version))
9236 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2"))))
9237 (properties `((upstream-name . "bayestestR")))
9238 (build-system r-build-system)
9240 `(("r-insight" ,r-insight)))
9242 `(("r-knitr" ,r-knitr)))
9243 (home-page "https://github.com/easystats/bayestestR")
9244 (synopsis "Describe Bayesian models and posterior distributions")
9246 "This package provides utilities to understand and describe posterior
9247 distributions and Bayesian models. It includes point-estimates such as
9248 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9249 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9250 ROPE percentage and pd).")
9251 (license license:gpl3)))
9253 (define-public r-performance
9255 (name "r-performance")
9260 (uri (cran-uri "performance" version))
9263 "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
9264 (build-system r-build-system)
9266 `(("r-bayestestr" ,r-bayestestr)
9267 ("r-insight" ,r-insight)))
9268 (home-page "https://easystats.github.io/performance/")
9269 (synopsis "Assessment of regression models performance")
9271 "This package provides utilities for computing measures to assess model
9272 quality, which are not directly provided by R's @code{base} or @code{stats}
9273 packages. These include e.g. measures like r-squared, intraclass correlation
9274 coefficient, root mean squared error or functions to check models for
9275 overdispersion, singularity or zero-inflation and more. Functions apply to a
9276 large variety of regression models, including generalized linear models, mixed
9277 effects models and Bayesian models.")
9278 (license license:gpl3)))
9280 (define-public r-ggeffects
9282 (name "r-ggeffects")
9287 (uri (cran-uri "ggeffects" version))
9290 "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
9291 (build-system r-build-system)
9293 `(("r-insight" ,r-insight)
9295 ("r-sjlabelled" ,r-sjlabelled)))
9297 `(("r-knitr" ,r-knitr)))
9298 (home-page "https://github.com/strengejacke/ggeffects")
9299 (synopsis "Create tidy data frames of marginal effects for ggplot")
9301 "This package provides tools to compute marginal effects from statistical
9302 models and return the result as tidy data frames. These data frames are ready
9303 to use with the @code{ggplot2} package. Marginal effects can be calculated
9304 for many different models. Interaction terms, splines and polynomial terms
9305 are also supported. The two main functions are @code{ggpredict()} and
9306 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9307 results using @code{ggplot2}.")
9308 (license license:gpl3)))
9310 (define-public r-effectsize
9312 (name "r-effectsize")
9317 (uri (cran-uri "effectsize" version))
9320 "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9"))))
9321 (properties `((upstream-name . "effectsize")))
9322 (build-system r-build-system)
9324 `(("r-bayestestr" ,r-bayestestr)
9325 ("r-insight" ,r-insight)
9326 ("r-parameters" ,r-parameters)))
9328 `(("r-knitr" ,r-knitr)))
9329 (home-page "https://github.com/easystats/effectsize")
9330 (synopsis "Indices of effect size and standardized parameters")
9332 "This package provides utilities to work with indices of effect size and
9333 standardized parameters for a wide variety of models, allowing computation and
9334 conversion of indices such as Cohen's d, r, odds, etc.")
9335 (license license:gpl3)))
9337 (define-public r-sjplot
9344 (uri (cran-uri "sjPlot" version))
9346 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9347 (properties `((upstream-name . "sjPlot")))
9348 (build-system r-build-system)
9350 `(("r-bayestestr" ,r-bayestestr)
9351 ("r-dplyr" ,r-dplyr)
9352 ("r-effectsize" ,r-effectsize)
9353 ("r-ggeffects" ,r-ggeffects)
9354 ("r-ggplot2" ,r-ggplot2)
9355 ("r-insight" ,r-insight)
9356 ("r-knitr" ,r-knitr)
9358 ("r-parameters" ,r-parameters)
9359 ("r-performance" ,r-performance)
9360 ("r-purrr" ,r-purrr)
9361 ("r-rlang" ,r-rlang)
9362 ("r-scales" ,r-scales)
9363 ("r-sjlabelled" ,r-sjlabelled)
9364 ("r-sjmisc" ,r-sjmisc)
9365 ("r-sjstats" ,r-sjstats)
9366 ("r-tidyr" ,r-tidyr)))
9368 `(("r-knitr" ,r-knitr)))
9369 (home-page "https://strengejacke.github.io/sjPlot/")
9370 (synopsis "Data visualization for statistics in social science")
9372 "This package represents a collection of plotting and table output
9373 functions for data visualization. Results of various statistical
9374 analyses (that are commonly used in social sciences) can be visualized using
9375 this package, including simple and cross tabulated frequencies, histograms,
9376 box plots, (generalized) linear models, mixed effects models, principal
9377 component analysis and correlation matrices, cluster analyses, scatter plots,
9378 stacked scales, effects plots of regression models (including interaction
9379 terms) and much more. This package supports labelled data.")
9380 (license license:gpl3)))
9382 (define-public r-ini
9389 (uri (cran-uri "ini" version))
9392 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9393 (build-system r-build-system)
9394 (home-page "https://github.com/dvdscripter/ini")
9395 (synopsis "Read and write configuration files")
9397 "This package provides tools to parse simple @code{.ini} configuration
9398 files to an structured list. Users can manipulate this resulting list with
9399 @code{lapply()} functions. This same structured list can be used to write
9400 back to file after modifications.")
9401 (license license:gpl3)))
9410 (uri (cran-uri "gh" version))
9413 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9414 (build-system r-build-system)
9419 ("r-jsonlite" ,r-jsonlite)))
9420 (home-page "https://github.com/r-lib/gh#readme")
9421 (synopsis "Access the GitHub API via R")
9423 "This package provides a minimal R client to access the GitHub API.")
9424 (license license:expat)))
9433 (uri (cran-uri "fs" version))
9436 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9437 (build-system r-build-system)
9439 `(("r-knitr" ,r-knitr)))
9440 (home-page "https://fs.r-lib.org")
9441 (synopsis "Cross-platform file system operations based on libuv")
9443 "This package provides a cross-platform interface to file system
9444 operations, built on top of the libuv C library.")
9445 (license license:gpl3)))
9447 (define-public r-clisymbols
9449 (name "r-clisymbols")
9454 (uri (cran-uri "clisymbols" version))
9457 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9458 (build-system r-build-system)
9459 (home-page "https://github.com/gaborcsardi/clisymbols")
9460 (synopsis "Unicode symbols at the R prompt")
9462 "This package provides a small subset of Unicode symbols, that are useful
9463 when building command line applications. They fall back to alternatives on
9464 terminals that do not support Unicode.")
9465 (license license:expat)))
9467 (define-public r-usethis
9474 (uri (cran-uri "usethis" version))
9477 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9478 (build-system r-build-system)
9481 ("r-clipr" ,r-clipr)
9482 ("r-crayon" ,r-crayon)
9487 ("r-git2r" ,r-git2r)
9489 ("r-purrr" ,r-purrr)
9490 ("r-rematch2" ,r-rematch2)
9491 ("r-rlang" ,r-rlang)
9492 ("r-rprojroot" ,r-rprojroot)
9493 ("r-rstudioapi" ,r-rstudioapi)
9494 ("r-whisker" ,r-whisker)
9495 ("r-withr" ,r-withr)
9496 ("r-yaml" ,r-yaml)))
9497 (home-page "https://github.com/r-lib/usethis")
9498 (synopsis "Automate R package and project setup")
9500 "This package helps you to automate R package and project setup tasks
9501 that are otherwise performed manually. This includes setting up unit testing,
9502 test coverage, continuous integration, Git, GitHub integration, licenses,
9503 Rcpp, RStudio projects, and more.")
9504 (license license:gpl3)))
9506 (define-public r-sessioninfo
9508 (name "r-sessioninfo")
9513 (uri (cran-uri "sessioninfo" version))
9516 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9517 (build-system r-build-system)
9520 ("r-withr" ,r-withr)))
9521 (home-page "https://github.com/r-lib/sessioninfo#readme")
9522 (synopsis "R session information")
9524 "This package provides tools to query and print information about the
9525 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9526 more information about packages, and where they were installed from.")
9527 (license license:gpl2)))
9529 (define-public r-remotes
9536 (uri (cran-uri "remotes" version))
9539 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9540 (build-system r-build-system)
9542 `(("r-knitr" ,r-knitr)))
9543 (home-page "https://github.com/r-lib/remotes#readme")
9544 (synopsis "R package installation from remote repositories")
9546 "Download and install R packages stored in GitHub, BitBucket, or plain
9547 subversion or git repositories. This package is a lightweight replacement of
9548 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9549 the code was copied over from @code{devtools}.")
9550 (license license:gpl2+)))
9552 (define-public r-xopen
9559 (uri (cran-uri "xopen" version))
9562 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9563 (build-system r-build-system)
9565 `(("r-processx" ,r-processx)))
9566 (home-page "https://github.com/r-lib/xopen#readme")
9567 (synopsis "Open system files, URLs, anything")
9569 "This package provides a cross-platform solution to open files,
9570 directories or URLs with their associated programs.")
9571 (license license:expat)))
9573 (define-public r-rcmdcheck
9575 (name "r-rcmdcheck")
9580 (uri (cran-uri "rcmdcheck" version))
9583 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9584 (build-system r-build-system)
9586 `(("r-callr" ,r-callr)
9588 ("r-crayon" ,r-crayon)
9590 ("r-digest" ,r-digest)
9591 ("r-pkgbuild" ,r-pkgbuild)
9592 ("r-prettyunits" ,r-prettyunits)
9594 ("r-rprojroot" ,r-rprojroot)
9595 ("r-sessioninfo" ,r-sessioninfo)
9596 ("r-withr" ,r-withr)
9597 ("r-xopen" ,r-xopen)))
9598 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9599 (synopsis "Run R CMD check from R and capture results")
9601 "Run @code{R CMD check} from R programmatically, and capture the results
9602 of the individual checks.")
9603 (license license:expat)))
9605 (define-public r-rapportools
9607 (name "r-rapportools")
9612 (uri (cran-uri "rapportools" version))
9615 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9616 (build-system r-build-system)
9618 `(("r-pander" ,r-pander)
9620 ("r-reshape" ,r-reshape)))
9621 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9622 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9624 "This package provides helper functions that act as wrappers to more
9625 advanced statistical methods with the advantage of having sane defaults for
9627 (license license:agpl3+)))
9629 (define-public r-pander
9636 (uri (cran-uri "pander" version))
9639 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9640 (build-system r-build-system)
9642 `(("r-digest" ,r-digest)
9643 ("r-rcpp" ,r-rcpp)))
9644 (home-page "https://rapporter.github.io/pander")
9645 (synopsis "Render R objects into Pandoc's markdown")
9647 "The main aim of the pander R package is to provide a minimal and easy
9648 tool for rendering R objects into Pandoc's markdown. The package is also
9649 capable of exporting/converting complex Pandoc documents (reports) in various
9651 ;; This package is licensed under either the AGPLv3+ or the very rarely
9653 (license license:agpl3+)))
9655 (define-public r-summarytools
9657 (name "r-summarytools")
9662 (uri (cran-uri "summarytools" version))
9665 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9666 (build-system r-build-system)
9668 `(("r-base64enc" ,r-base64enc)
9669 ("r-checkmate" ,r-checkmate)
9670 ("r-dplyr" ,r-dplyr)
9671 ("r-htmltools" ,r-htmltools)
9672 ("r-lubridate" ,r-lubridate)
9673 ("r-magick" ,r-magick)
9674 ("r-matrixstats" ,r-matrixstats)
9675 ("r-pander" ,r-pander)
9677 ("r-rapportools" ,r-rapportools)
9678 ("r-tibble" ,r-tibble)
9679 ("r-tidyr" ,r-tidyr)))
9680 (home-page "https://github.com/dcomtois/summarytools")
9681 (synopsis "Tools to quickly and neatly summarize data")
9683 "This package provides tools for data frame summaries, cross-tabulations,
9684 weight-enabled frequency tables and common univariate statistics in concise
9685 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9686 good point-of-entry for exploring data, both for experienced and new R
9688 (license license:gpl2)))
9690 (define-public r-lsei
9697 (uri (cran-uri "lsei" version))
9700 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9701 (build-system r-build-system)
9703 `(("gfortran" ,gfortran)))
9704 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9705 (synopsis "Solve regression problems under equality/inequality constraints")
9707 "It contains functions that solve least squares linear regression
9708 problems under linear equality/inequality constraints. Functions for solving
9709 quadratic programming problems are also available, which transform such
9710 problems into least squares ones first.")
9711 (license license:gpl2+)))
9713 (define-public r-npsurv
9720 (uri (cran-uri "npsurv" version))
9723 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9724 (build-system r-build-system)
9726 `(("r-lsei" ,r-lsei)))
9727 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9728 (synopsis "Nonparametric survival analysis")
9730 "This package contains functions for non-parametric survival analysis of
9731 exact and interval-censored observations.")
9732 (license license:gpl2+)))
9734 (define-public r-clusteval
9736 (name "r-clusteval")
9741 (uri (cran-uri "clusteval" version))
9744 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9745 (build-system r-build-system)
9747 `(("r-mvtnorm" ,r-mvtnorm)
9748 ("r-rcpp" ,r-rcpp)))
9749 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9750 (synopsis "Evaluation of clustering algorithms")
9752 "This R package provides a suite of tools to evaluate clustering
9753 algorithms, clusterings, and individual clusters.")
9754 (license license:expat)))
9756 (define-public r-tweedie
9763 (uri (cran-uri "tweedie" version))
9766 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9767 (build-system r-build-system)
9768 (native-inputs `(("gfortran" ,gfortran)))
9769 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9770 (synopsis "Evaluation of Tweedie exponential family models")
9772 "Maximum likelihood computations for Tweedie families, including the
9773 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9774 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9775 and related methods.")
9776 (license license:gpl2+)))
9778 (define-public r-rcppgsl
9785 (uri (cran-uri "RcppGSL" version))
9787 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9788 (properties `((upstream-name . "RcppGSL")))
9789 (build-system r-build-system)
9791 `(("r-rcpp" ,r-rcpp)
9793 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9794 (synopsis "Rcpp integration for GSL vectors and matrices")
9796 "The GNU Scientific Library (or GSL) is a collection of numerical
9797 routines for scientific computing. It is particularly useful for C and C++
9798 programs as it provides a standard C interface to a wide range of mathematical
9799 routines. There are over 1000 functions in total with an extensive test
9800 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9801 structures and R using concepts from Rcpp which is itself a package that eases
9802 the interfaces between R and C++.")
9803 (license license:gpl2+)))
9805 (define-public r-mvabund
9812 (uri (cran-uri "mvabund" version))
9815 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9816 (build-system r-build-system)
9818 `(("r-mass" ,r-mass)
9820 ("r-rcppgsl" ,r-rcppgsl)
9821 ("r-statmod" ,r-statmod)
9822 ("r-tweedie" ,r-tweedie)))
9823 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9824 (synopsis "Statistical methods for analysing multivariate abundance data")
9826 "This package provides a set of tools for displaying, modeling and
9827 analysing multivariate abundance data in community ecology.")
9828 (license license:lgpl2.1+)))
9830 (define-public r-afex
9837 (uri (cran-uri "afex" version))
9840 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9841 (build-system r-build-system)
9845 ("r-lmertest" ,r-lmertest)
9846 ("r-pbkrtest" ,r-pbkrtest)
9847 ("r-reshape2" ,r-reshape2)))
9849 `(("r-knitr" ,r-knitr)))
9850 (home-page "https://afex.singmann.science/")
9851 (synopsis "Analysis of factorial experiments")
9853 "This package provides convenience functions for analyzing factorial
9854 experiments using ANOVA or mixed models.")
9855 (license license:gpl2+)))
9857 (define-public r-lmertest
9864 (uri (cran-uri "lmerTest" version))
9867 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9868 (properties `((upstream-name . "lmerTest")))
9869 (build-system r-build-system)
9871 `(("r-ggplot2" ,r-ggplot2)
9874 ("r-numderiv" ,r-numderiv)))
9875 (home-page "https://github.com/runehaubo/lmerTestR")
9876 (synopsis "Tests in linear mixed effects models")
9878 "This package provides p-values in type I, II or III anova and summary
9879 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9880 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9881 package. Model selection methods include step, drop1 and anova-like tables
9882 for random effects (ranova). Methods for Least-Square means (LS-means) and
9883 tests of linear contrasts of fixed effects are also available.")
9884 (license license:gpl2+)))
9886 (define-public r-r2glmm
9893 (uri (cran-uri "r2glmm" version))
9896 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9897 (build-system r-build-system)
9899 `(("r-afex" ,r-afex)
9900 ("r-data-table" ,r-data-table)
9901 ("r-dplyr" ,r-dplyr)
9902 ("r-ggplot2" ,r-ggplot2)
9903 ("r-gridextra" ,r-gridextra)
9904 ("r-lmertest" ,r-lmertest)
9906 ("r-matrix" ,r-matrix)
9908 ("r-pbkrtest" ,r-pbkrtest)))
9909 (home-page "https://github.com/bcjaeger/r2glmm")
9910 (synopsis "Compute R squared for mixed (multilevel) models")
9912 "This package computes model and semi partial R squared with confidence
9913 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9914 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9915 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9917 (license license:gpl2)))
9919 (define-public r-weights
9926 (uri (cran-uri "weights" version))
9929 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9930 (build-system r-build-system)
9932 `(("r-gdata" ,r-gdata)
9933 ("r-hmisc" ,r-hmisc)
9934 ("r-mice" ,r-mice)))
9936 "https://cran.r-project.org/web/packages/weights/")
9937 (synopsis "Weighting and weighted statistics")
9938 (description "This package Provides a variety of functions for producing
9939 simple weighted statistics, such as weighted Pearson's correlations, partial
9940 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9941 includes some software for quickly recoding survey data and plotting point
9942 estimates from interaction terms in regressions (and multiply imputed
9943 regressions). NOTE: Weighted partial correlation calculations pulled to
9945 (license license:gpl2+)))
9947 (define-public r-rcppannoy
9949 (name "r-rcppannoy")
9954 (uri (cran-uri "RcppAnnoy" version))
9957 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9958 (properties `((upstream-name . "RcppAnnoy")))
9959 (build-system r-build-system)
9961 `(("r-rcpp" ,r-rcpp)))
9962 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9963 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9965 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9966 for efficient memory usage as well an ability to load from and save to disk.
9967 This package provides an R interface.")
9968 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9970 (license (list license:gpl2+ license:asl2.0))))
9972 (define-public r-rcpphnsw
9979 (uri (cran-uri "RcppHNSW" version))
9982 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9983 (properties `((upstream-name . "RcppHNSW")))
9984 (build-system r-build-system)
9985 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9986 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9987 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9989 "Hnswlib is a C++ library for approximate nearest neighbors. This
9990 package provides a minimal R interface by relying on the Rcpp package.")
9991 ;; hnswlib is released under Version 2.0 of the Apache License.
9992 (license (list license:gpl3 license:asl2.0))))
9994 (define-public r-rcppparallel
9996 (name "r-rcppparallel")
10001 (uri (cran-uri "RcppParallel" version))
10004 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10005 (properties `((upstream-name . "RcppParallel")))
10006 (build-system r-build-system)
10007 (home-page "https://rcppcore.github.io/RcppParallel/")
10008 (synopsis "Parallel programming tools for Rcpp")
10010 "This package provides high level functions for parallel programming with
10011 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10012 the work of a standard serial @code{for} loop into a parallel one and the
10013 @code{parallelReduce()} function can be used for accumulating aggregates or
10015 (license license:gpl2)))
10017 (define-public r-ncdf4
10024 (uri (cran-uri "ncdf4" version))
10027 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10028 (build-system r-build-system)
10030 `(("netcdf" ,netcdf)
10032 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10033 (synopsis "R interface to Unidata netCDF format data files")
10035 "This package provides a high-level R interface to data files written
10036 using Unidata's netCDF library (version 4 or earlier), which are binary data
10037 files that are portable across platforms and include metadata information in
10038 addition to the data sets. Using this package, netCDF files can be opened and
10039 data sets read in easily. It is also easy to create new netCDF dimensions,
10040 variables, and files, in either version 3 or 4 format, and manipulate existing
10042 (license license:gpl3+)))
10044 (define-public r-biocmanager
10046 (name "r-biocmanager")
10047 (version "1.30.10")
10051 (uri (cran-uri "BiocManager" version))
10053 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10054 (properties `((upstream-name . "BiocManager")))
10055 (build-system r-build-system)
10056 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10057 (synopsis "Access the Bioconductor project package repository")
10059 "This package provides a convenient tool to install and update
10060 Bioconductor packages.")
10061 (license license:artistic2.0)))
10063 (define-public r-rgl
10066 (version "0.100.54")
10070 (uri (cran-uri "rgl" version))
10073 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
10074 (build-system r-build-system)
10076 `(("pkg-config" ,pkg-config)))
10078 `(("freetype" ,freetype)
10085 `(("r-crosstalk" ,r-crosstalk)
10086 ("r-htmltools" ,r-htmltools)
10087 ("r-htmlwidgets" ,r-htmlwidgets)
10088 ("r-jsonlite" ,r-jsonlite)
10089 ("r-knitr" ,r-knitr)
10090 ("r-magrittr" ,r-magrittr)
10091 ("r-manipulatewidget" ,r-manipulatewidget)
10092 ("r-shiny" ,r-shiny)))
10093 (home-page "https://r-forge.r-project.org/projects/rgl/")
10094 (synopsis "3D visualization using OpenGL")
10096 "This package provides medium to high level functions for 3D interactive graphics,
10097 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
10098 as functions for constructing representations of geometric
10099 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
10100 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
10101 image formats, including PNG, Postscript, SVG, PGF.")
10102 ;; Any version of the GPL.
10103 (license (list license:gpl2+ license:gpl3+))))
10105 (define-public r-multicool
10107 (name "r-multicool")
10112 (uri (cran-uri "multicool" version))
10115 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
10116 (build-system r-build-system)
10117 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10118 (home-page "https://cran.r-project.org/web/packages/multicool/")
10119 (synopsis "Permutations of multisets in cool-lex order")
10121 "This package provides a set of tools to permute multisets without loops
10122 or hash tables and to generate integer partitions. Cool-lex order is similar
10123 to colexicographical order.")
10124 (license license:gpl2)))
10126 (define-public r-misc3d
10133 (uri (cran-uri "misc3d" version))
10136 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
10137 (build-system r-build-system)
10138 (home-page "https://cran.r-project.org/web/packages/misc3d/")
10139 (synopsis "Miscellaneous 3D Plots")
10141 "This package provides a collection of miscellaneous 3d plots, including
10143 ;; Any version of the GPL.
10144 (license (list license:gpl2+ license:gpl3+))))
10146 (define-public r-ks
10153 (uri (cran-uri "ks" version))
10155 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
10156 (build-system r-build-system)
10159 ("r-kernlab" ,r-kernlab)
10160 ("r-kernsmooth" ,r-kernsmooth)
10161 ("r-matrix" ,r-matrix)
10162 ("r-mclust" ,r-mclust)
10164 ("r-multicool" ,r-multicool)
10165 ("r-mvtnorm" ,r-mvtnorm)))
10166 (home-page "http://www.mvstat.net/tduong/")
10167 (synopsis "Kernel smoothing")
10169 "This package provides kernel smoothers for univariate and multivariate
10170 data, including density functions, density derivatives, cumulative
10171 distributions, modal clustering, discriminant analysis, and two-sample
10172 hypothesis testing.")
10173 ;; Either version of the GPL.
10174 (license (list license:gpl2 license:gpl3))))
10176 (define-public r-feature
10183 (uri (cran-uri "feature" version))
10186 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
10187 (build-system r-build-system)
10190 ("r-misc3d" ,r-misc3d)
10192 (home-page "http://www.mvstat.net/tduong/")
10193 (synopsis "Inferential feature significance for kernel density estimation")
10195 "The feature package contains functions to display and compute kernel
10196 density estimates, significant gradient and significant curvature regions.
10197 Significant gradient and/or curvature regions often correspond to significant
10198 features (e.g. local modes).")
10199 ;; Either version of the GPL.
10200 (license (list license:gpl2 license:gpl3))))
10202 (define-public r-arm
10209 (uri (cran-uri "arm" version))
10212 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10213 (build-system r-build-system)
10215 `(("r-abind" ,r-abind)
10217 ("r-hmisc" ,r-hmisc)
10220 ("r-matrix" ,r-matrix)
10221 ("r-nlme" ,r-nlme)))
10222 (home-page "https://cran.r-project.org/web/packages/arm/")
10223 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10225 "This package provides functions to accompany A. Gelman and J. Hill,
10226 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10227 University Press, 2007.")
10228 (license license:gpl3+)))
10230 (define-public r-circular
10232 (name "r-circular")
10237 (uri (cran-uri "circular" version))
10240 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10241 (build-system r-build-system)
10243 `(("r-boot" ,r-boot)
10244 ("r-mvtnorm" ,r-mvtnorm)))
10246 `(("gfortran" ,gfortran)))
10247 (home-page "https://cran.r-project.org/web/packages/circular/")
10248 (synopsis "Circular statistics")
10250 "This package provides tools for circular statistics, from \"Topics in
10251 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10253 (license license:gpl2+)))
10255 (define-public r-activity
10257 (name "r-activity")
10262 (uri (cran-uri "activity" version))
10265 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10266 (build-system r-build-system)
10268 `(("r-circular" ,r-circular)
10269 ("r-insol" ,r-insol)
10270 ("r-pbapply" ,r-pbapply)))
10271 (home-page "https://cran.r-project.org/web/packages/activity/")
10272 (synopsis "Animal activity statistics")
10274 "This package provides functions to fit kernel density functions to
10275 animal activity time data; plot activity distributions; quantify overall
10276 levels of activity; statistically compare activity metrics through
10277 bootstrapping; and evaluate variation in linear variables with time (or other
10278 circular variables).")
10279 (license license:gpl3)))
10281 (define-public r-ouch
10288 (uri (cran-uri "ouch" version))
10291 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10292 (build-system r-build-system)
10293 (propagated-inputs `(("r-subplex" ,r-subplex)))
10294 (home-page "https://kingaa.github.io/ouch/")
10295 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10297 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10298 for evolution along a phylogenetic tree.")
10299 (license license:gpl2+)))
10301 (define-public r-fmsb
10308 (uri (cran-uri "fmsb" version))
10311 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10312 (build-system r-build-system)
10313 (home-page "http://minato.sip21c.org/msb/")
10314 (synopsis "Functions for medical statistics book with demographic data")
10316 "This package provides several utility functions for the book entitled
10317 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10318 Japan, 2007) with Japanese demographic data and some demographic analysis
10319 related functions.")
10320 (license license:gpl2+)))
10322 (define-public r-stabledist
10324 (name "r-stabledist")
10329 (uri (cran-uri "stabledist" version))
10332 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10333 (build-system r-build-system)
10334 (home-page "https://www.rmetrics.org")
10335 (synopsis "Stable distribution functions")
10337 "This package provides density, probability and quantile functions, and
10338 random number generation for (skew) stable distributions, using the
10339 parametrizations of Nolan.")
10340 (license license:gpl2+)))
10342 (define-public r-gsl
10349 (uri (cran-uri "gsl" version))
10352 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10353 (build-system r-build-system)
10356 (home-page "https://cran.r-project.org/web/packages/gsl")
10357 (synopsis "Wrapper for the GNU Scientific Library")
10359 "This package provides an R wrapper for the special functions and quasi
10360 random number generators of the GNU Scientific Library.")
10361 (license license:gpl2+)))
10363 (define-public r-adgoftest
10365 (name "r-adgoftest")
10370 (uri (cran-uri "ADGofTest" version))
10373 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10374 (properties `((upstream-name . "ADGofTest")))
10375 (build-system r-build-system)
10376 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10377 (synopsis "Anderson-Darling GoF test")
10379 "This package provides an implementation of the Anderson-Darling GoF test
10380 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10381 Anderson-Darling Distribution\".")
10382 ;; Any version of the GPL.
10383 (license license:gpl3+)))
10385 (define-public r-softimpute
10387 (name "r-softimpute")
10392 (uri (cran-uri "softImpute" version))
10395 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10396 (properties `((upstream-name . "softImpute")))
10397 (build-system r-build-system)
10399 `(("r-matrix" ,r-matrix)))
10401 `(("gfortran" ,gfortran)))
10402 (home-page "https://cran.r-project.org/web/packages/softImpute")
10403 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10405 "This package provides iterative methods for matrix completion that use
10406 nuclear-norm regularization. The package includes procedures for centering
10407 and scaling rows, columns or both, and for computing low-rank @dfn{single
10408 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10410 (license license:gpl2)))
10412 (define-public r-fftwtools
10414 (name "r-fftwtools")
10419 (uri (cran-uri "fftwtools" version))
10422 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10423 (build-system r-build-system)
10424 (inputs `(("fftw" ,fftw)))
10425 (home-page "https://github.com/krahim/fftwtools")
10426 (synopsis "Wrapper for FFTW3")
10428 "This package provides a wrapper for several FFTW functions. It provides
10429 access to the two-dimensional FFT, the multivariate FFT, and the
10430 one-dimensional real to complex FFT using the FFTW3 library. The package
10431 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10432 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10433 The FFT functions have a parameter that allows them to not return the
10434 redundant complex conjugate when the input is real data.")
10435 (license license:gpl2+)))
10437 (define-public r-tiff
10444 (uri (cran-uri "tiff" version))
10447 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10448 (build-system r-build-system)
10450 `(("libtiff" ,libtiff)
10451 ("libjpeg" ,libjpeg-turbo)
10453 (home-page "https://www.rforge.net/tiff/")
10454 (synopsis "Read and write TIFF images")
10456 "This package provides an easy and simple way to read, write and display
10457 bitmap images stored in the TIFF format. It can read and write both files and
10458 in-memory raw vectors.")
10459 ;; Either of these two license versions.
10460 (license (list license:gpl2 license:gpl3))))
10462 (define-public r-nlp
10469 (uri (cran-uri "NLP" version))
10472 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10473 (properties `((upstream-name . "NLP")))
10474 (build-system r-build-system)
10475 (home-page "https://cran.r-project.org/web/packages/NLP/")
10476 (synopsis "Natural language processing infrastructure")
10478 "This package provides basic classes and methods for Natural Language
10480 (license license:gpl3)))
10482 (define-public r-tm
10489 (uri (cran-uri "tm" version))
10492 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10493 (properties `((upstream-name . "tm")))
10494 (build-system r-build-system)
10500 ("r-xml2" ,r-xml2)))
10501 (home-page "http://tm.r-forge.r-project.org/")
10502 (synopsis "Text mining package")
10504 "This package provides a framework for text mining applications within R.")
10505 (license license:gpl3)))
10507 (define-public r-waveslim
10509 (name "r-waveslim")
10514 (uri (cran-uri "waveslim" version))
10517 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10518 (build-system r-build-system)
10520 `(("gfortran" ,gfortran)))
10521 (home-page "http://waveslim.blogspot.com")
10522 (synopsis "Basic wavelet routines for signal processing")
10524 "This package provides basic wavelet routines for time series (1D),
10525 image (2D) and array (3D) analysis. The code provided here is based on
10526 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10527 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10528 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10529 pairs (Selesnick 2001, 2002).")
10530 (license license:bsd-3)))
10532 (define-public r-wordcloud
10534 (name "r-wordcloud")
10539 (uri (cran-uri "wordcloud" version))
10542 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10543 (build-system r-build-system)
10545 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10547 ;; The "tm" package is only "suggested" according to CRAN, but the
10548 ;; wordcloud package cannot be loaded without it.
10550 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10551 (synopsis "Word clouds")
10553 "This package provides functionality to create pretty word clouds,
10554 visualize differences and similarity between documents, and avoid
10555 over-plotting in scatter plots with text.")
10556 (license license:lgpl2.1)))
10558 (define-public r-colorramps
10560 (name "r-colorramps")
10565 (uri (cran-uri "colorRamps" version))
10568 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10569 (properties `((upstream-name . "colorRamps")))
10570 (build-system r-build-system)
10571 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10572 (synopsis "Build color tables")
10573 (description "This package provides features to build gradient color
10575 ;; Any version of the GPL
10576 (license license:gpl3+)))
10578 (define-public r-tidytree
10580 (name "r-tidytree")
10585 (uri (cran-uri "tidytree" version))
10587 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10588 (build-system r-build-system)
10591 ("r-dplyr" ,r-dplyr)
10592 ("r-lazyeval" ,r-lazyeval)
10593 ("r-magrittr" ,r-magrittr)
10594 ("r-rlang" ,r-rlang)
10595 ("r-tibble" ,r-tibble)))
10597 `(("r-knitr" ,r-knitr)))
10598 (home-page "https://github.com/GuangchuangYu/tidytree")
10599 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10601 "Phylogenetic trees generally contain multiple components including nodes,
10602 edges, branches and associated data. This package provides an approach to
10603 convert tree objects to tidy data frames. It also provides tidy interfaces to
10604 manipulate tree data.")
10605 (license license:artistic2.0)))
10607 (define-public r-rvcheck
10614 (uri (cran-uri "rvcheck" version))
10616 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10617 (build-system r-build-system)
10619 `(("r-biocmanager" ,r-biocmanager)
10620 ("r-rlang" ,r-rlang)))
10621 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10622 (synopsis "R package version check")
10624 "This package provides tools to check the latest release version of R and
10625 R packages (on CRAN, Bioconductor or Github).")
10626 (license license:artistic2.0)))
10628 (define-public r-docopt
10635 (uri (cran-uri "docopt" version))
10638 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10639 (build-system r-build-system)
10640 (home-page "https://github.com/docopt/docopt.R")
10641 (synopsis "Command-line interface specification language")
10643 "This package enables you to define a command-line interface by just
10644 giving it a description in the specific format.")
10645 (license license:expat)))
10647 (define-public r-sparsesvd
10649 (name "r-sparsesvd")
10654 (uri (cran-uri "sparsesvd" version))
10657 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10658 (build-system r-build-system)
10659 (propagated-inputs `(("r-matrix" ,r-matrix)))
10660 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10661 (synopsis "Sparse truncated singular value decomposition")
10663 "This package provides a Wrapper around the SVDLIBC library
10664 for (truncated) singular value decomposition of a sparse matrix. Currently,
10665 only sparse real matrices in Matrix package format are supported.")
10666 ;; SVDLIBC is released under BSD-2. The R interface is released under
10668 (license (list license:bsd-3 license:bsd-2))))
10670 (define-public r-speedglm
10672 (name "r-speedglm")
10677 (uri (cran-uri "speedglm" version))
10680 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10681 (build-system r-build-system)
10683 `(("r-mass" ,r-mass)
10684 ("r-matrix" ,r-matrix)))
10685 (home-page "https://cran.r-project.org/web/packages/speedglm")
10686 (synopsis "Fit linear and generalized linear models to large data sets")
10688 "This package provides tools for fitting linear models and generalized
10689 linear models to large data sets by updating algorithms.")
10690 ;; Any version of the GPL
10691 (license license:gpl2+)))
10693 (define-public r-densityclust
10695 (name "r-densityclust")
10700 (uri (cran-uri "densityClust" version))
10703 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10704 (properties `((upstream-name . "densityClust")))
10705 (build-system r-build-system)
10708 ("r-ggplot2" ,r-ggplot2)
10709 ("r-ggrepel" ,r-ggrepel)
10710 ("r-gridextra" ,r-gridextra)
10711 ("r-rcolorbrewer" ,r-rcolorbrewer)
10713 ("r-rtsne" ,r-rtsne)))
10714 (home-page "https://cran.r-project.org/web/packages/densityClust")
10715 (synopsis "Clustering by fast search and find of density peaks")
10717 "This package provides an improved implementation (based on k-nearest
10718 neighbors) of the density peak clustering algorithm, originally described by
10719 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10720 large datasets (> 100,000 samples) very efficiently.")
10721 (license license:gpl2+)))
10723 (define-public r-combinat
10725 (name "r-combinat")
10730 (uri (cran-uri "combinat" version))
10733 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10734 (build-system r-build-system)
10735 (home-page "https://cran.r-project.org/web/packages/combinat")
10736 (synopsis "Combinatorics utilities")
10737 (description "This package provides assorted routines for combinatorics.")
10738 (license license:gpl2)))
10740 (define-public r-qlcmatrix
10742 (name "r-qlcmatrix")
10747 (uri (cran-uri "qlcMatrix" version))
10750 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10751 (properties `((upstream-name . "qlcMatrix")))
10752 (build-system r-build-system)
10754 `(("r-docopt" ,r-docopt)
10755 ("r-matrix" ,r-matrix)
10757 ("r-sparsesvd" ,r-sparsesvd)))
10758 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10759 (synopsis "Sparse matrix functions for quantitative language comparison")
10761 "This package provides an extension of the functionality of the Matrix
10762 package for using sparse matrices. Some of the functions are very general,
10763 while other are highly specific for the special data format used for
10764 @dfn{quantitative language comparison} (QLC).")
10765 (license license:gpl3)))
10767 (define-public r-ddrtree
10774 (uri (cran-uri "DDRTree" version))
10777 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10778 (properties `((upstream-name . "DDRTree")))
10779 (build-system r-build-system)
10782 ("r-irlba" ,r-irlba)
10784 ("r-rcppeigen" ,r-rcppeigen)))
10785 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10786 (synopsis "Learning principal graphs with DDRTree")
10788 "This package provides an implementation of the framework of
10789 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10790 dimensional space while constructs a principal tree which passes through the
10791 middle of the data simultaneously. DDRTree shows superiority to
10792 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10793 intrinsic structure of single cell genomics data. In general, it could be
10794 used to reconstruct the temporal progression as well as the bifurcation
10795 structure of any data type.")
10796 (license license:asl2.0)))
10798 (define-public r-corpcor
10805 (uri (cran-uri "corpcor" version))
10808 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10809 (build-system r-build-system)
10810 (home-page "http://strimmerlab.org/software/corpcor/")
10811 (synopsis "Efficient estimation of covariance and (partial) correlation")
10813 "This package implements a James-Stein-type shrinkage estimator for the
10814 covariance matrix, with separate shrinkage for variances and correlations.
10815 Furthermore, functions are available for fast singular value decomposition,
10816 for computing the pseudoinverse, and for checking the rank and positive
10817 definiteness of a matrix.")
10818 (license license:gpl3+)))
10820 (define-public r-rspectra
10822 (name "r-rspectra")
10827 (uri (cran-uri "RSpectra" version))
10830 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10831 (properties `((upstream-name . "RSpectra")))
10832 (build-system r-build-system)
10834 `(("r-matrix" ,r-matrix)
10836 ("r-rcppeigen" ,r-rcppeigen)))
10837 (home-page "https://github.com/yixuan/RSpectra")
10838 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10840 "This package provides an R interface to the Spectra library for
10841 large-scale eigenvalue and SVD problems. It is typically used to compute a
10842 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10843 which is usually more efficient than @code{eigen()} if k << n.")
10845 (license license:mpl2.0)))
10847 (define-public r-vbsr
10854 (uri (cran-uri "vbsr" version))
10857 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10858 (build-system r-build-system)
10859 (home-page "https://cran.r-project.org/web/packages/vbsr")
10860 (synopsis "Variational Bayes spike regression regularized linear models")
10862 "This package provides an efficient algorithm for solving ultra-sparse
10863 regularized regression models using a variational Bayes algorithm with a spike
10864 prior. The algorithm is solved on a path, with coordinate updates, and is
10865 capable of generating very sparse models. Very general model
10866 diagnostics for controlling type-1 errors are also provided.")
10867 (license license:gpl2)))
10869 (define-public r-flare
10872 (version "1.6.0.2")
10876 (uri (cran-uri "flare" version))
10879 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10880 (build-system r-build-system)
10882 `(("r-igraph" ,r-igraph)
10883 ("r-lattice" ,r-lattice)
10885 ("r-matrix" ,r-matrix)))
10886 (home-page "https://cran.r-project.org/web/packages/flare")
10887 (synopsis "Family of Lasso regression implementations")
10889 "This package provides implementations of a family of Lasso variants
10890 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10891 high dimensional sparse linear models.")
10892 (license license:gpl2)))
10894 (define-public r-lassopv
10901 (uri (cran-uri "lassopv" version))
10904 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10905 (build-system r-build-system)
10906 (propagated-inputs `(("r-lars" ,r-lars)))
10907 (home-page "https://github.com/lingfeiwang/lassopv")
10908 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10910 "This package enables you to estimate the p-values for predictors x
10911 against target variable y in Lasso regression, using the regularization
10912 strength when each predictor enters the active set of regularization path for
10913 the first time as the statistic.")
10914 (license license:gpl3)))
10916 (define-public r-splitstackshape
10918 (name "r-splitstackshape")
10923 (uri (cran-uri "splitstackshape" version))
10926 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10927 (build-system r-build-system)
10929 `(("r-data-table" ,r-data-table)))
10930 (home-page "https://github.com/mrdwab/splitstackshape")
10931 (synopsis "Stack and reshape datasets after splitting concatenated values")
10933 "Online data collection tools like Google Forms often export
10934 multiple-response questions with data concatenated in cells. The
10935 @code{concat.split} (cSplit) family of functions provided by this package
10936 splits such data into separate cells. This package also includes functions to
10937 stack groups of columns and to reshape wide data, even when the data are
10938 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10939 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10941 (license license:gpl3)))
10943 (define-public r-tfmpvalue
10945 (name "r-tfmpvalue")
10950 (uri (cran-uri "TFMPvalue" version))
10953 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10954 (properties `((upstream-name . "TFMPvalue")))
10955 (build-system r-build-system)
10956 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10957 (home-page "https://github.com/ge11232002/TFMPvalue")
10958 (synopsis "P-value computation for position weight matrices")
10960 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10961 identification from sequence/alignments, we are interested in the significance
10962 of certain match scores. TFMPvalue provides the accurate calculation of a
10963 p-value with a score threshold for position weight matrices, or the score with
10964 a given p-value. It is an interface to code originally made available by
10965 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10966 Touzet and Varre (2007).")
10967 (license license:gpl2)))
10969 (define-public r-rnifti
10976 (uri (cran-uri "RNifti" version))
10979 "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
10980 (properties `((upstream-name . "RNifti")))
10981 (build-system r-build-system)
10982 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10983 (home-page "https://github.com/jonclayden/RNifti")
10984 (synopsis "Fast R and C++ access to NIfTI images")
10986 "This package provides very fast read and write access to images stored
10987 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10988 compiled C and interpreted R code. It also provides a C/C++ API that can be
10989 used by other packages.")
10990 (license license:gpl2)))
10992 (define-public r-shades
10999 (uri (cran-uri "shades" version))
11002 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
11003 (build-system r-build-system)
11004 (home-page "https://github.com/jonclayden/shades")
11005 (synopsis "Simple color manipulation")
11007 "This package provides functions for easily manipulating colors,
11008 creating color scales and calculating color distances.")
11009 (license license:bsd-3)))
11011 (define-public r-ore
11018 (uri (cran-uri "ore" version))
11020 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11021 (build-system r-build-system)
11022 (home-page "https://github.com/jonclayden/ore")
11023 (synopsis "R interface to the Onigmo regular expression library")
11025 "This package provides an alternative to R's built-in functionality for
11026 handling regular expressions, based on the Onigmo library. It offers
11027 first-class compiled regex objects, partial matching and function-based
11028 substitutions, amongst other features.")
11029 (license license:bsd-3)))
11031 (define-public r-reportr
11038 (uri (cran-uri "reportr" version))
11041 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11042 (build-system r-build-system)
11043 (propagated-inputs `(("r-ore" ,r-ore)))
11044 (home-page "https://github.com/jonclayden/reportr")
11045 (synopsis "General message and error reporting system")
11047 "This package provides a system for reporting messages, which offers
11048 certain useful features over the standard R system, such as the incorporation
11049 of output consolidation, message filtering, assertions, expression
11050 substitution, automatic generation of stack traces for debugging, and
11051 conditional reporting based on the current \"output level\".")
11052 (license license:gpl2)))
11054 (define-public r-tractor-base
11056 (name "r-tractor-base")
11061 (uri (cran-uri "tractor.base" version))
11064 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
11065 (properties `((upstream-name . "tractor.base")))
11066 (build-system r-build-system)
11069 ("r-reportr" ,r-reportr)
11070 ("r-rnifti" ,r-rnifti)
11071 ("r-shades" ,r-shades)))
11072 (home-page "https://www.tractor-mri.org.uk")
11073 (synopsis "Read, manipulate and visualize magnetic resonance images")
11075 "This package provides functions for working with magnetic resonance
11076 images. It supports reading and writing of popular file formats (DICOM,
11077 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
11078 visualization; flexible image manipulation; metadata and sparse image
11080 (license license:gpl2)))
11082 (define-public r-grimport
11084 (name "r-grimport")
11089 (uri (cran-uri "grImport" version))
11092 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
11093 (properties `((upstream-name . "grImport")))
11094 (build-system r-build-system)
11096 `(("ghostscript" ,ghostscript)))
11098 `(("r-xml" ,r-xml)))
11099 (home-page "https://cran.r-project.org/web/packages/grImport")
11100 (synopsis "Convert, import, and draw PostScript pictures")
11102 "This package provides functions for converting, importing, and drawing
11103 PostScript pictures in R plots.")
11104 (license license:gpl2+)))
11106 (define-public r-grimport2
11108 (name "r-grimport2")
11113 (uri (cran-uri "grImport2" version))
11116 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
11117 (properties `((upstream-name . "grImport2")))
11118 (build-system r-build-system)
11120 `(("r-base64enc" ,r-base64enc)
11124 (home-page "https://cran.r-project.org/web/packages/grImport2/")
11125 (synopsis "Import SVG graphics")
11127 "This package provides functions for importing external vector images and
11128 drawing them as part of R plots. This package is different from the
11129 @code{grImport} package because, where that package imports PostScript format
11130 images, this package imports SVG format images. Furthermore, this package
11131 imports a specific subset of SVG, so external images must be preprocessed
11132 using a package like @code{rsvg} to produce SVG that this package can import.
11133 SVG features that are not supported by R graphics, such as gradient fills, can
11134 be imported and then exported via the @code{gridSVG} package.")
11135 (license license:gpl2+)))
11137 (define-public r-kohonen
11144 (uri (cran-uri "kohonen" version))
11147 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
11148 (build-system r-build-system)
11150 `(("r-rcpp" ,r-rcpp)))
11151 (home-page "https://cran.r-project.org/web/packages/kohonen")
11152 (synopsis "Supervised and unsupervised self-organising maps")
11154 "This package provides functions to train @dfn{self-organising
11155 maps} (SOMs). Also interrogation of the maps and prediction using trained
11156 maps are supported. The name of the package refers to Teuvo Kohonen, the
11157 inventor of the SOM.")
11158 (license license:gpl2+)))
11160 (define-public r-nnls
11167 (uri (cran-uri "nnls" version))
11170 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
11171 (build-system r-build-system)
11172 (native-inputs `(("gfortran" ,gfortran)))
11173 (home-page "https://cran.r-project.org/web/packages/nnls")
11174 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
11176 "This package provides an R interface to the Lawson-Hanson implementation
11177 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
11178 the combination of non-negative and non-positive constraints.")
11179 (license license:gpl2+)))
11181 (define-public r-iso
11184 (version "0.0-18.1")
11188 (uri (cran-uri "Iso" version))
11191 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11192 (properties `((upstream-name . "Iso")))
11193 (build-system r-build-system)
11194 (native-inputs `(("gfortran" ,gfortran)))
11195 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11196 (synopsis "Functions to perform isotonic regression")
11198 "This package provides support for linear order and unimodal
11199 order (univariate) isotonic regression and bivariate isotonic regression with
11200 linear order on both variables.")
11201 (license license:gpl2+)))
11203 (define-public r-chemometricswithr
11205 (name "r-chemometricswithr")
11210 (uri (cran-uri "ChemometricsWithR" version))
11213 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11215 `((upstream-name . "ChemometricsWithR")))
11216 (build-system r-build-system)
11218 `(("r-devtools" ,r-devtools)
11219 ("r-kohonen" ,r-kohonen)
11222 (home-page "https://github.com/rwehrens/CWR")
11223 (synopsis "Chemometrics with R")
11225 "This package provides functions and scripts used in the book
11226 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11227 Life Sciences\" by Ron Wehrens, Springer (2011).")
11228 (license license:gpl2+)))
11230 (define-public r-als
11237 (uri (cran-uri "ALS" version))
11240 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11241 (properties `((upstream-name . "ALS")))
11242 (build-system r-build-system)
11245 ("r-nnls" ,r-nnls)))
11246 (home-page "https://cran.r-project.org/web/packages/ALS")
11247 (synopsis "Multivariate curve resolution alternating least squares")
11249 "Alternating least squares is often used to resolve components
11250 contributing to data with a bilinear structure; the basic technique may be
11251 extended to alternating constrained least squares. This package provides an
11252 implementation of @dfn{multivariate curve resolution alternating least
11253 squares} (MCR-ALS).
11255 Commonly applied constraints include unimodality, non-negativity, and
11256 normalization of components. Several data matrices may be decomposed
11257 simultaneously by assuming that one of the two matrices in the bilinear
11258 decomposition is shared between datasets.")
11259 (license license:gpl2+)))
11261 (define-public r-strucchange
11263 (name "r-strucchange")
11268 (uri (cran-uri "strucchange" version))
11271 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11272 (build-system r-build-system)
11274 `(("r-sandwich" ,r-sandwich)
11276 (home-page "https://cran.r-project.org/web/packages/strucchange")
11277 (synopsis "Testing, monitoring, and dating structural changes")
11279 "This package provides tools for testing, monitoring and dating
11280 structural changes in (linear) regression models. It features tests/methods
11281 from the generalized fluctuation test framework as well as from the F
11282 test (Chow test) framework. This includes methods to fit, plot and test
11283 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11284 statistics, respectively. It is possible to monitor incoming data online
11285 using fluctuation processes. Finally, the breakpoints in regression models
11286 with structural changes can be estimated together with confidence intervals.
11287 Emphasis is always given to methods for visualizing the data.")
11288 ;; Either of these two GPL versions
11289 (license (list license:gpl2 license:gpl3))))
11291 (define-public r-pixmap
11298 (uri (cran-uri "pixmap" version))
11301 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11302 (build-system r-build-system)
11303 (home-page "https://cran.r-project.org/web/packages/pixmap")
11304 (synopsis "Tools for bitmap images")
11306 "This package provides functions for importing, exporting, plotting and
11307 other manipulations of bitmapped images.")
11308 (license license:gpl2)))
11310 (define-public r-rapidjsonr
11312 (name "r-rapidjsonr")
11317 (uri (cran-uri "rapidjsonr" version))
11320 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11321 (build-system r-build-system)
11322 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11323 (synopsis "JSON parser")
11325 "This package provides JSON parsing capability through the Rapidjson
11327 (license license:expat)))
11329 (define-public r-ontologyindex
11331 (name "r-ontologyindex")
11336 (uri (cran-uri "ontologyIndex" version))
11339 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11340 (properties `((upstream-name . "ontologyIndex")))
11341 (build-system r-build-system)
11342 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11343 (synopsis "Functions for processing ontologies in R")
11345 "This package provides functions for reading ontologies into R as lists
11346 and manipulating sets of ontological terms.")
11347 (license license:gpl2+)))
11349 (define-public r-gargle
11356 (uri (cran-uri "gargle" version))
11359 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11360 (build-system r-build-system)
11365 ("r-jsonlite" ,r-jsonlite)
11366 ("r-rlang" ,r-rlang)
11367 ("r-withr" ,r-withr)))
11369 `(("r-knitr" ,r-knitr)))
11370 (home-page "https://gargle.r-lib.org")
11371 (synopsis "Utilities for working with Google APIs")
11373 "This package provides utilities for working with Google APIs. This
11374 includes functions and classes for handling common credential types and for
11375 preparing, executing, and processing HTTP requests.")
11376 (license license:expat)))
11378 (define-public r-bigrquery
11380 (name "r-bigrquery")
11385 (uri (cran-uri "bigrquery" version))
11388 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11389 (build-system r-build-system)
11391 `(("r-assertthat" ,r-assertthat)
11392 ("r-bit64" ,r-bit64)
11395 ("r-gargle" ,r-gargle)
11398 ("r-jsonlite" ,r-jsonlite)
11399 ("r-prettyunits" ,r-prettyunits)
11400 ("r-progress" ,r-progress)
11401 ("r-rapidjsonr" ,r-rapidjsonr)
11403 ("r-rlang" ,r-rlang)
11404 ("r-tibble" ,r-tibble)))
11405 (home-page "https://github.com/rstats-db/bigrquery")
11406 (synopsis "R interface to Google's BigQuery API")
11408 "This package provides an R interface to Google's BigQuery database.")
11409 (license license:gpl3)))
11411 (define-public r-gmp
11418 (uri (cran-uri "gmp" version))
11421 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11422 (build-system r-build-system)
11425 (modify-phases %standard-phases
11426 (add-after 'unpack 'set-CC
11427 (lambda _ (setenv "CC" "gcc") #t)))))
11428 (inputs `(("gmp" ,gmp)))
11429 (home-page "https://cran.r-project.org/web/packages/gmp")
11430 (synopsis "Multiple precision arithmetic")
11432 "This package supports multiple precision arithmetic (big integers and
11433 rationals, prime number tests, matrix computation), \"arithmetic without
11434 limitations\" using the GNU Multiple Precision library.")
11435 ;; Any version of the GPL.
11436 (license license:gpl3+)))
11438 (define-public r-rmpfr
11445 (uri (cran-uri "Rmpfr" version))
11448 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11449 (properties `((upstream-name . "Rmpfr")))
11450 (build-system r-build-system)
11455 `(("r-gmp" ,r-gmp)))
11457 `(("pkg-config" ,pkg-config)))
11458 (home-page "http://rmpfr.r-forge.r-project.org/")
11459 (synopsis "R bindings to the MPFR library")
11461 "This package supports arithmetic (via S4 classes and methods) for
11462 arbitrary precision floating point numbers, including transcendental
11463 functions. To this end, the package interfaces with the @dfn{Multiple
11464 Precision Floating-Point Reliable} (MPFR) library.")
11465 (license license:gpl2+)))
11467 (define-public r-assertive-base
11469 (name "r-assertive-base")
11474 (uri (cran-uri "assertive.base" version))
11477 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11479 `((upstream-name . "assertive.base")))
11480 (build-system r-build-system)
11481 (home-page "https://bitbucket.org/richierocks/assertive.base")
11482 (synopsis "Core of the assertive package")
11484 "This package provides a minimal set of predicates and assertions used by
11485 the assertive package. This is mainly for use by other package developers who
11486 want to include run-time testing features in their own packages.")
11487 (license license:gpl3+)))
11489 (define-public r-assertive-properties
11491 (name "r-assertive-properties")
11496 (uri (cran-uri "assertive.properties" version))
11499 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11501 `((upstream-name . "assertive.properties")))
11502 (build-system r-build-system)
11504 `(("r-assertive-base" ,r-assertive-base)))
11505 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11506 (synopsis "Assertions to check properties of variables")
11508 "This package provides a set of predicates and assertions for checking
11509 the properties of variables, such as length, names and attributes. This is
11510 mainly for use by other package developers who want to include run-time
11511 testing features in their own packages.")
11512 (license license:gpl3+)))
11514 (define-public r-assertive-numbers
11516 (name "r-assertive-numbers")
11521 (uri (cran-uri "assertive.numbers" version))
11524 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11526 `((upstream-name . "assertive.numbers")))
11527 (build-system r-build-system)
11529 `(("r-assertive-base" ,r-assertive-base)))
11530 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11531 (synopsis "Assertions to check properties of numbers")
11533 "This package provides a set of predicates and assertions for checking
11534 the properties of numbers. This is mainly for use by other package developers
11535 who want to include run-time testing features in their own packages.")
11536 (license license:gpl3+)))
11538 (define-public r-assertive-sets
11540 (name "r-assertive-sets")
11545 (uri (cran-uri "assertive.sets" version))
11548 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11550 `((upstream-name . "assertive.sets")))
11551 (build-system r-build-system)
11553 `(("r-assertive-base" ,r-assertive-base)))
11554 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11555 (synopsis "Assertions to check properties of sets")
11557 "This package provides a set of predicates and assertions for checking
11558 the properties of sets. This is mainly for use by other package developers
11559 who want to include run-time testing features in their own packages.")
11560 (license license:gpl3+)))
11562 (define-public r-assertive-matrices
11564 (name "r-assertive-matrices")
11569 (uri (cran-uri "assertive.matrices" version))
11572 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11574 `((upstream-name . "assertive.matrices")))
11575 (build-system r-build-system)
11577 `(("r-assertive-base" ,r-assertive-base)))
11578 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11579 (synopsis "Assertions to check properties of matrices")
11581 "This package provides a set of predicates and assertions for checking
11582 the properties of matrices. This is mainly for use by other package
11583 developers who want to include run-time testing features in their own
11585 (license license:gpl3+)))
11587 (define-public r-assertive-models
11589 (name "r-assertive-models")
11594 (uri (cran-uri "assertive.models" version))
11597 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11599 `((upstream-name . "assertive.models")))
11600 (build-system r-build-system)
11602 `(("r-assertive-base" ,r-assertive-base)))
11603 (home-page "https://bitbucket.org/richierocks/assertive.models")
11604 (synopsis "Assertions to check properties of models")
11606 "This package provides a set of predicates and assertions for checking
11607 the properties of models. This is mainly for use by other package developers
11608 who want to include run-time testing features in their own packages.")
11609 (license license:gpl3+)))
11611 (define-public r-assertive-reflection
11613 (name "r-assertive-reflection")
11618 (uri (cran-uri "assertive.reflection" version))
11621 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11623 `((upstream-name . "assertive.reflection")))
11624 (build-system r-build-system)
11626 `(("r-assertive-base" ,r-assertive-base)))
11627 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11628 (synopsis "Assertions for checking the state of R")
11630 "This package provides a set of predicates and assertions for checking
11631 the state and capabilities of R, the operating system it is running on, and
11632 the IDE being used. This is mainly for use by other package developers who
11633 want to include run-time testing features in their own packages.")
11634 (license license:gpl3+)))
11636 (define-public r-assertive-types
11638 (name "r-assertive-types")
11643 (uri (cran-uri "assertive.types" version))
11646 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11648 `((upstream-name . "assertive.types")))
11649 (build-system r-build-system)
11651 `(("r-assertive-base" ,r-assertive-base)
11652 ("r-assertive-properties" ,r-assertive-properties)
11653 ("r-codetools" ,r-codetools)))
11654 (home-page "https://bitbucket.org/richierocks/assertive.types")
11655 (synopsis "Assertions to check types of variables")
11657 "This package provides a set of predicates and assertions for checking
11658 the types of variables. This is mainly for use by other package developers
11659 who want to include run-time testing features in their own packages.")
11660 (license license:gpl3+)))
11662 (define-public r-assertive-files
11664 (name "r-assertive-files")
11669 (uri (cran-uri "assertive.files" version))
11672 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11674 `((upstream-name . "assertive.files")))
11675 (build-system r-build-system)
11677 `(("r-assertive-base" ,r-assertive-base)
11678 ("r-assertive-numbers" ,r-assertive-numbers)))
11679 (home-page "https://bitbucket.org/richierocks/assertive.files")
11680 (synopsis "Assertions to check properties of files")
11682 "This package provides a set of predicates and assertions for checking
11683 the properties of files and connections. This is mainly for use by other
11684 package developers who want to include run-time testing features in their own
11686 (license license:gpl3+)))
11688 (define-public r-assertive-code
11690 (name "r-assertive-code")
11695 (uri (cran-uri "assertive.code" version))
11698 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11700 `((upstream-name . "assertive.code")))
11701 (build-system r-build-system)
11703 `(("r-assertive-base" ,r-assertive-base)
11704 ("r-assertive-properties" ,r-assertive-properties)
11705 ("r-assertive-types" ,r-assertive-types)))
11706 (home-page "https://bitbucket.org/richierocks/assertive.code")
11707 (synopsis "Assertions to check properties of code")
11709 "This package provides a set of predicates and assertions for checking
11710 the properties of code. This is mainly for use by other package developers
11711 who want to include run-time testing features in their own packages.")
11712 (license license:gpl3+)))
11714 (define-public r-assertive-datetimes
11716 (name "r-assertive-datetimes")
11721 (uri (cran-uri "assertive.datetimes" version))
11724 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11726 `((upstream-name . "assertive.datetimes")))
11727 (build-system r-build-system)
11729 `(("r-assertive-base" ,r-assertive-base)
11730 ("r-assertive-types" ,r-assertive-types)))
11731 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11732 (synopsis "Assertions to check properties of dates and times")
11734 "This package provides a set of predicates and assertions for checking
11735 the properties of dates and times. This is mainly for use by other package
11736 developers who want to include run-time testing features in their own
11738 (license license:gpl3+)))
11740 (define-public r-assertive-strings
11742 (name "r-assertive-strings")
11747 (uri (cran-uri "assertive.strings" version))
11750 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11752 `((upstream-name . "assertive.strings")))
11753 (build-system r-build-system)
11755 `(("r-assertive-base" ,r-assertive-base)
11756 ("r-assertive-types" ,r-assertive-types)
11757 ("r-stringi" ,r-stringi)))
11758 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11759 (synopsis "Assertions to check properties of strings")
11761 "This package provides a set of predicates and assertions for checking
11762 the properties of strings. This is mainly for use by other package developers
11763 who want to include run-time testing features in their own packages.")
11764 (license license:gpl3+)))
11766 (define-public r-assertive-data-us
11768 (name "r-assertive-data-us")
11773 (uri (cran-uri "assertive.data.us" version))
11776 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11778 `((upstream-name . "assertive.data.us")))
11779 (build-system r-build-system)
11781 `(("r-assertive-base" ,r-assertive-base)
11782 ("r-assertive-strings" ,r-assertive-strings)))
11783 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11784 (synopsis "Assertions to check properties of strings")
11786 "This package provides a set of predicates and assertions for checking
11787 the properties of US-specific complex data types. This is mainly for use by
11788 other package developers who want to include run-time testing features in
11789 their own packages.")
11790 (license license:gpl3+)))
11792 (define-public r-assertive-data-uk
11794 (name "r-assertive-data-uk")
11799 (uri (cran-uri "assertive.data.uk" version))
11802 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11804 `((upstream-name . "assertive.data.uk")))
11805 (build-system r-build-system)
11807 `(("r-assertive-base" ,r-assertive-base)
11808 ("r-assertive-strings" ,r-assertive-strings)))
11809 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11810 (synopsis "Assertions to check properties of strings")
11812 "This package provides a set of predicates and assertions for checking
11813 the properties of UK-specific complex data types. This is mainly for use by
11814 other package developers who want to include run-time testing features in
11815 their own packages.")
11816 (license license:gpl3+)))
11818 (define-public r-assertive-data
11820 (name "r-assertive-data")
11825 (uri (cran-uri "assertive.data" version))
11828 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11830 `((upstream-name . "assertive.data")))
11831 (build-system r-build-system)
11833 `(("r-assertive-base" ,r-assertive-base)
11834 ("r-assertive-strings" ,r-assertive-strings)))
11835 (home-page "https://bitbucket.org/richierocks/assertive.data")
11836 (synopsis "Assertions to check properties of data")
11838 "This package provides a set of predicates and assertions for checking
11839 the properties of (country independent) complex data types. This is mainly
11840 for use by other package developers who want to include run-time testing
11841 features in their own packages.")
11842 (license license:gpl3+)))
11844 (define-public r-assertive
11846 (name "r-assertive")
11851 (uri (cran-uri "assertive" version))
11854 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11855 (build-system r-build-system)
11857 `(("r-assertive-base" ,r-assertive-base)
11858 ("r-assertive-code" ,r-assertive-code)
11859 ("r-assertive-data" ,r-assertive-data)
11860 ("r-assertive-data-uk" ,r-assertive-data-uk)
11861 ("r-assertive-data-us" ,r-assertive-data-us)
11862 ("r-assertive-datetimes" ,r-assertive-datetimes)
11863 ("r-assertive-files" ,r-assertive-files)
11864 ("r-assertive-matrices" ,r-assertive-matrices)
11865 ("r-assertive-models" ,r-assertive-models)
11866 ("r-assertive-numbers" ,r-assertive-numbers)
11867 ("r-assertive-properties" ,r-assertive-properties)
11868 ("r-assertive-reflection" ,r-assertive-reflection)
11869 ("r-assertive-sets" ,r-assertive-sets)
11870 ("r-assertive-strings" ,r-assertive-strings)
11871 ("r-assertive-types" ,r-assertive-types)
11872 ("r-knitr" ,r-knitr)))
11874 `(("r-knitr" ,r-knitr)))
11875 (home-page "https://bitbucket.org/richierocks/assertive")
11876 (synopsis "Readable check functions to ensure code integrity")
11878 "This package provides lots of predicates (@code{is_*} functions) to
11879 check the state of your variables, and assertions (@code{assert_*} functions)
11880 to throw errors if they aren't in the right form.")
11881 (license license:gpl3+)))
11883 (define-public r-dotcall64
11885 (name "r-dotcall64")
11890 (uri (cran-uri "dotCall64" version))
11893 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11894 (properties `((upstream-name . "dotCall64")))
11895 (build-system r-build-system)
11896 (native-inputs `(("gfortran" ,gfortran)))
11897 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11898 (synopsis "Enhanced foreign function interface supporting long vectors")
11900 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11901 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11902 supports long vectors, arguments of type 64-bit integer, and provides a
11903 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11904 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11905 (license license:gpl2+)))
11907 (define-public r-spam
11914 (uri (cran-uri "spam" version))
11916 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11917 (build-system r-build-system)
11919 `(("r-dotcall64" ,r-dotcall64)))
11920 (native-inputs `(("gfortran" ,gfortran)))
11921 (home-page "https://www.math.uzh.ch/pages/spam/")
11922 (synopsis "Sparse matrix algebra")
11924 "This package provides a set of functions for sparse matrix algebra.
11925 Differences with other sparse matrix packages are:
11928 @item it only supports (essentially) one sparse matrix format;
11929 @item it is based on transparent and simple structure(s);
11930 @item it is tailored for MCMC calculations within G(M)RF;
11931 @item and it is fast and scalable (with the extension package @code{spam64}).
11933 ;; Either of these licenses
11934 (license (list license:bsd-3 license:lgpl2.0))))
11936 (define-public r-fields
11943 (uri (cran-uri "fields" version))
11945 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11946 (build-system r-build-system)
11948 `(("r-maps" ,r-maps)
11949 ("r-spam" ,r-spam)))
11951 `(("gfortran" ,gfortran)))
11952 (home-page "https://www.image.ucar.edu/fields")
11953 (synopsis "Tools for spatial data")
11955 "This is a package for curve, surface and function fitting with an
11956 emphasis on splines, spatial data and spatial statistics. The major methods
11957 include cubic, and thin plate splines, Kriging, and compactly supported
11958 covariance functions for large data sets.")
11959 (license license:gpl2+)))
11961 (define-public r-spatialextremes
11963 (name "r-spatialextremes")
11968 (uri (cran-uri "SpatialExtremes" version))
11971 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11973 `((upstream-name . "SpatialExtremes")))
11974 (build-system r-build-system)
11976 `(("r-fields" ,r-fields)
11977 ("r-maps" ,r-maps)))
11978 (home-page "http://spatialextremes.r-forge.r-project.org/")
11979 (synopsis "Modelling spatial extremes")
11981 "This package provides tools for the statistical modelling of spatial
11982 extremes using max-stable processes, copula or Bayesian hierarchical models.
11983 More precisely, this package allows (conditional) simulations from various
11984 parametric max-stable models, analysis of the extremal spatial dependence, the
11985 fitting of such processes using composite likelihoods or least square (simple
11986 max-stable processes only), model checking and selection and prediction.")
11987 (license license:gpl2+)))
11989 (define-public r-drc
11996 (uri (cran-uri "drc" version))
11999 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
12000 (build-system r-build-system)
12003 ("r-gtools" ,r-gtools)
12005 ("r-multcomp" ,r-multcomp)
12006 ("r-plotrix" ,r-plotrix)
12007 ("r-scales" ,r-scales)))
12008 (home-page "https://cran.r-project.org/web/packages/drc")
12009 (synopsis "Analysis of dose-response curves")
12011 "This package provides a suite of flexible and versatile model fitting
12012 and after-fitting functions for the analysis of dose-response data.")
12013 (license license:gpl2+)))
12015 (define-public r-rmeta
12022 (uri (cran-uri "rmeta" version))
12025 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12026 (build-system r-build-system)
12027 (home-page "https://cran.r-project.org/web/packages/rmeta")
12028 (synopsis "Tools for meta-analysis")
12030 "This package provides functions for simple fixed and random effects
12031 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12032 draws standard summary plots, funnel plots, and computes summaries and tests
12033 for association and heterogeneity.")
12034 (license license:gpl2)))
12036 (define-public r-bootstrap
12038 (name "r-bootstrap")
12043 (uri (cran-uri "bootstrap" version))
12046 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
12047 (build-system r-build-system)
12048 (native-inputs `(("gfortran" ,gfortran)))
12049 (home-page "https://cran.r-project.org/web/packages/bootstrap")
12050 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
12052 "This package provides software and data for the book \"An Introduction
12053 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
12054 This package is primarily provided for projects already based on it, and for
12055 support of the book. New projects should preferentially use the recommended
12056 package \"boot\".")
12057 (license license:bsd-3)))
12059 (define-public r-survivalroc
12061 (name "r-survivalroc")
12066 (uri (cran-uri "survivalROC" version))
12069 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
12070 (properties `((upstream-name . "survivalROC")))
12071 (build-system r-build-system)
12072 (home-page "https://cran.r-project.org/web/packages/survivalROC")
12073 (synopsis "Time-dependent ROC curve estimation from censored survival data")
12075 "Compute time-dependent ROC curve from censored survival data using
12076 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
12077 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
12078 (license license:gpl2+)))
12080 (define-public r-longitudinal
12082 (name "r-longitudinal")
12087 (uri (cran-uri "longitudinal" version))
12090 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
12091 (build-system r-build-system)
12092 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
12093 (home-page "http://strimmerlab.org/software/longitudinal/")
12094 (synopsis "Analysis of multiple time course data")
12096 "This package contains general data structures and functions for
12097 longitudinal data with multiple variables, repeated measurements, and
12098 irregularly spaced time points. It also implements a shrinkage estimator of
12099 dynamical correlation and dynamical covariance.")
12100 (license license:gpl3+)))
12102 (define-public r-genenet
12109 (uri (cran-uri "GeneNet" version))
12112 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
12113 (properties `((upstream-name . "GeneNet")))
12114 (build-system r-build-system)
12116 `(("r-corpcor" ,r-corpcor)
12117 ("r-fdrtool" ,r-fdrtool)
12118 ("r-longitudinal" ,r-longitudinal)))
12119 (home-page "http://strimmerlab.org/software/genenet/")
12120 (synopsis "Modeling and inferring gene networks")
12122 "This package analyzes gene expression (time series) data with focus on
12123 the inference of gene networks. In particular, GeneNet implements the methods
12124 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
12125 for learning large-scale gene association networks (including assignment of
12126 putative directions).")
12127 (license license:gpl3+)))
12129 (define-public r-rbamtools
12131 (name "r-rbamtools")
12132 (version "2.16.17")
12136 (uri (cran-uri "rbamtools" version))
12139 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
12140 (build-system r-build-system)
12141 (inputs `(("zlib" ,zlib)))
12143 `(("r-refgenome" ,r-refgenome)))
12144 (home-page "https://cran.r-project.org/web/packages/rbamtools")
12145 (synopsis "Read and write BAM (binary alignment) files")
12147 "This package provides an R interface to functions of the SAMtools
12149 (license license:artistic2.0)))
12151 (define-public r-protviz
12158 (uri (cran-uri "protViz" version))
12161 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
12162 (properties `((upstream-name . "protViz")))
12163 (build-system r-build-system)
12164 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12165 (home-page "https://github.com/protViz/protViz/")
12166 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
12168 "This package helps with quality checks, visualizations and analysis of
12169 mass spectrometry data, coming from proteomics experiments. The package is
12170 developed, tested and used at the Functional Genomics Center Zurich, where it
12171 is used mainly for prototyping, teaching, and having fun with proteomics data.
12172 But it can also be used to do data analysis for small scale data sets.")
12173 (license license:gpl3)))
12175 (define-public r-cmprsk
12182 (uri (cran-uri "cmprsk" version))
12184 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
12185 (build-system r-build-system)
12187 `(("r-survival" ,r-survival)))
12189 `(("gfortran" ,gfortran)))
12190 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12191 (synopsis "Subdistribution analysis of competing risks")
12193 "This package provides tool for estimation, testing and regression
12194 modeling of subdistribution functions in competing risks, as described in
12195 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12196 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12197 A proportional hazards model for the subdistribution of a competing risk,
12198 JASA, 94:496-509.")
12199 (license license:gpl2+)))
12201 (define-public r-etm
12208 (uri (cran-uri "etm" version))
12211 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
12212 (build-system r-build-system)
12214 `(("r-data-table" ,r-data-table)
12215 ("r-lattice" ,r-lattice)
12217 ("r-rcpparmadillo" ,r-rcpparmadillo)
12218 ("r-survival" ,r-survival)))
12219 (home-page "https://cran.r-project.org/web/packages/etm")
12220 (synopsis "Empirical transition matrix")
12222 "The @dfn{empirical transition matrix} (etm) package estimates
12223 the matrix of transition probabilities for any time-inhomogeneous multistate
12224 model with finite state space using the Aalen-Johansen estimator.")
12225 (license license:expat)))
12227 (define-public r-epi
12234 (uri (cran-uri "Epi" version))
12237 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12238 (properties `((upstream-name . "Epi")))
12239 (build-system r-build-system)
12241 `(("r-cmprsk" ,r-cmprsk)
12242 ("r-data-table" ,r-data-table)
12245 ("r-matrix" ,r-matrix)
12247 ("r-numderiv" ,r-numderiv)
12249 ("r-survival" ,r-survival)
12251 (home-page "https://BendixCarstensen.com/Epi/")
12252 (synopsis "Statistical analysis in epidemiology")
12254 "This package provides functions for demographic and epidemiological
12255 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12256 particular representation, manipulation and simulation of multistate data -
12257 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12258 @code{etm} and @code{cmprsk} packages. It also contains functions for
12259 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12260 data and some useful functions for tabulation and plotting, as well as a
12261 number of epidemiological data sets.")
12262 (license license:gpl2)))
12264 (define-public r-ppls
12267 (version "1.6-1.1")
12271 (uri (cran-uri "ppls" version))
12274 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12275 (build-system r-build-system)
12276 (propagated-inputs `(("r-mass" ,r-mass)))
12277 (home-page "https://cran.r-project.org/web/packages/ppls")
12278 (synopsis "Penalized partial least squares")
12280 "This package contains linear and nonlinear regression methods based on
12281 partial least squares and penalization techniques. Model parameters are
12282 selected via cross-validation, and confidence intervals ans tests for the
12283 regression coefficients can be conducted via jackknifing.")
12284 (license license:gpl2+)))
12286 (define-public r-huge
12289 (version "1.3.4.1")
12293 (uri (cran-uri "huge" version))
12295 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12296 (build-system r-build-system)
12298 `(("r-igraph" ,r-igraph)
12300 ("r-matrix" ,r-matrix)
12302 ("r-rcppeigen" ,r-rcppeigen)))
12303 (home-page "https://cran.r-project.org/web/packages/huge")
12304 (synopsis "High-dimensional undirected graph estimation")
12306 "This package provides a general framework for high-dimensional
12307 undirected graph estimation. It integrates data preprocessing, neighborhood
12308 screening, graph estimation, and model selection techniques into a pipeline.")
12309 (license license:gpl2)))
12311 (define-public r-parcor
12318 (uri (cran-uri "parcor" version))
12321 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12322 (build-system r-build-system)
12325 ("r-genenet" ,r-genenet)
12326 ("r-glmnet" ,r-glmnet)
12328 ("r-ppls" ,r-ppls)))
12329 (home-page "https://cran.r-project.org/web/packages/parcor")
12330 (synopsis "Regularized estimation of partial correlation matrices")
12332 "This package estimates the matrix of partial correlations based on
12333 different regularized regression methods: lasso, adaptive lasso, PLS, and
12334 Ridge Regression. In addition, the package provides model selection for
12335 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12336 (license license:gpl2+)))
12338 (define-public r-mcmc
12345 (uri (cran-uri "mcmc" version))
12348 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12349 (build-system r-build-system)
12350 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12351 (synopsis "Markov chain Monte Carlo")
12353 "This package simulates continuous distributions of random vectors using
12354 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12355 function that evaluates the log unnormalized density. Algorithms are random
12356 walk Metropolis algorithm (function @code{metrop}), simulated
12357 tempering (function @code{temper}), and morphometric random walk
12358 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12359 by change of variable.")
12360 (license license:expat)))
12362 (define-public r-listenv
12369 (uri (cran-uri "listenv" version))
12372 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12373 (build-system r-build-system)
12375 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12376 (home-page "https://github.com/HenrikBengtsson/listenv")
12377 (synopsis "Environments behaving (almost) as lists")
12379 "This package implements list environments. List environments are
12380 environments that have list-like properties. For instance, the elements of a
12381 list environment are ordered and can be accessed and iterated over using index
12383 (license license:lgpl2.1+)))
12385 (define-public r-globals
12392 (uri (cran-uri "globals" version))
12395 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12396 (build-system r-build-system)
12398 `(("r-codetools" ,r-codetools)))
12399 (home-page "https://github.com/HenrikBengtsson/globals")
12400 (synopsis "Identify global objects in R expressions")
12402 "This package provides tools to identify global (\"unknown\" or \"free\")
12403 objects in R expressions by code inspection using various strategies, e.g.
12404 conservative or liberal. The objective of this package is to make it as
12405 simple as possible to identify global objects for the purpose of exporting
12406 them in distributed compute environments.")
12407 (license license:lgpl2.1+)))
12409 (define-public r-future
12416 (uri (cran-uri "future" version))
12419 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12420 (build-system r-build-system)
12422 `(("r-digest" ,r-digest)
12423 ("r-globals" ,r-globals)
12424 ("r-listenv" ,r-listenv)))
12426 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12427 (home-page "https://github.com/HenrikBengtsson/future")
12428 (synopsis "Unified parallel and distributed processing in R")
12430 "The purpose of this package is to provide a lightweight and unified
12431 Future API for sequential and parallel processing of R expression via futures.
12432 This package implements sequential, multicore, multisession, and cluster
12433 futures. With these, R expressions can be evaluated on the local machine, in
12434 parallel a set of local machines, or distributed on a mix of local and remote
12435 machines. Extensions to this package implement additional backends for
12436 processing futures via compute cluster schedulers etc. Because of its unified
12437 API, there is no need to modify any code in order to switch from sequential on
12438 the local machine to, say, distributed processing on a remote compute cluster.")
12439 (license license:lgpl2.1+)))
12441 (define-public r-future-apply
12443 (name "r-future-apply")
12448 (uri (cran-uri "future.apply" version))
12451 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12452 (properties `((upstream-name . "future.apply")))
12453 (build-system r-build-system)
12455 `(("r-future" ,r-future)
12456 ("r-globals" ,r-globals)))
12458 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12459 (home-page "https://github.com/HenrikBengtsson/future.apply")
12460 (synopsis "Apply function to elements in parallel using futures")
12462 "This package provides implementations of @code{apply()},
12463 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12464 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12465 can be resolved using any future-supported backend, e.g. parallel on the local
12466 machine or distributed on a compute cluster.")
12467 (license license:gpl2+)))
12469 (define-public r-rsvd
12476 (uri (cran-uri "rsvd" version))
12479 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12480 (build-system r-build-system)
12482 `(("r-matrix" ,r-matrix)))
12483 (home-page "https://github.com/erichson/rSVD")
12484 (synopsis "Randomized singular value decomposition")
12486 "Low-rank matrix decompositions are fundamental tools and widely used for
12487 data analysis, dimension reduction, and data compression. Classically, highly
12488 accurate deterministic matrix algorithms are used for this task. However, the
12489 emergence of large-scale data has severely challenged our computational
12490 ability to analyze big data. The concept of randomness has been demonstrated
12491 as an effective strategy to quickly produce approximate answers to familiar
12492 problems such as the @dfn{singular value decomposition} (SVD). This package
12493 provides several randomized matrix algorithms such as the randomized singular
12494 value decomposition (@code{rsvd}), randomized principal component
12495 analysis (@code{rpca}), randomized robust principal component
12496 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12497 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12498 functions are provided.")
12499 (license license:gpl3+)))
12501 (define-public r-sloop
12508 (uri (cran-uri "sloop" version))
12511 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12512 (build-system r-build-system)
12514 `(("r-codetools" ,r-codetools)
12515 ("r-crayon" ,r-crayon)
12516 ("r-purrr" ,r-purrr)
12517 ("r-rlang" ,r-rlang)
12518 ("r-tibble" ,r-tibble)))
12519 (home-page "https://github.com/r-lib/sloop")
12520 (synopsis "Helpers for object-oriented programming in R")
12522 "This package provides a collection of helper functions designed to
12523 help you to better understand object oriented programming in R, particularly
12525 (license license:gpl3)))
12527 (define-public r-capushe
12534 (uri (cran-uri "capushe" version))
12537 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12538 (build-system r-build-system)
12539 (propagated-inputs `(("r-mass" ,r-mass)))
12540 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12541 (synopsis "Calibrating penalties using slope heuristics")
12543 "This package provides tools for the calibration of penalized criteria
12544 for model selection. The calibration methods available are based on the slope
12546 (license license:gpl2+)))
12548 (define-public r-dorng
12555 (uri (cran-uri "doRNG" version))
12558 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12559 (properties `((upstream-name . "doRNG")))
12560 (build-system r-build-system)
12562 `(("r-foreach" ,r-foreach)
12563 ("r-iterators" ,r-iterators)
12564 ("r-rngtools" ,r-rngtools)))
12565 (home-page "https://renozao.github.io/doRNG/")
12566 (synopsis "Generic reproducible parallel backend for foreach loops")
12568 "This package provides functions to perform reproducible parallel
12569 @code{foreach} loops, using independent random streams as generated by
12570 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12571 convert standard @code{%dopar%} loops into fully reproducible loops,
12572 independently of the number of workers, the task scheduling strategy, or the
12573 chosen parallel environment and associated foreach backend.")
12574 (license license:gpl2+)))
12576 (define-public r-blockmodeling
12578 (name "r-blockmodeling")
12583 (uri (cran-uri "blockmodeling" version))
12586 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12587 (build-system r-build-system)
12589 `(("r-matrix" ,r-matrix)))
12590 (native-inputs `(("gfortran" ,gfortran)))
12591 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12592 (synopsis "Generalized and classical blockmodeling of valued networks")
12594 "This package is primarily meant as an implementation of generalized
12595 blockmodeling for valued networks. In addition, measures of similarity or
12596 dissimilarity based on structural equivalence and regular equivalence (REGE
12597 algorithms) can be computed and partitioned matrices can be plotted.")
12598 (license license:gpl2+)))
12600 (define-public r-upsetr
12607 (uri (cran-uri "UpSetR" version))
12610 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12611 (properties `((upstream-name . "UpSetR")))
12612 (build-system r-build-system)
12614 `(("r-ggplot2" ,r-ggplot2)
12615 ("r-gridextra" ,r-gridextra)
12617 ("r-scales" ,r-scales)))
12618 (home-page "https://github.com/hms-dbmi/UpSetR")
12619 (synopsis "Visualize intersecting sets")
12621 "This package provides a more scalable alternative to Venn and Euler
12622 diagrams for visualizing intersecting sets. Create visualizations of
12623 intersecting sets using a novel matrix design, along with visualizations of
12624 several common set, element and attribute related tasks.")
12625 (license license:expat)))
12627 ;; This package includes a JavaScript file, which is not minified. When
12628 ;; upgrading please check that there are no new minified JavaScript files.
12629 (define-public r-shinybs
12636 (uri (cran-uri "shinyBS" version))
12639 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12640 (properties `((upstream-name . "shinyBS")))
12641 (build-system r-build-system)
12642 ;; The tests spawn Shiny browser apps. They cannot be run
12643 ;; non-interactively.
12644 (arguments '(#:tests? #f))
12646 `(("r-htmltools" ,r-htmltools)
12647 ("r-shiny" ,r-shiny)))
12648 (home-page "https://ebailey78.github.io/shinyBS/")
12649 (synopsis "Twitter Bootstrap components for Shiny")
12651 "This package adds additional Twitter Bootstrap components to Shiny.")
12652 (license license:gpl3)))
12654 (define-public r-outliers
12656 (name "r-outliers")
12661 (uri (cran-uri "outliers" version))
12664 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12665 (build-system r-build-system)
12666 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12667 (synopsis "Tests for outliers")
12669 "This package provides a collection of some tests commonly used for
12670 identifying outliers.")
12671 (license license:gpl2+)))
12673 (define-public r-bayesm
12680 (uri (cran-uri "bayesm" version))
12682 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12683 (build-system r-build-system)
12685 `(("r-rcpp" ,r-rcpp)
12686 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12687 (home-page "http://www.perossi.org/home/bsm-1")
12688 (synopsis "Bayesian inference for marketing/micro-econometrics")
12690 "This package covers many important models used in marketing and
12691 micro-econometrics applications, including Bayes Regression (univariate or
12692 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12693 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12694 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12695 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12696 Estimation with normal base, Hierarchical Linear Models with normal prior and
12697 covariates, Hierarchical Linear Models with a mixture of normals prior and
12698 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12699 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12700 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12701 analysis of choice-based conjoint data, Bayesian treatment of linear
12702 instrumental variables models, Analysis of Multivariate Ordinal survey data
12703 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12704 Coefficient Logit Models.")
12705 (license license:gpl2+)))
12707 (define-public r-tensora
12714 (uri (cran-uri "tensorA" version))
12717 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12718 (properties `((upstream-name . "tensorA")))
12719 (build-system r-build-system)
12720 (home-page "http://www.stat.boogaart.de/tensorA")
12721 (synopsis "Advanced tensor arithmetic with named indices")
12723 "This package provides convenience functions for advanced linear algebra
12724 with tensors and computation with datasets of tensors on a higher level
12725 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12726 co- and contravariate indices, and parallel computations on sequences of
12728 (license license:gpl2+)))
12730 (define-public r-rarpack
12737 (uri (cran-uri "rARPACK" version))
12740 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12741 (properties `((upstream-name . "rARPACK")))
12742 (build-system r-build-system)
12743 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12744 (home-page "https://github.com/yixuan/rARPACK")
12745 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12747 "This package was previously an R wrapper of the ARPACK library, and now
12748 a shell of the R package RSpectra, an R interface to the Spectra library for
12749 solving large scale eigenvalue/vector problems. The current version of
12750 rARPACK simply imports and exports the functions provided by RSpectra. New
12751 users of rARPACK are advised to switch to the RSpectra package.")
12752 (license license:bsd-3)))
12754 (define-public r-compositions
12756 (name "r-compositions")
12761 (uri (cran-uri "compositions" version))
12764 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12765 (build-system r-build-system)
12767 `(("r-bayesm" ,r-bayesm)
12769 ("r-robustbase" ,r-robustbase)
12770 ("r-tensora" ,r-tensora)))
12772 `(("r-knitr" ,r-knitr)))
12773 (home-page "http://www.stat.boogaart.de/compositions")
12774 (synopsis "Compositional data analysis")
12776 "This package provides functions for the consistent analysis of
12777 compositional data (e.g. portions of substances) and positive
12778 numbers (e.g. concentrations).")
12779 (license license:gpl2+)))
12781 (define-public r-cobs
12788 (uri (cran-uri "cobs" version))
12791 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12792 (build-system r-build-system)
12794 `(("r-quantreg" ,r-quantreg)
12795 ("r-sparsem" ,r-sparsem)))
12796 (home-page "https://cran.r-project.org/web/packages/cobs")
12797 (synopsis "Constrained B-Splines (sparse matrix based)")
12799 "This package provides qualitatively constrained (regression) smoothing
12800 splines via linear programming and sparse matrices.")
12801 (license license:gpl2+)))
12803 (define-public r-drimpute
12805 (name "r-drimpute")
12810 (uri (cran-uri "DrImpute" version))
12813 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12814 (properties `((upstream-name . "DrImpute")))
12815 (build-system r-build-system)
12817 `(("r-rcpp" ,r-rcpp)
12818 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12819 (home-page "https://github.com/ikwak2/DrImpute")
12820 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12822 "This is an R package for imputing dropout events. Many statistical
12823 methods in cell type identification, visualization and lineage reconstruction
12824 do not account for dropout events. DrImpute can improve the performance of
12825 such software by imputing dropout events.")
12826 (license license:gpl3)))
12828 (define-public r-gamlss-dist
12830 (name "r-gamlss-dist")
12835 (uri (cran-uri "gamlss.dist" version))
12837 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12838 (properties `((upstream-name . "gamlss.dist")))
12839 (build-system r-build-system)
12840 (propagated-inputs `(("r-mass" ,r-mass)))
12841 (home-page "http://www.gamlss.org/")
12842 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12844 "This package provides a set of distributions which can be used for
12845 modelling the response variables in Generalized Additive Models for Location
12846 Scale and Shape. The distributions can be continuous, discrete or mixed
12847 distributions. Extra distributions can be created, by transforming, any
12848 continuous distribution defined on the real line, to a distribution defined on
12849 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12850 transformation, respectively.")
12851 ;; Either version of the GPL.
12852 (license (list license:gpl2 license:gpl3))))
12854 ;; This package includes JavaScript files, which are not minified. When
12855 ;; upgrading please check that there are no new minified JavaScript files.
12856 (define-public r-shinyjs
12863 (uri (cran-uri "shinyjs" version))
12866 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12867 (build-system r-build-system)
12869 `(("r-digest" ,r-digest)
12870 ("r-htmltools" ,r-htmltools)
12871 ("r-jsonlite" ,r-jsonlite)
12872 ("r-shiny" ,r-shiny)))
12873 (home-page "https://deanattali.com/shinyjs")
12874 (synopsis "Improve the user experience of your Shiny apps")
12876 "Perform common useful JavaScript operations in Shiny apps that will
12877 greatly improve your apps without having to know any JavaScript. Examples
12878 include: hiding an element, disabling an input, resetting an input back to its
12879 original value, delaying code execution by a few seconds, and many more useful
12880 functions for both the end user and the developer. Shinyjs can also be used
12881 to easily call your own custom JavaScript functions from R.")
12882 (license license:agpl3+)))
12884 ;; This package includes minified JavaScript files. When upgrading please
12885 ;; check that there are no new minified JavaScript files.
12886 (define-public r-colourpicker
12888 (name "r-colourpicker")
12893 (uri (cran-uri "colourpicker" version))
12896 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12897 (build-system r-build-system)
12899 `(#:modules ((guix build utils)
12900 (guix build r-build-system)
12904 (modify-phases %standard-phases
12905 (add-after 'unpack 'process-javascript
12906 (lambda* (#:key inputs #:allow-other-keys)
12907 (with-directory-excursion "inst"
12911 `((,(assoc-ref inputs "js-salvattore")
12912 "examples/colourInput/www/salvattore.min.js")
12913 (,(assoc-ref inputs "js-jquery")
12914 "htmlwidgets/lib/jquery/jquery.min.js")
12915 ("www/shared/colourpicker/js/colourpicker.js"
12916 "www/shared/colourpicker/js/colourpicker.min.js"))))
12917 (lambda (sources targets)
12918 (for-each (lambda (source target)
12919 (format #t "Processing ~a --> ~a~%"
12921 (delete-file target)
12922 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12923 (call-with-output-file target
12925 (dump-port minified port)))))
12926 sources targets))))
12929 `(("r-ggplot2" ,r-ggplot2)
12930 ("r-htmltools" ,r-htmltools)
12931 ("r-htmlwidgets" ,r-htmlwidgets)
12932 ("r-jsonlite" ,r-jsonlite)
12933 ("r-miniui" ,r-miniui)
12934 ("r-shiny" ,r-shiny)
12935 ("r-shinyjs" ,r-shinyjs)))
12937 `(("uglify-js" ,uglify-js)
12941 (uri "https://code.jquery.com/jquery-3.3.1.js")
12944 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12948 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12951 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12952 (home-page "https://github.com/daattali/colourpicker")
12953 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12955 "This package provides a color picker that can be used as an input in
12956 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12957 custom color palettes, and many more options. A plot color helper tool is
12958 available as an RStudio Addin, which helps you pick colors to use in your
12959 plots. A more generic color picker RStudio Addin is also provided to let you
12960 select colors to use in your R code.")
12961 (license license:expat)))
12963 (define-public r-ggextra
12970 (uri (cran-uri "ggExtra" version))
12973 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12974 (properties `((upstream-name . "ggExtra")))
12975 (build-system r-build-system)
12977 `(("r-colourpicker" ,r-colourpicker)
12978 ("r-ggplot2" ,r-ggplot2)
12979 ("r-gtable" ,r-gtable)
12980 ("r-miniui" ,r-miniui)
12982 ("r-scales" ,r-scales)
12983 ("r-shiny" ,r-shiny)
12984 ("r-shinyjs" ,r-shinyjs)))
12986 `(("r-knitr" ,r-knitr)))
12987 (home-page "https://github.com/daattali/ggExtra")
12988 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12990 "This package is a collection of functions and layers to enhance ggplot2.
12991 The flagship function is @code{ggMarginal()}, which can be used to add
12992 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12993 (license license:expat)))
12995 (define-public r-minpack-lm
12997 (name "r-minpack-lm")
13002 (uri (cran-uri "minpack.lm" version))
13005 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
13006 (properties `((upstream-name . "minpack.lm")))
13007 (build-system r-build-system)
13008 (native-inputs `(("gfortran" ,gfortran)))
13009 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
13010 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
13012 "The @code{nls.lm} function provides an R interface to @code{lmder} and
13013 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
13014 problems by a modification of the Levenberg-Marquardt algorithm, with support
13015 for lower and upper parameter bounds. The implementation can be used via
13016 @code{nls}-like calls using the @code{nlsLM} function.")
13017 (license license:gpl3)))
13019 (define-public r-moments
13026 (uri (cran-uri "moments" version))
13029 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
13030 (build-system r-build-system)
13031 (home-page "https://cran.r-project.org/web/packages/moments")
13032 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
13034 "This package provides functions to calculate: moments, Pearson's
13035 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
13036 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
13037 (license license:gpl2+)))
13039 (define-public r-msir
13046 (uri (cran-uri "msir" version))
13049 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
13050 (build-system r-build-system)
13052 `(("r-mclust" ,r-mclust)))
13053 (home-page "https://cran.r-project.org/web/packages/msir")
13054 (synopsis "Model-based sliced inverse regression")
13056 "This is an R package for dimension reduction based on finite Gaussian
13057 mixture modeling of inverse regression.")
13058 (license license:gpl2+)))
13060 (define-public r-pbivnorm
13062 (name "r-pbivnorm")
13067 (uri (cran-uri "pbivnorm" version))
13070 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
13071 (build-system r-build-system)
13072 (native-inputs `(("gfortran" ,gfortran)))
13073 (home-page "https://github.com/brentonk/pbivnorm")
13074 (synopsis "Vectorized bivariate normal CDF")
13076 "This package provides a vectorized R function for calculating
13077 probabilities from a standard bivariate normal CDF.")
13078 (license license:gpl2+)))
13080 (define-public r-lavaan
13087 (uri (cran-uri "lavaan" version))
13090 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
13091 (build-system r-build-system)
13093 `(("r-mass" ,r-mass)
13094 ("r-mnormt" ,r-mnormt)
13095 ("r-numderiv" ,r-numderiv)
13096 ("r-pbivnorm" ,r-pbivnorm)))
13097 (home-page "http://lavaan.ugent.be")
13098 (synopsis "Latent variable analysis")
13100 "This package provides tools to fit a variety of latent variable models,
13101 including confirmatory factor analysis, structural equation modeling and
13102 latent growth curve models.")
13103 (license license:gpl2+)))
13105 (define-public r-nonnest2
13107 (name "r-nonnest2")
13112 (uri (cran-uri "nonnest2" version))
13115 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
13116 (build-system r-build-system)
13118 `(("r-compquadform" ,r-compquadform)
13119 ("r-lavaan" ,r-lavaan)
13120 ("r-mvtnorm" ,r-mvtnorm)
13121 ("r-sandwich" ,r-sandwich)))
13123 `(("r-knitr" ,r-knitr)))
13124 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
13125 (synopsis "Tests of non-nested models")
13127 "This package allows for testing of non-nested models. It includes tests
13128 of model distinguishability and of model fit that can be applied to both
13129 nested and non-nested models. The package also includes functionality to
13130 obtain confidence intervals associated with AIC and BIC.")
13131 ;; Either version of the GPL.
13132 (license (list license:gpl2 license:gpl3))))
13134 (define-public r-penalized
13136 (name "r-penalized")
13141 (uri (cran-uri "penalized" version))
13144 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
13145 (build-system r-build-system)
13147 `(("r-rcpp" ,r-rcpp)
13148 ("r-rcpparmadillo" ,r-rcpparmadillo)
13149 ("r-survival" ,r-survival)))
13150 (home-page "https://cran.r-project.org/web/packages/penalized/")
13151 (synopsis "Penalized estimation in GLMs and in the Cox model")
13153 "This package provides tools for fitting possibly high dimensional
13154 penalized regression models. The penalty structure can be any combination of
13155 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
13156 constraint on the regression coefficients. The supported regression models
13157 are linear, logistic and Poisson regression and the Cox Proportional Hazards
13158 model. Cross-validation routines allow optimization of the tuning
13160 (license license:gpl2+)))
13162 (define-public r-zim
13169 (uri (cran-uri "ZIM" version))
13172 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
13173 (properties `((upstream-name . "ZIM")))
13174 (build-system r-build-system)
13175 (propagated-inputs `(("r-mass" ,r-mass)))
13176 (home-page "https://github.com/biostatstudio/ZIM")
13177 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
13179 "Analyze count time series with excess zeros. Two types of statistical
13180 models are supported: Markov regression and state-space models. They are also
13181 known as observation-driven and parameter-driven models respectively in the
13182 time series literature. The functions used for Markov regression or
13183 observation-driven models can also be used to fit ordinary regression models
13184 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
13185 negative binomial (ZINB) assumption. The package also contains miscellaneous
13186 functions to compute density, distribution, quantile, and generate random
13187 numbers from ZIP and ZINB distributions.")
13188 (license license:gpl3)))
13190 (define-public r-nor1mix
13197 (uri (cran-uri "nor1mix" version))
13200 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13201 (build-system r-build-system)
13202 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13203 (synopsis "Normal (1-d) mixture models")
13205 "This package provides S3 classes and methods for one-dimensional normal
13206 mixture models, for, e.g., density estimation or clustering algorithms
13207 research and teaching; it provides the widely used Marron-Wand densities. It
13208 also provides tools for efficient random number generation and graphics.")
13209 (license license:gpl2+)))
13211 (define-public r-beanplot
13213 (name "r-beanplot")
13218 (uri (cran-uri "beanplot" version))
13221 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13222 (build-system r-build-system)
13223 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13224 (synopsis "Visualization via beanplots")
13226 "This package provides beanplots, an alternative to
13227 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13229 (license license:gpl2)))
13231 (define-public r-pbdzmq
13238 (uri (cran-uri "pbdZMQ" version))
13241 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13242 (properties `((upstream-name . "pbdZMQ")))
13243 (build-system r-build-system)
13245 `(("zeromq" ,zeromq)
13248 `(("pkg-config" ,pkg-config)))
13249 (home-page "https://pbdr.org/")
13250 (synopsis "R interface to ZeroMQ")
13252 "ZeroMQ is a well-known library for high-performance asynchronous
13253 messaging in scalable, distributed applications. This package provides high
13254 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13255 interactive client/server programming frameworks. A few wrapper functions
13256 compatible with @code{rzmq} are also provided.")
13257 (license license:gpl3)))
13259 (define-public r-repr
13266 (uri (cran-uri "repr" version))
13269 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13270 (build-system r-build-system)
13272 `(("r-base64enc" ,r-base64enc)
13273 ("r-htmltools" ,r-htmltools)
13274 ("r-jsonlite" ,r-jsonlite)
13275 ("r-pillar" ,r-pillar)))
13276 (home-page "https://cran.r-project.org/web/packages/repr/")
13277 (synopsis "Serializable representations")
13279 "This package provides string and binary representations of objects for
13280 several formats and MIME types.")
13281 (license license:gpl3)))
13283 (define-public r-irdisplay
13285 (name "r-irdisplay")
13290 (uri (cran-uri "IRdisplay" version))
13293 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13294 (properties `((upstream-name . "IRdisplay")))
13295 (build-system r-build-system)
13297 `(("r-repr" ,r-repr)))
13298 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13299 (synopsis "Jupyter display machinery")
13301 "This package provides an interface to the rich display capabilities of
13302 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13303 running IRkernel session.")
13304 (license license:expat)))
13306 (define-public r-irkernel
13308 (name "r-irkernel")
13313 (uri (cran-uri "IRkernel" version))
13316 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13317 (properties `((upstream-name . "IRkernel")))
13318 (build-system r-build-system)
13321 (modify-phases %standard-phases
13322 (add-after 'install 'install-kernelspec
13323 (lambda* (#:key outputs #:allow-other-keys)
13324 (let ((out (assoc-ref outputs "out")))
13325 (setenv "HOME" "/tmp")
13326 (invoke "jupyter" "kernelspec" "install"
13329 (string-append out "/site-library/IRkernel/kernelspec"))
13330 ;; Record the absolute file name of the 'R' executable in
13332 (substitute* (string-append out "/share/jupyter"
13333 "/kernels/ir/kernel.json")
13335 (string-append "[\"" (which "R") "\",")))
13338 `(("jupyter" ,jupyter)))
13340 `(("r-crayon" ,r-crayon)
13341 ("r-digest" ,r-digest)
13342 ("r-evaluate" ,r-evaluate)
13343 ("r-irdisplay" ,r-irdisplay)
13344 ("r-jsonlite" ,r-jsonlite)
13345 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13346 ("r-minimal" ,r-minimal)
13347 ("r-pbdzmq" ,r-pbdzmq)
13349 ("r-uuid" ,r-uuid)))
13350 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13351 (synopsis "Native R kernel for Jupyter")
13353 "The R kernel for the Jupyter environment executes R code which the
13354 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13356 (license license:expat)))
13358 (define-public r-gmodels
13365 (uri (cran-uri "gmodels" version))
13368 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13369 (build-system r-build-system)
13371 `(("r-gdata" ,r-gdata)
13372 ("r-mass" ,r-mass)))
13373 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13374 (synopsis "Various R programming tools for model fitting")
13376 "This package provides various R programming tools for model fitting.")
13377 (license license:gpl2)))
13379 (define-public r-apcluster
13381 (name "r-apcluster")
13386 (uri (cran-uri "apcluster" version))
13389 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13390 (build-system r-build-system)
13392 `(("r-matrix" ,r-matrix)
13393 ("r-rcpp" ,r-rcpp)))
13394 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13395 (synopsis "Affinity propagation clustering")
13397 "This package implements affinity propagation clustering introduced by
13398 Frey and Dueck (2007). The package further provides leveraged affinity
13399 propagation and an algorithm for exemplar-based agglomerative clustering that
13400 can also be used to join clusters obtained from affinity propagation. Various
13401 plotting functions are available for analyzing clustering results.")
13402 (license license:gpl2+)))
13404 (define-public r-valr
13411 (uri (cran-uri "valr" version))
13414 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13415 (build-system r-build-system)
13417 `(("r-broom" ,r-broom)
13418 ("r-dplyr" ,r-dplyr)
13419 ("r-ggplot2" ,r-ggplot2)
13421 ("r-readr" ,r-readr)
13422 ("r-rlang" ,r-rlang)
13423 ("r-stringr" ,r-stringr)
13424 ("r-tibble" ,r-tibble)))
13426 `(("r-knitr" ,r-knitr)))
13427 (home-page "https://github.com/rnabioco/valr")
13428 (synopsis "Genome interval arithmetic in R")
13430 "This package enables you to read and manipulate genome intervals and
13431 signals. It provides functionality similar to command-line tool suites within
13432 R, enabling interactive analysis and visualization of genome-scale data.")
13433 (license license:expat)))
13435 (define-public r-rematch2
13437 (name "r-rematch2")
13442 (uri (cran-uri "rematch2" version))
13445 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13446 (build-system r-build-system)
13448 `(("r-tibble" ,r-tibble)))
13449 (home-page "https://github.com/r-lib/rematch2")
13450 (synopsis "Tidy output from regular expression matching")
13452 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13453 return the match results in tidy data frames.")
13454 (license license:expat)))
13456 (define-public r-picante
13463 (uri (cran-uri "picante" version))
13466 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13467 (build-system r-build-system)
13471 ("r-vegan" ,r-vegan)))
13472 (home-page "https://cran.r-project.org/web/packages/picante/")
13473 (synopsis "Integrating phylogenies and ecology")
13475 "This package provides functions for phylocom integration, community
13476 analyses, null-models, traits and evolution. It implements numerous
13477 ecophylogenetic approaches including measures of community phylogenetic and
13478 trait diversity, phylogenetic signal, estimation of trait values for
13479 unobserved taxa, null models for community and phylogeny randomizations, and
13480 utility functions for data input/output and phylogeny plotting. A full
13481 description of package functionality and methods are provided by Kembel et
13483 (license license:gpl2)))
13485 (define-public r-reinforcelearn
13487 (name "r-reinforcelearn")
13492 (uri (cran-uri "reinforcelearn" version))
13495 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13496 (build-system r-build-system)
13498 `(("r-checkmate" ,r-checkmate)
13500 ("r-purrr" ,r-purrr)
13502 (home-page "https://markusdumke.github.io/reinforcelearn")
13503 (synopsis "Reinforcement learning")
13505 "This package implements reinforcement learning environments and
13506 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13507 can be used with function approximation, eligibility traces (Singh & Sutton,
13508 1996) and experience replay (Mnih et al., 2013).")
13509 (license license:expat)))
13511 (define-public r-lemon
13518 (uri (cran-uri "lemon" version))
13521 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13522 (build-system r-build-system)
13524 `(("r-ggplot2" ,r-ggplot2)
13525 ("r-gridextra" ,r-gridextra)
13526 ("r-gtable" ,r-gtable)
13527 ("r-knitr" ,r-knitr)
13528 ("r-lattice" ,r-lattice)
13530 ("r-rlang" ,r-rlang)
13531 ("r-scales" ,r-scales)))
13533 `(("r-knitr" ,r-knitr)))
13534 (home-page "https://github.com/stefanedwards/lemon")
13535 (synopsis "Freshen up your ggplot2 plots")
13537 "This package provides functions for working with legends and axis lines
13538 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13540 (license license:gpl3)))
13542 (define-public r-wgaim
13549 (uri (cran-uri "wgaim" version))
13551 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13552 (build-system r-build-system)
13554 `(("r-ggplot2" ,r-ggplot2)
13556 (home-page "https://cran.r-project.org/web/packages/wgaim")
13557 (synopsis "Whole genome average interval mapping for QTL detection")
13559 "This package integrates sophisticated mixed modelling methods with a
13560 whole genome approach to detecting significant QTL in linkage maps.")
13561 (license license:gpl2+)))
13563 (define-public r-bedr
13570 (uri (cran-uri "bedr" version))
13573 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13574 (build-system r-build-system)
13576 `(("r-data-table" ,r-data-table)
13577 ("r-r-utils" ,r-r-utils)
13578 ("r-testthat" ,r-testthat)
13579 ("r-venndiagram" ,r-venndiagram)
13582 ("bedtools" ,bedtools)
13583 ("htslib" ,htslib))) ; for tabix
13585 `(("r-knitr" ,r-knitr))) ; for vignettes
13586 (home-page "https://cran.r-project.org/web/packages/bedr")
13587 (synopsis "Genomic region processing")
13589 "This package is for genomic regions processing using command line tools
13590 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13591 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13592 The bedr package's API enhances access to these tools as well as offers
13593 additional utilities for genomic regions processing.")
13594 (license license:gpl2)))
13596 (define-public r-sets
13603 (uri (cran-uri "sets" version))
13606 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13607 (properties `((upstream-name . "sets")))
13608 (build-system r-build-system)
13609 (home-page "https://cran.r-project.org/web/packages/sets")
13610 (synopsis "Sets, generalized sets, customizable sets and intervals")
13612 "This package provides data structures and basic operations for ordinary
13613 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13614 customizable sets, and intervals.")
13615 (license license:gpl2)))
13617 (define-public r-partitions
13619 (name "r-partitions")
13624 (uri (cran-uri "partitions" version))
13627 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13628 (build-system r-build-system)
13631 ("r-polynom" ,r-polynom)
13632 ("r-sets" ,r-sets)))
13633 (home-page "https://cran.r-project.org/web/packages/partitions")
13634 (synopsis "Additive partitions of integers")
13636 "This package provides tools to enumerates the partitions, unequal
13637 partitions, and restricted partitions of an integer; the three corresponding
13638 partition functions are also given.")
13639 ;; Any version of the GPL
13640 (license license:gpl2+)))
13642 (define-public r-brobdingnag
13644 (name "r-brobdingnag")
13649 (uri (cran-uri "Brobdingnag" version))
13652 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13653 (properties `((upstream-name . "Brobdingnag")))
13654 (build-system r-build-system)
13655 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13656 (synopsis "Very large numbers in R")
13658 "This package handles very large numbers in R. Real numbers are held
13659 using their natural logarithms, plus a logical flag indicating sign. The
13660 package includes a vignette that gives a step-by-step introduction to using S4
13662 ;; Any version of the GPL
13663 (license license:gpl2+)))
13665 (define-public r-untb
13672 (uri (cran-uri "untb" version))
13675 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13676 (build-system r-build-system)
13678 `(("r-brobdingnag" ,r-brobdingnag)
13679 ("r-partitions" ,r-partitions)
13680 ("r-polynom" ,r-polynom)))
13681 (home-page "https://github.com/RobinHankin/untb.git")
13682 (synopsis "Ecological drift under the UNTB")
13684 "This package provides numerical simulations, and visualizations, of
13685 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13686 (license license:gpl2+)))
13688 (define-public r-stepwise
13690 (name "r-stepwise")
13695 (uri (cran-uri "stepwise" version))
13698 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13699 (build-system r-build-system)
13700 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13701 (synopsis "Stepwise detection of recombination breakpoints")
13703 "This package provides a stepwise approach to identifying recombination
13704 breakpoints in a genomic sequence alignment.")
13705 (license license:gpl2+)))
13707 (define-public r-snpmaxsel
13709 (name "r-snpmaxsel")
13714 (uri (cran-uri "SNPmaxsel" version))
13717 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13718 (properties `((upstream-name . "SNPmaxsel")))
13719 (build-system r-build-system)
13721 `(("r-combinat" ,r-combinat)
13722 ("r-mvtnorm" ,r-mvtnorm)))
13723 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13724 (synopsis "Maximally selected statistics for SNP data")
13726 "This package implements asymptotic methods related to maximally selected
13727 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13729 (license license:gpl2+)))
13731 (define-public r-acsnminer
13733 (name "r-acsnminer")
13734 (version "0.16.8.25")
13737 (uri (cran-uri "ACSNMineR" version))
13740 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13741 (properties `((upstream-name . "ACSNMineR")))
13742 (build-system r-build-system)
13744 `(("r-ggplot2" ,r-ggplot2)
13745 ("r-gridextra" ,r-gridextra)))
13746 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13747 (synopsis "Gene enrichment analysis")
13749 "This package provides tools to compute and represent gene set enrichment
13750 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13751 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13752 enrichment can be run with hypergeometric test or Fisher exact test, and can
13753 use multiple corrections. Visualization of data can be done either by
13754 barplots or heatmaps.")
13755 (license license:gpl2+)))
13757 (define-public r-seqinr
13764 (uri (cran-uri "seqinr" version))
13767 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13768 (build-system r-build-system)
13770 `(("r-ade4" ,r-ade4)
13771 ("r-segmented" ,r-segmented)))
13774 (home-page "http://seqinr.r-forge.r-project.org/")
13775 (synopsis "Biological sequences retrieval and analysis")
13777 "This package provides tools for exploratory data analysis and data
13778 visualization of biological sequence (DNA and protein) data. It also includes
13779 utilities for sequence data management under the ACNUC system.")
13780 (license license:gpl2+)))
13782 (define-public r-units
13789 (uri (cran-uri "units" version))
13792 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13793 (build-system r-build-system)
13795 `(("udunits" ,udunits)))
13797 `(("r-rcpp" ,r-rcpp)))
13799 `(("r-knitr" ,r-knitr)))
13800 (home-page "https://github.com/r-quantities/units/")
13801 (synopsis "Measurement Units for R Vectors")
13803 "This package provides support for measurement units in R vectors,
13804 matrices and arrays: automatic propagation, conversion, derivation and
13805 simplification of units; raising errors in case of unit incompatibility. It
13806 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13808 (license license:gpl2)))
13810 (define-public r-classint
13812 (name "r-classint")
13817 (uri (cran-uri "classInt" version))
13820 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13821 (properties `((upstream-name . "classInt")))
13822 (build-system r-build-system)
13824 `(("r-class" ,r-class)
13825 ("r-e1071" ,r-e1071)
13826 ("r-kernsmooth" ,r-kernsmooth)))
13828 `(("gfortran" ,gfortran)
13829 ("r-knitr" ,r-knitr)))
13830 (home-page "https://github.com/r-spatial/classInt/")
13831 (synopsis "Choose univariate class intervals")
13833 "This package provides selected commonly used methods for choosing
13834 univariate class intervals for mapping or other graphics purposes.")
13835 (license license:gpl2+)))
13837 (define-public r-spdata
13844 (uri (cran-uri "spData" version))
13847 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13848 (properties `((upstream-name . "spData")))
13849 (build-system r-build-system)
13851 `(("r-raster" ,r-raster)
13853 (home-page "https://github.com/Nowosad/spData")
13854 (synopsis "Datasets for spatial analysis")
13856 "This a package containing diverse spatial datasets for demonstrating,
13857 benchmarking and teaching spatial data analysis. It includes R data of class
13858 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13859 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13860 of the datasets are designed to illustrate specific analysis techniques.
13861 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13862 illustrate point pattern analysis techniques.")
13863 (license license:cc0)))
13865 (define-public r-learnbayes
13867 (name "r-learnbayes")
13872 (uri (cran-uri "LearnBayes" version))
13875 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13876 (properties `((upstream-name . "LearnBayes")))
13877 (build-system r-build-system)
13878 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13879 (synopsis "Functions for learning Bayesian inference")
13881 "This package provides a collection of functions helpful in learning the
13882 basic tenets of Bayesian statistical inference. It contains functions for
13883 summarizing basic one and two parameter posterior distributions and predictive
13884 distributions. It contains MCMC algorithms for summarizing posterior
13885 distributions defined by the user. It also contains functions for regression
13886 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13888 (license license:gpl2+)))
13890 (define-public r-deldir
13897 (uri (cran-uri "deldir" version))
13900 "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
13901 (build-system r-build-system)
13902 (native-inputs `(("gfortran" ,gfortran)))
13903 (home-page "https://cran.r-project.org/web/packages/deldir")
13904 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13906 "This package provides tools for calculating the Delaunay triangulation
13907 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13908 of a planar point set. It plots triangulations and tessellations in various
13909 ways, clips tessellations to sub-windows, calculates perimeters of
13910 tessellations, and summarizes information about the tiles of the
13912 (license license:gpl2+)))
13914 (define-public r-sf
13921 (uri (cran-uri "sf" version))
13924 "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
13925 (build-system r-build-system)
13932 `(("r-classint" ,r-classint)
13934 ("r-magrittr" ,r-magrittr)
13936 ("r-units" ,r-units)))
13938 `(("pkg-config" ,pkg-config)
13939 ("r-knitr" ,r-knitr)))
13940 (home-page "https://github.com/r-spatial/sf/")
13941 (synopsis "Simple features for R")
13943 "This package provides support for simple features, a standardized way to
13944 encode spatial vector data. It binds to GDAL for reading and writing data, to
13945 GEOS for geometrical operations, and to PROJ for projection conversions and
13946 datum transformations.")
13947 ;; Either of these licenses
13948 (license (list license:gpl2 license:expat))))
13950 (define-public r-spdep
13957 (uri (cran-uri "spdep" version))
13960 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13961 (build-system r-build-system)
13963 `(("r-boot" ,r-boot)
13965 ("r-deldir" ,r-deldir)
13967 ("r-gmodels" ,r-gmodels)
13968 ("r-learnbayes" ,r-learnbayes)
13970 ("r-matrix" ,r-matrix)
13974 ("r-spdata" ,r-spdata)))
13976 `(("r-knitr" ,r-knitr)))
13977 (home-page "https://github.com/r-spatial/spdep/")
13978 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13980 "This package provides a collection of functions to create spatial
13981 weights matrix objects from polygon contiguities, from point patterns by
13982 distance and tessellations, for summarizing these objects, and for permitting
13983 their use in spatial data analysis, including regional aggregation by minimum
13985 (license license:gpl2+)))
13987 (define-public r-adegenet
13989 (name "r-adegenet")
13994 (uri (cran-uri "adegenet" version))
13997 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13998 (build-system r-build-system)
14000 `(("r-ade4" ,r-ade4)
14003 ("r-dplyr" ,r-dplyr)
14004 ("r-ggplot2" ,r-ggplot2)
14005 ("r-igraph" ,r-igraph)
14007 ("r-reshape2" ,r-reshape2)
14008 ("r-seqinr" ,r-seqinr)
14009 ("r-shiny" ,r-shiny)
14010 ("r-spdep" ,r-spdep)
14011 ("r-vegan" ,r-vegan)))
14012 (home-page "https://github.com/thibautjombart/adegenet")
14013 (synopsis "Exploratory analysis of genetic and genomic data")
14015 "This package provides a toolset for the exploration of genetic and
14016 genomic data. Adegenet provides formal (S4) classes for storing and handling
14017 various genetic data, including genetic markers with varying ploidy and
14018 hierarchical population structure (@code{genind} class), alleles counts by
14019 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
14020 also implements original multivariate methods (DAPC, sPCA), graphics,
14021 statistical tests, simulation tools, distance and similarity measures, and
14022 several spatial methods. A range of both empirical and simulated datasets is
14023 also provided to illustrate various methods.")
14024 (license license:gpl2+)))
14026 (define-public r-pegas
14033 (uri (cran-uri "pegas" version))
14035 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
14036 (build-system r-build-system)
14038 `(("r-adegenet" ,r-adegenet)
14040 (home-page "http://ape-package.ird.fr/pegas.html")
14041 (synopsis "Population and evolutionary genetics analysis system")
14043 "This package provides functions for reading, writing, plotting,
14044 analysing, and manipulating allelic and haplotypic data, including from VCF
14045 files, and for the analysis of population nucleotide sequences and
14046 micro-satellites including coalescent analyses, linkage disequilibrium,
14047 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
14048 minimum spanning tree and network, and median-joining networks.")
14049 (license license:gpl2+)))
14051 (define-public r-rmetasim
14053 (name "r-rmetasim")
14058 (uri (cran-uri "rmetasim" version))
14061 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
14062 (build-system r-build-system)
14064 `(("r-ade4" ,r-ade4)
14065 ("r-adegenet" ,r-adegenet)
14066 ("r-gtools" ,r-gtools)
14067 ("r-pegas" ,r-pegas)))
14068 (home-page "https://cran.r-project.org/web/packages/rmetasim")
14069 (synopsis "Individual-based population genetic simulation environment")
14071 "This package provides an interface between R and the metasim simulation
14072 engine. The simulation environment is documented in: Strand, A.(2002),
14073 Metasim 1.0: an individual-based environment for simulating population
14074 genetics of complex population dynamics.")
14076 (license license:gpl2+)))
14078 (define-public r-genetics
14080 (name "r-genetics")
14081 (version "1.3.8.1.2")
14085 (uri (cran-uri "genetics" version))
14088 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
14089 (build-system r-build-system)
14091 `(("r-combinat" ,r-combinat)
14092 ("r-gdata" ,r-gdata)
14093 ("r-gtools" ,r-gtools)
14095 ("r-mvtnorm" ,r-mvtnorm)))
14096 (home-page "https://cran.r-project.org/web/packages/genetics/")
14097 (synopsis "Population genetics")
14099 "This package provides classes and methods for handling genetic data.
14100 It includes classes to represent genotypes and haplotypes at single markers up
14101 to multiple markers on multiple chromosomes. Function include allele
14102 frequencies, flagging homo/heterozygotes, flagging carriers of certain
14103 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
14104 and testing for linkage disequilibrium, ...")
14105 ;; Any GPL version.
14106 (license license:gpl2+)))
14108 (define-public r-snp-plotter
14110 (name "r-snp-plotter")
14115 (uri (cran-uri "snp.plotter" version))
14118 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
14119 (properties `((upstream-name . "snp.plotter")))
14120 (build-system r-build-system)
14121 (propagated-inputs `(("r-genetics" ,r-genetics)))
14122 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
14123 (synopsis "Plot p-values using single SNP and/or haplotype data")
14125 "This package helps you create plots of p-values using single SNP and/or
14126 haplotype data. Main features of the package include options to display a
14127 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
14128 datasets simultaneously. Plots can be created using global and/or individual
14129 haplotype p-values along with single SNP p-values. Images are created as
14130 either PDF/EPS files.")
14131 (license license:gpl2+)))
14133 (define-public r-polspline
14135 (name "r-polspline")
14140 (uri (cran-uri "polspline" version))
14142 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
14143 (build-system r-build-system)
14144 (native-inputs `(("gfortran" ,gfortran)))
14145 (home-page "https://cran.r-project.org/web/packages/polspline/")
14146 (synopsis "Polynomial spline routines")
14148 "This package provides routines for the polynomial spline fitting
14149 routines hazard regression, hazard estimation with flexible tails, logspline,
14150 lspec, polyclass, and polymars.")
14151 (license license:gpl2+)))
14153 (define-public r-rms
14160 (uri (cran-uri "rms" version))
14162 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
14163 (build-system r-build-system)
14165 `(("r-cluster" ,r-cluster)
14166 ("r-digest" ,r-digest)
14167 ("r-ggplot2" ,r-ggplot2)
14168 ("r-hmisc" ,r-hmisc)
14169 ("r-htmltable" ,r-htmltable)
14170 ("r-htmltools" ,r-htmltools)
14171 ("r-lattice" ,r-lattice)
14173 ("r-multcomp" ,r-multcomp)
14175 ("r-polspline" ,r-polspline)
14176 ("r-quantreg" ,r-quantreg)
14177 ("r-rpart" ,r-rpart)
14178 ("r-sparsem" ,r-sparsem)
14179 ("r-survival" ,r-survival)))
14180 (native-inputs `(("gfortran" ,gfortran)))
14181 (home-page "http://biostat.mc.vanderbilt.edu/rms")
14182 (synopsis "Regression modeling strategies")
14184 "This is a package for regression modeling, testing, estimation,
14185 validation, graphics, prediction, and typesetting by storing enhanced model
14186 design attributes in the fit. The rms package is a collection of functions
14187 that assist with and streamline modeling. It also contains functions for
14188 binary and ordinal logistic regression models, ordinal models for continuous Y
14189 with a variety of distribution families, and the Buckley-James multiple
14190 regression model for right-censored responses, and implements penalized
14191 maximum likelihood estimation for logistic and ordinary linear models. The
14192 package works with almost any regression model, but it was especially written
14193 to work with binary or ordinal regression models, Cox regression, accelerated
14194 failure time models, ordinary linear models, the Buckley-James model,
14195 generalized least squares for serially or spatially correlated observations,
14196 generalized linear models, and quantile regression.")
14197 (license license:gpl2+)))
14199 (define-public r-arsenal
14206 (uri (cran-uri "arsenal" version))
14209 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14210 (properties `((upstream-name . "arsenal")))
14211 (build-system r-build-system)
14212 (propagated-inputs `(("r-knitr" ,r-knitr)))
14213 (native-inputs `(("r-knitr" ,r-knitr)))
14214 (home-page "https://github.com/mayoverse/arsenal")
14215 (synopsis "Functions for large-scale statistical summaries")
14217 "This package provides an arsenal of R functions for large-scale
14218 statistical summaries, which are streamlined to work within the latest
14219 reporting tools in R and RStudio and which use formulas and versatile
14220 summary statistics for summary tables and models. The primary functions
14224 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14225 levels of one or more categorical variables;
14226 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14227 across two time points;
14228 @item @code{modelsum}, which performs simple model fits on one or more
14229 endpoints for many variables (univariate or adjusted for covariates);
14230 @item @code{freqlist}, a powerful frequency table across many categorical
14232 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14233 @item @code{write2}, a function to output tables to a document.
14236 (license license:gpl2+)))
14238 (define-public r-haplo-stats
14240 (name "r-haplo-stats")
14245 (uri (cran-uri "haplo.stats" version))
14248 "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9"))))
14249 (properties `((upstream-name . "haplo.stats")))
14250 (build-system r-build-system)
14252 `(("r-arsenal" ,r-arsenal)
14255 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14256 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14257 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14259 "This package provides routines for the analysis of indirectly measured
14260 haplotypes. The statistical methods assume that all subjects are unrelated
14261 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14262 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14263 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14264 examples in the vignette.")
14265 (license license:gpl2+)))
14267 (define-public r-bqtl
14274 (uri (cran-uri "bqtl" version))
14277 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14278 (build-system r-build-system)
14279 (native-inputs `(("gfortran" ,gfortran)))
14280 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14281 (synopsis "Bayesian QTL mapping toolkit")
14283 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14284 lines. It includes maximum likelihood and Bayesian tools.")
14285 (license license:gpl2+)))
14287 (define-public r-ibdreg
14294 (uri (cran-uri "ibdreg" version))
14297 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14298 (build-system r-build-system)
14299 (home-page "https://www.mayo.edu/research/labs/\
14300 statistical-genetics-genetic-epidemiology/software")
14301 (synopsis "Regression methods for IBD linkage with covariates")
14303 "This package provides a method to test genetic linkage with covariates
14304 by regression methods with response IBD sharing for relative pairs. Account
14305 for correlations of IBD statistics and covariates for relative pairs within
14306 the same pedigree.")
14307 (license license:gpl2+)))
14309 (define-public r-dlmap
14316 (uri (cran-uri "dlmap" version))
14319 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14320 (build-system r-build-system)
14322 `(("r-ibdreg" ,r-ibdreg)
14326 ("r-wgaim" ,r-wgaim)))
14327 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14328 (synopsis "Detection localization mapping for QTL")
14330 "This is package for QTL mapping in a mixed model framework with separate
14331 detection and localization stages. The first stage detects the number of QTL
14332 on each chromosome based on the genetic variation due to grouped markers on
14333 the chromosome; the second stage uses this information to determine the most
14334 likely QTL positions. The mixed model can accommodate general fixed and
14335 random effects, including spatial effects in field trials and pedigree
14336 effects. It is applicable to backcrosses, doubled haploids, recombinant
14337 inbred lines, F2 intercrosses, and association mapping populations.")
14338 (license license:gpl2)))
14340 (define-public r-ldheatmap
14342 (name "r-ldheatmap")
14347 (uri (cran-uri "LDheatmap" version))
14350 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14351 (properties `((upstream-name . "LDheatmap")))
14352 (build-system r-build-system)
14354 `(("r-genetics" ,r-genetics)
14356 ("r-snpstats" ,r-snpstats)))
14357 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14358 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14360 "This package provides tools to produce a graphical display, as a heat
14361 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14362 optionally include the physical locations or genetic map distances of each SNP
14364 (license license:gpl3)))
14366 (define-public r-hwde
14373 (uri (cran-uri "hwde" version))
14376 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14377 (build-system r-build-system)
14378 (home-page "https://cran.r-project.org/web/packages/hwde/")
14379 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14381 "This package fits models for genotypic disequilibria, as described in
14382 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14383 terms are available that account for first order interactions between loci.
14384 It also implements, for a single locus in a single population, a conditional
14385 exact test for Hardy-Weinberg equilibrium.")
14386 (license license:gpl2+)))
14388 (define-public r-tdthap
14395 (uri (cran-uri "tdthap" version))
14398 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14399 (build-system r-build-system)
14400 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14401 (synopsis "TDT tests for extended haplotypes")
14403 "Functions and examples are provided for transmission/disequilibrium
14404 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14405 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14406 (license license:artistic2.0)))
14408 (define-public r-sparql
14414 (uri (cran-uri "SPARQL" version))
14417 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14418 (properties `((upstream-name . "SPARQL")))
14419 (build-system r-build-system)
14421 `(("r-rcurl" ,r-rcurl)
14423 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14424 (synopsis "SPARQL client for R")
14425 (description "This package provides an interface to use SPARQL to pose
14426 SELECT or UPDATE queries to an end-point.")
14427 ;; The only license indication is found in the DESCRIPTION file,
14428 ;; which states GPL-3. So we cannot assume GPLv3+.
14429 (license license:gpl3)))
14431 (define-public r-bookdown
14433 (name "r-bookdown")
14437 (uri (cran-uri "bookdown" version))
14440 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14441 (build-system r-build-system)
14443 `(("r-htmltools" ,r-htmltools)
14444 ("r-knitr" ,r-knitr)
14445 ("r-rmarkdown" ,r-rmarkdown)
14446 ("r-tinytex" ,r-tinytex)
14448 ("pandoc" ,pandoc)))
14449 (home-page "https://github.com/rstudio/bookdown")
14450 (synopsis "Authoring books and technical documents with R markdown")
14451 (description "This package provides output formats and utilities for
14452 authoring books and technical documents with R Markdown.")
14453 (license license:gpl3)))
14455 (define-public r-optparse
14457 (name "r-optparse")
14462 (uri (cran-uri "optparse" version))
14465 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14466 (build-system r-build-system)
14468 `(("r-getopt" ,r-getopt)))
14470 `(("r-knitr" ,r-knitr)))
14471 (home-page "https://github.com/trevorld/optparse")
14472 (synopsis "Command line option parser")
14474 "This package provides a command line parser inspired by Python's
14475 @code{optparse} library to be used with Rscript to write shebang scripts
14476 that accept short and long options.")
14477 (license license:gpl2+)))
14479 (define-public r-wgcna
14486 (uri (cran-uri "WGCNA" version))
14489 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14490 (properties `((upstream-name . "WGCNA")))
14491 (build-system r-build-system)
14493 `(("r-annotationdbi" ,r-annotationdbi)
14494 ("r-doparallel" ,r-doparallel)
14495 ("r-dynamictreecut" ,r-dynamictreecut)
14496 ("r-fastcluster" ,r-fastcluster)
14497 ("r-foreach" ,r-foreach)
14498 ("r-go-db" ,r-go-db)
14499 ("r-hmisc" ,r-hmisc)
14500 ("r-impute" ,r-impute)
14502 ("r-survival" ,r-survival)
14503 ("r-matrixstats" ,r-matrixstats)
14504 ("r-preprocesscore" ,r-preprocesscore)))
14506 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14507 (synopsis "Weighted correlation network analysis")
14509 "This package provides functions necessary to perform Weighted
14510 Correlation Network Analysis on high-dimensional data. It includes functions
14511 for rudimentary data cleaning, construction and summarization of correlation
14512 networks, module identification and functions for relating both variables and
14513 modules to sample traits. It also includes a number of utility functions for
14514 data manipulation and visualization.")
14515 (license license:gpl2+)))
14517 (define-public r-kernlab
14524 (uri (cran-uri "kernlab" version))
14526 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14527 (build-system r-build-system)
14528 (home-page "https://cran.r-project.org/web/packages/kernlab")
14529 (synopsis "Kernel-based machine learning tools")
14531 "This package provides kernel-based machine learning methods for
14532 classification, regression, clustering, novelty detection, quantile regression
14533 and dimensionality reduction. Among other methods @code{kernlab} includes
14534 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14536 (license license:gpl2)))
14538 (define-public r-hierfstat
14540 (name "r-hierfstat")
14545 (uri (cran-uri "hierfstat" version))
14548 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14549 (build-system r-build-system)
14551 `(("r-ade4" ,r-ade4)
14552 ("r-adegenet" ,r-adegenet)
14553 ("r-gaston" ,r-gaston)
14554 ("r-gtools" ,r-gtools)))
14556 `(("r-knitr" ,r-knitr)))
14557 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14558 (synopsis "Estimation and tests of hierarchical F-statistics")
14560 "This package allows the estimation of hierarchical F-statistics from
14561 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14562 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14563 are also given to test via randomisations the significance of each F and
14564 variance components, using the likelihood-ratio statistics G.")
14565 (license license:gpl2+)))
14567 (define-public r-hapassoc
14569 (name "r-hapassoc")
14574 (uri (cran-uri "hapassoc" version))
14577 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14578 (build-system r-build-system)
14579 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14580 (synopsis "Inference of trait associations with SNP haplotypes")
14582 "Hapassoc performs likelihood inference of trait associations with
14583 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14584 functions are developed primarily for data collected in cohort or
14585 cross-sectional studies. They can accommodate uncertain haplotype phase and
14586 handle missing genotypes at some SNPs.")
14587 (license license:gpl2)))
14589 (define-public r-sampling
14591 (name "r-sampling")
14596 (uri (cran-uri "sampling" version))
14599 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14600 (build-system r-build-system)
14602 `(("r-lpsolve" ,r-lpsolve)
14603 ("r-mass" ,r-mass)))
14604 (home-page "https://cran.r-project.org/web/packages/sampling/")
14605 (synopsis "Survey sampling")
14607 "This package provides functions for drawing and calibrating samples.")
14608 (license license:gpl2+)))
14610 (define-public r-r2html
14617 (uri (cran-uri "R2HTML" version))
14620 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14621 (properties `((upstream-name . "R2HTML")))
14622 (build-system r-build-system)
14623 (home-page "https://github.com/nalimilan/R2HTML")
14624 (synopsis "HTML export for R objects")
14626 "This package includes HTML functions and methods to write in an HTML
14627 file. Thus, making HTML reports is easy. It includes a function that allows
14628 redirection on the fly, which appears to be very useful for teaching purposes,
14629 as the student can keep a copy of the produced output to keep all that they
14630 did during the course. The package comes with a vignette describing how to
14631 write HTML reports for statistical analysis. Finally, a driver for Sweave
14632 parses HTML flat files containing R code and to automatically write
14633 the corresponding outputs (tables and graphs).")
14634 (license license:gpl2+)))
14636 (define-public r-rjava
14643 (uri (cran-uri "rJava" version))
14646 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14647 (properties `((upstream-name . "rJava")))
14648 (build-system r-build-system)
14650 `(#:modules ((guix build utils)
14651 (guix build r-build-system)
14654 (modify-phases %standard-phases
14655 (add-after 'unpack 'set-JAVA_HOME
14656 (lambda* (#:key inputs #:allow-other-keys)
14657 (let ((jdk (assoc-ref inputs "jdk")))
14658 (setenv "JAVA_HOME" jdk)
14659 (setenv "JAVA" (which "java"))
14660 (setenv "JAR" (which "jar"))
14661 (setenv "JAVAC" (which "javac"))
14662 (setenv "JAVAH" (which "javah"))
14663 (setenv "JAVA_CPPFLAGS"
14664 (string-append "-I" jdk "/include "
14665 "-I" jdk "/include/linux"))
14666 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14667 ((lib) (setenv "JAVA_LIBS" lib))
14668 (_ (error "Could not find libjvm.so"))))
14672 ("jdk" ,icedtea-8 "jdk")
14675 (home-page "https://www.rforge.net/rJava/")
14676 (synopsis "Low-Level R to Java interface")
14678 "This package provides a low-level interface to the Java VM very much
14679 like .C/.Call and friends. It allows the creation of objects, calling methods
14680 and accessing fields.")
14681 (license license:gpl2)))
14683 (define-public r-svmisc
14690 (uri (cran-uri "svMisc" version))
14693 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14694 (properties `((upstream-name . "svMisc")))
14695 (build-system r-build-system)
14696 (home-page "https://github.com/SciViews/svMisc")
14697 (synopsis "Miscellaneous functions for SciViews")
14699 "This package provides miscellaneous functions for SciViews or general
14700 use, including tools to manage a temporary environment attached to the search
14701 path for temporary variables you do not want to @code{save()} or
14702 @code{load()}; test the current platform; showing progress bars, etc.")
14703 (license license:gpl2)))
14705 (define-public r-xyz
14712 (uri (cran-uri "xyz" version))
14715 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14716 (build-system r-build-system)
14718 `(("r-rcpp" ,r-rcpp)))
14719 (home-page "https://cran.r-project.org/web/packages/xyz/")
14720 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14722 "High dimensional interaction search by brute force requires a quadratic
14723 computational cost in the number of variables. The xyz algorithm provably
14724 finds strong interactions in almost linear time. For details of the algorithm
14725 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14726 interaction search in high-dimensional data.")
14727 ;; Any version of the GPL.
14728 (license license:gpl2+)))
14730 (define-public r-rttf2pt1
14732 (name "r-rttf2pt1")
14737 (uri (cran-uri "Rttf2pt1" version))
14740 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14741 (properties `((upstream-name . "Rttf2pt1")))
14742 (build-system r-build-system)
14743 (home-page "https://github.com/wch/Rttf2pt1")
14744 (synopsis "Font conversion utility")
14746 "This package contains the program @code{ttf2pt1}, for use with the
14747 @code{extrafont} package.")
14748 ;; Most of the files are covered under the Expat license. Some files are
14749 ;; covered under BSD-3. Deviations for individual files are recorded in
14750 ;; the LICENSE file.
14751 (license (list license:bsd-3 license:expat
14752 (license:non-copyleft "file://LICENSE")))))
14754 (define-public r-extrafontdb
14756 (name "r-extrafontdb")
14761 (uri (cran-uri "extrafontdb" version))
14764 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14765 (build-system r-build-system)
14766 (home-page "https://github.com/wch/extrafontdb")
14767 (synopsis "Database for the extrafont package")
14769 "This package holds the database for the @code{extrafont} package.")
14770 (license license:gpl2)))
14772 (define-public r-extrafont
14774 (name "r-extrafont")
14779 (uri (cran-uri "extrafont" version))
14782 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14783 (build-system r-build-system)
14785 `(("r-extrafontdb" ,r-extrafontdb)
14786 ("r-rttf2pt1" ,r-rttf2pt1)))
14787 (home-page "https://github.com/wch/extrafont")
14788 (synopsis "Tools for using fonts in R")
14790 "The extrafont package makes it easier to use fonts other than the basic
14791 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14792 used with PDF or PostScript output files. There are two hurdles for using
14793 fonts in PDF (or Postscript) output files:
14796 @item Making R aware of the font and the dimensions of the characters.
14797 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14798 properly on a device that doesn't have the font. This is usually needed if
14799 you want to print the PDF file or share it with others.
14802 The extrafont package makes both of these things easier.")
14803 (license license:gpl2)))
14805 (define-public r-xkcd
14812 (uri (cran-uri "xkcd" version))
14815 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14816 (build-system r-build-system)
14818 `(("r-extrafont" ,r-extrafont)
14819 ("r-ggplot2" ,r-ggplot2)
14820 ("r-hmisc" ,r-hmisc)))
14821 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14822 (synopsis "Plot ggplot2 graphics in the XKCD style")
14824 "This package provides the means to plot ggplot2 graphs in the style of
14825 the XKCD web comic.")
14826 (license license:gpl3)))
14828 (define-public r-msigdbr
14835 (uri (cran-uri "msigdbr" version))
14838 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14839 (build-system r-build-system)
14841 `(("r-dplyr" ,r-dplyr)
14842 ("r-magrittr" ,r-magrittr)
14843 ("r-rlang" ,r-rlang)
14844 ("r-tibble" ,r-tibble)))
14846 `(("r-knitr" ,r-knitr)))
14847 (home-page "https://github.com/igordot/msigdbr")
14848 (synopsis "MSigDB gene sets for multiple organisms")
14850 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14851 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14852 software in a standard R data frame with key-value pairs. Included are the
14853 original human gene symbols and Entrez IDs as well as the equivalents for
14854 various frequently studied model organisms such as mouse, rat, pig, fly, and
14856 ;; The package is covered under the Expat license, but the upstream MSigDB
14857 ;; files are made available under the Creative Commons Attribution 4.0
14858 ;; International license.
14859 (license (list license:expat license:cc-by4.0))))
14861 (define-public r-gridgraphics
14863 (name "r-gridgraphics")
14868 (uri (cran-uri "gridGraphics" version))
14871 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14872 (properties `((upstream-name . "gridGraphics")))
14873 (build-system r-build-system)
14874 (home-page "https://github.com/pmur002/gridgraphics")
14875 (synopsis "Redraw base graphics using @code{grid} graphics")
14877 "This package provides functions to convert a page of plots drawn with
14878 the @code{graphics} package into identical output drawn with the @code{grid}
14879 package. The result looks like the original @code{graphics}-based plot, but
14880 consists of @code{grid} grobs and viewports that can then be manipulated with
14881 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14882 (license license:gpl2+)))
14884 (define-public r-farver
14891 (uri (cran-uri "farver" version))
14894 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14895 (build-system r-build-system)
14896 (home-page "https://github.com/thomasp85/farver")
14897 (synopsis "Vectorized color conversion and comparison")
14899 "The encoding of color can be handled in many different ways, using
14900 different color spaces. As different color spaces have different uses,
14901 efficient conversion between these representations are important. This
14902 package provides a set of functions that gives access to very fast color space
14903 conversion and comparisons implemented in C++, and offers 100-fold speed
14904 improvements over the @code{convertColor} function in the @code{grDevices}
14906 (license license:expat)))
14908 (define-public r-ggplotify
14910 (name "r-ggplotify")
14915 (uri (cran-uri "ggplotify" version))
14918 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14919 (build-system r-build-system)
14921 `(("r-ggplot2" ,r-ggplot2)
14922 ("r-gridgraphics" ,r-gridgraphics)
14923 ("r-rvcheck" ,r-rvcheck)))
14925 `(("r-knitr" ,r-knitr)))
14926 (home-page "https://github.com/GuangchuangYu/ggplotify")
14927 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14929 "This package provides tools to convert plot function calls (using
14930 expression or formula) to @code{grob} or @code{ggplot} objects that are
14931 compatible with the @code{grid} and @code{ggplot2} environment. With this
14932 package, we are able to e.g. use @code{cowplot} to align plots produced by
14933 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14934 converting them to @code{ggplot} objects.")
14935 (license license:artistic2.0)))
14937 (define-public r-triebeard
14939 (name "r-triebeard")
14944 (uri (cran-uri "triebeard" version))
14947 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14948 (build-system r-build-system)
14949 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14950 (home-page "https://github.com/Ironholds/triebeard/")
14951 (synopsis "Radix trees in Rcpp")
14953 "Radix trees, or tries, are key-value data structures optimized for
14954 efficient lookups, similar in purpose to hash tables. This package provides
14955 an implementation of radix trees for use in R programming and in developing
14956 packages with Rcpp.")
14957 (license license:expat)))
14959 (define-public r-tweenr
14966 (uri (cran-uri "tweenr" version))
14969 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14970 (build-system r-build-system)
14972 `(("r-farver" ,r-farver)
14973 ("r-magrittr" ,r-magrittr)
14975 ("r-rlang" ,r-rlang)))
14976 (home-page "https://github.com/thomasp85/tweenr")
14977 (synopsis "Interpolate data for smooth animations")
14979 "In order to create smooth animation between states of data, tweening is
14980 necessary. This package provides a range of functions for creating tweened
14981 data that can be used as basis for animation. Furthermore it adds a number of
14982 vectorized interpolaters for common R data types such as numeric, date and
14984 (license license:expat)))
14986 (define-public r-polyclip
14988 (name "r-polyclip")
14993 (uri (cran-uri "polyclip" version))
14996 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14997 (build-system r-build-system)
14998 (native-inputs `(("pkg-config" ,pkg-config)))
14999 (home-page "http://www.angusj.com/delphi/clipper.php")
15000 (synopsis "Polygon clipping")
15002 "This package provides an R port of the library Clipper. It performs
15003 polygon clipping operations (intersection, union, set minus, set difference)
15004 for polygonal regions of arbitrary complexity, including holes. It computes
15005 offset polygons (spatial buffer zones, morphological dilations, Minkowski
15006 dilations) for polygonal regions and polygonal lines. It computes the
15007 Minkowski Sum of general polygons. There is a function for removing
15008 self-intersections from polygon data.")
15009 (license license:boost1.0)))
15011 (define-public r-urltools
15013 (name "r-urltools")
15018 (uri (cran-uri "urltools" version))
15021 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
15022 (build-system r-build-system)
15024 `(("r-rcpp" ,r-rcpp)
15025 ("r-triebeard" ,r-triebeard)))
15026 (home-page "https://github.com/Ironholds/urltools/")
15027 (synopsis "Vectorized tools for URL handling and parsing")
15029 "This package provides a toolkit for all URL-handling needs, including
15030 encoding and decoding, parsing, parameter extraction and modification. All
15031 functions are designed to be both fast and entirely vectorized. It is
15032 intended to be useful for people dealing with web-related datasets, such as
15033 server-side logs, although may be useful for other situations involving large
15035 (license license:expat)))
15037 (define-public r-ggforce
15044 (uri (cran-uri "ggforce" version))
15047 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
15048 (build-system r-build-system)
15050 `(("r-ggplot2" ,r-ggplot2)
15051 ("r-gtable" ,r-gtable)
15053 ("r-polyclip" ,r-polyclip)
15055 ("r-rcppeigen" ,r-rcppeigen)
15056 ("r-rlang" ,r-rlang)
15057 ("r-scales" ,r-scales)
15058 ("r-tidyselect" ,r-tidyselect)
15059 ("r-tweenr" ,r-tweenr)
15060 ("r-withr" ,r-withr)))
15061 (home-page "https://ggforce.data-imaginist.com")
15062 (synopsis "Accelerating ggplot2")
15064 "The aim of the ggplot2 package is to aid in visual data investigations.
15065 This focus has led to a lack of facilities for composing specialized plots.
15066 Thi package aims to be a collection of mainly new statistics and geometries
15067 that fills this gap.")
15068 (license license:expat)))
15070 (define-public r-europepmc
15072 (name "r-europepmc")
15077 (uri (cran-uri "europepmc" version))
15080 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
15081 (build-system r-build-system)
15083 `(("r-dplyr" ,r-dplyr)
15085 ("r-jsonlite" ,r-jsonlite)
15087 ("r-progress" ,r-progress)
15088 ("r-purrr" ,r-purrr)
15089 ("r-rlang" ,r-rlang)
15090 ("r-tibble" ,r-tibble)
15091 ("r-tidyr" ,r-tidyr)
15092 ("r-urltools" ,r-urltools)
15093 ("r-xml2" ,r-xml2)))
15095 `(("r-knitr" ,r-knitr)))
15096 (home-page "https://github.com/ropensci/europepmc/")
15097 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
15099 "This package provides an R Client for the
15100 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
15101 Service}. It gives access to both metadata on life science literature and
15102 open access full texts. Europe PMC indexes all PubMed content and other
15103 literature sources including Agricola, a bibliographic database of citations
15104 to the agricultural literature, or Biological Patents. In addition to
15105 bibliographic metadata, the client allows users to fetch citations and
15106 reference lists. Links between life-science literature and other EBI
15107 databases, including ENA, PDB or ChEMBL are also accessible.")
15108 (license license:gpl3)))
15110 (define-public r-ggraph
15117 (uri (cran-uri "ggraph" version))
15120 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
15121 (build-system r-build-system)
15123 `(("r-digest" ,r-digest)
15124 ("r-dplyr" ,r-dplyr)
15125 ("r-ggforce" ,r-ggforce)
15126 ("r-ggplot2" ,r-ggplot2)
15127 ("r-ggrepel" ,r-ggrepel)
15128 ("r-graphlayouts" ,r-graphlayouts)
15129 ("r-gtable" ,r-gtable)
15130 ("r-igraph" ,r-igraph)
15133 ("r-rlang" ,r-rlang)
15134 ("r-scales" ,r-scales)
15135 ("r-tidygraph" ,r-tidygraph)
15136 ("r-viridis" ,r-viridis)))
15138 `(("r-knitr" ,r-knitr)))
15139 (home-page "https://cran.r-project.org/web/packages/ggraph/")
15140 (synopsis "Implementation of grammar of graphics for graphs and networks")
15142 "The grammar of graphics as implemented in ggplot2 is a poor fit for
15143 graph and network visualizations due to its reliance on tabular data input.
15144 The ggraph package is an extension of the ggplot2 API tailored to graph
15145 visualizations and provides the same flexible approach to building up plots
15147 (license license:gpl3)))
15149 (define-public r-varselrf
15151 (name "r-varselrf")
15156 (uri (cran-uri "varSelRF" version))
15159 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
15160 (properties `((upstream-name . "varSelRF")))
15161 (build-system r-build-system)
15163 `(("r-randomforest" ,r-randomforest)))
15164 (home-page "https://www.ligarto.org/rdiaz/software/software")
15165 (synopsis "Variable selection using random forests")
15167 "This package provides tools for the variable selection from random
15168 forests using both backwards variable elimination (for the selection of small
15169 sets of non-redundant variables) and selection based on the importance
15170 spectrum (somewhat similar to scree plots; for the selection of large,
15171 potentially highly-correlated variables). The main applications are in
15172 high-dimensional data (e.g., microarray data, and other genomics and
15173 proteomics applications).")
15174 (license license:gpl2+)))
15176 (define-public r-pamr
15183 (uri (cran-uri "pamr" version))
15186 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
15187 (build-system r-build-system)
15189 `(("r-cluster" ,r-cluster)
15190 ("r-survival" ,r-survival)))
15191 (native-inputs `(("gfortran" ,gfortran)))
15192 (home-page "https://cran.r-project.org/web/packages/pamr/")
15193 (synopsis "Prediction Analysis for Microarrays")
15195 "This package provides some functions for sample classification in
15197 (license license:gpl2)))
15199 (define-public r-rda
15202 (version "1.0.2-2.1")
15206 (uri (cran-uri "rda" version))
15209 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15210 (build-system r-build-system)
15211 (home-page "https://cran.r-project.org/web/packages/rda/")
15212 (synopsis "Shrunken centroids regularized discriminant analysis")
15214 "This package provides tools for shrunken centroids regularized
15215 discriminant analysis for the purpose of classifying high dimensional data.")
15216 (license license:gpl2+)))
15218 (define-public r-ggvis
15225 (uri (cran-uri "ggvis" version))
15228 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
15229 (build-system r-build-system)
15231 `(("r-assertthat" ,r-assertthat)
15232 ("r-dplyr" ,r-dplyr)
15233 ("r-htmltools" ,r-htmltools)
15234 ("r-jsonlite" ,r-jsonlite)
15235 ("r-lazyeval" ,r-lazyeval)
15236 ("r-magrittr" ,r-magrittr)
15237 ("r-shiny" ,r-shiny)))
15238 (home-page "https://ggvis.rstudio.com/")
15239 (synopsis "Interactive grammar of graphics")
15241 "This package is a data visualization package for R providing an
15242 implementation of an interactive grammar of graphics, taking the best parts of
15243 ggplot2, combining them with the reactive framework of Shiny and drawing web
15244 graphics using Vega.")
15245 (license license:gpl2)))
15247 (define-public r-gbm
15254 (uri (cran-uri "gbm" version))
15257 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15258 (build-system r-build-system)
15260 `(("r-lattice" ,r-lattice)
15261 ("r-survival" ,r-survival)))
15263 `(("r-knitr" ,r-knitr)))
15264 (home-page "https://github.com/gbm-developers/gbm")
15265 (synopsis "Generalized boosted regression models")
15267 "This package is an implementation of extensions to Freund and Schapire's
15268 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15269 regression methods for least squares, absolute loss, t-distribution loss,
15270 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15271 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15272 and Learning to Rank measures (LambdaMart).")
15273 (license license:gpl2+)))
15275 (define-public r-threejs
15282 (uri (cran-uri "threejs" version))
15285 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15286 (build-system r-build-system)
15288 `(#:modules ((guix build utils)
15289 (guix build r-build-system)
15293 (modify-phases %standard-phases
15294 (add-after 'unpack 'process-javascript
15295 (lambda* (#:key inputs #:allow-other-keys)
15296 (with-directory-excursion "inst"
15300 `((,(assoc-ref inputs "js-jquery")
15301 "htmlwidgets/lib/jquery/jquery.min.js")
15302 (,(assoc-ref inputs "js-threejs-111")
15303 "htmlwidgets/lib/threejs-111/three.min.js"))))
15304 (lambda (sources targets)
15305 (for-each (lambda (source target)
15306 (format #t "Processing ~a --> ~a~%"
15308 (delete-file target)
15309 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15310 (call-with-output-file target
15312 (dump-port minified port)))))
15313 sources targets))))
15316 `(("r-base64enc" ,r-base64enc)
15317 ("r-crosstalk" ,r-crosstalk)
15318 ("r-htmlwidgets" ,r-htmlwidgets)
15319 ("r-igraph" ,r-igraph)))
15321 `(("uglify-js" ,uglify-js)
15325 (uri "https://code.jquery.com/jquery-1.12.4.js")
15328 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15332 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15335 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15336 (home-page "https://bwlewis.github.io/rthreejs")
15337 (synopsis "Interactive 3D scatter plots, networks and globes")
15339 "Create interactive 3D scatter plots, network plots, and globes in R
15340 using the three.js visualization library.")
15341 (license license:expat)))
15343 (define-public r-mlbench
15350 (uri (cran-uri "mlbench" version))
15353 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15354 (build-system r-build-system)
15355 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15356 (synopsis "Machine learning benchmark problems")
15358 "This package provides a collection of artificial and real-world machine
15359 learning benchmark problems, including, e.g., several data sets from the UCI
15361 (license license:gpl2)))
15363 (define-public r-mpm
15370 (uri (cran-uri "mpm" version))
15373 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15374 (build-system r-build-system)
15376 `(("r-kernsmooth" ,r-kernsmooth)
15377 ("r-mass" ,r-mass)))
15378 (home-page "http://mpm.r-forge.r-project.org")
15379 (synopsis "Multivariate projection methods")
15381 "This is a package for exploratory graphical analysis of multivariate
15382 data, specifically gene expression data with different projection methods:
15383 principal component analysis, correspondence analysis, spectral map
15385 (license license:gpl2+)))
15387 (define-public r-png
15393 (uri (cran-uri "png" version))
15396 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15397 (build-system r-build-system)
15399 `(("libpng" ,libpng)
15401 (home-page "https://www.rforge.net/png/")
15402 (synopsis "Read and write PNG images")
15404 "This package provides an easy and simple way to read, write and display
15405 bitmap images stored in the PNG format. It can read and write both files and
15406 in-memory raw vectors.")
15407 ;; Any of these GPL versions.
15408 (license (list license:gpl2 license:gpl3))))
15410 (define-public r-ggcorrplot
15412 (name "r-ggcorrplot")
15417 (uri (cran-uri "ggcorrplot" version))
15420 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15421 (build-system r-build-system)
15423 `(("r-ggplot2" ,r-ggplot2)
15424 ("r-reshape2" ,r-reshape2)))
15425 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15426 (synopsis "Visualization of a correlation matrix using ggplot2")
15428 "The ggcorrplot package can be used to visualize easily a correlation
15429 matrix using ggplot2. It provides a solution for reordering the correlation
15430 matrix and displays the significance level on the plot. It also includes a
15431 function for computing a matrix of correlation p-values.")
15432 (license license:gpl2)))
15434 ;; This package includes minified JavaScript files. When upgrading please
15435 ;; check that there are no new minified JavaScript files.
15436 (define-public r-flexdashboard
15438 (name "r-flexdashboard")
15443 (uri (cran-uri "flexdashboard" version))
15446 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15447 (modules '((guix build utils)))
15450 ;; Delete bundled minified JavaScript files
15451 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15452 (delete-file "inst/www/sly/sly.min.js")
15453 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15454 (delete-file "inst/www/prism/prism.js")
15456 (build-system r-build-system)
15458 `(#:modules ((guix build utils)
15459 (guix build r-build-system)
15463 (ice-9 textual-ports))
15465 (modify-phases %standard-phases
15466 (add-after 'unpack 'process-javascript
15467 (lambda* (#:key inputs #:allow-other-keys)
15468 (with-directory-excursion "inst"
15469 ;; Concatenate all components of prism.js
15470 (let ((contents (string-join
15471 (map (lambda (name)
15472 (call-with-input-file
15473 (assoc-ref inputs name)
15477 "js-prism-line-numbers"))
15479 (call-with-output-file "prism-src.js"
15480 (cut display contents <>)))
15484 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15485 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15487 "www/sly/sly.min.js")
15489 "www/prism/prism.js")
15490 (,(assoc-ref inputs "js-raphael")
15491 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15492 (,(assoc-ref inputs "js-featherlight")
15493 "www/featherlight/featherlight.min.js"))))
15494 (lambda (sources targets)
15495 (for-each (lambda (source target)
15496 (format #t "Processing ~a --> ~a~%"
15498 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15499 (call-with-output-file target
15501 (dump-port minified port)))))
15502 sources targets))))
15505 `(("r-htmltools" ,r-htmltools)
15506 ("r-htmlwidgets" ,r-htmlwidgets)
15507 ("r-jsonlite" ,r-jsonlite)
15508 ("r-knitr" ,r-knitr)
15509 ("r-rmarkdown" ,r-rmarkdown)
15510 ("r-shiny" ,r-shiny)))
15512 `(("uglify-js" ,uglify-js)
15516 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15519 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15523 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15526 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15530 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15533 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15534 ("js-prism-line-numbers"
15537 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15540 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15544 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15547 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15548 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15549 (synopsis "R Markdown format for flexible dashboards")
15551 "This package provides an R Markdown format for converting an R Markdown
15552 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15553 of its components to the containing web page.")
15554 (license license:expat)))
15556 (define-public r-preseqr
15563 (uri (cran-uri "preseqR" version))
15566 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15567 (properties `((upstream-name . "preseqR")))
15568 (build-system r-build-system)
15570 `(("r-polynom" ,r-polynom)))
15571 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15572 (synopsis "Predicting species accumulation curves")
15574 "This package can be used to predict the r-species accumulation
15575 curve (r-SAC), which is the number of species represented at least r times as
15576 a function of the sampling effort. When r = 1, the curve is known as the
15577 species accumulation curve, or the library complexity curve in high-throughput
15578 genomic sequencing. The package includes both parametric and nonparametric
15579 methods, as described by Deng C, et al. (2018).")
15580 (license license:gpl3)))
15582 (define-public r-mapplots
15584 (name "r-mapplots")
15589 (uri (cran-uri "mapplots" version))
15592 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15593 (build-system r-build-system)
15594 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15595 (synopsis "Data visualization on maps")
15597 "This package helps you create simple maps; add sub-plots like pie plots
15598 to a map or any other plot; format, plot and export gridded data. The package
15599 was developed for displaying fisheries data but most functions can be used for
15600 more generic data visualisation.")
15601 (license license:gpl2+)))
15603 (define-public r-pmcmr
15610 (uri (cran-uri "PMCMR" version))
15613 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15614 (properties `((upstream-name . "PMCMR")))
15615 (build-system r-build-system)
15616 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15617 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15619 "This is a deprecated package for calculating pairwise multiple
15620 comparisons of mean rank sums. This package is superseded by the novel
15621 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15622 compatibility of dependent packages for some time.")
15623 (license license:gpl3+)))
15625 (define-public r-downloader
15627 (name "r-downloader")
15632 (uri (cran-uri "downloader" version))
15635 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15636 (build-system r-build-system)
15638 `(("r-digest" ,r-digest)))
15639 (home-page "https://github.com/wch/downloader")
15640 (synopsis "Download files over HTTP and HTTPS")
15642 "This package provides a wrapper for the @code{download.file} function,
15643 making it possible to download files over HTTPS across platforms. The
15644 @code{RCurl} package provides this functionality (and much more) but has
15645 external dependencies. This package has is implemented purely in R.")
15646 (license license:gpl2)))
15648 (define-public r-rex
15655 (uri (cran-uri "rex" version))
15658 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15659 (build-system r-build-system)
15661 `(("r-lazyeval" ,r-lazyeval)))
15663 `(("r-knitr" ,r-knitr)))
15664 (home-page "https://github.com/kevinushey/rex")
15665 (synopsis "Friendly regular expressions")
15667 "This package provides a friendly interface for the construction of
15668 regular expressions. Regular expressions are a very powerful feature, however
15669 they are often difficult to interpret. Rex allows you to build complex
15670 regular expressions from human readable expressions")
15671 (license license:expat)))
15673 (define-public r-xmlparsedata
15675 (name "r-xmlparsedata")
15680 (uri (cran-uri "xmlparsedata" version))
15683 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
15684 (properties `((upstream-name . "xmlparsedata")))
15685 (build-system r-build-system)
15686 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15687 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15689 "This package provides tools to convert the output of
15690 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15691 @code{XPath}, and is easier to manipulate in general.")
15692 (license license:expat)))
15694 (define-public r-cyclocomp
15696 (name "r-cyclocomp")
15701 (uri (cran-uri "cyclocomp" version))
15704 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15705 (properties `((upstream-name . "cyclocomp")))
15706 (build-system r-build-system)
15708 `(("r-callr" ,r-callr)
15709 ("r-crayon" ,r-crayon)
15711 ("r-remotes" ,r-remotes)
15712 ("r-withr" ,r-withr)))
15713 (home-page "https://github.com/MangoTheCat/cyclocomp")
15714 (synopsis "Cyclomatic complexity of R code")
15716 "Cyclomatic complexity is a software metric, used to indicate the
15717 complexity of a program. It is a quantitative measure of the number of
15718 linearly independent paths through a program's source code. This package
15719 provides tools to compute this metric.")
15720 (license license:expat)))
15722 (define-public r-lintr
15729 (uri (cran-uri "lintr" version))
15732 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15733 (properties `((upstream-name . "lintr")))
15734 (build-system r-build-system)
15736 `(("r-codetools" ,r-codetools)
15737 ("r-crayon" ,r-crayon)
15738 ("r-cyclocomp" ,r-cyclocomp)
15739 ("r-digest" ,r-digest)
15741 ("r-jsonlite" ,r-jsonlite)
15742 ("r-knitr" ,r-knitr)
15744 ("r-rstudioapi" ,r-rstudioapi)
15745 ("r-testthat" ,r-testthat)
15747 ("r-xmlparsedata" ,r-xmlparsedata)))
15748 (home-page "https://github.com/jimhester/lintr")
15749 (synopsis "Linter for R code")
15750 (description "This package checks adherence to a given style, syntax
15751 errors and possible semantic issues. It supports on the fly checking of R
15752 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15753 (license license:expat)))
15755 (define-public r-sctransform
15757 (name "r-sctransform")
15762 (uri (cran-uri "sctransform" version))
15765 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15766 (build-system r-build-system)
15768 `(("r-future-apply" ,r-future-apply)
15769 ("r-ggplot2" ,r-ggplot2)
15770 ("r-gridextra" ,r-gridextra)
15772 ("r-matrix" ,r-matrix)
15774 ("r-rcppeigen" ,r-rcppeigen)
15775 ("r-reshape2" ,r-reshape2)))
15776 (home-page "https://github.com/ChristophH/sctransform")
15777 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15779 "This package provides a normalization method for single-cell UMI count
15780 data using a variance stabilizing transformation. The transformation is based
15781 on a negative binomial regression model with regularized parameters. As part
15782 of the same regression framework, this package also provides functions for
15783 batch correction, and data correction.")
15784 (license license:gpl3)))
15786 (define-public r-styler
15793 (uri (cran-uri "styler" version))
15796 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15797 (build-system r-build-system)
15799 `(("r-backports" ,r-backports)
15801 ("r-magrittr" ,r-magrittr)
15802 ("r-purrr" ,r-purrr)
15803 ("r-r-cache" ,r-r-cache)
15804 ("r-rematch2" ,r-rematch2)
15805 ("r-rlang" ,r-rlang)
15806 ("r-rprojroot" ,r-rprojroot)
15807 ("r-tibble" ,r-tibble)
15808 ("r-withr" ,r-withr)
15809 ("r-xfun" ,r-xfun)))
15810 (home-page "https://github.com/r-lib/styler")
15811 (synopsis "Non-invasive pretty printing of R code")
15813 "This is a package for pretty-printing R code without changing the user's
15814 formatting intent.")
15815 (license license:gpl3)))
15817 (define-public r-scrime
15824 (uri (cran-uri "scrime" version))
15827 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15828 (build-system r-build-system)
15829 (home-page "https://cran.r-project.org/web/packages/scrime/")
15830 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15832 "This package provides tools for the analysis of high-dimensional data
15833 developed/implemented at the group \"Statistical Complexity Reduction In
15834 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15835 the functions can also be applied to other types of categorical data.")
15836 (license license:gpl2)))
15838 (define-public r-pbmcapply
15840 (name "r-pbmcapply")
15845 (uri (cran-uri "pbmcapply" version))
15848 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15849 (build-system r-build-system)
15850 (home-page "https://github.com/kvnkuang/pbmcapply")
15851 (synopsis "Track the progress of apply procedures with a progress bar")
15853 "This light-weight package helps you track and visualize the progress of
15854 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15855 (license license:expat)))
15857 (define-public r-blme
15864 (uri (cran-uri "blme" version))
15867 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15868 (build-system r-build-system)
15869 (propagated-inputs `(("r-lme4" ,r-lme4)))
15870 (home-page "https://github.com/vdorie/blme")
15871 (synopsis "Bayesian linear mixed-effects models")
15873 "This package provides tools for maximum a posteriori estimation for
15874 linear and generalized linear mixed-effects models in a Bayesian setting. It
15875 extends the lme4 package.")
15876 (license license:gpl2+)))
15878 (define-public r-batchtools
15880 (name "r-batchtools")
15885 (uri (cran-uri "batchtools" version))
15888 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15889 (build-system r-build-system)
15891 `(("r-backports" ,r-backports)
15892 ("r-base64url" ,r-base64url)
15894 ("r-checkmate" ,r-checkmate)
15895 ("r-data-table" ,r-data-table)
15896 ("r-digest" ,r-digest)
15898 ("r-progress" ,r-progress)
15900 ("r-rappdirs" ,r-rappdirs)
15901 ("r-stringi" ,r-stringi)
15902 ("r-withr" ,r-withr)))
15904 `(("r-knitr" ,r-knitr)))
15905 (home-page "https://github.com/mllg/batchtools")
15906 (synopsis "Tools for computation on batch systems")
15908 "As a successor of the packages BatchJobs and BatchExperiments, this
15909 package provides a parallel implementation of the Map function for high
15910 performance computing systems managed by various schedulers. A multicore and
15911 socket mode allow the parallelization on a local machines, and multiple
15912 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15913 the package provides an abstraction mechanism to define large-scale computer
15914 experiments in a well-organized and reproducible way.")
15915 (license license:lgpl3)))
15917 (define-public r-clue
15924 (uri (cran-uri "clue" version))
15927 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15928 (build-system r-build-system)
15929 (propagated-inputs `(("r-cluster" ,r-cluster)))
15930 (home-page "https://cran.r-project.org/web/packages/clue/")
15931 (synopsis "Tools for analyzing cluster ensembles")
15932 (description "Cluster ensembles are collections of individual solutions to
15933 a given clustering problem which are useful or necessary to consider in a wide
15934 range of applications. This R package provides an extensible computational
15935 environment for creating and analyzing cluster ensembles, with basic data
15936 structures for representing partitions and hierarchies, and facilities for
15937 computing on them, including methods for measuring proximity and obtaining
15938 consensus and secondary clusterings.")
15939 (license license:gpl2)))
15941 (define-public r-sitmo
15948 (uri (cran-uri "sitmo" version))
15951 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15952 (build-system r-build-system)
15953 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15954 (home-page "https://github.com/coatless/sitmo/")
15955 (synopsis "Parallel pseudo random number generator header files")
15957 "This package provides two high quality and fast PPRNGs that may be used
15958 in an OpenMP parallel environment. In addition, there is a generator for one
15959 dimensional low-discrepancy sequence.")
15960 (license license:expat)))
15962 (define-public r-dqrng
15969 (uri (cran-uri "dqrng" version))
15972 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15973 (build-system r-build-system)
15977 ("r-sitmo" ,r-sitmo)))
15978 (home-page "https://www.daqana.org/dqrng")
15979 (synopsis "Fast pseudo random number generators")
15981 "Several fast random number generators are provided as C++ header-only
15982 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15983 Additionally, fast functions for generating random numbers according to a
15984 uniform, normal and exponential distribution are included. The latter two use
15985 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15986 functions are exported to R and as a C++ interface and are enabled for use
15987 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15988 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15989 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15990 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15991 ;; whole is distributed under the terms of the AGPL 3.
15992 (license license:agpl3)))
15994 (define-public r-ingredients
15996 (name "r-ingredients")
16001 (uri (cran-uri "ingredients" version))
16004 "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
16005 (properties `((upstream-name . "ingredients")))
16006 (build-system r-build-system)
16008 `(("r-ggplot2" ,r-ggplot2)
16009 ("r-gridextra" ,r-gridextra)
16010 ("r-scales" ,r-scales)))
16011 (native-inputs `(("r-knitr" ,r-knitr)))
16012 (home-page "https://ModelOriented.github.io/ingredients/")
16013 (synopsis "Effects and importances of model ingredients")
16015 "This is a collection of tools for assessment of feature importance and
16016 feature effects. Key functions are:
16019 @item @code{feature_importance()} for assessment of global level feature
16021 @item @code{ceteris_paribus()} for calculation of the what-if plots,
16022 @item @code{partial_dependence()} for partial dependence plots,
16023 @item @code{conditional_dependence()} for conditional dependence plots,
16024 @item @code{accumulated_dependence()} for accumulated local effects plots,
16025 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
16026 aggregation of ceteris paribus profiles,
16027 @item generic @code{print()} and @code{plot()} for better usability of
16028 selected explainers,
16029 @item generic @code{plotD3()} for interactive, D3 based explanations, and
16030 @item generic @code{describe()} for explanations in natural language.
16032 (license license:gpl3)))
16034 (define-public r-ibreakdown
16036 (name "r-ibreakdown")
16041 (uri (cran-uri "iBreakDown" version))
16044 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
16045 (properties `((upstream-name . "iBreakDown")))
16046 (build-system r-build-system)
16047 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
16048 (native-inputs `(("r-knitr" ,r-knitr)))
16049 (home-page "https://ModelOriented.github.io/iBreakDown/")
16050 (synopsis "Model agnostic instance level variable attributions")
16052 "This package provides a model agnostic tool for decomposition of
16053 predictions from black boxes. It supports additive attributions and
16054 attributions with interactions. The Break Down Table shows contributions of
16055 every variable to a final prediction. The Break Down Plot presents variable
16056 contributions in a concise graphical way. This package works for
16057 classification and regression models.")
16058 (license license:gpl3)))
16060 (define-public r-dae
16067 (uri (cran-uri "dae" version))
16070 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
16071 (build-system r-build-system)
16073 `(("r-ggplot2" ,r-ggplot2)
16074 ("r-plyr" ,r-plyr)))
16076 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
16077 (home-page "http://chris.brien.name")
16078 (synopsis "Functions useful in the design and ANOVA of experiments")
16080 "This package provides functions useful in the design and ANOVA of
16081 experiments. The content falls into the following groupings:
16085 @item factor manipulation functions,
16086 @item design functions,
16087 @item ANOVA functions,
16088 @item matrix functions,
16089 @item projector and canonical efficiency functions, and
16090 @item miscellaneous functions.
16093 There is a vignette called @code{DesignNotes} describing how to use the design
16094 functions for randomizing and assessing designs. The ANOVA functions
16095 facilitate the extraction of information when the @code{Error} function has
16096 been used in the call to @code{aov}.")
16097 (license license:gpl2)))
16099 (define-public r-dalex
16102 (version "1.3.1.1")
16106 (uri (cran-uri "DALEX" version))
16109 "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
16110 (properties `((upstream-name . "DALEX")))
16111 (build-system r-build-system)
16113 `(("r-ggplot2" ,r-ggplot2)
16114 ("r-ibreakdown" ,r-ibreakdown)
16115 ("r-ingredients" ,r-ingredients)))
16116 (home-page "https://pbiecek.github.io/DALEX/")
16117 (synopsis "Descriptive machine learning explanations")
16119 "Machine Learning models are widely used and have various applications in
16120 classification or regression. Models created with boosting, bagging, stacking
16121 or similar techniques are often used due to their high performance, but such
16122 black-box models usually lack interpretability. The DALEX package contains
16123 various explainers that help to understand the link between input variables
16124 and model output.")
16125 ;; Any version of the GPL
16126 (license license:gpl3+)))
16128 (define-public r-enrichr
16135 (uri (cran-uri "enrichR" version))
16138 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
16139 (properties `((upstream-name . "enrichR")))
16140 (build-system r-build-system)
16142 `(("r-httr" ,r-httr)
16143 ("r-rjson" ,r-rjson)))
16144 (home-page "https://cran.r-project.org/web/packages/enrichR/")
16145 (synopsis "R Interface to Enrichr database for analyzing gene sets")
16147 "This package provides an R interface to all Enrichr databases, a
16148 web-based tool for analyzing gene sets and returns any enrichment of common
16149 annotated biological functions.")
16150 (license license:gpl2+)))
16152 (define-public r-plot3d
16159 (uri (cran-uri "plot3D" version))
16162 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
16163 (properties `((upstream-name . "plot3D")))
16164 (build-system r-build-system)
16165 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
16166 (home-page "https://cran.r-project.org/web/packages/plot3D")
16167 (synopsis "Plot multi-dimensional data")
16169 "This package provides functions for viewing 2D and 3D data, including
16170 perspective plots, slice plots, surface plots, scatter plots, etc. It
16171 includes data sets from oceanography.")
16172 (license license:gpl3+)))
16174 (define-public r-ggfortify
16176 (name "r-ggfortify")
16181 (uri (cran-uri "ggfortify" version))
16184 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
16185 (build-system r-build-system)
16187 `(("r-dplyr" ,r-dplyr)
16188 ("r-ggplot2" ,r-ggplot2)
16189 ("r-gridextra" ,r-gridextra)
16190 ("r-scales" ,r-scales)
16191 ("r-stringr" ,r-stringr)
16192 ("r-tibble" ,r-tibble)
16193 ("r-tidyr" ,r-tidyr)))
16195 `(("r-knitr" ,r-knitr)))
16196 (home-page "https://github.com/sinhrks/ggfortify")
16197 (synopsis "Data visualization tools for statistical analysis results")
16199 "This package provides unified plotting tools for statistics commonly
16200 used, such as GLM, time series, PCA families, clustering and survival
16201 analysis. The package offers a single plotting interface for these analysis
16202 results and plots in a unified style using the @code{ggplot2} package.")
16203 (license license:gpl2)))
16205 (define-public r-refmanager
16207 (name "r-refmanager")
16212 (uri (cran-uri "RefManageR" version))
16215 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16216 (properties `((upstream-name . "RefManageR")))
16217 (build-system r-build-system)
16219 `(("r-bibtex" ,r-bibtex)
16221 ("r-jsonlite" ,r-jsonlite)
16222 ("r-lubridate" ,r-lubridate)
16224 ("r-stringr" ,r-stringr)
16225 ("r-xml2" ,r-xml2)))
16226 (home-page "https://github.com/ropensci/RefManageR/")
16227 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16229 "This package provides tools for importing and working with bibliographic
16230 references. It greatly enhances the @code{bibentry} class by providing a
16231 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16232 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16233 by various formats for name lists (author by last names, translator by full
16234 names, etc.). Entries can be updated, combined, sorted, printed in a number
16235 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16236 into R and converted to @code{BibEntry} objects.")
16237 ;; Any of these licenses may be picked.
16238 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16240 (define-public r-citr
16247 (uri (cran-uri "citr" version))
16250 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16251 (build-system r-build-system)
16253 `(("r-assertthat" ,r-assertthat)
16256 ("r-miniui" ,r-miniui)
16257 ("r-refmanager" ,r-refmanager)
16258 ("r-rstudioapi" ,r-rstudioapi)
16259 ("r-shiny" ,r-shiny)
16260 ("r-shinyjs" ,r-shinyjs)
16261 ("r-yaml" ,r-yaml)))
16262 (home-page "https://github.com/crsh/citr")
16263 (synopsis "RStudio add-in to insert Markdown citations")
16265 "This package provides functions and an RStudio add-in that search a
16266 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16267 the current document.")
16268 (license license:expat)))
16270 (define-public r-xgboost
16273 (version "1.2.0.1")
16277 (uri (cran-uri "xgboost" version))
16280 "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
16281 (build-system r-build-system)
16283 `(("r-data-table" ,r-data-table)
16284 ("r-magrittr" ,r-magrittr)
16285 ("r-matrix" ,r-matrix)
16286 ("r-stringi" ,r-stringi)))
16288 `(("r-knitr" ,r-knitr)))
16289 (home-page "https://github.com/dmlc/xgboost")
16290 (synopsis "Extreme gradient boosting")
16292 "This package provides an R interface to Extreme Gradient Boosting, which
16293 is an efficient implementation of the gradient boosting framework from Chen
16294 and Guestrin (2016). The package includes efficient linear model solver and
16295 tree learning algorithms. The package can automatically do parallel
16296 computation on a single machine. It supports various objective functions,
16297 including regression, classification and ranking. The package is made to be
16298 extensible, so that users are also allowed to define their own objectives
16300 (license license:asl2.0)))
16302 (define-public r-umap
16305 (version "0.2.6.0")
16309 (uri (cran-uri "umap" version))
16312 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16313 (build-system r-build-system)
16315 `(("r-openssl" ,r-openssl)
16317 ("r-reticulate" ,r-reticulate)
16318 ("r-rspectra" ,r-rspectra)))
16320 `(("r-knitr" ,r-knitr)))
16321 (home-page "https://github.com/tkonopka/umap")
16322 (synopsis "Uniform manifold approximation and projection")
16324 "Uniform manifold approximation and projection is a technique for
16325 dimension reduction. This package provides an interface to the UMAP algorithm
16326 in R, including a translation of the original algorithm into R.")
16327 (license license:expat)))
16329 (define-public r-uwot
16336 (uri (cran-uri "uwot" version))
16339 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16340 (build-system r-build-system)
16342 `(("r-dqrng" ,r-dqrng)
16344 ("r-irlba" ,r-irlba)
16345 ("r-matrix" ,r-matrix)
16347 ("r-rcppannoy" ,r-rcppannoy)
16348 ("r-rcppprogress" ,r-rcppprogress)
16349 ("r-rspectra" ,r-rspectra)))
16350 (home-page "https://github.com/jlmelville/uwot")
16351 (synopsis "Uniform manifold approximation and projection")
16353 "This package provides an implementation of the Uniform Manifold
16354 Approximation and Projection dimensionality reduction by McInnes et
16355 al. (2018). It also provides means to transform new data and to carry out
16356 supervised dimensionality reduction. An implementation of the related
16357 LargeVis method of Tang et al. (2016) is also provided.")
16358 (license license:gpl3)))
16360 (define-public r-kableextra
16362 (name "r-kableextra")
16367 (uri (cran-uri "kableExtra" version))
16370 "0n25y7zwpspvkd62rd6x8c22dg2ys27smlpdz5brqs5ddv7x9dis"))))
16371 (properties `((upstream-name . "kableExtra")))
16372 (build-system r-build-system)
16374 `(("r-digest" ,r-digest)
16376 ("r-htmltools" ,r-htmltools)
16377 ("r-knitr" ,r-knitr)
16378 ("r-magrittr" ,r-magrittr)
16379 ("r-rmarkdown" ,r-rmarkdown)
16380 ("r-rstudioapi" ,r-rstudioapi)
16381 ("r-rvest" ,r-rvest)
16382 ("r-scales" ,r-scales)
16383 ("r-stringr" ,r-stringr)
16384 ("r-viridislite" ,r-viridislite)
16385 ("r-webshot" ,r-webshot)
16386 ("r-xml2" ,r-xml2)))
16388 `(("r-knitr" ,r-knitr)))
16389 (home-page "https://haozhu233.github.io/kableExtra/")
16390 (synopsis "Construct complex tables with pipe syntax")
16392 "Build complex HTML or LaTeX tables using @code{kable()} from
16393 @code{knitr} and the piping syntax from @code{magrittr}. The function
16394 @code{kable()} is a light weight table generator coming from @code{knitr}.
16395 This package simplifies the way to manipulate the HTML or LaTeX codes
16396 generated by @code{kable()} and allows users to construct complex tables and
16397 customize styles using a readable syntax.")
16398 (license license:expat)))
16400 (define-public r-glasso
16407 (uri (cran-uri "glasso" version))
16409 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16410 (build-system r-build-system)
16411 (native-inputs `(("gfortran" ,gfortran)))
16412 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16413 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16415 "This is a package for estimation of a sparse inverse covariance matrix
16416 using a lasso (L1) penalty. Facilities are provided for estimates along a
16417 path of values for the regularization parameter.")
16418 (license license:gpl2)))
16420 (define-public r-rhpcblasctl
16422 (name "r-rhpcblasctl")
16423 (version "0.20-137")
16427 (uri (cran-uri "RhpcBLASctl" version))
16430 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16431 (properties `((upstream-name . "RhpcBLASctl")))
16432 (build-system r-build-system)
16433 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16434 (synopsis "Control the number of threads on BLAS")
16436 "This package allows you to control the number of threads the BLAS
16437 library uses. It is also possible to control the number of threads in
16439 (license license:agpl3+)))
16441 (define-public r-lda
16448 (uri (cran-uri "lda" version))
16451 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16452 (build-system r-build-system)
16453 (home-page "https://cran.r-project.org/web/packages/lda/")
16454 (synopsis "Collapsed Gibbs sampling methods for topic models")
16456 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16457 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16458 mixed-membership stochastic blockmodel. Inference for all of these models is
16459 implemented via a fast collapsed Gibbs sampler written in C. Utility
16460 functions for reading/writing data typically used in topic models, as well as
16461 tools for examining posterior distributions are also included.")
16462 ;; Any version of the LGPL
16463 (license license:lgpl3+)))
16465 (define-public r-rann-l1
16472 (uri (cran-uri "RANN.L1" version))
16475 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16476 (properties `((upstream-name . "RANN.L1")))
16477 (build-system r-build-system)
16478 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16479 (synopsis "Fast nearest neighbour search using L1 metric")
16481 "This package provides tools to find the k nearest neighbours for every
16482 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16483 library. There is support for approximate as well as exact searches, fixed
16484 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16485 computed using the L1 (Manhattan, taxicab) metric.")
16486 (license license:gpl3+)))
16488 (define-public r-leiden
16495 (uri (cran-uri "leiden" version))
16498 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16499 (properties `((upstream-name . "leiden")))
16500 (build-system r-build-system)
16502 `(("r-igraph" ,r-igraph)
16503 ("r-matrix" ,r-matrix)
16504 ("r-reticulate" ,r-reticulate)))
16505 (home-page "https://github.com/TomKellyGenetics/leiden")
16506 (synopsis "R implementation of Leiden clustering algorithm")
16508 "This package implements the Python @code{leidenalg} module to be called
16509 in R. It enables clustering using the Leiden algorithm for partitioning a
16510 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16511 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16512 (license license:gpl3)))
16514 (define-public r-patchwork
16516 (name "r-patchwork")
16521 (uri (cran-uri "patchwork" version))
16524 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16525 (build-system r-build-system)
16527 `(("r-ggplot2" ,r-ggplot2)
16528 ("r-gtable" ,r-gtable)))
16530 `(("r-knitr" ,r-knitr)))
16531 (home-page "https://github.com/thomasp85/patchwork")
16532 (synopsis "Compose ggplot2 plots")
16534 "The @code{ggplot2} package provides a strong API for sequentially
16535 building up a plot, but does not concern itself with composition of multiple
16536 plots. Patchwork is a package that expands the API to allow for arbitrarily
16537 complex composition of plots by providing mathmatical operators for combining
16539 (license license:expat)))
16541 (define-public r-liger
16548 (uri (git-reference
16549 (url "https://github.com/MacoskoLab/liger")
16550 (commit (string-append "v" version))))
16551 (file-name (git-file-name name version))
16554 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16555 (modules '((guix build utils)))
16558 (delete-file "inst/java/ModularityOptimizer.jar")
16560 (build-system r-build-system)
16563 (modify-phases %standard-phases
16564 (add-after 'unpack 'build-java-part
16565 (lambda* (#:key inputs #:allow-other-keys)
16566 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16567 (for-each (lambda (file) (invoke "javac" file))
16568 (find-files "." "\\.java$"))
16569 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16570 (find-files "." "\\.class$"))
16573 `(("r-cowplot" ,r-cowplot)
16574 ("r-dosnow" ,r-dosnow)
16575 ("r-dplyr" ,r-dplyr)
16577 ("r-foreach" ,r-foreach)
16578 ("r-ggplot2" ,r-ggplot2)
16579 ("r-ggrepel" ,r-ggrepel)
16580 ("r-hmisc" ,r-hmisc)
16582 ("r-irlba" ,r-irlba)
16583 ("r-matrix" ,r-matrix)
16584 ("r-mclust" ,r-mclust)
16585 ("r-patchwork" ,r-patchwork)
16587 ("r-rann-l1" ,r-rann-l1)
16589 ("r-rcpparmadillo" ,r-rcpparmadillo)
16590 ("r-riverplot" ,r-riverplot)
16591 ("r-rtsne" ,r-rtsne)
16592 ("r-snow" ,r-snow)))
16594 `(("jdk" ,icedtea "jdk")
16595 ;; See https://github.com/MacoskoLab/liger/issues/96
16596 ;; The optimizer is released under the Expat license.
16600 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16603 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16605 ("r-knitr" ,r-knitr))) ; for vignettes
16606 (home-page "https://github.com/MacoskoLab/liger")
16607 (synopsis "Integrate and analyze multiple single-cell datasets")
16609 "LIGER is a package for integrating and analyzing multiple single-cell
16610 datasets, developed and maintained by the Macosko lab. It relies on
16611 integrative non-negative matrix factorization to identify shared and
16612 dataset-specific factors.")
16613 (license license:gpl3)))
16615 (define-public r-harmony
16622 (uri (git-reference
16623 (url "https://github.com/immunogenomics/harmony")
16625 (file-name (git-file-name name version))
16628 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16629 (modules '((guix build utils)))
16632 (for-each delete-file '("config.status" "configure"))
16634 (build-system r-build-system)
16636 `(("r-cowplot" ,r-cowplot)
16637 ("r-dplyr" ,r-dplyr)
16638 ("r-ggplot2" ,r-ggplot2)
16639 ("r-irlba" ,r-irlba)
16640 ("r-matrix" ,r-matrix)
16642 ("r-rcpparmadillo" ,r-rcpparmadillo)
16643 ("r-rcppprogress" ,r-rcppprogress)
16644 ("r-rlang" ,r-rlang)
16645 ("r-tibble" ,r-tibble)
16646 ("r-tidyr" ,r-tidyr)))
16648 `(("autoconf" ,autoconf)))
16649 (home-page "https://github.com/immunogenomics/harmony")
16650 (synopsis "Integration of single cell sequencing data")
16652 "This package provides an implementation of the Harmony algorithm for
16653 single cell integration, described in Korsunsky et al
16654 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16655 function and interfaces to external frameworks.")
16656 (license license:gpl3)))
16658 (define-public r-covr
16665 (uri (cran-uri "covr" version))
16667 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16668 (properties `((upstream-name . "covr")))
16669 (build-system r-build-system)
16671 `(("r-crayon" ,r-crayon)
16672 ("r-digest" ,r-digest)
16674 ("r-jsonlite" ,r-jsonlite)
16676 ("r-withr" ,r-withr)
16677 ("r-yaml" ,r-yaml)))
16679 `(("r-knitr" ,r-knitr))) ; for vignettes
16680 (home-page "https://github.com/r-lib/covr")
16681 (synopsis "Test coverage for R packages")
16683 "Thisp package enables you to track and report code coverage for your
16684 package and (optionally) upload the results to a coverage service. Code
16685 coverage is a measure of the amount of code being exercised by a set of tests.
16686 It is an indirect measure of test quality and completeness. This package is
16687 compatible with any testing methodology or framework and tracks coverage of
16688 both R code and compiled C/C++/FORTRAN code.")
16689 (license license:gpl3)))
16691 (define-public r-systemfonts
16693 (name "r-systemfonts")
16698 (uri (cran-uri "systemfonts" version))
16701 "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
16702 (properties `((upstream-name . "systemfonts")))
16703 (build-system r-build-system)
16705 `(("r-cpp11" ,r-cpp11)))
16707 `(("fontconfig" ,fontconfig)
16710 `(("pkg-config" ,pkg-config)
16711 ("r-knitr" ,r-knitr)))
16712 (home-page "https://github.com/r-lib/systemfonts")
16713 (synopsis "System native font finding")
16715 "This package provides system native access to the font catalogue. As
16716 font handling varies between systems it is difficult to correctly locate
16717 installed fonts across different operating systems. The 'systemfonts' package
16718 provides bindings to the native libraries for finding font files that can then
16719 be used further by e.g. graphic devices.")
16720 (license license:expat)))
16722 (define-public r-graphlayouts
16724 (name "r-graphlayouts")
16729 (uri (cran-uri "graphlayouts" version))
16732 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16733 (properties `((upstream-name . "graphlayouts")))
16734 (build-system r-build-system)
16736 `(("r-igraph" ,r-igraph)
16738 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16739 (home-page "https://github.com/schochastics/graphlayouts")
16740 (synopsis "Additional layout algorithms for network visualizations")
16742 "This package provides several layout algorithms to visualize networks
16743 which are not part of the igraph library. Most are based on the concept of
16744 stress majorization by Gansner et al. (2004)
16745 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16746 emphasize hidden group structures in networks or focus on specific nodes.")
16747 (license license:expat)))
16749 (define-public r-tidygraph
16751 (name "r-tidygraph")
16756 (uri (cran-uri "tidygraph" version))
16759 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16760 (properties `((upstream-name . "tidygraph")))
16761 (build-system r-build-system)
16763 `(("r-dplyr" ,r-dplyr)
16764 ("r-igraph" ,r-igraph)
16765 ("r-magrittr" ,r-magrittr)
16766 ("r-pillar" ,r-pillar)
16769 ("r-rlang" ,r-rlang)
16770 ("r-tibble" ,r-tibble)
16771 ("r-tidyr" ,r-tidyr)))
16772 (home-page "https://github.com/thomasp85/tidygraph")
16773 (synopsis "Tidy API for graph manipulation")
16775 "This package provides a graph implementation that can be thought of as
16776 two tidy data frames describing node and edge data respectively. It provides
16777 an approach to manipulate these two virtual data frames using the API defined
16778 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16779 common graph algorithms.")
16780 (license license:expat)))
16782 (define-public r-soupx
16783 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16787 (version (git-version "0.3.1" revision commit))
16791 (uri (git-reference
16792 (url "https://github.com/constantAmateur/SoupX")
16794 (file-name (git-file-name name version))
16797 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16798 (properties `((upstream-name . "SoupX")))
16799 (build-system r-build-system)
16801 `(("r-ggplot2" ,r-ggplot2)
16802 ("r-matrix" ,r-matrix)
16803 ("r-seurat" ,r-seurat)))
16804 (home-page "https://github.com/constantAmateur/SoupX")
16805 (synopsis "Single cell mRNA Soup eXterminator")
16807 "This package provides a package for quantifying, profiling and
16808 removing cell free mRNA contamination (the \"soup\") from droplet based single
16809 cell RNA-seq experiments.")
16810 (license license:gpl2))))
16812 (define-public r-assertr
16819 (uri (cran-uri "assertr" version))
16822 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16823 (build-system r-build-system)
16825 `(("r-dplyr" ,r-dplyr)
16827 ("r-rlang" ,r-rlang)))
16829 `(("r-knitr" ,r-knitr))) ; needed for vignette
16830 (home-page "https://github.com/ropensci/assertr")
16831 (synopsis "Assertive programming for R analysis pipelines")
16833 "This package provides functionality to assert conditions that have to be
16834 met so that errors in data used in analysis pipelines can fail quickly. It is
16835 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16837 (license license:expat)))
16839 (define-public r-parameters
16841 (name "r-parameters")
16846 (uri (cran-uri "parameters" version))
16849 "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
16850 (properties `((upstream-name . "parameters")))
16851 (build-system r-build-system)
16853 `(("r-bayestestr" ,r-bayestestr)
16854 ("r-insight" ,r-insight)))
16856 `(("r-knitr" ,r-knitr)))
16857 (home-page "https://cran.r-project.org/web/packages/parameters")
16858 (synopsis "Processing of model parameters")
16860 "This package provides utilities for processing the parameters of various
16861 statistical models. Beyond computing p values, CIs, and other indices for a
16862 wide variety of models, this package implements features like standardization
16863 or bootstrapping of parameters and models, feature reduction (feature
16864 extraction and variable selection) as well as conversion between indices of
16866 (license license:gpl3)))
16868 (define-public r-rgdal
16875 (uri (cran-uri "rgdal" version))
16877 (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp"))))
16878 (properties `((upstream-name . "rgdal")))
16879 (build-system r-build-system)
16887 `(("pkg-config" ,pkg-config)
16888 ("r-knitr" ,r-knitr)))
16889 (home-page "http://rgdal.r-forge.r-project.org")
16890 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16892 "This package provides bindings to the Geospatial Data Abstraction
16893 Library (GDAL) and access to projection/transformation operations from the
16895 (license license:gpl2+)))
16897 (define-public r-insol
16904 (uri (cran-uri "insol" version))
16907 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16908 (properties `((upstream-name . "insol")))
16909 (build-system r-build-system)
16911 `(("r-raster" ,r-raster)))
16913 `(("gfortran" ,gfortran)))
16914 (home-page "https://meteoexploration.com/R/insol/index.html")
16915 (synopsis "Tools for calculating solar radiation")
16917 "This package provides functions to compute insolation on tilted
16918 surfaces, computes atmospheric transmittance and related parameters such as:
16919 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16920 time, vector in the direction of the sun, vector normal to surface, and some
16921 atmospheric physics.")
16922 (license license:gpl2+)))
16924 (define-public r-lifecycle
16926 (name "r-lifecycle")
16931 (uri (cran-uri "lifecycle" version))
16934 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16935 (properties `((upstream-name . "lifecycle")))
16936 (build-system r-build-system)
16938 `(("r-glue" ,r-glue)
16939 ("r-rlang" ,r-rlang)))
16941 `(("r-knitr" ,r-knitr))) ; for vignettes
16942 (home-page "https://github.com/r-lib/lifecycle")
16943 (synopsis "Manage the life cycle of your package functions")
16945 "Manage the life cycle of your exported functions with shared
16946 conventions, documentation badges, and non-invasive deprecation warnings. The
16947 lifecycle package defines four development stages (experimental, maturing,
16948 stable, and questioning) and three deprecation stages (soft-deprecated,
16949 deprecated, and defunct). It makes it easy to insert badges corresponding to
16950 these stages in your documentation. Usage of deprecated functions are
16951 signalled with increasing levels of non-invasive verbosity.")
16952 (license license:gpl3)))
16954 (define-public r-assertable
16956 (name "r-assertable")
16961 (uri (cran-uri "assertable" version))
16964 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16965 (build-system r-build-system)
16967 `(("r-data-table" ,r-data-table)))
16968 (home-page "https://cran.r-project.org/web/packages/assertable/")
16969 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16970 (description "This package provides simple, flexible assertions on
16971 data.frame or data.table objects with verbose output for vetting. While other
16972 assertion packages apply towards more general use-cases, @code{assertable} is
16973 tailored towards tabular data. It includes functions to check variable names
16974 and values, whether the dataset contains all combinations of a given set of
16975 unique identifiers, and whether it is a certain length. In addition,
16976 @code{assertable} includes utility functions to check the existence of target
16977 files and to efficiently import multiple tabular data files into one
16979 (license license:gpl3)))
16981 (define-public r-quadprog
16983 (name "r-quadprog")
16988 (uri (cran-uri "quadprog" version))
16990 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16991 (build-system r-build-system)
16993 `(("gfortran" ,gfortran)))
16994 (home-page "https://cran.r-project.org/web/packages/quadprog")
16995 (synopsis "Functions to solve quadratic programming problems")
16997 "This package contains routines and documentation for solving quadratic
16998 programming problems.")
16999 (license license:gpl3+)))
17001 (define-public r-desolve
17008 (uri (cran-uri "deSolve" version))
17010 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
17011 (properties `((upstream-name . "deSolve")))
17012 (build-system r-build-system)
17014 `(("gfortran" ,gfortran)))
17015 (home-page "https://desolve.r-forge.r-project.org/")
17016 (synopsis "Solvers for initial value problems of differential equations")
17017 (description "This package provides functions that solve initial value
17018 problems of a system of first-order @dfn{ordinary differential
17019 equations} (ODE), of @dfn{partial differential equations} (PDE), of
17020 @dfn{differential algebraic equations} (DAE), and of delay differential
17021 equations. The functions provide an interface to the FORTRAN functions
17022 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
17023 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
17024 C-implementation of solvers of the Runge-Kutta family with fixed or variable
17025 time steps. The package contains routines designed for solving ODEs resulting
17026 from 1-D, 2-D and 3-D partial differential equations that have been converted
17027 to ODEs by numerical differencing.")
17028 (license license:gpl2+)))
17030 (define-public r-pracma
17036 (uri (cran-uri "pracma" version))
17038 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
17039 (build-system r-build-system)
17040 (home-page "https://cran.r-project.org/web/packages/pracma/")
17041 (synopsis "Practical numerical math functions")
17042 (description "This package provides functions for numerical analysis and
17043 linear algebra, numerical optimization, differential equations, plus some
17044 special functions. It uses Matlab function names where appropriate to simplify
17046 (license license:gpl3+)))
17048 (define-public r-subplex
17055 (uri (cran-uri "subplex" version))
17058 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
17059 (build-system r-build-system)
17061 `(("gfortran" ,gfortran)))
17062 (home-page "https://cran.r-project.org/web/packages/subplex")
17063 (synopsis "Unconstrained optimization using the subplex algorithm")
17065 "This package implements the Subplex optimization algorithm.
17066 It solves unconstrained optimization problems using a simplex method on
17067 subspaces. The method is well suited for optimizing objective functions that
17068 are noisy or are discontinuous at the solution.")
17069 (license license:gpl3+)))
17071 (define-public r-txtplot
17078 (uri (cran-uri "txtplot" version))
17081 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
17082 (build-system r-build-system)
17083 (home-page "https://cran.r-project.org/web/packages/txtplot/")
17084 (synopsis "Text-based plotting")
17085 (description "This package provides functions to produce rudimentary ASCII
17086 graphics directly in the terminal window. This package provides a basic
17087 plotting function (and equivalents of curve, density, acf and barplot) as well
17088 as a boxplot function.")
17089 (license license:lgpl3+)))
17091 (define-public r-bio3d
17098 (uri (cran-uri "bio3d" version))
17101 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
17102 (properties `((upstream-name . "bio3d")))
17103 (build-system r-build-system)
17104 (inputs `(("zlib" ,zlib)))
17105 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17106 (home-page "http://thegrantlab.org/bio3d/")
17107 (synopsis "Biological structure analysis")
17109 "This package provides utilities to process, organize and explore protein
17110 structure, sequence and dynamics data. Features include the ability to read
17111 and write structure, sequence and dynamic trajectory data, perform sequence
17112 and structure database searches, data summaries, atom selection, alignment,
17113 superposition, rigid core identification, clustering, torsion analysis,
17114 distance matrix analysis, structure and sequence conservation analysis, normal
17115 mode analysis, principal component analysis of heterogeneous structure data,
17116 and correlation network analysis from normal mode and molecular dynamics data.
17117 In addition, various utility functions are provided to enable the statistical
17118 and graphical power of the R environment to work with biological sequence and
17120 (license license:gpl2+)))
17122 (define-public r-bios2cor
17124 (name "r-bios2cor")
17129 (uri (cran-uri "Bios2cor" version))
17132 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
17133 (properties `((upstream-name . "Bios2cor")))
17134 (build-system r-build-system)
17136 `(("r-bigmemory" ,r-bigmemory)
17137 ("r-bio3d" ,r-bio3d)
17138 ("r-circular" ,r-circular)
17139 ("r-igraph" ,r-igraph)))
17140 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
17141 (synopsis "From biological sequences and simulations to correlation analysis")
17143 "This package provides utilities for computation and analysis of
17144 correlation/covariation in multiple sequence alignments and in side chain
17145 motions during molecular dynamics simulations. Features include the
17146 computation of correlation/covariation scores using a variety of scoring
17147 functions between either sequence positions in alignments or side chain
17148 dihedral angles in molecular dynamics simulations and utilities to analyze the
17149 correlation/covariation matrix through a variety of tools including network
17150 representation and principal components analysis. In addition, several
17151 utility functions are based on the R graphical environment to provide friendly
17152 tools for help in data interpretation.")
17153 (license license:gpl2+)))
17155 ;; This package includes minified JavaScript files. When upgrading please
17156 ;; check that there are no new minified JavaScript files.
17157 (define-public r-networkd3
17159 (name "r-networkd3")
17164 (uri (cran-uri "networkD3" version))
17167 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
17170 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
17172 (properties `((upstream-name . "networkD3")))
17173 (build-system r-build-system)
17175 `(#:modules ((guix build utils)
17176 (guix build r-build-system)
17180 (modify-phases %standard-phases
17181 (add-after 'unpack 'process-javascript
17182 (lambda* (#:key inputs #:allow-other-keys)
17183 (with-directory-excursion "inst/htmlwidgets/lib/"
17187 `((,(assoc-ref inputs "d3.v4.js")
17188 "d3-4.5.0/d3.min.js"))))
17189 (lambda (sources targets)
17190 (for-each (lambda (source target)
17191 (format #t "Processing ~a --> ~a~%"
17193 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17194 (call-with-output-file target
17196 (dump-port minified port)))))
17197 sources targets))))
17200 `(("uglify-js" ,uglify-js)
17201 ;; NOTE: Make sure that this version of d3 is still valid when
17202 ;; upgrading the package.
17206 (uri "https://d3js.org/d3.v4.js")
17209 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17211 `(("r-htmlwidgets" ,r-htmlwidgets)
17212 ("r-igraph" ,r-igraph)
17213 ("r-magrittr" ,r-magrittr)))
17214 (home-page "https://cran.r-project.org/package=networkD3")
17215 (synopsis "D3 JavaScript network graphs from R")
17217 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17219 (license license:gpl3+)))
17221 (define-public r-aasea
17228 (uri (cran-uri "aaSEA" version))
17231 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17232 (properties `((upstream-name . "aaSEA")))
17233 (build-system r-build-system)
17235 `(("r-bios2cor" ,r-bios2cor)
17237 ("r-hmisc" ,r-hmisc)
17238 ("r-magrittr" ,r-magrittr)
17239 ("r-networkd3" ,r-networkd3)
17240 ("r-plotly" ,r-plotly)
17241 ("r-seqinr" ,r-seqinr)
17242 ("r-shiny" ,r-shiny)
17243 ("r-shinydashboard" ,r-shinydashboard)))
17244 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17245 (synopsis "Amino acid substitution effect analyzer")
17247 "Given a protein multiple sequence alignment, it is a daunting task to
17248 assess the effects of substitutions along sequence length. The aaSEA package
17249 is intended to help researchers to rapidly analyze property changes caused by
17250 single, multiple and correlated amino acid substitutions in proteins.")
17251 (license license:gpl3)))
17253 (define-public r-abacus
17260 (uri (cran-uri "ABACUS" version))
17263 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17264 (properties `((upstream-name . "ABACUS")))
17265 (build-system r-build-system)
17267 `(("r-ggplot2" ,r-ggplot2)
17268 ("r-shiny" ,r-shiny)))
17269 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17270 (synopsis "Apps-based activities for communicating and understanding statistics")
17272 "This package provides a set of Shiny apps for effective communication
17273 and understanding in statistics. The current version includes properties of
17274 normal distribution, properties of sampling distribution, one-sample z and t
17275 tests, two samples independent (unpaired) t test and analysis of variance.")
17276 (license license:gpl3)))
17278 (define-public r-abc-rap
17285 (uri (cran-uri "ABC.RAP" version))
17288 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17289 (properties `((upstream-name . "ABC.RAP")))
17290 (build-system r-build-system)
17291 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17292 (synopsis "Array-based CpG region analysis pipeline")
17294 "This package aims to identify candidate genes that are differentially
17295 methylated between cases and controls. It applies Student's t-test and delta
17296 beta analysis to identify candidate genes containing multiple CpG sites.")
17297 (license license:gpl3)))
17299 (define-public r-abcadm
17306 (uri (cran-uri "abcADM" version))
17309 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17310 (properties `((upstream-name . "abcADM")))
17311 (build-system r-build-system)
17314 ("r-rcpp" ,r-rcpp)))
17315 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17316 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17318 "This package provides tools to estimate parameters of accumulated
17319 damage (load duration) models based on failure time data under a Bayesian
17320 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17321 long-term reliability under stochastic load profiles.")
17322 (license license:gpl3)))
17324 (define-public r-rglpk
17331 (uri (cran-uri "Rglpk" version))
17334 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17335 (properties `((upstream-name . "Rglpk")))
17336 (build-system r-build-system)
17338 `(("r-slam" ,r-slam)))
17341 (home-page "https://r-forge.r-project.org/projects/rglp/")
17342 (synopsis "R interface to the GNU Linear Programming Kit")
17344 "This package provides an R interface to the GNU Linear Programming Kit,
17345 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17346 integer linear programming} (MILP) and other related problems.")
17348 (license (list license:gpl2 license:gpl3))))
17350 (define-public r-abcdefba
17352 (name "r-abcdefba")
17357 (uri (cran-uri "abcdeFBA" version))
17360 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17361 (properties `((upstream-name . "abcdeFBA")))
17362 (build-system r-build-system)
17364 `(("r-corrplot" ,r-corrplot)
17365 ("r-lattice" ,r-lattice)
17367 ("r-rglpk" ,r-rglpk)))
17368 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17369 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17371 "This package provides functions for Constraint Based Simulation using
17372 Flux Balance Analysis and informative analysis of the data generated during
17374 (license license:gpl2)))
17376 (define-public r-abcrlda
17383 (uri (cran-uri "abcrlda" version))
17386 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17387 (properties `((upstream-name . "abcrlda")))
17388 (build-system r-build-system)
17389 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17390 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17392 "This package offers methods to perform @dfn{asymptotically
17393 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17394 cost-sensitive binary classification. The bias-correction is an estimate of
17395 the bias term added to regularized discriminant analysis that minimizes the
17397 (license license:gpl3)))
17399 (define-public r-abemus
17406 (uri (cran-uri "abemus" version))
17409 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17410 (properties `((upstream-name . "abemus")))
17411 (build-system r-build-system)
17413 `(("r-data-table" ,r-data-table)))
17414 (home-page "https://cran.r-project.org/web/packages/abemus/")
17415 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17417 "This package provides an implementation of @dfn{Adaptive Base Error
17418 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17419 platform-specific genetic knowledge and empirical signal to readily detect and
17420 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17421 cell free DNA} (cfDNA).")
17422 (license license:gpl3)))
17424 ;; This package includes minified JavaScript files. When upgrading please
17425 ;; check that there are no new minified JavaScript files.
17426 (define-public r-rintrojs
17428 (name "r-rintrojs")
17433 (uri (cran-uri "rintrojs" version))
17436 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17437 (properties `((upstream-name . "rintrojs")))
17438 (build-system r-build-system)
17440 `(#:modules ((guix build utils)
17441 (guix build r-build-system)
17445 (modify-phases %standard-phases
17446 (add-after 'unpack 'process-javascript
17447 (lambda* (#:key inputs #:allow-other-keys)
17448 (with-directory-excursion "inst/javascript/introjs/"
17452 `((,(assoc-ref inputs "intro.js")
17454 (lambda (sources targets)
17455 (for-each (lambda (source target)
17456 (format #t "Processing ~a --> ~a~%"
17458 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17459 (call-with-output-file target
17461 (dump-port minified port)))))
17462 sources targets))))
17465 `(("uglify-js" ,uglify-js)
17469 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17472 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17474 `(("r-jsonlite" ,r-jsonlite)
17475 ("r-shiny" ,r-shiny)))
17476 (home-page "https://github.com/carlganz/rintrojs")
17477 (synopsis "Wrapper for the Intro.js library")
17479 "This package provides a wrapper for the @url{http://www.introjs.com,
17480 Intro.js} library. This package makes it easy to include step-by-step
17481 introductions, and clickable hints in a Shiny application. It supports both
17482 static introductions in the UI, and programmatic introductions from the
17484 (license license:agpl3+)))
17486 (define-public r-sysfonts
17488 (name "r-sysfonts")
17493 (uri (cran-uri "sysfonts" version))
17496 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17497 (properties `((upstream-name . "sysfonts")))
17498 (build-system r-build-system)
17500 `(("freetype" ,freetype)
17504 `(("pkg-config" ,pkg-config)))
17505 (home-page "https://github.com/yixuan/sysfonts")
17506 (synopsis "Loading fonts into R")
17508 "This is a package to simplify loading of system fonts and Google Fonts
17509 into R, in order to support other packages.")
17510 (license license:gpl2)))
17512 (define-public r-showtextdb
17514 (name "r-showtextdb")
17519 (uri (cran-uri "showtextdb" version))
17522 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17523 (properties `((upstream-name . "showtextdb")))
17524 (build-system r-build-system)
17526 `(("r-sysfonts" ,r-sysfonts)))
17527 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17528 (synopsis "Font files for the 'showtext' package")
17530 "This package provides font files that can be used by the @code{showtext}
17532 (license license:asl2.0)))
17534 (define-public r-showtext
17536 (name "r-showtext")
17541 (uri (cran-uri "showtext" version))
17544 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17545 (properties `((upstream-name . "showtext")))
17546 (build-system r-build-system)
17548 `(("freetype" ,freetype)
17552 `(("r-showtextdb" ,r-showtextdb)
17553 ("r-sysfonts" ,r-sysfonts)))
17555 `(("pkg-config" ,pkg-config)
17556 ("r-knitr" ,r-knitr)))
17557 (home-page "https://github.com/yixuan/showtext")
17558 (synopsis "Using fonts more easily in R graphs")
17560 "This package aims to make it easy to use various types of
17561 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17562 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17563 will be converted into polygons or raster images, hence after the plot has
17564 been created, it no longer relies on the font files. No external software
17565 such as Ghostscript is needed to use this package.")
17566 (license license:asl2.0)))
17568 (define-public r-emojifont
17570 (name "r-emojifont")
17575 (uri (cran-uri "emojifont" version))
17578 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17579 (properties `((upstream-name . "emojifont")))
17580 (build-system r-build-system)
17582 `(("r-ggplot2" ,r-ggplot2)
17583 ("r-proto" ,r-proto)
17584 ("r-showtext" ,r-showtext)
17585 ("r-sysfonts" ,r-sysfonts)))
17586 (home-page "https://guangchuangyu.github.io/emojifont")
17587 (synopsis "Emoji and Font Awesome in R graphics")
17589 "This package enables the use of emoji and the Font Awesome glyphs in
17590 both base and ggplot2 graphics.")
17591 (license license:artistic2.0)))
17593 (define-public r-abstractr
17595 (name "r-abstractr")
17600 (uri (cran-uri "abstractr" version))
17603 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17604 (properties `((upstream-name . "abstractr")))
17605 (build-system r-build-system)
17607 `(("r-colourpicker" ,r-colourpicker)
17608 ("r-emojifont" ,r-emojifont)
17609 ("r-ggplot2" ,r-ggplot2)
17610 ("r-gridextra" ,r-gridextra)
17611 ("r-rintrojs" ,r-rintrojs)
17612 ("r-shiny" ,r-shiny)
17613 ("r-shinythemes" ,r-shinythemes)))
17614 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17615 (synopsis "R-Shiny application for creating visual abstracts")
17617 "This package provides an R Shiny application to create visual abstracts
17618 for original research. A variety of user defined options and formatting are
17620 (license license:gpl3)))
17622 (define-public r-qgam
17629 (uri (cran-uri "qgam" version))
17632 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17633 (properties `((upstream-name . "qgam")))
17634 (build-system r-build-system)
17636 `(("r-doparallel" ,r-doparallel)
17639 ("r-shiny" ,r-shiny)))
17640 (native-inputs `(("r-knitr" ,r-knitr)))
17641 (home-page "https://cran.r-project.org/web/packages/qgam/")
17642 (synopsis "Smooth additive quantile regression models")
17644 "This package provides smooth additive quantile regression models, fitted
17645 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17646 the smoothing parameters are estimated automatically by marginal loss
17647 minimization, while the regression coefficients are estimated using either
17648 PIRLS or Newton algorithm. The learning rate is determined so that the
17649 Bayesian credible intervals of the estimated effects have approximately the
17650 correct coverage. The main function is @code{qgam()} which is similar to
17651 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17652 regression models.")
17653 (license license:gpl2+)))
17655 (define-public r-abtest
17662 (uri (cran-uri "abtest" version))
17665 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17666 (properties `((upstream-name . "abtest")))
17667 (build-system r-build-system)
17669 `(("r-matrix" ,r-matrix)
17670 ("r-mvtnorm" ,r-mvtnorm)
17671 ("r-plotrix" ,r-plotrix)
17673 ("r-rcolorbrewer" ,r-rcolorbrewer)
17676 ("r-truncnorm" ,r-truncnorm)))
17677 (home-page "https://cran.r-project.org/web/packages/abtest/")
17678 (synopsis "Bayesian A/B testing")
17680 "This package provides functions for Bayesian A/B testing including prior
17681 elicitation options based on Kass and Vaidyanathan (1992)
17682 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17683 (license license:gpl2+)))
17685 (define-public r-accept
17692 (uri (cran-uri "accept" version))
17695 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17696 (properties `((upstream-name . "accept")))
17697 (build-system r-build-system)
17699 `(("r-dplyr" ,r-dplyr)
17700 ("r-extrafont" ,r-extrafont)
17702 ("r-plotly" ,r-plotly)
17703 ("r-stringr" ,r-stringr)
17704 ("r-viridis" ,r-viridis)))
17705 (home-page "https://cran.r-project.org/web/packages/accept/")
17706 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17708 "This package allows clinicians to predict the rate and severity of
17709 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17710 Disease} (COPD) patients, based on the clinical prediction model published in
17711 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17712 (license license:gpl3)))
17714 (define-public r-smpracticals
17716 (name "r-smpracticals")
17721 (uri (cran-uri "SMPracticals" version))
17724 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17725 (properties `((upstream-name . "SMPracticals")))
17726 (build-system r-build-system)
17728 `(("r-ellipse" ,r-ellipse)
17731 ("r-survival" ,r-survival)))
17732 (home-page "http://statwww.epfl.ch/davison/SM/")
17733 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17735 "This package contains the datasets and a few functions for use with the
17736 practicals outlined in Appendix A of the book Statistical Models (Davison,
17737 2003, Cambridge University Press). The practicals themselves can be found at
17738 @url{http://statwww.epfl.ch/davison/SM/}.")
17739 (license license:gpl2+)))
17741 (define-public r-fgui
17748 (uri (cran-uri "fgui" version))
17751 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17752 (properties `((upstream-name . "fgui")))
17753 (build-system r-build-system)
17755 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17756 (synopsis "Create GUI for R functions")
17758 "Rapidly create a GUI for a function you created by automatically
17759 creating widgets for arguments of the function. This package automatically
17760 parses help routines for context-sensitive help to these arguments. The
17761 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17762 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17763 incorporated into the interface for greater customization for the more
17765 ;; Any version of the GPL.
17766 (license (list license:gpl2+ license:gpl3+))))
17768 (define-public r-tcltk2
17775 (uri (cran-uri "tcltk2" version))
17778 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17779 (properties `((upstream-name . "tcltk2")))
17780 (build-system r-build-system)
17784 (home-page "https://www.sciviews.org/SciViews-R")
17785 (synopsis "Tcl/Tk additions")
17787 "This package provides a series of additional Tcl commands and Tk widgets
17788 with style and various functions to supplement the tcltk package")
17789 (license license:lgpl3)))
17791 (define-public r-accrual
17798 (uri (cran-uri "accrual" version))
17801 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17802 (properties `((upstream-name . "accrual")))
17803 (build-system r-build-system)
17805 `(("r-fgui" ,r-fgui)
17806 ("r-smpracticals" ,r-smpracticals)
17807 ("r-tcltk2" ,r-tcltk2)))
17808 (home-page "https://cran.r-project.org/web/packages/accrual/")
17809 (synopsis "Bayesian accrual prediction")
17811 "Subject recruitment for medical research is challenging. Slow patient
17812 accrual leads to delay in research. Accrual monitoring during the process of
17813 recruitment is critical. Researchers need reliable tools to manage the
17814 accrual rate. This package provides an implementation of a Bayesian method
17815 that integrates researcher's experience on previous trials and data from the
17816 current study, providing reliable prediction on accrual rate for clinical
17817 studies. It provides functions for Bayesian accrual prediction which can be
17818 easily used by statisticians and clinical researchers.")
17819 (license license:gpl2)))
17821 (define-public r-accrued
17828 (uri (cran-uri "accrued" version))
17831 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17832 (properties `((upstream-name . "accrued")))
17833 (build-system r-build-system)
17834 (home-page "https://cran.r-project.org/web/packages/accrued/")
17835 (synopsis "Data quality visualization tools for partially accruing data")
17837 "This is a package for visualizing data quality of partially accruing
17839 (license license:gpl3)))
17841 (define-public r-mda
17848 (uri (cran-uri "mda" version))
17851 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17852 (properties `((upstream-name . "mda")))
17853 (build-system r-build-system)
17854 (propagated-inputs `(("r-class" ,r-class)))
17855 (native-inputs `(("gfortran" ,gfortran)))
17856 (home-page "https://cran.r-project.org/web/packages/mda/")
17857 (synopsis "Mixture and flexible discriminant analysis")
17859 "This is a package for mixture and flexible discriminant analysis,
17860 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17861 (license license:gpl2)))
17863 (define-public r-elasticnet
17865 (name "r-elasticnet")
17870 (uri (cran-uri "elasticnet" version))
17873 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17874 (properties `((upstream-name . "elasticnet")))
17875 (build-system r-build-system)
17877 `(("r-lars" ,r-lars)))
17878 (home-page "http://users.stat.umn.edu/~zouxx019/")
17879 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17881 "This package provides functions for fitting the entire solution path of
17882 the Elastic-Net and also provides functions for estimating sparse Principal
17883 Components. The Lasso solution paths can be computed by the same function.")
17884 (license license:gpl2+)))
17886 (define-public r-sparselda
17888 (name "r-sparselda")
17893 (uri (cran-uri "sparseLDA" version))
17896 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17897 (properties `((upstream-name . "sparseLDA")))
17898 (build-system r-build-system)
17900 `(("r-elasticnet" ,r-elasticnet)
17903 (home-page "https://www.imm.dtu.dk/~lkhc/")
17904 (synopsis "Sparse discriminant analysis")
17906 "This package performs sparse linear discriminant analysis for Gaussians
17907 and mixture of Gaussian models.")
17908 (license license:gpl2+)))
17910 (define-public r-accsda
17917 (uri (cran-uri "accSDA" version))
17920 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17921 (properties `((upstream-name . "accSDA")))
17922 (build-system r-build-system)
17924 `(("r-ggplot2" ,r-ggplot2)
17925 ("r-ggthemes" ,r-ggthemes)
17926 ("r-gridextra" ,r-gridextra)
17928 ("r-rarpack" ,r-rarpack)
17929 ("r-sparselda" ,r-sparselda)))
17930 (home-page "https://github.com/gumeo/accSDA/wiki")
17931 (synopsis "Accelerated sparse discriminant analysis")
17933 "This package provides an implementation of sparse linear discriminant
17934 analysis, which is a supervised classification method for multiple classes.
17935 Various novel optimization approaches to this problem are implemented
17936 including @dfn{alternating direction method of multipliers} (ADMM),
17937 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17938 Functions for performing cross validation are also supplied along with basic
17939 prediction and plotting functions. @dfn{Sparse zero variance
17940 discriminant} (SZVD) analysis is also included in the package.")
17941 (license license:gpl2+)))
17943 (define-public r-ace2fastq
17945 (name "r-ace2fastq")
17950 (uri (cran-uri "ace2fastq" version))
17953 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17954 (properties `((upstream-name . "ace2fastq")))
17955 (build-system r-build-system)
17957 `(("r-stringr" ,r-stringr)))
17958 (home-page "https://github.com/c5sire/ace2fastq")
17959 (synopsis "ACE file to FASTQ converter")
17961 "The ACE file format is used in genomics to store contigs from sequencing
17962 machines. This tools converts it into FASTQ format. Both formats contain the
17963 sequence characters and their corresponding quality information. Unlike the
17964 FASTQ file, the ACE file stores the quality values numerically. The
17965 conversion algorithm uses the standard Sanger formula. The package
17966 facilitates insertion into pipelines, and content inspection.")
17967 (license license:gpl3)))
17969 (define-public r-rngwell
17976 (uri (cran-uri "rngWELL" version))
17979 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17980 (properties `((upstream-name . "rngWELL")))
17981 (build-system r-build-system)
17982 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17983 (synopsis "Toolbox for WELL random number generators")
17985 "This is a dedicated package to WELL pseudo random generators, which were
17986 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17987 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17988 (license license:bsd-3)))
17990 (define-public r-randtoolbox
17992 (name "r-randtoolbox")
17997 (uri (cran-uri "randtoolbox" version))
18000 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
18001 (properties `((upstream-name . "randtoolbox")))
18002 (build-system r-build-system)
18004 `(("r-rngwell" ,r-rngwell)))
18006 `(("gfortran" ,gfortran)))
18007 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
18008 (synopsis "Toolbox for pseudo and quasi random number generation")
18010 "This package provides
18013 @item pseudo random generators, such as general linear
18014 congruential generators, multiple recursive generators and generalized
18015 feedback shift register (SF-Mersenne Twister algorithm and WELL
18018 @item quasi random generators, such as the Torus algorithm, the Sobol
18019 sequence, the Halton sequence (including the Van der Corput sequence), and
18021 @item some generator tests: the gap test, the serial test, the poker test.
18024 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
18025 (license license:bsd-3)))
18027 (define-public r-lhs
18034 (uri (cran-uri "lhs" version))
18037 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
18038 (properties `((upstream-name . "lhs")))
18039 (build-system r-build-system)
18040 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18042 `(("r-knitr" ,r-knitr)))
18043 (home-page "https://github.com/bertcarnell/lhs")
18044 (synopsis "Latin Hypercube Samples")
18046 "This package provides a number of methods for creating and augmenting
18047 Latin Hypercube Samples.")
18048 (license license:gpl3)))
18050 (define-public r-acebayes
18052 (name "r-acebayes")
18057 (uri (cran-uri "acebayes" version))
18060 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
18061 (properties `((upstream-name . "acebayes")))
18062 (build-system r-build-system)
18064 `(("r-compare" ,r-compare)
18066 ("r-randtoolbox" ,r-randtoolbox)
18068 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18069 (home-page "https://cran.r-project.org/web/packages/acebayes/")
18070 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
18072 "Finding an optimal Bayesian experimental design involves maximizing an
18073 objective function given by the expectation of some appropriately chosen
18074 utility function with respect to the joint distribution of unknown
18075 quantities (including responses). This objective function is usually not
18076 available in closed form and the design space can be continuous and of high
18077 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
18078 to maximise an approximation to the expectation of the utility function.")
18079 (license license:gpl2)))
18081 (define-public r-acet
18088 (uri (cran-uri "ACEt" version))
18091 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
18092 (properties `((upstream-name . "ACEt")))
18093 (build-system r-build-system)
18098 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18099 (home-page "https://cran.r-project.org/web/packages/ACEt/")
18100 (synopsis "Estimating dynamic heritability and twin model comparison")
18102 "This package supports twin models that are able to estimate the dynamic
18103 behaviour of the variance components in the classical twin models with respect
18104 to age using B-splines and P-splines.")
18105 (license license:gpl2+)))
18107 (define-public r-acfmperiod
18109 (name "r-acfmperiod")
18114 (uri (cran-uri "acfMPeriod" version))
18117 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
18118 (properties `((upstream-name . "acfMPeriod")))
18119 (build-system r-build-system)
18121 `(("r-mass" ,r-mass)))
18122 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
18123 (synopsis "Estimation of the ACF from the M-periodogram")
18125 "This package support non-robust and robust computations of the sample
18126 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
18127 univariate and multivariate processes. The methodology consists in reversing
18128 the diagonalization procedure involving the periodogram or the
18129 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
18130 ACOVF or the ACF as discussed in Fuller (1995)
18131 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
18132 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
18133 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
18134 (license license:gpl2+)))
18136 (define-public r-gamlss-data
18138 (name "r-gamlss-data")
18143 (uri (cran-uri "gamlss.data" version))
18146 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
18147 (properties `((upstream-name . "gamlss.data")))
18148 (build-system r-build-system)
18149 (home-page "http://www.gamlss.org/")
18150 (synopsis "GAMLSS data")
18152 "This package provides data used as examples to demonstrate GAMLSS
18154 ;; Either version of the license
18155 (license (list license:gpl2 license:gpl3))))
18157 (define-public r-gamlss
18164 (uri (cran-uri "gamlss" version))
18167 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
18168 (properties `((upstream-name . "gamlss")))
18169 (build-system r-build-system)
18171 `(("r-gamlss-data" ,r-gamlss-data)
18172 ("r-gamlss-dist" ,r-gamlss-dist)
18175 ("r-survival" ,r-survival)))
18176 (home-page "http://www.gamlss.org/")
18177 (synopsis "Generalized additive models for location scale and shape")
18179 "This package provides functions for fitting the generalized additive
18180 models for location scale and shape introduced by Rigby and
18181 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
18182 use a distributional regression approach where all the parameters of the
18183 conditional distribution of the response variable are modelled using
18184 explanatory variables.")
18185 ;; Either version of the license
18186 (license (list license:gpl2 license:gpl3))))
18188 (define-public r-acid
18195 (uri (cran-uri "acid" version))
18198 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18199 (properties `((upstream-name . "acid")))
18200 (build-system r-build-system)
18202 `(("r-gamlss" ,r-gamlss)
18203 ("r-gamlss-dist" ,r-gamlss-dist)
18204 ("r-hmisc" ,r-hmisc)))
18205 (home-page "https://cran.r-project.org/web/packages/acid/")
18206 (synopsis "Analysing conditional income distributions")
18208 "This package provides functions for the analysis of income distributions
18209 for subgroups of the population as defined by a set of variables like age,
18210 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18211 distribution as well as functions for moments, inequality measures, entropy
18212 measures and polarisation measures of income distributions. This package thus
18213 aides the analysis of income inequality by offering tools for the exploratory
18214 analysis of income distributions at the disaggregated level.")
18215 (license license:gpl3)))
18217 (define-public r-acm4r
18224 (uri (cran-uri "acm4r" version))
18227 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18228 (properties `((upstream-name . "acm4r")))
18229 (build-system r-build-system)
18230 (propagated-inputs `(("r-mass" ,r-mass)))
18231 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18232 (synopsis "Align-and-count method comparisons of RFLP data")
18234 "This is a package to compare sequence fragment lengths or molecular
18235 weights from pairs of lanes. The number of matching bands in the
18236 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18237 the align-and-count method.")
18238 ;; Any version of the GPL
18239 (license (list license:gpl2+ license:gpl3+))))
18241 (define-public r-filematrix
18243 (name "r-filematrix")
18248 (uri (cran-uri "filematrix" version))
18251 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18252 (properties `((upstream-name . "filematrix")))
18253 (build-system r-build-system)
18254 ;; These inputs are needed for vignettes
18256 `(("r-knitr" ,r-knitr)
18257 ("r-rmarkdown" ,r-rmarkdown)
18258 ("pandoc-citeproc" ,pandoc-citeproc)))
18259 (home-page "https://github.com/andreyshabalin/filematrix")
18260 (synopsis "File-backed matrix class with convenient read and write access")
18262 "This package provides an interface for working with large matrices
18263 stored in files, not in computer memory. It supports multiple non-character
18264 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18265 byte real values). Access to parts of the matrix is done by indexing, exactly
18266 as with usual R matrices. It supports very large matrices; the package has
18267 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18268 columns, ad allows for quick addition of extra columns to a filematrix.")
18269 (license license:lgpl3)))
18271 (define-public r-acmeeqtl
18273 (name "r-acmeeqtl")
18278 (uri (cran-uri "ACMEeqtl" version))
18281 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18282 (properties `((upstream-name . "ACMEeqtl")))
18283 (build-system r-build-system)
18285 `(("r-filematrix" ,r-filematrix)))
18286 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18287 (synopsis "Estimation of interpretable eQTL effect sizes")
18289 "This package provides a non-linear model, termed ACME, that reflects a
18290 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18291 With non-linear least-squares algorithm the maximum likelihood parameters can
18292 be estimated. The ACME model provides interpretable effect size estimates and
18293 p-values with well controlled Type-I error.")
18294 (license license:lgpl3)))
18296 (define-public r-acmer
18303 (uri (cran-uri "acmeR" version))
18306 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18307 (properties `((upstream-name . "acmeR")))
18308 (build-system r-build-system)
18309 (propagated-inputs `(("r-foreign" ,r-foreign)))
18310 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18311 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18313 "This package provides an implementation of the ACME estimator, described
18314 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18315 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18316 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18317 as carcasses age; variable bleed-through at successive searches; and interval
18318 mortality estimates. The package provides, based on search data, functions
18319 for estimating the mortality inflation factor in Frequentist and Bayesian
18321 (license license:expat)))
18323 (define-public r-r-huge
18330 (uri (cran-uri "R.huge" version))
18333 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18334 (properties `((upstream-name . "R.huge")))
18335 (build-system r-build-system)
18337 `(("r-r-methodss3" ,r-r-methodss3)
18339 ("r-r-utils" ,r-r-utils)))
18340 (home-page "https://github.com/HenrikBengtsson/R.huge")
18341 (synopsis "Methods for accessing huge amounts of data")
18343 "This is a deprecated package for accessing huge amounts of data.
18344 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18345 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18346 the @code{aroma.affymetrix} package.")
18347 (license license:lgpl2.1+)))
18349 (define-public r-r-filesets
18351 (name "r-r-filesets")
18356 (uri (cran-uri "R.filesets" version))
18359 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18360 (properties `((upstream-name . "R.filesets")))
18361 (build-system r-build-system)
18363 `(("r-digest" ,r-digest)
18364 ("r-r-cache" ,r-r-cache)
18365 ("r-r-methodss3" ,r-r-methodss3)
18367 ("r-r-utils" ,r-r-utils)))
18368 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18369 (synopsis "Easy handling of and access to files")
18371 "This package provides classes and methods to locate, setup, subset,
18372 navigate and iterate file sets, i.e. sets of files located in one or more
18373 directories on the file system. The API is designed such that these classes
18374 can be extended via inheritance to provide a richer API for special file
18375 formats. Moreover, a specific name format is defined such that filenames and
18376 directories can be considered to have full names which consists of a name
18377 followed by comma-separated tags. This adds additional flexibility to
18378 identify file sets and individual files.")
18379 (license license:lgpl2.1+)))
18381 (define-public r-r-devices
18383 (name "r-r-devices")
18388 (uri (cran-uri "R.devices" version))
18391 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18392 (properties `((upstream-name . "R.devices")))
18393 (build-system r-build-system)
18395 `(("r-base64enc" ,r-base64enc)
18396 ("r-r-methodss3" ,r-r-methodss3)
18398 ("r-r-utils" ,r-r-utils)))
18399 (home-page "https://github.com/HenrikBengtsson/R.devices")
18400 (synopsis "Unified handling of graphics devices")
18402 "This package provides functions for creating plots and image files in a
18403 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18404 Default device options as well as scales and aspect ratios are controlled in a
18405 uniform way across all device types. Switching output format requires minimal
18406 changes in code. This package is ideal for large-scale batch processing,
18407 because it will never leave open graphics devices or incomplete image files
18408 behind, even on errors or user interrupts.")
18409 (license license:lgpl2.1+)))
18411 (define-public r-acnr
18418 (uri (cran-uri "acnr" version))
18421 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18422 (properties `((upstream-name . "acnr")))
18423 (build-system r-build-system)
18424 (home-page "https://github.com/mpierrejean/acnr")
18425 (synopsis "Annotated copy-number regions")
18427 "This package provides SNP array data from different types of copy-number
18428 regions. These regions were identified manually by the authors of the package
18429 and may be used to generate realistic data sets with known truth.")
18430 (license license:lgpl2.1+)))
18432 (define-public r-acopula
18439 (uri (cran-uri "acopula" version))
18442 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18443 (properties `((upstream-name . "acopula")))
18444 (build-system r-build-system)
18445 (home-page "https://cran.r-project.org/web/packages/acopula/")
18446 (synopsis "Modelling dependence with multivariate Archimax copulas")
18448 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18449 package provides definitions of several parametric families of generator and
18450 dependence function, computes CDF and PDF, estimates parameters, tests for
18451 goodness of fit, generates random sample and checks copula properties for
18452 custom constructs. In the 2-dimensional case explicit formulas for density
18453 are used, contrary to higher dimensions when all derivatives are linearly
18454 approximated. Several non-archimax families (normal, FGM, Plackett) are
18455 provided as well.")
18456 (license license:gpl2)))
18458 (define-public r-tuner
18465 (uri (cran-uri "tuneR" version))
18468 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18469 (properties `((upstream-name . "tuneR")))
18470 (build-system r-build-system)
18471 (propagated-inputs `(("r-signal" ,r-signal)))
18472 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18473 (synopsis "Analysis of music and speech")
18475 "This is a package for the analysis of music and speech. Analyze music
18476 and speech, extract features like MFCCs, handle wave files and their
18477 representation in various ways, read MP3, read MIDI, perform steps of a
18478 transcription, ...")
18479 ;; Either of these versions.
18480 (license (list license:gpl2 license:gpl3))))
18482 (define-public r-seewave
18489 (uri (cran-uri "seewave" version))
18492 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18493 (properties `((upstream-name . "seewave")))
18494 (build-system r-build-system)
18496 `(("libsndfile" ,libsndfile)))
18498 `(("r-tuner" ,r-tuner)))
18499 (home-page "http://rug.mnhn.fr/seewave")
18500 (synopsis "Sound analysis and synthesis")
18502 "This package provides functions for analysing, manipulating, displaying,
18503 editing and synthesizing time waves (particularly sound). This package
18504 processes time analysis (oscillograms and envelopes), spectral content,
18505 resonance quality factor, entropy, cross correlation and autocorrelation,
18506 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18507 and 3D spectrograms and many other analyses.")
18508 (license license:gpl2+)))
18510 (define-public r-acousticndlcoder
18512 (name "r-acousticndlcoder")
18517 (uri (cran-uri "AcousticNDLCodeR" version))
18520 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18522 `((upstream-name . "AcousticNDLCodeR")))
18523 (build-system r-build-system)
18525 `(("r-seewave" ,r-seewave)
18526 ("r-tuner" ,r-tuner)
18528 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18529 (synopsis "Coding sound files for use with NDL")
18531 "Make acoustic cues to use with the R package @code{ndl}.
18532 The package implements functions used in the PLoS ONE paper \"Words from
18533 spontaneous conversational speech can be recognized with human-like accuracy
18534 by an error-driven learning algorithm that discriminates between meanings
18535 straight from smart acoustic features, bypassing the phoneme as recognition
18536 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18537 (license license:gpl2+)))
18539 (define-public r-acp
18546 (uri (cran-uri "acp" version))
18549 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18550 (properties `((upstream-name . "acp")))
18551 (build-system r-build-system)
18553 `(("r-quantmod" ,r-quantmod)
18554 ("r-tseries" ,r-tseries)))
18555 (home-page "https://cran.r-project.org/web/packages/acp/")
18556 (synopsis "Autoregressive conditional Poisson")
18558 "This package supports the analysis of count data exhibiting
18559 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18560 model (ACP(p,q)) proposed by Heinen (2003).")
18561 (license license:gpl2)))
18563 (define-public r-ada
18570 (uri (cran-uri "ada" version))
18573 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18574 (properties `((upstream-name . "ada")))
18575 (build-system r-build-system)
18576 (propagated-inputs `(("r-rpart" ,r-rpart)))
18577 (home-page "https://cran.r-project.org/web/packages/ada/")
18578 (synopsis "Stochastic boosting")
18580 "This package provides a straightforward, well-documented, and broad
18581 boosting routine for classification, ideally suited for small to
18582 moderate-sized data sets. It performs discrete, real, and gentle boost under
18583 both exponential and logistic loss on a given data set.")
18584 ;; Any version of the GPL.
18585 (license (list license:gpl2+ license:gpl3+))))
18587 (define-public r-genalg
18594 (uri (cran-uri "genalg" version))
18597 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18598 (properties `((upstream-name . "genalg")))
18599 (build-system r-build-system)
18600 (home-page "https://github.com/egonw/genalg")
18601 (synopsis "R based genetic algorithm")
18603 "This package provides an R based genetic algorithm for binary and
18604 floating point chromosomes.")
18605 (license license:gpl2)))
18607 (define-public r-kernelfactory
18609 (name "r-kernelfactory")
18614 (uri (cran-uri "kernelFactory" version))
18617 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18618 (properties `((upstream-name . "kernelFactory")))
18619 (build-system r-build-system)
18622 ("r-genalg" ,r-genalg)
18623 ("r-kernlab" ,r-kernlab)
18624 ("r-randomforest" ,r-randomforest)))
18625 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18626 (synopsis "Ensemble of kernel machines")
18628 "Kernel factory is an ensemble method where each base classifier (random
18629 forest) is fit on the kernel matrix of a subset of the training data.")
18630 (license license:gpl2+)))
18632 (define-public r-dummies
18639 (uri (cran-uri "dummies" version))
18642 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18643 (properties `((upstream-name . "dummies")))
18644 (build-system r-build-system)
18645 (home-page "https://decisionpatterns.com")
18646 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18648 "This package lets you expand factors, characters and other eligible
18649 classes into dummy/indicator variables.")
18650 (license license:gpl2+)))
18652 (define-public r-acrm
18659 (uri (cran-uri "aCRM" version))
18662 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18663 (properties `((upstream-name . "aCRM")))
18664 (build-system r-build-system)
18667 ("r-dummies" ,r-dummies)
18668 ("r-kernelfactory" ,r-kernelfactory)
18669 ("r-randomforest" ,r-randomforest)))
18670 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18671 (synopsis "Convenience functions for analytical customer relationship management")
18673 "This package provides convenience functions for data preparation and
18674 modeling often used in @dfn{analytical customer relationship
18675 management} (aCRM).")
18676 (license license:gpl2+)))
18678 (define-public r-treeclust
18680 (name "r-treeclust")
18685 (uri (cran-uri "treeClust" version))
18688 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18689 (properties `((upstream-name . "treeClust")))
18690 (build-system r-build-system)
18692 `(("r-cluster" ,r-cluster)
18693 ("r-rpart" ,r-rpart)))
18694 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18695 (synopsis "Cluster distances through trees")
18697 "This package provides tools to create a measure of inter-point
18698 dissimilarity useful for clustering mixed data, and, optionally, perform the
18700 (license license:gpl2+)))
18702 (define-public r-acrosstic
18704 (name "r-acrosstic")
18709 (uri (cran-uri "AcrossTic" version))
18712 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18713 (properties `((upstream-name . "AcrossTic")))
18714 (build-system r-build-system)
18716 `(("r-lpsolve" ,r-lpsolve)
18717 ("r-treeclust" ,r-treeclust)))
18718 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18719 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18721 "This is a package for constructing minimum-cost regular spanning
18722 subgraph as part of a non-parametric two-sample test for equality of
18724 (license license:gpl2+)))
18726 (define-public r-acrt
18733 (uri (cran-uri "acrt" version))
18736 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18737 (properties `((upstream-name . "acrt")))
18738 (build-system r-build-system)
18740 `(("r-rcpp" ,r-rcpp)
18741 ("r-rcppeigen" ,r-rcppeigen)
18742 ("r-sandwich" ,r-sandwich)))
18743 (home-page "https://cran.r-project.org/web/packages/acrt/")
18744 (synopsis "Autocorrelation robust testing")
18746 "This package provides functions for testing affine hypotheses on the
18747 regression coefficient vector in regression models with autocorrelated
18749 (license license:gpl2)))
18751 (define-public r-acs
18758 (uri (cran-uri "acs" version))
18761 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18762 (properties `((upstream-name . "acs")))
18763 (build-system r-build-system)
18765 `(("r-httr" ,r-httr)
18768 ("r-stringr" ,r-stringr)
18770 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18771 (synopsis "Work with data from the US Census")
18773 "This package provides a general toolkit for downloading, managing,
18774 analyzing, and presenting data from the
18775 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18776 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18777 American Community Survey (ACS). Confidence intervals provided with ACS data
18778 are converted to standard errors to be bundled with estimates in complex
18779 @code{acs} objects. The package provides new methods to conduct standard
18780 operations on @code{acs} objects and present/plot data in statistically
18781 appropriate ways.")
18782 (license license:gpl3)))
18784 (define-public r-acss-data
18786 (name "r-acss-data")
18791 (uri (cran-uri "acss.data" version))
18794 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18795 (properties `((upstream-name . "acss.data")))
18796 (build-system r-build-system)
18797 (home-page "http://complexitycalculator.com/methodology.html")
18798 (synopsis "Data for algorithmic complexity of short strings")
18800 "This is a data only package providing the algorithmic complexity of
18801 short strings, computed using the coding theorem method. For a given set of
18802 symbols in a string, all possible or a large number of random samples of
18803 Turing machines with a given number of states (e.g., 5) and number of symbols
18804 corresponding to the number of symbols in the strings were simulated until
18805 they reached a halting state or failed to end. This package contains data on
18806 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18807 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18808 distribution of the halting states.")
18809 (license license:gpl2+)))
18811 (define-public r-acss
18818 (uri (cran-uri "acss" version))
18821 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18822 (properties `((upstream-name . "acss")))
18823 (build-system r-build-system)
18825 `(("r-acss-data" ,r-acss-data)
18827 (home-page "http://complexitycalculator.com/methodology.html")
18828 (synopsis "Algorithmic complexity for short strings")
18830 "The main purpose of this package is to provide the algorithmic
18831 complexity for short strings, an approximation of the Kolmogorov Complexity of
18832 a short string using the coding theorem method. While the database containing
18833 the complexity is provided in the data only package @code{acss.data}, this
18834 package provides functions accessing the data such as @code{prob_random}
18835 returning the posterior probability that a given string was produced by a
18836 random process. In addition, two traditional (but problematic) measures of
18837 complexity are also provided: entropy and change complexity.")
18838 (license license:gpl2+)))
18840 (define-public r-acswr
18847 (uri (cran-uri "ACSWR" version))
18850 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18851 (properties `((upstream-name . "ACSWR")))
18852 (build-system r-build-system)
18854 `(("r-mass" ,r-mass)))
18855 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18856 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18858 "This is a companion package for the book \"A Course in Statistics with
18859 R\" (ISBN 978-1-119-15272-9.)")
18860 (license license:gpl2)))
18862 (define-public r-alabama
18865 (version "2015.3-1")
18869 (uri (cran-uri "alabama" version))
18872 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18873 (properties `((upstream-name . "alabama")))
18874 (build-system r-build-system)
18875 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18876 (home-page "https://cran.r-project.org/web/packages/alabama/")
18877 (synopsis "Constrained nonlinear optimization")
18879 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18880 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18881 constraints. Linear or nonlinear equality and inequality constraints are
18883 (license license:gpl2+)))
18885 (define-public r-gdina
18892 (uri (cran-uri "GDINA" version))
18895 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18896 (properties `((upstream-name . "GDINA")))
18897 (build-system r-build-system)
18899 `(("r-alabama" ,r-alabama)
18900 ("r-ggplot2" ,r-ggplot2)
18902 ("r-nloptr" ,r-nloptr)
18903 ("r-numderiv" ,r-numderiv)
18905 ("r-rcpparmadillo" ,r-rcpparmadillo)
18906 ("r-rsolnp" ,r-rsolnp)
18907 ("r-shiny" ,r-shiny)
18908 ("r-shinydashboard" ,r-shinydashboard)))
18910 `(("r-knitr" ,r-knitr)))
18911 (home-page "https://github.com/Wenchao-Ma/GDINA")
18912 (synopsis "Generalized DINA model framework")
18914 "This package provides a set of psychometric tools for cognitive
18915 diagnosis modeling based on the generalized deterministic inputs, noisy and
18916 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18917 and its extensions, including the sequential G-DINA model by Ma and de la
18918 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18919 polytomous G-DINA model by Chen and de la Torre
18920 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18921 distribution can be independent, saturated, higher-order, loglinear smoothed
18922 or structured. Q-matrix validation, item and model fit statistics, model
18923 comparison at test and item level and differential item functioning can also
18924 be conducted. A graphical user interface is also provided.")
18925 (license license:gpl3)))
18927 (define-public r-actcd
18934 (uri (cran-uri "ACTCD" version))
18937 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18938 (properties `((upstream-name . "ACTCD")))
18939 (build-system r-build-system)
18941 `(("r-gdina" ,r-gdina)
18942 ("r-r-methodss3" ,r-r-methodss3)))
18944 `(("gfortran" ,gfortran)))
18945 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18946 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18948 "This is a package supporting cluster analysis for cognitive diagnosis
18949 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18950 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18951 sum-scores, cluster analysis techniques can be used to classify examinees into
18952 latent classes based on their attribute patterns. In addition to the
18953 algorithms used to classify data, three labeling approaches are proposed to
18954 label clusters so that examinees' attribute profiles can be obtained.")
18955 (license license:gpl2+)))
18957 (define-public r-ineq
18964 (uri (cran-uri "ineq" version))
18967 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18968 (properties `((upstream-name . "ineq")))
18969 (build-system r-build-system)
18970 (home-page "https://cran.r-project.org/web/packages/ineq/")
18971 (synopsis "Measuring inequality, concentration, and poverty")
18973 "This package provides tools for measuring inequality, concentration, and
18974 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18975 ;; Either of these two versions.
18976 (license (list license:gpl2 license:gpl3))))
18978 (define-public r-actfrag
18985 (uri (cran-uri "ActFrag" version))
18988 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18989 (properties `((upstream-name . "ActFrag")))
18990 (build-system r-build-system)
18992 `(("r-accelerometry" ,r-accelerometry)
18993 ("r-dplyr" ,r-dplyr)
18995 ("r-survival" ,r-survival)
18996 ("r-tidyr" ,r-tidyr)))
18997 (home-page "https://github.com/junruidi/ActFrag")
18998 (synopsis "Activity fragmentation metrics extraction")
19000 "This package provides functions to extract commonly used fragmentation
19001 metrics to quantify time accumulation strategies based on minute level
19002 actigraphy-measured activity counts data.")
19003 (license license:gpl3)))
19005 (define-public r-fda
19008 (version "5.1.5.1")
19012 (uri (cran-uri "fda" version))
19015 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
19016 (properties `((upstream-name . "fda")))
19017 (build-system r-build-system)
19019 `(("r-matrix" ,r-matrix)))
19020 (home-page "https://www.functionaldata.org")
19021 (synopsis "Functional data analysis")
19023 "These functions were developed to support functional data analysis as
19024 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
19025 Analysis. The package includes data sets and script files working many
19027 (license license:gpl2+)))
19029 (define-public r-actigraphy
19031 (name "r-actigraphy")
19036 (uri (cran-uri "Actigraphy" version))
19039 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
19040 (properties `((upstream-name . "Actigraphy")))
19041 (build-system r-build-system)
19043 `(("r-fda" ,r-fda)))
19044 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
19045 (synopsis "Actigraphy data analysis")
19047 "This package provides tools for functional linear modeling and analysis
19048 of actigraphy data.")
19049 (license license:asl2.0)))
19051 (define-public r-activedriver
19053 (name "r-activedriver")
19058 (uri (cran-uri "ActiveDriver" version))
19061 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
19062 (properties `((upstream-name . "ActiveDriver")))
19063 (build-system r-build-system)
19065 `(("r-mass" ,r-mass)))
19066 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
19067 (synopsis "Tools for finding cancer driver proteins")
19069 "This package provides a mutation analysis tool that discovers cancer
19070 driver genes with frequent mutations in protein signalling sites such as
19071 post-translational modifications (phosphorylation, ubiquitination, etc). The
19072 Poisson generalized linear regression model identifies genes where cancer
19073 mutations in signalling sites are more frequent than expected from the
19074 sequence of the entire gene. Integration of mutations with signalling
19075 information helps find new driver genes and propose candidate mechanisms to
19077 (license license:gpl2+)))
19079 (define-public r-activitycounts
19081 (name "r-activitycounts")
19086 (uri (cran-uri "activityCounts" version))
19089 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
19091 `((upstream-name . "activityCounts")))
19092 (build-system r-build-system)
19094 `(("r-lubridate" ,r-lubridate)
19095 ("r-magrittr" ,r-magrittr)
19096 ("r-seewave" ,r-seewave)
19097 ("r-signal" ,r-signal)
19098 ("r-tibble" ,r-tibble)))
19099 (home-page "https://github.com/walkabillylab/activityCounts")
19100 (synopsis "Generate ActiLife counts")
19102 "ActiLife generates activity counts from data collected by Actigraph
19103 accelerometers. Actigraph is one of the most common research-grade
19104 accelerometers. There is considerable research validating and developing
19105 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
19106 counts are proprietary and difficult to implement if researchers use different
19107 accelerometer brands. The code creates ActiLife counts from raw acceleration
19108 data for different accelerometer brands.")
19109 (license license:gpl3)))
19111 (define-public r-activityindex
19113 (name "r-activityindex")
19118 (uri (cran-uri "ActivityIndex" version))
19121 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
19122 (properties `((upstream-name . "ActivityIndex")))
19123 (build-system r-build-system)
19125 `(("r-data-table" ,r-data-table)
19126 ("r-matrixstats" ,r-matrixstats)
19127 ("r-r-utils" ,r-r-utils)))
19128 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
19129 (synopsis "Activity Index calculation using raw accelerometry data")
19131 "This is a package to read raw accelerometry from GT3X+ accelerometry
19132 data and plain table data to calculate the Activity Index from Bai et
19133 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
19134 (license license:gpl3)))
19136 (define-public r-activpal
19138 (name "r-activpal")
19143 (uri (cran-uri "activPAL" version))
19146 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
19147 (properties `((upstream-name . "activPAL")))
19148 (build-system r-build-system)
19150 `(("r-devtools" ,r-devtools)
19151 ("r-dplyr" ,r-dplyr)
19152 ("r-ggplot2" ,r-ggplot2)
19153 ("r-lubridate" ,r-lubridate)
19154 ("r-magrittr" ,r-magrittr)
19155 ("r-tidyr" ,r-tidyr)))
19156 (home-page "https://cran.r-project.org/web/packages/activPAL")
19157 (synopsis "Processing and chart generation from activPAL events files")
19159 "This package contains functions to generate pre-defined summary
19160 statistics from activPAL events files. The package also contains functions to
19161 produce informative graphics that visualize physical activity behaviour and
19162 trends. This includes generating graphs that align physical activity
19163 behaviour with additional time based observations described by other data
19164 sets, such as sleep diaries and continuous glucose monitoring data.")
19165 (license license:gpl3)))
19167 (define-public r-activpalprocessing
19169 (name "r-activpalprocessing")
19174 (uri (cran-uri "activpalProcessing" version))
19177 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
19179 `((upstream-name . "activpalProcessing")))
19180 (build-system r-build-system)
19182 `(("r-chron" ,r-chron)))
19183 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
19184 (synopsis "Process activPAL events files")
19186 "This package performs estimation of physical activity and sedentary
19187 behavior variables from activPAL events files.")
19188 ;; Either version of the GPL.
19189 (license (list license:gpl2 license:gpl3))))
19191 (define-public r-actogrammr
19193 (name "r-actogrammr")
19198 (uri (cran-uri "actogrammr" version))
19201 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19202 (properties `((upstream-name . "actogrammr")))
19203 (build-system r-build-system)
19205 `(("r-dplyr" ,r-dplyr)
19206 ("r-ggplot2" ,r-ggplot2)
19207 ("r-lubridate" ,r-lubridate)
19208 ("r-readr" ,r-readr)
19209 ("r-tidyr" ,r-tidyr)))
19210 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19211 (synopsis "Read in activity data and plot actograms")
19213 "Read in activity measurements from standard file formats used by
19214 circadian rhythm researchers, currently only ClockLab format, and process and
19215 plot the data. The central type of plot is the actogram, as first described
19216 in \"Activity and distribution of certain wild mice in relation to biotic
19217 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19218 (license license:gpl3)))
19220 (define-public r-expint
19227 (uri (cran-uri "expint" version))
19230 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19231 (properties `((upstream-name . "expint")))
19232 (build-system r-build-system)
19233 (home-page "https://gitlab.com/vigou3/expint")
19234 (synopsis "Exponential integral and incomplete Gamma function")
19236 "This package provides the exponential integrals @code{E_1(x)},
19237 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19238 function @code{G(a, x)} defined for negative values of its first argument.
19239 The package also gives easy access to the underlying C routines through an
19240 API; see the package vignette for details.")
19241 (license license:gpl2+)))
19243 (define-public r-actuar
19250 (uri (cran-uri "actuar" version))
19253 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19254 (properties `((upstream-name . "actuar")))
19255 (build-system r-build-system)
19256 (propagated-inputs `(("r-expint" ,r-expint)))
19257 (home-page "https://gitlab.com/vigou3/actuar")
19258 (synopsis "Actuarial functions and heavy tailed distributions")
19260 "This package provides functions and data sets for actuarial science:
19261 modeling of loss distributions; risk theory and ruin theory; simulation of
19262 compound models, discrete mixtures and compound hierarchical models;
19263 credibility theory. It boasts support for many additional probability
19264 distributions to model insurance loss amounts and loss frequency: 19
19265 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19266 distribution; zero-truncated and zero-modified extensions of the standard
19267 discrete distributions. It also supports phase-type distributions commonly
19268 used to compute ruin probabilities.")
19269 (license license:gpl2+)))
19271 (define-public r-bmp
19278 (uri (cran-uri "bmp" version))
19281 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19282 (properties `((upstream-name . "bmp")))
19283 (build-system r-build-system)
19284 (home-page "https://cran.r-project.org/web/packages/bmp/")
19285 (synopsis "Read Bitmap (BMP) images")
19287 "This package provides pure R tools to read BMP format images. It is
19288 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19289 (license license:gpl2+)))
19291 (define-public r-readbitmap
19293 (name "r-readbitmap")
19298 (uri (cran-uri "readbitmap" version))
19301 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19302 (properties `((upstream-name . "readbitmap")))
19303 (build-system r-build-system)
19305 `(("libjpeg" ,libjpeg-turbo)
19306 ("libpng" ,libpng)))
19311 ("r-tiff" ,r-tiff)))
19312 (home-page "https://github.com/jefferis/readbitmap")
19313 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19315 "This package provides tools to identify and read BMP, JPEG, PNG, and
19316 TIFF format bitmap images. Identification defaults to the use of the magic
19317 number embedded in the file rather than the file extension.")
19318 (license license:gpl2+)))
19320 (define-public r-imager
19327 (uri (cran-uri "imager" version))
19330 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19331 (properties `((upstream-name . "imager")))
19332 (build-system r-build-system)
19335 ("libtiff" ,libtiff)
19339 `(("r-downloader" ,r-downloader)
19340 ("r-igraph" ,r-igraph)
19342 ("r-magrittr" ,r-magrittr)
19344 ("r-purrr" ,r-purrr)
19346 ("r-readbitmap" ,r-readbitmap)
19347 ("r-stringr" ,r-stringr)))
19349 `(("pkg-config" ,pkg-config)
19350 ("r-knitr" ,r-knitr)))
19351 (home-page "https://dahtah.github.io/imager/")
19352 (synopsis "Image processing library")
19354 "This is a package for fast image processing for images in up to 4
19355 dimensions (two spatial dimensions, one time/depth dimension, one color
19356 dimension). It provides most traditional image processing tools (filtering,
19357 morphology, transformations, etc.) as well as various functions for easily
19358 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19359 simple, modern C++ library for image processing.")
19360 (license license:lgpl3)))
19362 (define-public r-acuityview
19364 (name "r-acuityview")
19369 (uri (cran-uri "AcuityView" version))
19372 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19373 (properties `((upstream-name . "AcuityView")))
19374 (build-system r-build-system)
19376 `(("r-fftwtools" ,r-fftwtools)
19377 ("r-imager" ,r-imager)
19378 ("r-plotrix" ,r-plotrix)))
19379 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19380 (synopsis "Display scenes as seen by an animal with less acute vision")
19382 "This package provides a simple method for representing a visual scene as
19383 it may be seen by an animal with less acute vision.")
19384 (license license:gpl2+)))
19386 (define-public r-caret
19393 (uri (cran-uri "caret" version))
19396 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19397 (build-system r-build-system)
19399 `(("r-foreach" ,r-foreach)
19400 ("r-ggplot2" ,r-ggplot2)
19401 ("r-lattice" ,r-lattice)
19402 ("r-modelmetrics" ,r-modelmetrics)
19406 ("r-recipes" ,r-recipes)
19407 ("r-reshape2" ,r-reshape2)
19408 ("r-withr" ,r-withr)))
19410 `(("r-knitr" ,r-knitr)))
19411 (home-page "https://github.com/topepo/caret")
19412 (synopsis "Classification and regression training")
19414 "This package provides miscellaneous functions for training and plotting
19415 classification and regression models.")
19416 (license license:gpl2+)))
19418 (define-public r-adabag
19425 (uri (cran-uri "adabag" version))
19428 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19429 (properties `((upstream-name . "adabag")))
19430 (build-system r-build-system)
19432 `(("r-caret" ,r-caret)
19433 ("r-doparallel" ,r-doparallel)
19434 ("r-foreach" ,r-foreach)
19435 ("r-rpart" ,r-rpart)))
19436 (home-page "https://cran.r-project.org/web/packages/adabag/")
19437 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19439 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19440 Breiman's Bagging algorithm using classification trees as individual
19441 classifiers. Once these classifiers have been trained, they can be used to
19442 predict on new data. Also, cross validation estimation of the error can be
19444 (license license:gpl2+)))
19446 (define-public r-adagio
19453 (uri (cran-uri "adagio" version))
19456 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19457 (properties `((upstream-name . "adagio")))
19458 (build-system r-build-system)
19459 (native-inputs `(("gfortran" ,gfortran)))
19460 (home-page "https://cran.r-project.org/web/packages/adagio/")
19461 (synopsis "Discrete and global optimization routines")
19463 "This package provides methods and algorithms for discrete optimization,
19464 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19465 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19467 (license license:gpl3+)))
19469 (define-public r-univoutl
19471 (name "r-univoutl")
19476 (uri (cran-uri "univOutl" version))
19479 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19480 (properties `((upstream-name . "univOutl")))
19481 (build-system r-build-system)
19483 `(("r-hmisc" ,r-hmisc)
19484 ("r-robustbase" ,r-robustbase)))
19485 (home-page "https://github.com/marcellodo/univOutl")
19486 (synopsis "Detection of univariate outliers")
19488 "This package provides well-known outlier detection techniques in the
19489 univariate case. Methods to deal with skewed distribution are included too.
19490 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19491 historical data is implemented as well. When available, survey weights can be
19492 used in outliers detection.")
19493 (license license:gpl2+)))
19495 (define-public r-tolerance
19497 (name "r-tolerance")
19502 (uri (cran-uri "tolerance" version))
19505 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19506 (properties `((upstream-name . "tolerance")))
19507 (build-system r-build-system)
19509 `(("r-mass" ,r-mass)
19511 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19512 (synopsis "Statistical tolerance intervals and regions")
19514 "This package provides functions for estimating tolerance
19515 limits (intervals) for various univariate distributions (binomial, Cauchy,
19516 discrete Pareto, exponential, two-parameter exponential, extreme value,
19517 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19518 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19519 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19520 nonparametric tolerance intervals, tolerance bands for regression
19521 settings (linear regression, nonlinear regression, nonparametric regression,
19522 and multivariate regression), and analysis of variance tolerance intervals.
19523 Visualizations are also available for most of these settings.")
19524 (license license:gpl2+)))
19526 (define-public r-additivitytests
19528 (name "r-additivitytests")
19533 (uri (cran-uri "additivityTests" version))
19536 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19538 `((upstream-name . "additivityTests")))
19539 (build-system r-build-system)
19540 (home-page "https://github.com/simecek/additivityTests")
19541 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19543 "This package provides an implementation of the Tukey, Mandel,
19544 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19545 (license license:gpl3)))
19547 (define-public r-flexclust
19549 (name "r-flexclust")
19554 (uri (cran-uri "flexclust" version))
19557 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19558 (properties `((upstream-name . "flexclust")))
19559 (build-system r-build-system)
19561 `(("r-class" ,r-class)
19562 ("r-lattice" ,r-lattice)
19563 ("r-modeltools" ,r-modeltools)))
19564 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19565 (synopsis "Flexible cluster algorithms")
19567 "The main function @code{kcca} implements a general framework for
19568 k-centroids cluster analysis supporting arbitrary distance measures and
19569 centroid computation. Further cluster methods include hard competitive
19570 learning, neural gas, and QT clustering. There are numerous visualization
19571 methods for cluster results (neighborhood graphs, convex cluster hulls,
19572 barcharts of centroids, ...), and bootstrap methods for the analysis of
19573 cluster stability.")
19574 (license license:gpl2)))
19576 (define-public r-biclust
19583 (uri (cran-uri "biclust" version))
19586 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19587 (properties `((upstream-name . "biclust")))
19588 (build-system r-build-system)
19590 `(("r-additivitytests" ,r-additivitytests)
19591 ("r-colorspace" ,r-colorspace)
19592 ("r-flexclust" ,r-flexclust)
19593 ("r-ggplot2" ,r-ggplot2)
19594 ("r-lattice" ,r-lattice)
19596 ("r-tidyr" ,r-tidyr)))
19597 (home-page "https://cran.r-project.org/web/packages/biclust/")
19598 (synopsis "BiCluster algorithms")
19600 "The main function @code{biclust()} provides several algorithms to find
19601 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19602 In addition, the package provides methods for data
19603 preprocessing (normalization and discretization), visualization, and
19604 validation of bicluster solutions.")
19605 (license license:gpl3)))
19607 (define-public r-icge
19614 (uri (cran-uri "ICGE" version))
19617 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19618 (properties `((upstream-name . "ICGE")))
19619 (build-system r-build-system)
19621 `(("r-cluster" ,r-cluster)
19622 ("r-mass" ,r-mass)))
19623 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19624 (synopsis "Cluster estimation and identification of atypical units")
19626 "ICGE is a package that helps to estimate the number of real clusters in
19627 data as well as to identify atypical units. The underlying methods are based
19628 on distances rather than on unit x variables.")
19629 (license license:gpl2+)))
19631 (define-public r-depth
19634 (version "2.1-1.1")
19638 (uri (cran-uri "depth" version))
19641 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19642 (properties `((upstream-name . "depth")))
19643 (build-system r-build-system)
19645 `(("r-abind" ,r-abind)
19646 ("r-circular" ,r-circular)
19649 `(("gfortran" ,gfortran)))
19650 (home-page "https://cran.r-project.org/web/packages/depth/")
19651 (synopsis "Nonparametric depth functions for multivariate analysis")
19653 "This package provides tools for depth functions methodology applied to
19654 multivariate analysis. Besides allowing calculation of depth values and
19655 depth-based location estimators, the package includes functions or drawing
19656 contour plots and perspective plots of depth functions. Euclidian and
19657 spherical depths are supported.")
19658 (license license:gpl2)))
19660 (define-public r-archetypes
19662 (name "r-archetypes")
19663 (version "2.2-0.1")
19667 (uri (cran-uri "archetypes" version))
19670 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19671 (properties `((upstream-name . "archetypes")))
19672 (build-system r-build-system)
19674 `(("r-modeltools" ,r-modeltools)
19675 ("r-nnls" ,r-nnls)))
19676 (home-page "https://cran.r-project.org/web/packages/archetypes")
19677 (synopsis "Archetypal analysis")
19679 "The main function @code{archetypes} implements a framework for
19680 archetypal analysis supporting arbitrary problem solving mechanisms for the
19681 different conceptual parts of the algorithm.")
19682 (license license:gpl2+)))
19684 (define-public r-shapes
19691 (uri (cran-uri "shapes" version))
19694 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19695 (properties `((upstream-name . "shapes")))
19696 (build-system r-build-system)
19698 `(("r-mass" ,r-mass)
19699 ("r-minpack-lm" ,r-minpack-lm)
19701 ("r-scatterplot3d" ,r-scatterplot3d)))
19702 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19703 (synopsis "Statistical shape analysis")
19705 "This package provides routines for the statistical analysis of landmark
19706 shapes, including Procrustes analysis, graphical displays, principal
19707 components analysis, permutation and bootstrap tests, thin-plate spline
19708 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19709 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19710 Edition), John Wiley and Sons.")
19711 (license license:gpl2)))
19713 (define-public r-anthropometry
19715 (name "r-anthropometry")
19720 (uri (cran-uri "Anthropometry" version))
19723 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19724 (properties `((upstream-name . "Anthropometry")))
19725 (build-system r-build-system)
19727 `(("r-archetypes" ,r-archetypes)
19728 ("r-biclust" ,r-biclust)
19729 ("r-cluster" ,r-cluster)
19730 ("r-depth" ,r-depth)
19735 ("r-shapes" ,r-shapes)))
19737 `(("r-knitr" ,r-knitr)))
19738 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19739 (synopsis "Statistical methods for anthropometric data")
19741 "This package provides statistical methods especially developed to
19742 analyze anthropometric data. These methods are aimed at providing effective
19743 solutions to some commons problems related to Ergonomics and Anthropometry.
19744 They are based on clustering, the statistical concept of data depth,
19745 statistical shape analysis and archetypal analysis.")
19746 (license license:gpl2+)))
19748 (define-public r-adamethods
19750 (name "r-adamethods")
19755 (uri (cran-uri "adamethods" version))
19758 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19759 (properties `((upstream-name . "adamethods")))
19760 (build-system r-build-system)
19762 `(("r-anthropometry" ,r-anthropometry)
19763 ("r-archetypes" ,r-archetypes)
19765 ("r-foreach" ,r-foreach)
19767 ("r-tolerance" ,r-tolerance)
19768 ("r-univoutl" ,r-univoutl)))
19769 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19770 (synopsis "Archetypoid algorithms and anomaly detection")
19772 "This package is a collection of several algorithms to obtain
19773 archetypoids with small and large databases and with both classical
19774 multivariate data and functional data (univariate and multivariate). Some of
19775 these algorithms also allow to detect anomalies (outliers).")
19776 (license license:gpl2+)))
19778 (define-public r-idpmisc
19785 (uri (cran-uri "IDPmisc" version))
19788 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19789 (properties `((upstream-name . "IDPmisc")))
19790 (build-system r-build-system)
19792 `(("r-lattice" ,r-lattice)))
19793 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19794 (synopsis "Functions for data analyses and visualization")
19796 "This package provides different high-level graphics functions for
19797 displaying large datasets, displaying circular data in a very flexible way,
19798 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19799 2D-plots, creating figures with differently colored margin and plot region.
19800 In addition, the package contains auxiliary functions for data manipulation
19801 like omitting observations with irregular values or selecting data by logical
19802 vectors, which include NAs. Other functions are especially useful in
19803 spectroscopy and analyses of environmental data: robust baseline fitting,
19804 finding peaks in spectra, converting humidity measures.")
19805 (license license:gpl3+)))
19807 (define-public r-qqman
19814 (uri (cran-uri "qqman" version))
19817 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19818 (properties `((upstream-name . "qqman")))
19819 (build-system r-build-system)
19821 `(("r-calibrate" ,r-calibrate)))
19822 (home-page "https://cran.r-project.org/web/packages/qqman/")
19823 (synopsis "Q-Q and Manhattan plots for GWAS data")
19825 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19826 from PLINK results.")
19827 (license license:gpl3)))
19829 (define-public r-ggplot-multistats
19831 (name "r-ggplot-multistats")
19836 (uri (cran-uri "ggplot.multistats" version))
19839 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19841 `((upstream-name . "ggplot.multistats")))
19842 (build-system r-build-system)
19844 `(("r-ggplot2" ,r-ggplot2)
19845 ("r-hexbin" ,r-hexbin)
19846 ("r-rlang" ,r-rlang)
19847 ("r-scales" ,r-scales)))
19848 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19849 (synopsis "Multiple summary statistics for binned stats/geometries")
19851 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19852 which functions similar to its singular form, but allows the use of multiple
19853 statistics per bin. Those statistics can be mapped to multiple bin
19855 (license license:gpl3)))
19857 (define-public r-knn-covertree
19859 (name "r-knn-covertree")
19864 (uri (cran-uri "knn.covertree" version))
19867 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19868 (properties `((upstream-name . "knn.covertree")))
19869 (build-system r-build-system)
19871 `(("r-matrix" ,r-matrix)
19873 ("r-rcppeigen" ,r-rcppeigen)))
19874 (home-page "https://github.com/flying-sheep/knn.covertree")
19875 (synopsis "Accurate kNN Implementation with multiple distance measures")
19877 "Similarly to the FNN package, this package allows calculation of the k
19878 nearest neighbors (kNN) of a data matrix. The implementation is based on
19879 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19880 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19881 (license license:agpl3+)))
19883 (define-public r-poibin
19890 (uri (cran-uri "poibin" version))
19893 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19894 (properties `((upstream-name . "poibin")))
19895 (build-system r-build-system)
19896 (home-page "https://cran.r-project.org/web/packages/poibin/")
19897 (synopsis "Poisson binomial distribution")
19899 "This package provides an implementation of both the exact and
19900 approximation methods for computing the @dfn{cumulative distribution
19901 function} (CDF) of the Poisson binomial distribution. It also provides the
19902 @dfn{probability mass function} (PMF), quantile function, and random number
19903 generation for the Poisson binomial distribution.")
19904 (license license:gpl2)))
19906 (define-public r-diagram
19913 (uri (cran-uri "diagram" version))
19916 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19917 (properties `((upstream-name . "diagram")))
19918 (build-system r-build-system)
19920 `(("r-shape" ,r-shape)))
19921 (home-page "https://cran.r-project.org/web/packages/diagram/")
19922 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19924 "This package provides tools to visualize simple graphs (networks) based
19925 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19926 electrical networks, etc. It also includes supporting material for the book
19927 \"A practical guide to ecological modelling - using R as a simulation
19928 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19929 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19930 Francesca Mazzia (2012).")
19931 (license license:gpl2+)))
19933 (define-public r-lim
19940 (uri (cran-uri "LIM" version))
19943 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19944 (properties `((upstream-name . "LIM")))
19945 (build-system r-build-system)
19947 `(("r-diagram" ,r-diagram)
19948 ("r-limsolve" ,r-limsolve)))
19949 (home-page "https://cran.r-project.org/web/packages/LIM/")
19950 (synopsis "Linear inverse model examples and solution methods")
19952 "This package provides functions that read and solve linear inverse
19953 problems (food web problems, linear programming problems).")
19954 (license license:gpl2+)))
19956 (define-public r-shinycssloaders
19958 (name "r-shinycssloaders")
19963 (uri (cran-uri "shinycssloaders" version))
19966 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19968 `((upstream-name . "shinycssloaders")))
19969 (build-system r-build-system)
19971 `(("r-digest" ,r-digest)
19973 ("r-shiny" ,r-shiny)))
19974 (home-page "https://github.com/andrewsali/shinycssloaders")
19975 (synopsis "Add CSS loading animations to Shiny outputs")
19977 "This package provides tools to create a lightweight Shiny wrapper for
19978 the css-loaders created by Luke Hass
19979 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19980 automatically show a loader when the output is (re)calculating.")
19981 (license license:gpl3)))
19983 (define-public r-rsvg
19990 (uri (cran-uri "rsvg" version))
19993 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19994 (properties `((upstream-name . "rsvg")))
19995 (build-system r-build-system)
19997 `(("librsvg" ,librsvg)
20000 `(("pkg-config" ,pkg-config)
20001 ("r-knitr" ,r-knitr)))
20002 (home-page "https://github.com/jeroen/rsvg#readme")
20003 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
20005 "This package allows you to render vector-based SVG images into
20006 high-quality custom-size bitmap arrays using the librsvg2 library. The
20007 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
20008 addition, the package can convert images directly to various formats such as
20009 PDF or PostScript.")
20010 (license license:expat)))
20012 (define-public r-influencer
20014 (name "r-influencer")
20019 (uri (cran-uri "influenceR" version))
20022 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
20023 (properties `((upstream-name . "influenceR")))
20024 (build-system r-build-system)
20026 `(("r-igraph" ,r-igraph)
20027 ("r-matrix" ,r-matrix)))
20028 (home-page "https://github.com/rcc-uchicago/influenceR")
20029 (synopsis "Tools to quantify structural importance of nodes in a network")
20031 "This package provides functionality to compute various node centrality
20032 measures on networks. Included are functions to compute betweenness
20033 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
20034 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
20035 algorithm to identify key players, and Valente's bridging metric. The
20036 betweenness, Key Players, and bridging implementations are parallelized with
20038 (license license:gpl2)))
20040 (define-public r-emplik
20047 (uri (cran-uri "emplik" version))
20050 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
20051 (properties `((upstream-name . "emplik")))
20052 (build-system r-build-system)
20054 `(("r-quantreg" ,r-quantreg)))
20055 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
20056 (synopsis "Empirical likelihood ratio for censored/truncated data")
20058 "This package provides empirical likelihood ratio tests for
20059 means/quantiles/hazards from possibly censored and/or truncated data. It also
20061 (license license:gpl2+)))
20063 (define-public r-imputeyn
20065 (name "r-imputeyn")
20070 (uri (cran-uri "imputeYn" version))
20073 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
20074 (properties `((upstream-name . "imputeYn")))
20075 (build-system r-build-system)
20077 `(("r-boot" ,r-boot)
20078 ("r-emplik" ,r-emplik)
20079 ("r-mvtnorm" ,r-mvtnorm)
20080 ("r-quadprog" ,r-quadprog)
20081 ("r-survival" ,r-survival)))
20082 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
20083 (synopsis "Impute last largest censored observation under weighted least squares")
20085 "This package allows for the imputation of the last largest censored
20086 observantions. This method brings less bias and more efficient estimates for
20088 (license license:gpl2)))
20090 (define-public r-adapenetclass
20092 (name "r-adapenetclass")
20097 (uri (cran-uri "AdapEnetClass" version))
20100 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
20101 (properties `((upstream-name . "AdapEnetClass")))
20102 (build-system r-build-system)
20104 `(("r-glmnet" ,r-glmnet)
20105 ("r-imputeyn" ,r-imputeyn)
20107 ("r-quadprog" ,r-quadprog)))
20108 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
20109 (synopsis "Class of adaptive elastic net methods for censored data")
20111 "This package provides methods for variable selection for AFT models.")
20112 (license license:gpl2)))
20114 (define-public r-flock
20121 (uri (cran-uri "flock" version))
20124 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
20125 (properties `((upstream-name . "flock")))
20126 (build-system r-build-system)
20127 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
20128 (home-page "https://cran.r-project.org/web/packages/flock/")
20129 (synopsis "Process synchronization using file locks")
20131 "This package implements synchronization between R processes (spawned by
20132 using the @code{parallel} package for instance) using file locks. It supports
20133 both exclusive and shared locking.")
20134 (license license:asl2.0)))
20136 (define-public r-archivist
20138 (name "r-archivist")
20143 (uri (cran-uri "archivist" version))
20146 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
20147 (properties `((upstream-name . "archivist")))
20148 (build-system r-build-system)
20151 ("r-digest" ,r-digest)
20152 ("r-flock" ,r-flock)
20154 ("r-lubridate" ,r-lubridate)
20155 ("r-magrittr" ,r-magrittr)
20156 ("r-rcurl" ,r-rcurl)
20157 ("r-rsqlite" ,r-rsqlite)))
20158 (home-page "https://pbiecek.github.io/archivist/")
20159 (synopsis "Tools for storing, restoring and searching for R objects")
20161 "Data exploration and modelling is a process in which a lot of data
20162 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
20163 statistical models, different versions of data sets and different versions of
20164 results. Archivist helps to store and manage artifacts created in R. It
20165 allows you to store selected artifacts as binary files together with their
20166 metadata and relations. Archivist allows sharing artifacts with others. It
20167 can look for already created artifacts by using its class, name, date of the
20168 creation or other properties. It also makes it easy to restore such
20170 (license license:gpl2)))
20172 (define-public r-versions
20174 (name "r-versions")
20179 (uri (cran-uri "versions" version))
20182 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
20183 (properties `((upstream-name . "versions")))
20184 (build-system r-build-system)
20185 (home-page "https://cran.r-project.org/web/packages/versions/")
20186 (synopsis "Query and install specific versions of CRAN packages")
20188 "This package allows you to install specified versions of R packages
20189 hosted on CRAN and provides functions to list available versions and the
20190 versions of currently installed packages.")
20191 (license license:bsd-3)))
20193 (define-public r-adapr
20200 (uri (cran-uri "adapr" version))
20203 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20204 (properties `((upstream-name . "adapr")))
20205 (build-system r-build-system)
20207 `(("r-archivist" ,r-archivist)
20208 ("r-devtools" ,r-devtools)
20209 ("r-digest" ,r-digest)
20210 ("r-doparallel" ,r-doparallel)
20211 ("r-gdata" ,r-gdata)
20212 ("r-ggplot2" ,r-ggplot2)
20213 ("r-git2r" ,r-git2r)
20214 ("r-igraph" ,r-igraph)
20215 ("r-knitr" ,r-knitr)
20216 ("r-plotly" ,r-plotly)
20218 ("r-rmarkdown" ,r-rmarkdown)
20219 ("r-shiny" ,r-shiny)
20220 ("r-shinydashboard" ,r-shinydashboard)
20221 ("r-versions" ,r-versions)))
20222 (home-page "https://cran.r-project.org/web/packages/adapr/")
20223 (synopsis "Implementation of an accountable data analysis process")
20225 "This package tracks reading and writing within R scripts that are
20226 organized into a directed acyclic graph. It contains an interactive Shiny
20227 application @code{adaprApp()}. It uses Git and file hashes to track version
20228 histories of inputs and outputs.")
20229 (license license:lgpl2.0)))
20231 (define-public r-adapsamp
20233 (name "r-adapsamp")
20238 (uri (cran-uri "AdapSamp" version))
20241 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20242 (properties `((upstream-name . "AdapSamp")))
20243 (build-system r-build-system)
20244 (propagated-inputs `(("r-pracma" ,r-pracma)))
20245 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20246 (synopsis "Adaptive sampling algorithms")
20248 "For distributions whose probability density functions are log-concave,
20249 the adaptive rejection sampling algorithm can be used to build envelope
20250 functions for sampling. For others, the modified adaptive rejection sampling
20251 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20252 adaptive slice sampling algorithm can be used. This R package mainly includes
20253 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20254 @code{rASS()}. These functions can realize sampling based on the algorithms
20256 (license license:gpl2)))
20258 (define-public r-adaptalint
20260 (name "r-adaptalint")
20265 (uri (cran-uri "adaptalint" version))
20268 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20269 (properties `((upstream-name . "adaptalint")))
20270 (build-system r-build-system)
20272 `(("r-dplyr" ,r-dplyr)
20273 ("r-lintr" ,r-lintr)
20274 ("r-purrr" ,r-purrr)))
20275 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20276 (synopsis "Check R code style")
20278 "This package provides tools to infer the code style (which style rules
20279 are followed and which ones are not) from one package and use it to check
20280 another. This makes it easier to find and correct the most important problems
20282 (license license:gpl3)))
20284 (define-public r-fracdiff
20286 (name "r-fracdiff")
20291 (uri (cran-uri "fracdiff" version))
20294 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20295 (properties `((upstream-name . "fracdiff")))
20296 (build-system r-build-system)
20297 (home-page "https://github.com/mmaechler/fracdiff")
20299 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20301 "This package provides tools for the maximum likelihood estimation of the
20302 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20303 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20304 (license license:gpl2+)))
20306 (define-public r-forecast
20308 (name "r-forecast")
20313 (uri (cran-uri "forecast" version))
20316 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20317 (properties `((upstream-name . "forecast")))
20318 (build-system r-build-system)
20320 `(("r-colorspace" ,r-colorspace)
20321 ("r-fracdiff" ,r-fracdiff)
20322 ("r-ggplot2" ,r-ggplot2)
20323 ("r-lmtest" ,r-lmtest)
20324 ("r-magrittr" ,r-magrittr)
20327 ("r-rcpparmadillo" ,r-rcpparmadillo)
20328 ("r-timedate" ,r-timedate)
20329 ("r-tseries" ,r-tseries)
20333 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20334 (home-page "https://pkg.robjhyndman.com/forecast/")
20335 (synopsis "Forecasting functions for time series and linear models")
20337 "This package provides methods and tools for displaying and analysing
20338 univariate time series forecasts including exponential smoothing via state
20339 space models and automatic ARIMA modelling.")
20340 (license license:gpl3)))
20342 (define-public r-xmisc
20349 (uri (cran-uri "Xmisc" version))
20352 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20353 (properties `((upstream-name . "Xmisc")))
20354 (build-system r-build-system)
20355 (home-page "https://cran.r-project.org/package=Xmisc")
20357 "Xiaobei's miscellaneous classes and functions")
20359 "This package provides Xiaobei's miscellaneous classes and functions,
20360 which are useful when developing R packages for @dfn{object oriented
20361 programming} (OOP) using R Reference Class.")
20362 (license license:gpl2+)))
20364 (define-public r-proxyc
20371 (uri (cran-uri "proxyC" version))
20374 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20375 (properties `((upstream-name . "proxyC")))
20376 (build-system r-build-system)
20378 `(("r-matrix" ,r-matrix)
20380 ("r-rcpparmadillo" ,r-rcpparmadillo)
20381 ("r-rcppparallel" ,r-rcppparallel)))
20382 (home-page "https://cran.r-project.org/package=proxyC")
20383 (synopsis "Compute proximity in large sparse matrices")
20385 "This package provides efficient tools to compute the proximity between
20386 rows or columns of large matrices. Functions are optimised for large sparse
20387 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20388 similarity/distance measures, computation of correlation, cosine similarity
20389 and Euclidean distance is particularly fast.")
20390 (license license:gpl3)))
20392 (define-public r-isocodes
20394 (name "r-isocodes")
20395 (version "2020.03.16")
20399 (uri (cran-uri "ISOcodes" version))
20402 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20403 (properties `((upstream-name . "ISOcodes")))
20404 (build-system r-build-system)
20405 (home-page "https://cran.r-project.org/package=ISOcodes")
20406 (synopsis "Selected ISO codes")
20408 "This package provides ISO language, territory, currency, script and
20409 character codes. It provides ISO 639 language codes, ISO 3166 territory
20410 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20411 character codes as well as the UN M.49 area codes.")
20412 (license license:gpl2)))
20414 (define-public r-stopwords
20416 (name "r-stopwords")
20421 (uri (cran-uri "stopwords" version))
20424 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20425 (properties `((upstream-name . "stopwords")))
20426 (build-system r-build-system)
20428 `(("r-desc" ,r-desc)
20429 ("r-isocodes" ,r-isocodes)
20430 ("r-usethis" ,r-usethis)))
20431 (home-page "https://github.com/quanteda/stopwords")
20432 (synopsis "Multilingual stopword lists")
20434 "This package provides multiple sources of stopwords, for use in text
20435 analysis and natural language processing.")
20436 (license license:expat)))
20438 (define-public r-spacyr
20445 (uri (cran-uri "spacyr" version))
20448 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20449 (properties `((upstream-name . "spacyr")))
20450 (build-system r-build-system)
20452 `(("r-data-table" ,r-data-table)
20453 ("r-reticulate" ,r-reticulate)))
20454 (home-page "https://spacyr.quanteda.io")
20455 (synopsis "R wrapper for the spaCy NLP library")
20457 "This package provides an R wrapper to the Python @dfn{natural language
20458 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20459 (license license:gpl3)))
20461 (define-public r-snowballc
20463 (name "r-snowballc")
20468 (uri (cran-uri "SnowballC" version))
20471 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20472 (properties `((upstream-name . "SnowballC")))
20473 (build-system r-build-system)
20474 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20475 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20477 "This package provides an R interface to the C @code{libstemmer} library
20478 that implements Porter's word stemming algorithm for collapsing words to a
20479 common root to aid comparison of vocabulary. Currently supported languages
20480 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20481 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20482 (license license:bsd-3)))
20484 (define-public r-quanteda
20486 (name "r-quanteda")
20491 (uri (cran-uri "quanteda" version))
20494 "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8"))))
20495 (properties `((upstream-name . "quanteda")))
20496 (build-system r-build-system)
20498 `(("r-data-table" ,r-data-table)
20499 ("r-digest" ,r-digest)
20500 ("r-extrafont" ,r-extrafont)
20501 ("r-fastmatch" ,r-fastmatch)
20502 ("r-ggplot2" ,r-ggplot2)
20503 ("r-ggrepel" ,r-ggrepel)
20504 ("r-jsonlite" ,r-jsonlite)
20505 ("r-magrittr" ,r-magrittr)
20506 ("r-matrix" ,r-matrix)
20507 ("r-network" ,r-network)
20508 ("r-proxyc" ,r-proxyc)
20510 ("r-rcpparmadillo" ,r-rcpparmadillo)
20511 ("r-rcppparallel" ,r-rcppparallel)
20513 ("r-snowballc" ,r-snowballc)
20514 ("r-stopwords" ,r-stopwords)
20515 ("r-stringi" ,r-stringi)
20517 ("r-yaml" ,r-yaml)))
20519 `(("r-knitr" ,r-knitr)))
20520 (home-page "https://quanteda.io")
20521 (synopsis "Quantitative analysis of textual data")
20523 "This package provides a fast, flexible, and comprehensive framework for
20524 quantitative text analysis in R. It provides functionality for corpus
20525 management, creating and manipulating tokens and ngrams, exploring keywords in
20526 context, forming and manipulating sparse matrices of documents by features and
20527 feature co-occurrences, analyzing keywords, computing feature similarities and
20528 distances, applying content dictionaries, applying supervised and unsupervised
20529 machine learning, visually representing text and text analyses, and more.")
20530 (license license:gpl3)))
20532 (define-public r-topicmodels
20534 (name "r-topicmodels")
20539 (uri (cran-uri "topicmodels" version))
20542 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20543 (properties `((upstream-name . "topicmodels")))
20544 (build-system r-build-system)
20548 `(("r-modeltools" ,r-modeltools)
20551 (home-page "https://cran.r-project.org/package=topicmodels")
20552 (synopsis "Topic models")
20554 "This package provides an interface to the C code for @dfn{Latent
20555 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20556 David M. Blei and co-authors and the C++ code for fitting LDA models using
20557 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20558 (license license:gpl2)))
20560 (define-public r-stm
20567 (uri (cran-uri "stm" version))
20570 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20571 (properties `((upstream-name . "stm")))
20572 (build-system r-build-system)
20574 `(("r-data-table" ,r-data-table)
20575 ("r-glmnet" ,r-glmnet)
20577 ("r-matrix" ,r-matrix)
20578 ("r-matrixstats" ,r-matrixstats)
20579 ("r-quadprog" ,r-quadprog)
20580 ("r-quanteda" ,r-quanteda)
20582 ("r-rcpparmadillo" ,r-rcpparmadillo)
20584 ("r-stringr" ,r-stringr)))
20585 (home-page "http://www.structuraltopicmodel.com/")
20586 (synopsis "Estimation of the Structural Topic Model")
20588 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20589 topic models with document-level covariates. The package also includes tools
20590 for model selection, visualization, and estimation of topic-covariate
20592 (license license:expat)))
20594 (define-public r-polycor
20601 (uri (cran-uri "polycor" version))
20604 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20605 (properties `((upstream-name . "polycor")))
20606 (build-system r-build-system)
20608 `(("r-matrix" ,r-matrix)
20609 ("r-mvtnorm" ,r-mvtnorm)))
20610 (home-page "https://r-forge.r-project.org/projects/polycor/")
20611 (synopsis "Polychoric and polyserial correlations")
20613 "This package provides tools to compute polychoric and polyserial
20614 correlations by quick \"two-step\" methods or ML, optionally with standard
20615 errors; tetrachoric and biserial correlations are special cases.")
20616 (license license:gpl2+)))
20618 (define-public r-msm
20625 (uri (cran-uri "msm" version))
20628 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20629 (properties `((upstream-name . "msm")))
20630 (build-system r-build-system)
20632 `(("r-expm" ,r-expm)
20633 ("r-mvtnorm" ,r-mvtnorm)
20634 ("r-survival" ,r-survival)))
20635 (home-page "https://github.com/chjackson/msm")
20636 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20638 "This package provides functions for fitting continuous-time Markov and
20639 hidden Markov multi-state models to longitudinal data. It was designed for
20640 processes observed at arbitrary times in continuous time (panel data) but some
20641 other observation schemes are supported. Both Markov transition rates and the
20642 hidden Markov output process can be modelled in terms of covariates, which may
20643 be constant or piecewise-constant in time.")
20644 (license license:gpl2+)))
20646 (define-public r-ltm
20653 (uri (cran-uri "ltm" version))
20656 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20657 (properties `((upstream-name . "ltm")))
20658 (build-system r-build-system)
20660 `(("r-mass" ,r-mass)
20662 ("r-polycor" ,r-polycor)))
20663 (home-page "https://github.com/drizopoulos/ltm")
20664 (synopsis "Latent trait models under IRT")
20666 "This is a package supporting the analysis of multivariate dichotomous
20667 and polytomous data using latent trait models under the Item Response Theory
20668 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20669 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20671 (license license:gpl2+)))
20673 (define-public r-mi
20680 (uri (cran-uri "mi" version))
20683 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20684 (properties `((upstream-name . "mi")))
20685 (build-system r-build-system)
20688 ("r-matrix" ,r-matrix)))
20689 (home-page "http://www.stat.columbia.edu/~gelman/")
20690 (synopsis "Missing data imputation and model checking")
20692 "This package provides functions for data manipulation, imputing missing
20693 values in an approximate Bayesian framework, diagnostics of the models used to
20694 generate the imputations, confidence-building mechanisms to validate some of
20695 the assumptions of the imputation algorithm, and functions to analyze multiply
20696 imputed data sets with the appropriate degree of sampling uncertainty.")
20697 (license license:gpl2+)))
20699 (define-public r-matrixcalc
20701 (name "r-matrixcalc")
20706 (uri (cran-uri "matrixcalc" version))
20709 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20710 (properties `((upstream-name . "matrixcalc")))
20711 (build-system r-build-system)
20712 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20713 (synopsis "Collection of functions for matrix calculations")
20715 "This package provides a collection of functions to support matrix
20716 calculations for probability, econometric and numerical analysis. There are
20717 additional functions that are comparable to APL functions which are useful for
20718 actuarial models such as pension mathematics.")
20719 (license license:gpl2+)))
20721 (define-public r-sem
20728 (uri (cran-uri "sem" version))
20731 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20732 (properties `((upstream-name . "sem")))
20733 (build-system r-build-system)
20735 `(("r-boot" ,r-boot)
20737 ("r-matrixcalc" ,r-matrixcalc)
20739 (home-page "https://cran.r-project.org/package=sem")
20740 (synopsis "Structural equation models")
20742 "This package provides functions for fitting general linear structural
20743 equation models (with observed and latent variables) using the RAM approach,
20744 and for fitting structural equations in observed-variable models by two-stage
20746 (license license:gpl2+)))
20748 (define-public r-semtools
20750 (name "r-semtools")
20755 (uri (cran-uri "semTools" version))
20758 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20759 (properties `((upstream-name . "semTools")))
20760 (build-system r-build-system)
20762 `(("r-lavaan" ,r-lavaan)))
20763 (home-page "https://github.com/simsem/semTools/wiki")
20764 (synopsis "Useful tools for structural equation modeling")
20766 "This package provides useful tools for structural equation modeling.")
20767 (license license:gpl2+)))
20769 (define-public r-regsem
20776 (uri (cran-uri "regsem" version))
20779 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20780 (properties `((upstream-name . "regsem")))
20781 (build-system r-build-system)
20783 `(("r-lavaan" ,r-lavaan)
20785 ("r-rcpparmadillo" ,r-rcpparmadillo)
20786 ("r-rsolnp" ,r-rsolnp)))
20787 (home-page "https://cran.r-project.org/package=regsem")
20788 (synopsis "Regularized structural equation modeling")
20790 "This package uses both ridge and lasso penalties (and extensions) to
20791 penalize specific parameters in structural equation models. The package
20792 offers additional cost functions, cross validation, and other extensions
20793 beyond traditional structural equation models. It also contains a function to
20794 perform @dfn{exploratory mediation} (XMed).")
20795 (license license:gpl2+)))
20797 (define-public r-stanheaders
20799 (name "r-stanheaders")
20800 (version "2.21.0-6")
20804 (uri (cran-uri "StanHeaders" version))
20807 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20808 (properties `((upstream-name . "StanHeaders")))
20809 (build-system r-build-system)
20810 (inputs `(("pandoc" ,pandoc)))
20812 `(("r-rcppeigen" ,r-rcppeigen)
20813 ("r-rcppparallel" ,r-rcppparallel)))
20815 `(("gfortran" ,gfortran)
20816 ("r-knitr" ,r-knitr))) ; for vignettes
20817 (home-page "https://mc-stan.org/")
20818 (synopsis "C++ header files for Stan")
20820 "The C++ header files of the Stan project are provided by this package.
20821 There is a shared object containing part of the @code{CVODES} library, but it
20822 is not accessible from R. @code{r-stanheaders} is only useful for developers
20823 who want to utilize the @code{LinkingTo} directive of their package's
20824 DESCRIPTION file to build on the Stan library without incurring unnecessary
20827 The Stan project develops a probabilistic programming language that implements
20828 full or approximate Bayesian statistical inference via Markov Chain Monte
20829 Carlo or variational methods and implements (optionally penalized) maximum
20830 likelihood estimation via optimization. The Stan library includes an advanced
20831 automatic differentiation scheme, templated statistical and linear algebra
20832 functions that can handle the automatically differentiable scalar types (and
20833 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20834 package provides user-facing R functions to parse, compile, test, estimate,
20835 and analyze Stan models.")
20836 (license license:bsd-3)))
20838 (define-public r-rpf
20845 (uri (cran-uri "rpf" version))
20848 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20849 (properties `((upstream-name . "rpf")))
20850 (build-system r-build-system)
20852 `(("r-lifecycle" ,r-lifecycle)
20853 ("r-mvtnorm" ,r-mvtnorm)
20855 ("r-rcppeigen" ,r-rcppeigen)))
20857 `(("r-knitr" ,r-knitr)))
20858 (home-page "https://github.com/jpritikin/rpf")
20859 (synopsis "Response probability functions")
20861 "The purpose of this package is to factor out logic and math common to
20862 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20863 core support code suitable for more specialized IRT packages to build upon.
20864 Complete access to optimized C functions is made available with
20865 @code{R_RegisterCCallable()}.")
20866 (license license:gpl3+)))
20868 (define-public r-openmx
20875 (uri (cran-uri "OpenMx" version))
20878 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
20879 (properties `((upstream-name . "OpenMx")))
20880 (build-system r-build-system)
20883 ("r-digest" ,r-digest)
20884 ("r-lifecycle" ,r-lifecycle)
20886 ("r-matrix" ,r-matrix)
20888 ("r-rcppeigen" ,r-rcppeigen)
20890 ("r-stanheaders" ,r-stanheaders)))
20891 (native-inputs `(("gfortran" ,gfortran)))
20892 (home-page "http://openmx.ssri.psu.edu")
20893 (synopsis "Extended structural equation modelling")
20895 "This package allows for the estimation of a wide variety of advanced
20896 multivariate statistical models. It consists of a library of functions and
20897 optimizers that allow you to quickly and flexibly define an SEM model and
20898 estimate parameters given observed data.")
20899 (license license:asl2.0)))
20901 (define-public r-kutils
20908 (uri (cran-uri "kutils" version))
20911 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20912 (properties `((upstream-name . "kutils")))
20913 (build-system r-build-system)
20915 `(("r-foreign" ,r-foreign)
20916 ("r-openxlsx" ,r-openxlsx)
20918 ("r-runit" ,r-runit)
20919 ("r-xtable" ,r-xtable)))
20920 (home-page "https://cran.r-project.org/package=kutils")
20921 (synopsis "Project management tools")
20923 "This package provides tools for data importation, recoding, and
20924 inspection. There are functions to create new project folders, R code
20925 templates, create uniquely named output directories, and to quickly obtain a
20926 visual summary for each variable in a data frame. The main feature here is
20927 the systematic implementation of the \"variable key\" framework for data
20928 importation and recoding.")
20929 (license license:gpl2)))
20931 (define-public r-rockchalk
20933 (name "r-rockchalk")
20934 (version "1.8.144")
20938 (uri (cran-uri "rockchalk" version))
20941 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20942 (properties `((upstream-name . "rockchalk")))
20943 (build-system r-build-system)
20945 `(("r-cardata" ,r-cardata)
20946 ("r-kutils" ,r-kutils)
20948 ("r-mass" ,r-mass)))
20949 (home-page "https://cran.r-project.org/package=rockchalk")
20950 (synopsis "Regression estimation and presentation")
20952 "This package provides a collection of functions for interpretation and
20953 presentation of regression analysis. These functions are used to produce the
20954 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20955 includes regression diagnostics, regression tables, and plots of interactions
20956 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20957 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20958 fairly comprehensive overview.")
20959 (license license:gpl3+)))
20961 (define-public r-lisreltor
20963 (name "r-lisreltor")
20968 (uri (cran-uri "lisrelToR" version))
20971 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20972 (properties `((upstream-name . "lisrelToR")))
20973 (build-system r-build-system)
20974 (home-page "https://cran.r-project.org/package=lisrelToR")
20975 (synopsis "Import output from LISREL into R")
20977 "This is an unofficial package aimed at automating the import of LISREL
20979 (license license:gpl2)))
20981 (define-public r-bdgraph
20988 (uri (cran-uri "BDgraph" version))
20991 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
20992 (properties `((upstream-name . "BDgraph")))
20993 (build-system r-build-system)
20995 `(("r-igraph" ,r-igraph)))
20996 (home-page "https://www.uva.nl/profile/a.mohammadi")
20997 (synopsis "Bayesian structure learning in graphical models")
20999 "This package provides statistical tools for Bayesian structure learning
21000 in undirected graphical models for continuous, discrete, and mixed data. It
21001 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
21002 on a continuous-time birth-death process.")
21003 (license license:gpl2+)))
21005 (define-public r-d3network
21007 (name "r-d3network")
21008 (version "0.5.2.1")
21012 (uri (cran-uri "d3Network" version))
21015 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
21016 (properties `((upstream-name . "d3Network")))
21017 (build-system r-build-system)
21019 `(("r-plyr" ,r-plyr)
21020 ("r-rjson" ,r-rjson)
21021 ("r-whisker" ,r-whisker)))
21022 (home-page "http://christophergandrud.github.io/d3Network/")
21023 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
21025 "This package is intended to make it easy to create D3 JavaScript
21026 network, tree, dendrogram, and Sankey graphs from R using data frames.")
21027 (license license:gpl3+)))
21029 (define-public r-qgraph
21036 (uri (cran-uri "qgraph" version))
21039 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
21040 (properties `((upstream-name . "qgraph")))
21041 (build-system r-build-system)
21043 `(("r-abind" ,r-abind)
21044 ("r-bdgraph" ,r-bdgraph)
21045 ("r-colorspace" ,r-colorspace)
21046 ("r-corpcor" ,r-corpcor)
21047 ("r-d3network" ,r-d3network)
21048 ("r-dplyr" ,r-dplyr)
21049 ("r-fdrtool" ,r-fdrtool)
21050 ("r-ggplot2" ,r-ggplot2)
21051 ("r-ggraph" ,r-ggraph)
21052 ("r-glasso" ,r-glasso)
21053 ("r-gtools" ,r-gtools)
21054 ("r-hmisc" ,r-hmisc)
21056 ("r-igraph" ,r-igraph)
21058 ("r-lavaan" ,r-lavaan)
21059 ("r-matrix" ,r-matrix)
21060 ("r-pbapply" ,r-pbapply)
21063 ("r-psych" ,r-psych)
21065 ("r-reshape2" ,r-reshape2)
21066 ("r-tidygraph" ,r-tidygraph)))
21067 (home-page "http://sachaepskamp.com/qgraph/")
21068 (synopsis "Weighted network visualization and analysis")
21070 "This package implements tools for weighted network visualization and
21071 analysis, as well as Gaussian graphical model computation. It contains graph
21072 plotting methods, and tools for psychometric data visualization and graphical
21073 model estimation. See Epskamp et al. (2012)
21074 @url{doi:10.18637/jss.v048.i04}.")
21075 (license license:gpl2)))
21077 (define-public r-semplot
21084 (uri (cran-uri "semPlot" version))
21087 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
21088 (properties `((upstream-name . "semPlot")))
21089 (build-system r-build-system)
21091 `(("r-colorspace" ,r-colorspace)
21092 ("r-corpcor" ,r-corpcor)
21093 ("r-igraph" ,r-igraph)
21094 ("r-lavaan" ,r-lavaan)
21095 ("r-lisreltor" ,r-lisreltor)
21096 ("r-openmx" ,r-openmx)
21098 ("r-qgraph" ,r-qgraph)
21099 ("r-regsem" ,r-regsem)
21100 ("r-rockchalk" ,r-rockchalk)
21103 (home-page "https://github.com/SachaEpskamp/semPlot")
21104 (synopsis "Unified visualizations of structural equation models")
21106 "Structural equation modeling (SEM) has a long history of representing
21107 models graphically as path diagrams. The semPlot package for R fills the gap
21108 between advanced, but time-consuming, graphical software and the limited
21109 graphics produced automatically by SEM software. In addition, semPlot offers
21110 more functionality than drawing path diagrams: it can act as a common ground
21111 for importing SEM results into R. Any result usable as input to semPlot can
21112 also be represented in any of the three popular SEM frame-works, as well as
21113 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
21114 (license license:gpl2)))
21116 (define-public r-cdm
21123 (uri (cran-uri "CDM" version))
21126 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
21127 (properties `((upstream-name . "CDM")))
21128 (build-system r-build-system)
21130 `(("r-mvtnorm" ,r-mvtnorm)
21131 ("r-polycor" ,r-polycor)
21133 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21135 "https://github.com/alexanderrobitzsch/CDM")
21136 (synopsis "Cognitive diagnosis modeling")
21138 "This package provides functions for cognitive diagnosis modeling and
21139 multidimensional item response modeling for dichotomous and polytomous item
21140 responses. It enables the estimation of the DINA and DINO model, the multiple
21141 group (polytomous) GDINA model, the multiple choice DINA model, the general
21142 diagnostic model (GDM), the structured latent class model (SLCA), and
21143 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
21144 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
21145 estimation and the package structure. For tutorials on how to use the CDM
21146 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
21147 well as Ravand and Robitzsch (2015).")
21148 (license license:gpl2+)))
21150 (define-public r-tam
21157 (uri (cran-uri "TAM" version))
21160 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
21161 (properties `((upstream-name . "TAM")))
21162 (build-system r-build-system)
21166 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21167 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
21168 (synopsis "Test analysis modules")
21170 "This package includes tools for marginal maximum likelihood estimation
21171 and joint maximum likelihood estimation for unidimensional and
21172 multidimensional item response models. The package functionality covers the
21173 Rasch model, 2PL model, 3PL model, generalized partial credit model,
21174 multi-faceted Rasch model, nominal item response model, structured latent
21175 class model, mixture distribution IRT models, and located latent class models.
21176 Latent regression models and plausible value imputation are also supported.")
21177 (license license:gpl2+)))
21179 (define-public r-erm
21186 (uri (cran-uri "eRm" version))
21189 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
21190 (properties `((upstream-name . "eRm")))
21191 (build-system r-build-system)
21193 `(("r-colorspace" ,r-colorspace)
21194 ("r-lattice" ,r-lattice)
21196 ("r-matrix" ,r-matrix)
21197 ("r-psych" ,r-psych)))
21198 (native-inputs `(("gfortran" ,gfortran)))
21199 (home-page "https://cran.r-project.org/package=eRm")
21200 (synopsis "Extended Rasch modeling")
21202 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21203 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21204 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21205 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21206 data matrix. Additional features are the ML estimation of the person
21207 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21208 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21209 infit and outfit measures, ICC and other plots, automated stepwise item
21210 elimination, and a simulation module for various binary data matrices.")
21211 (license license:gpl3)))
21213 (define-public r-irtoys
21220 (uri (cran-uri "irtoys" version))
21223 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21224 (properties `((upstream-name . "irtoys")))
21225 (build-system r-build-system)
21229 (home-page "https://cran.r-project.org/package=irtoys")
21230 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21232 "This package provides a collection of functions useful in learning and
21233 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21234 programs. It provides basic CTT analysis, a simple common interface to the
21235 estimation of item parameters in IRT models for binary responses with three
21236 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21237 EAP, WLE, plausible values), item and person fit statistics, scaling
21238 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21239 array of parametric and non-parametric (kernel) plots. It estimates and plots
21240 Haberman's interaction model when all items are dichotomously scored.")
21241 (license license:gpl2+)))
21243 (define-public r-iheatmapr
21245 (name "r-iheatmapr")
21250 (uri (cran-uri "iheatmapr" version))
21253 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21254 (properties `((upstream-name . "iheatmapr")))
21255 (build-system r-build-system)
21257 `(("r-fastcluster" ,r-fastcluster)
21258 ("r-ggdendro" ,r-ggdendro)
21259 ("r-htmlwidgets" ,r-htmlwidgets)
21260 ("r-jsonlite" ,r-jsonlite)
21261 ("r-knitr" ,r-knitr)
21262 ("r-magrittr" ,r-magrittr)
21263 ("r-rcolorbrewer" ,r-rcolorbrewer)
21264 ("r-scales" ,r-scales)))
21266 `(("r-knitr" ,r-knitr)))
21267 (home-page "https://docs.ropensci.org/iheatmapr")
21268 (synopsis "Interactive, Complex Heatmaps")
21270 "iheatmapr is an R package for building complex, interactive heatmaps
21271 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21272 subplots along the rows or columns of the main heatmap add more information
21273 about each row or column. For example, a one column additional heatmap may
21274 indicate what group a particular row or column belongs to. Complex heatmaps
21275 may also include multiple side by side heatmaps which show different types of
21276 data for the same conditions. Interactivity can improve complex heatmaps by
21277 providing tooltips with information about each cell and enabling zooming into
21278 interesting features. iheatmapr uses the plotly library for interactivity.")
21279 (license license:expat)))
21281 (define-public r-packrat
21288 (uri (cran-uri "packrat" version))
21291 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21292 (properties `((upstream-name . "packrat")))
21293 (build-system r-build-system)
21294 (home-page "https://github.com/rstudio/packrat/")
21295 (synopsis "Dependency management R projects")
21297 "This package provides a dependency manager for R projects that allows
21298 you to manage the R packages your project depends on in an isolated, portable,
21299 and reproducible way.")
21300 (license license:gpl2)))
21302 (define-public r-rsconnect
21304 (name "r-rsconnect")
21309 (uri (cran-uri "rsconnect" version))
21312 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21313 (properties `((upstream-name . "rsconnect")))
21314 (build-system r-build-system)
21316 `(("r-curl" ,r-curl)
21317 ("r-digest" ,r-digest)
21318 ("r-jsonlite" ,r-jsonlite)
21319 ("r-openssl" ,r-openssl)
21320 ("r-packrat" ,r-packrat)
21321 ("r-rstudioapi" ,r-rstudioapi)
21322 ("r-yaml" ,r-yaml)))
21323 (home-page "https://github.com/rstudio/rsconnect")
21324 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21326 "This package provides a programmatic deployment interface for RPubs,
21327 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21328 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21329 (license license:gpl2)))
21331 ;; This package includes minified JavaScript files. When upgrading please
21332 ;; check that there are no new minified JavaScript files.
21333 (define-public r-dygraphs
21335 (name "r-dygraphs")
21336 (version "1.1.1.6")
21340 (uri (cran-uri "dygraphs" version))
21343 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21344 (properties `((upstream-name . "dygraphs")))
21345 (build-system r-build-system)
21347 `(#:modules ((guix build utils)
21348 (guix build r-build-system)
21352 (modify-phases %standard-phases
21353 (add-after 'unpack 'process-javascript
21354 (lambda* (#:key inputs #:allow-other-keys)
21355 (with-directory-excursion "inst/htmlwidgets/lib/"
21359 `(("dygraphs/dygraph-combined-dev.js"
21360 "dygraph-combined.js")
21361 (,(assoc-ref inputs "js-jquery")
21362 "jquery/jquery.min.js")
21363 (,(assoc-ref inputs "js-fquarter")
21364 "fquarter/moment-fquarter.min.js"))))
21365 (lambda (sources targets)
21366 (for-each (lambda (source target)
21367 (format #t "Processing ~a --> ~a~%"
21369 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21370 (call-with-output-file target
21372 (dump-port minified port)))))
21373 sources targets))))
21376 `(("uglify-js" ,uglify-js)
21377 ;; They actually use version 1.11.1, but this more recent version
21378 ;; should be just fine.
21382 (uri "https://code.jquery.com/jquery-1.12.4.js")
21385 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21389 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21390 "moment-fquarter/1.0.1/moment-fquarter.js"))
21393 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21395 `(("r-htmltools" ,r-htmltools)
21396 ("r-htmlwidgets" ,r-htmlwidgets)
21397 ("r-magrittr" ,r-magrittr)
21400 (home-page "https://github.com/rstudio/dygraphs")
21401 (synopsis "Interface to Dygraphs interactive time series charting library")
21403 "This package provides an R interface to the dygraphs JavaScript charting
21404 library (a copy of which is included in the package). It provides rich
21405 facilities for charting time-series data in R, including highly configurable
21406 series- and axis-display and interactive features like zoom/pan and
21407 series/point highlighting.")
21408 (license license:expat)))
21410 (define-public r-shinystan
21412 (name "r-shinystan")
21417 (uri (cran-uri "shinystan" version))
21420 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21421 (properties `((upstream-name . "shinystan")))
21422 (build-system r-build-system)
21424 `(("r-bayesplot" ,r-bayesplot)
21425 ("r-colourpicker" ,r-colourpicker)
21427 ("r-dygraphs" ,r-dygraphs)
21428 ("r-ggplot2" ,r-ggplot2)
21429 ("r-gridextra" ,r-gridextra)
21430 ("r-gtools" ,r-gtools)
21431 ("r-markdown" ,r-markdown)
21432 ("r-reshape2" ,r-reshape2)
21433 ("r-rsconnect" ,r-rsconnect)
21434 ("r-rstan" ,r-rstan)
21435 ("r-shiny" ,r-shiny)
21436 ("r-shinyjs" ,r-shinyjs)
21437 ("r-shinythemes" ,r-shinythemes)
21438 ("r-threejs" ,r-threejs)
21439 ("r-xtable" ,r-xtable)
21441 (home-page "https://mc-stan.org/")
21442 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21444 "This package provides a graphical user interface for interactive
21445 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21446 for analyzing a posterior sample. The interface is powered by the Shiny web
21447 application framework and works with the output of MCMC programs written in
21448 any programming language (and has extended functionality for Stan models fit
21449 using the @code{rstan} and @code{rstanarm} packages).")
21450 (license license:gpl3+)))
21452 (define-public r-rstantools
21454 (name "r-rstantools")
21459 (uri (cran-uri "rstantools" version))
21462 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21463 (properties `((upstream-name . "rstantools")))
21464 (build-system r-build-system)
21465 (inputs `(("pandoc" ,pandoc)))
21467 `(("r-desc" ,r-desc)
21469 ("r-rcppparallel" ,r-rcppparallel)))
21471 `(("r-knitr" ,r-knitr)))
21472 (home-page "https://mc-stan.org/rstantools/")
21473 (synopsis "Tools for developing R packages interfacing with Stan")
21475 "This package provides various tools for developers of R packages
21476 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21477 up the required package structure, S3 generics and default methods to unify
21478 function naming across Stan-based R packages, and vignettes with
21479 recommendations for developers.")
21480 (license license:gpl3+)))
21482 (define-public r-loo
21489 (uri (cran-uri "loo" version))
21491 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21492 (properties `((upstream-name . "loo")))
21493 (build-system r-build-system)
21495 `(("pandoc" ,pandoc)
21496 ("pandoc-citeproc" ,pandoc-citeproc)))
21498 `(("r-checkmate" ,r-checkmate)
21499 ("r-matrixstats" ,r-matrixstats)))
21501 `(("r-knitr" ,r-knitr)))
21502 (home-page "https://mc-stan.org/loo/")
21503 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21505 "This package provides an implementation of efficient approximate
21506 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21507 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21508 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21509 procedure for regularizing importance weights. As a byproduct of the
21510 calculations, we also obtain approximate standard errors for estimated
21511 predictive errors and for the comparison of predictive errors between models.
21512 The package also provides methods for using stacking and other model weighting
21513 techniques to average Bayesian predictive distributions.")
21514 (license license:gpl3+)))
21516 (define-public r-rstan
21523 (uri (cran-uri "rstan" version))
21526 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21527 (properties `((upstream-name . "rstan")))
21528 (build-system r-build-system)
21531 (modify-phases %standard-phases
21532 (add-before 'install 'set-timezone
21533 ;; This package is picky about timezones.
21534 (lambda* (#:key inputs #:allow-other-keys)
21535 (setenv "TZ" "UTC+1")
21537 (string-append (assoc-ref inputs "tzdata")
21538 "/share/zoneinfo"))
21541 `(("tzdata" ,tzdata-for-tests)
21543 ("r-knitr" ,r-knitr)))
21546 ("r-ggplot2" ,r-ggplot2)
21547 ("r-gridextra" ,r-gridextra)
21548 ("r-inline" ,r-inline)
21550 ("r-pkgbuild" ,r-pkgbuild)
21552 ("r-rcppeigen" ,r-rcppeigen)
21553 ("r-rcppparallel" ,r-rcppparallel)
21554 ("r-stanheaders" ,r-stanheaders)
21556 ("r-withr" ,r-withr)))
21557 (home-page "https://discourse.mc-stan.org/")
21558 (synopsis "R interface to Stan")
21560 "User-facing R functions are provided to parse, compile, test, estimate,
21561 and analyze Stan models by accessing the header-only Stan library provided by
21562 the StanHeaders package. The Stan project develops a probabilistic
21563 programming language that implements full Bayesian statistical inference via
21564 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21565 approximation, and (optionally penalized) maximum likelihood estimation via
21566 optimization. In all three cases, automatic differentiation is used to
21567 quickly and accurately evaluate gradients without burdening the user with the
21568 need to derive the partial derivatives.")
21569 (license license:gpl3+)))
21571 (define-public r-rstanarm
21573 (name "r-rstanarm")
21578 (uri (cran-uri "rstanarm" version))
21581 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21582 (properties `((upstream-name . "rstanarm")))
21583 (build-system r-build-system)
21585 `(("pandoc" ,pandoc)
21586 ("pandoc-citeproc" ,pandoc-citeproc)))
21588 `(("r-bayesplot" ,r-bayesplot)
21590 ("r-ggplot2" ,r-ggplot2)
21593 ("r-matrix" ,r-matrix)
21596 ("r-rcppeigen" ,r-rcppeigen)
21597 ("r-rcppparallel" ,r-rcppparallel)
21598 ("r-rstan" ,r-rstan)
21599 ("r-rstantools" ,r-rstantools)
21600 ("r-shinystan" ,r-shinystan)
21601 ("r-stanheaders" ,r-stanheaders)
21602 ("r-survival" ,r-survival)))
21604 `(("r-knitr" ,r-knitr)))
21605 (home-page "https://mc-stan.org/rstanarm/")
21606 (synopsis "Bayesian applied regression modeling via Stan")
21608 "This package estimates previously compiled regression models using the
21609 @code{rstan} package, which provides the R interface to the Stan C++ library
21610 for Bayesian estimation. Users specify models via the customary R syntax with
21611 a formula and @code{data.frame} plus some additional arguments for priors.")
21612 (license license:gpl3+)))
21614 (define-public r-kendall
21621 (uri (cran-uri "Kendall" version))
21624 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21625 (properties `((upstream-name . "Kendall")))
21626 (build-system r-build-system)
21628 `(("r-boot" ,r-boot)))
21630 `(("gfortran" ,gfortran)))
21631 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21632 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21634 "This package computes the Kendall rank correlation and Mann-Kendall
21636 (license license:gpl2+)))
21638 (define-public r-zyp
21641 (version "0.10-1.1")
21645 (uri (cran-uri "zyp" version))
21648 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21649 (properties `((upstream-name . "zyp")))
21650 (build-system r-build-system)
21652 `(("r-kendall" ,r-kendall)))
21653 (home-page "https://cran.r-project.org/web/packages/zyp/")
21654 (synopsis "Zhang + Yue-Pilon Trends Package")
21656 "This package contains an efficient implementation of Sen's slope
21657 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21658 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21660 (license license:lgpl2.1)))
21662 (define-public r-rlinsolve
21664 (name "r-rlinsolve")
21669 (uri (cran-uri "Rlinsolve" version))
21672 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21673 (properties `((upstream-name . "Rlinsolve")))
21674 (build-system r-build-system)
21676 `(("r-matrix" ,r-matrix)
21678 ("r-rcpparmadillo" ,r-rcpparmadillo)
21679 ("r-rdpack" ,r-rdpack)))
21680 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21681 (synopsis "Iterative solvers for (sparse) linear system of equations")
21683 "Solving a system of linear equations is one of the most fundamental
21684 computational problems for many fields of mathematical studies, such as
21685 regression problems from statistics or numerical partial differential
21686 equations. This package provides basic stationary iterative solvers such as
21687 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21688 Nonstationary, also known as Krylov subspace methods are also provided.
21689 Sparse matrix computation is also supported in that solving large and sparse
21690 linear systems can be manageable using the @code{Matrix} package along with
21691 @code{RcppArmadillo}.")
21692 (license license:gpl3+)))
21694 (define-public r-zvcv
21701 (uri (cran-uri "ZVCV" version))
21704 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21705 (properties `((upstream-name . "ZVCV")))
21706 (build-system r-build-system)
21708 `(("r-abind" ,r-abind)
21710 ("r-dplyr" ,r-dplyr)
21711 ("r-glmnet" ,r-glmnet)
21712 ("r-magrittr" ,r-magrittr)
21713 ("r-mvtnorm" ,r-mvtnorm)
21715 ("r-rcpparmadillo" ,r-rcpparmadillo)
21716 ("r-rlinsolve" ,r-rlinsolve)))
21717 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21718 (synopsis "Zero-Variance Control Variates")
21720 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21721 to reduce the variance of Monte Carlo estimators of expectations using the
21722 derivatives of the log target. Once the derivatives are available, the only
21723 additional computational effort is in solving a linear regression problem.
21724 This method has been extended to higher dimensions using regularisation. This
21725 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21726 samples, derivatives and function evaluations are available. Additional
21727 functions for applying ZV-CV to two estimators for the normalising constant of
21728 the posterior distribution in Bayesian statistics are also supplied.")
21729 (license license:gpl2+)))
21731 (define-public r-ztype
21738 (uri (cran-uri "ztype" version))
21741 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21742 (properties `((upstream-name . "ztype")))
21743 (build-system r-build-system)
21745 `(("r-assertthat" ,r-assertthat)
21746 ("r-dplyr" ,r-dplyr)
21747 ("r-ggplot2" ,r-ggplot2)
21748 ("r-lubridate" ,r-lubridate)
21749 ("r-magrittr" ,r-magrittr)
21750 ("r-rvest" ,r-rvest)
21751 ("r-stringr" ,r-stringr)))
21752 (home-page "https://cran.r-project.org/web/packages/ztype/")
21753 (synopsis "Run a Ztype game loaded with R functions")
21755 "How fast can you type R functions on your keyboard? Find out by running
21756 a @code{zty.pe} game: export R functions as instructions to type to destroy
21757 opponents' vessels.")
21758 (license license:gpl3)))
21760 (define-public r-zseq
21767 (uri (cran-uri "Zseq" version))
21770 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21771 (properties `((upstream-name . "Zseq")))
21772 (build-system r-build-system)
21774 `(("r-gmp" ,r-gmp)))
21775 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21776 (synopsis "Integer sequence generator")
21778 "This package generates well-known integer sequences. The @code{gmp}
21779 package is adopted for computing with arbitrarily large numbers. Every
21780 function has a hyperlink to its corresponding item in the @dfn{On-Line
21781 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21782 (license license:gpl3+)))
21784 (define-public r-isoband
21791 (uri (cran-uri "isoband" version))
21794 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21795 (properties `((upstream-name . "isoband")))
21796 (build-system r-build-system)
21798 `(("r-testthat" ,r-testthat)))
21800 `(("r-knitr" ,r-knitr)))
21801 (home-page "https://github.com/wilkelab/isoband")
21802 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21804 "This package provides a fast C++ implementation to generate contour
21805 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21806 containing elevation data.")
21807 (license license:expat)))
21809 (define-public r-ppcor
21816 (uri (cran-uri "ppcor" version))
21819 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21820 (properties `((upstream-name . "ppcor")))
21821 (build-system r-build-system)
21823 `(("r-mass" ,r-mass)))
21824 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21825 (synopsis "Partial and semi-partial correlation")
21827 "This package provides users not only with a function to readily
21828 calculate the higher-order partial and semi-partial correlations but also with
21829 statistics and p-values of the correlation coefficients.")
21830 (license license:gpl2)))
21832 (define-public r-hrbrthemes
21834 (name "r-hrbrthemes")
21839 (uri (cran-uri "hrbrthemes" version))
21841 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21842 (properties `((upstream-name . "hrbrthemes")))
21843 (build-system r-build-system)
21845 `(("r-extrafont" ,r-extrafont)
21846 ("r-gdtools" ,r-gdtools)
21847 ("r-ggplot2" ,r-ggplot2)
21848 ("r-htmltools" ,r-htmltools)
21849 ("r-knitr" ,r-knitr)
21850 ("r-magrittr" ,r-magrittr)
21851 ("r-rmarkdown" ,r-rmarkdown)
21852 ("r-scales" ,r-scales)))
21854 `(("r-knitr" ,r-knitr)))
21855 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21856 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21858 "This package provides a compilation of extra @code{ggplot2} themes,
21859 scales and utilities, including a spell check function for plot label fields
21860 and an overall emphasis on typography.")
21861 (license license:expat)))
21863 (define-public r-crochet
21870 (uri (cran-uri "crochet" version))
21873 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21874 (build-system r-build-system)
21876 `(("r-knitr" ,r-knitr)))
21877 (home-page "https://github.com/agrueneberg/crochet")
21878 (synopsis "Implementation Helper for Matrix-Like Types")
21880 "Functions to help implement the extraction / subsetting / indexing
21881 function @code{[} and replacement function @code{[<-} of custom matrix-like
21882 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21883 as possible (with tests to prove it).")
21884 (license license:expat)))
21886 (define-public r-boa
21889 (version "1.1.8-2")
21893 (uri (cran-uri "boa" version))
21896 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21897 (properties `((upstream-name . "boa")))
21898 (build-system r-build-system)
21899 (home-page "http://www.jstatsoft.org/v21/i11")
21900 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21902 "This package provides a menu-driven program and library of functions for
21903 carrying out convergence diagnostics and statistical and graphical analysis of
21904 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21905 (license license:gpl2+)))
21907 (define-public r-httpcode
21909 (name "r-httpcode")
21913 (uri (cran-uri "httpcode" version))
21916 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21917 (build-system r-build-system)
21918 (home-page "https://github.com/sckott/httpcode")
21919 (synopsis "HTTP status code helper")
21920 (description "@code{httpcode} provides functionality for finding and
21921 explaining the meaning of @code{HTTP} status codes. Functions are included for
21922 searching for codes by full or partial number, by message, and to get
21923 appropriate dog and cat images for many status codes.")
21924 (license license:expat)))
21926 (define-public r-latex2exp
21928 (name "r-latex2exp")
21932 (uri (cran-uri "latex2exp" version))
21935 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21936 (build-system r-build-system)
21938 `(("r-stringr" ,r-stringr)
21939 ("r-magrittr", r-magrittr)))
21940 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21941 (synopsis "Use LaTeX expressions in plots")
21942 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21943 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21944 rendered as text, axis labels, etc. throughout R's plotting system.")
21945 (license license:expat)))
21947 (define-public r-oai
21953 (uri (cran-uri "oai" version))
21956 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21957 (build-system r-build-system)
21959 `(("r-xml2" ,r-xml2)
21962 ("r-stringr" ,r-stringr)
21963 ("r-tibble" ,r-tibble)))
21964 (home-page "https://github.com/ropensci/oai/")
21965 (synopsis "General purpose OAI-PMH services client")
21966 (description "@code{oai} provides a general purpose client to work with
21967 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21968 service. Functions are provided to work with the OAI-PMH verbs:
21969 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21970 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21971 (license license:expat)))
21973 (define-public r-argon2
21980 (uri (cran-uri "argon2" version))
21983 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21984 (properties `((upstream-name . "argon2")))
21985 (build-system r-build-system)
21986 (home-page "https://github.com/wrathematics/argon2")
21987 (synopsis "Secure password hashing based on the argon2 algorithm")
21989 "This package provides utilities for secure password hashing via the
21990 argon2 algorithm.")
21991 (license license:bsd-2)))
21993 (define-public r-getpass
22000 (uri (cran-uri "getPass" version))
22003 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
22004 (properties `((upstream-name . "getPass")))
22005 (build-system r-build-system)
22007 `(("r-rstudioapi" ,r-rstudioapi)))
22008 (home-page "https://github.com/wrathematics/getPass")
22009 (synopsis "Masked user input")
22011 "This package provides a micro-package for reading \"passwords\", i.e.
22012 reading user input with masking, so that the input is not displayed as it is
22013 typed. Currently, RStudio, the command line (every OS), and any platform
22014 where tcltk is present are supported.")
22015 (license license:bsd-2)))
22017 (define-public r-remoter
22024 (uri (cran-uri "remoter" version))
22027 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
22028 (properties `((upstream-name . "remoter")))
22029 (build-system r-build-system)
22031 `(("r-argon2" ,r-argon2)
22032 ("r-getpass" ,r-getpass)
22033 ("r-pbdzmq" ,r-pbdzmq)
22035 (home-page "https://github.com/RBigData/remoter")
22036 (synopsis "Control a remote R session from a local one")
22038 "This package provides a set of utilities for client/server computing
22039 with R, controlling a remote R session (the server) from a local one (the
22041 (license license:bsd-2)))
22043 (define-public r-asd
22050 (uri (cran-uri "asd" version))
22053 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
22054 (properties `((upstream-name . "asd")))
22055 (build-system r-build-system)
22057 `(("r-mvtnorm" ,r-mvtnorm)))
22058 (home-page "https://cran.r-project.org/web/packages/asd")
22059 (synopsis "Simulations for Adaptive Seamless Designs")
22061 "This package provdes means to run simulations for adaptive seamless
22062 designs with and without early outcomes for treatment selection and
22063 subpopulation type designs.")
22064 (license license:gpl3)))
22066 (define-public r-nbconvertr
22068 (name "r-nbconvertr")
22073 (uri (cran-uri "nbconvertR" version))
22076 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
22077 (properties `((upstream-name . "nbconvertR")))
22078 (build-system r-build-system)
22080 `(("jupyter" ,python-nbconvert)
22081 ("pandoc" ,pandoc)))
22082 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
22083 (synopsis "Vignette engine wrapping Jupyter notebooks")
22085 "This package calls the Jupyter script @code{nbconvert} to create
22086 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
22087 containing rich text, code, and its output. Code cells can be edited and
22088 evaluated interactively.")
22089 (license license:gpl3)))
22091 (define-public r-bridgesampling
22093 (name "r-bridgesampling")
22098 (uri (cran-uri "bridgesampling" version))
22101 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
22103 `((upstream-name . "bridgesampling")))
22104 (build-system r-build-system)
22106 `(("r-brobdingnag" ,r-brobdingnag)
22108 ("r-matrix" ,r-matrix)
22109 ("r-mvtnorm" ,r-mvtnorm)
22110 ("r-scales" ,r-scales)
22111 ("r-stringr" ,r-stringr)))
22113 `(("r-knitr" ,r-knitr)))
22114 (home-page "https://github.com/quentingronau/bridgesampling")
22115 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
22117 "This package provides functions for estimating marginal likelihoods,
22118 Bayes factors, posterior model probabilities, and normalizing constants in
22119 general, via different versions of bridge sampling.")
22120 (license license:gpl2+)))
22122 (define-public r-tea
22129 (uri (cran-uri "tea" version))
22132 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
22134 `((upstream-name . "tea")))
22135 (build-system r-build-system)
22137 `(("r-matrix" ,r-matrix)))
22138 (home-page "https://cran.r-project.org/web/packages/tea/")
22139 (synopsis "Threshold estimation approaches")
22141 "This package provides different approaches for selecting the threshold
22142 in generalized Pareto distributions. Most of them are based on minimizing the
22143 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
22144 Others are heuristically motivated by searching for stable sample paths, i.e.
22145 a nearly constant region of the tail index estimator with respect to k, which
22146 is the number of data in the tail. The third class is motivated by graphical
22147 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
22148 is also implemented here.")
22149 (license license:gpl3)))
22151 (define-public r-awsmethods
22153 (name "r-awsmethods")
22158 (uri (cran-uri "awsMethods" version))
22161 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
22163 `((upstream-name . "awsMethods")))
22164 (build-system r-build-system)
22165 (home-page "http://www.wias-berlin.de/software/imaging/")
22166 (synopsis "Class and methods definitions")
22168 "This package defines the generic method @code{extract} and provides
22169 @code{openMP} support as needed in several packages like
22170 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
22171 (license license:gpl2+)))
22173 (define-public r-aws
22180 (uri (cran-uri "aws" version))
22183 "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5"))))
22185 `((upstream-name . "aws")))
22186 (build-system r-build-system)
22188 `(("r-awsmethods" ,r-awsmethods)
22191 `(("gfortran" ,gfortran)))
22192 (home-page "https://cran.r-project.org/web/packages/aws/")
22193 (synopsis "Adaptive weights smoothing")
22195 "This package provides a collection of R-functions implementing adaptive
22196 smoothing procedures in 1D, 2D and 3D. This includes the
22197 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22198 Confidence Intervals} (ICI), variational approaches, and a non-local means
22200 (license license:gpl2+)))
22202 (define-public r-sgloptim
22204 (name "r-sgloptim")
22209 (uri (cran-uri "sglOptim" version))
22212 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22214 `((upstream-name . "sglOptim")))
22215 (build-system r-build-system)
22218 ("r-doparallel" ,r-doparallel)
22219 ("r-foreach" ,r-foreach)
22220 ("r-matrix" ,r-matrix)
22222 ("r-rcpparmadillo" ,r-rcpparmadillo)
22223 ("r-rcppprogress" ,r-rcppprogress)))
22225 `(("r-knitr" ,r-knitr)))
22226 (home-page "https://github.com/nielsrhansen/sglOptim")
22227 (synopsis "Generic sparse group Lasso solver")
22229 "This package provides a fast generic solver for sparse group lasso
22230 optimization problems. The loss (objective) function must be defined in a C++
22231 module. The optimization problem is solved using a coordinate gradient
22232 descent algorithm. Convergence of the algorithm is established and the
22233 algorithm is applicable to a broad class of loss functions. Use of parallel
22234 computing for cross validation and subsampling is supported through the
22235 @code{foreach} and @code{doParallel} packages.")
22236 (license license:gpl2+)))
22238 (define-public r-grouped
22245 (uri (cran-uri "grouped" version))
22248 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22250 `((upstream-name . "grouped")))
22251 (build-system r-build-system)
22253 `(("r-mass" ,r-mass)))
22254 (home-page "https://cran.r-project.org/web/packages/grouped/")
22255 (synopsis "Regression analysis of grouped and coarse data")
22257 "This package provides regression models for grouped and coarse data,
22258 under the coarsened at random assumption.")
22259 (license license:gpl2+)))
22261 (define-public r-stam
22268 (uri (cran-uri "stam" version))
22271 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22273 `((upstream-name . "stam")))
22274 (build-system r-build-system)
22278 (home-page "https://cran.r-project.org/web/packages/stam")
22279 (synopsis "Spatio-temporal analysis and modelling")
22281 "This package provides various methods to conduct Spatio-Temporal
22282 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22283 Inferred Spatio-Temporal Modelling.")
22284 (license license:gpl2+)))
22286 (define-public r-dcv
22293 (uri (cran-uri "dcv" version))
22296 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22298 `((upstream-name . "dcv")))
22299 (build-system r-build-system)
22301 `(("r-lmtest" ,r-lmtest)))
22302 (home-page "https://cran.r-project.org/web/packages/dcv/")
22303 (synopsis "Conventional cross-validation statistics for climate-growth model")
22305 "This package performs several conventional cross-validation statistical
22306 methods for climate-growth model in the climate reconstruction from tree
22307 rings, including Sign Test statistic, Reduction of Error statistic, Product
22308 Mean Test, Durbin-Watson statistic etc.")
22309 (license license:gpl2)))
22311 (define-public r-rcdd
22318 (uri (cran-uri "rcdd" version))
22321 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22323 `((upstream-name . "rcdd")))
22324 (build-system r-build-system)
22327 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22328 (synopsis "Computational geometry")
22330 "This package converts back and forth between two representations of a
22331 convex polytope: as solution of a set of linear equalities and inequalities
22332 and as convex hull of set of points and rays. Also does linear programming
22333 and redundant generator elimination. All functions can use exact
22334 infinite-precision rational arithmetic.")
22335 (license license:gpl2)))
22337 (define-public r-rxnat
22344 (uri (cran-uri "Rxnat" version))
22347 "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb"))))
22349 `((upstream-name . "Rxnat")))
22350 (build-system r-build-system)
22352 `(("r-dplyr" ,r-dplyr)
22354 ("r-rcurl" ,r-rcurl)))
22356 `(("r-knitr" ,r-knitr)))
22357 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22358 (synopsis "Queries and extracts images from neuroimaging datasets")
22360 "This package allows communication with the Extensible Neuroimaging
22361 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22363 (license license:gpl2)))
22365 (define-public r-rserve
22372 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22373 version ".tar.gz"))
22376 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22377 (build-system r-build-system)
22379 `(("r-checkmate" ,r-checkmate)
22381 ("r-jsonlite" ,r-jsonlite)
22382 ("r-knitr" ,r-knitr)
22385 ("r-uuid" ,r-uuid)))
22387 `(("openssl" ,openssl)
22389 (home-page "https://github.com/s-u/Rserve")
22391 "Server providing access to R from many languages and systems")
22393 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22394 binary requests to be sent to R. Every connection has a separate workspace
22395 and working directory. Client-side implementations are available for popular
22396 languages such as C/C++ and Java, allowing any application to use facilities
22397 of R without the need of linking to R code. Rserve supports remote
22398 connection, user authentication and file transfer. A simple R client is
22399 included in this package as well.")
22400 (license license:gpl2)))
22402 (define-public r-brms
22409 (uri (cran-uri "brms" version))
22412 "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69"))))
22413 (properties `((upstream-name . "brms")))
22414 (build-system r-build-system)
22416 `(("r-abind" ,r-abind)
22417 ("r-backports" ,r-backports)
22418 ("r-bayesplot" ,r-bayesplot)
22419 ("r-bridgesampling" ,r-bridgesampling)
22421 ("r-future" ,r-future)
22422 ("r-ggplot2" ,r-ggplot2)
22425 ("r-matrix" ,r-matrix)
22426 ("r-matrixstats" ,r-matrixstats)
22428 ("r-nleqslv" ,r-nleqslv)
22431 ("r-rstan" ,r-rstan)
22432 ("r-rstantools" ,r-rstantools)
22433 ("r-shinystan" ,r-shinystan)))
22434 (native-inputs `(("r-knitr" ,r-knitr)))
22436 "https://github.com/paul-buerkner/brms")
22438 "Bayesian Regression Models using 'Stan'")
22440 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22441 using 'Stan' for full Bayesian inference. A wide range of distributions and
22442 link functions are supported, allowing users to fit -- among others -- linear,
22443 robust linear, count data, survival, response times, ordinal, zero-inflated,
22444 hurdle, and even self-defined mixture models all in a multilevel context.
22445 Further modeling options include non-linear and smooth terms, auto-correlation
22446 structures, censored data, meta-analytic standard errors, and quite a few
22447 more. In addition, all parameters of the response distribution can be
22448 predicted in order to perform distributional regression. Prior specifications
22449 are flexible and explicitly encourage users to apply prior distributions that
22450 actually reflect their beliefs. Model fit can easily be assessed and compared
22451 with posterior predictive checks and leave-one-out cross-validation.")
22452 (license license:gpl2)))
22454 (define-public r-mstate
22461 (uri (cran-uri "mstate" version))
22464 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22465 (properties `((upstream-name . "mstate")))
22466 (build-system r-build-system)
22468 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22469 ("r-survival" ,r-survival)))
22471 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22473 "Data Preparation, Estimation and Prediction in Multi-State Models")
22475 "Contains functions for data preparation, descriptives, hazard estimation
22476 and prediction with Aalen-Johansen or simulation in competing risks and
22477 multi-state models.")
22478 (license license:gpl2+)))
22480 (define-public r-scatterpie
22482 (name "r-scatterpie")
22487 (uri (cran-uri "scatterpie" version))
22490 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22491 (properties `((upstream-name . "scatterpie")))
22492 (build-system r-build-system)
22494 `(("r-ggforce" ,r-ggforce)
22495 ("r-ggplot2" ,r-ggplot2)
22496 ("r-rlang" ,r-rlang)
22497 ("r-rvcheck" ,r-rvcheck)
22498 ("r-tidyr" ,r-tidyr)))
22500 `(("r-knitr" ,r-knitr)))
22501 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22502 (synopsis "Scatter pie plot")
22504 "This package creates scatterpie plots, especially useful for plotting
22506 (license license:artistic2.0)))
22508 (define-public r-boruta
22515 (uri (cran-uri "Boruta" version))
22518 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22519 (properties `((upstream-name . "Boruta")))
22520 (build-system r-build-system)
22521 (propagated-inputs `(("r-ranger" ,r-ranger)))
22522 (home-page "https://gitlab.com/mbq/Boruta/")
22523 (synopsis "Wrapper algorithm for all relevant feature selection")
22525 "This package provides an all relevant feature selection wrapper
22526 algorithm. It finds relevant features by comparing original attributes'
22527 importance with importance achievable at random, estimated using their
22528 permuted copies (shadows).")
22529 (license license:gpl2+)))
22531 (define-public r-directlabels
22533 (name "r-directlabels")
22534 (version "2020.6.17")
22538 (uri (cran-uri "directlabels" version))
22541 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22542 (build-system r-build-system)
22544 `(("r-quadprog" ,r-quadprog)))
22546 `(("r-knitr" ,r-knitr)))
22547 (home-page "http://directlabels.r-forge.r-project.org/")
22548 (synopsis "Direct labels for multicolor plots")
22550 "This package provides an extensible framework for automatically placing
22551 direct labels onto multicolor plots. Label positions are described using
22552 positioning methods that can be re-used across several different plots. There
22553 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22554 inferring an appropriate positioning method.")
22555 (license license:gpl3)))
22557 (define-public r-lsd
22564 (uri (cran-uri "LSD" version))
22566 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22567 (properties `((upstream-name . "LSD")))
22568 (build-system r-build-system)
22569 (home-page "https://cran.r-project.org/web/packages/LSD/")
22570 (synopsis "Lots of superior depictions tool creates colorful plots")
22572 "This package creates lots of colorful plots in a multitude of variations.
22573 Try a demo of the LSD by running @code{demotour()}.")
22575 (license (list license:gpl2 license:gpl3))))
22577 (define-public r-fourcseq
22579 (name "r-fourcseq")
22584 (uri (bioconductor-uri "FourCSeq" version))
22586 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
22587 (properties `((upstream-name . "FourCSeq")))
22588 (build-system r-build-system)
22590 `(("r-biobase" ,r-biobase)
22591 ("r-biostrings" ,r-biostrings)
22592 ("r-deseq2" ,r-deseq2)
22594 ("r-genomicalignments" ,r-genomicalignments)
22595 ("r-genomicranges" ,r-genomicranges)
22596 ("r-ggbio" ,r-ggbio)
22597 ("r-ggplot2" ,r-ggplot2)
22598 ("r-gtools" ,r-gtools)
22600 ("r-matrix" ,r-matrix)
22601 ("r-reshape2" ,r-reshape2)
22602 ("r-rsamtools" ,r-rsamtools)
22603 ("r-rtracklayer" ,r-rtracklayer)
22604 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22606 `(("r-knitr" ,r-knitr)))
22608 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22609 (synopsis "Analysis of multiplexed 4C sequencing data")
22611 "This package is an R package dedicated to the analysis of (multiplexed)
22612 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22613 interactions between DNA elements and identify differential interactions
22614 between conditions. The statistical analysis in R starts with individual bam
22615 files for each sample as inputs. To obtain these files, the package contains
22616 a Python script to demultiplex libraries and trim off primer sequences. With
22617 a standard alignment software the required bam files can be then be
22619 (license license:gpl3+)))
22621 (define-public r-phylogram
22623 (name "r-phylogram")
22628 (uri (cran-uri "phylogram" version))
22630 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22631 (properties `((upstream-name . "phylogram")))
22632 (build-system r-build-system)
22633 (propagated-inputs `(("r-ape" ,r-ape)))
22634 (home-page "https://github.com/ropensci/phylogram/")
22635 (synopsis "Dendrograms for evolutionary analysis")
22637 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22638 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22639 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22640 as well as several tools for command-line tree manipulation and import/export
22641 via Newick parenthetic text. This improves accessibility to the comprehensive
22642 range of object-specific analytical and tree-visualization functions found
22643 across a wide array of bioinformatic R packages.")
22644 (license license:gpl3)))
22646 (define-public r-kmer
22653 (uri (cran-uri "kmer" version))
22655 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22656 (properties `((upstream-name . "kmer")))
22657 (build-system r-build-system)
22659 `(("r-openssl" ,r-openssl)
22660 ("r-phylogram" ,r-phylogram)
22661 ("r-rcpp" ,r-rcpp)))
22662 (home-page "https://github.com/shaunpwilkinson/kmer/")
22663 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22665 "@code{r-kmer} is an R package for rapidly computing distance matrices
22666 and clustering large sequence datasets using fast alignment-free k-mer
22667 counting and recursive k-means partitioning.")
22668 (license license:gpl3)))
22670 (define-public r-hardhat
22677 (uri (cran-uri "hardhat" version))
22680 "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
22681 (properties `((upstream-name . "hardhat")))
22682 (build-system r-build-system)
22684 `(("r-glue" ,r-glue)
22685 ("r-rlang" ,r-rlang)
22686 ("r-tibble" ,r-tibble)
22687 ("r-vctrs" ,r-vctrs)))
22689 `(("r-knitr" ,r-knitr)))
22690 (home-page "https://github.com/tidymodels/hardhat")
22691 (synopsis "Construct modeling packages")
22693 "Building modeling packages is hard. A large amount of effort generally
22694 goes into providing an implementation for a new method that is efficient,
22695 fast, and correct, but often less emphasis is put on the user interface. A
22696 good interface requires specialized knowledge about S3 methods and formulas,
22697 which the average package developer might not have. The goal of
22698 @code{hardhat} is to reduce the burden around building new modeling packages
22699 by providing functionality for preprocessing, predicting, and validating
22701 (license license:expat)))
22703 (define-public r-shapforxgboost
22705 (name "r-shapforxgboost")
22710 (uri (cran-uri "SHAPforxgboost" version))
22713 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22715 `((upstream-name . "SHAPforxgboost")))
22716 (build-system r-build-system)
22718 `(("r-bbmisc" ,r-bbmisc)
22719 ("r-data-table" ,r-data-table)
22720 ("r-ggextra" ,r-ggextra)
22721 ("r-ggforce" ,r-ggforce)
22722 ("r-ggplot2" ,r-ggplot2)
22723 ("r-ggpubr" ,r-ggpubr)
22724 ("r-rcolorbrewer" ,r-rcolorbrewer)
22725 ("r-xgboost" ,r-xgboost)))
22726 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22727 (synopsis "SHAP Plots for XGBoost")
22729 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22730 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22731 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22732 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22734 (license license:expat)))
22736 (define-public r-rismed
22743 (uri (cran-uri "RISmed" version))
22746 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22747 (properties `((upstream-name . "RISmed")))
22748 (build-system r-build-system)
22749 (home-page "https://cran.r-project.org/web/packages/RISmed")
22750 (synopsis "Download content from NCBI databases")
22752 "This package provides a set of tools to extract bibliographic
22753 content from the National Center for Biotechnology Information (NCBI)
22754 databases, including PubMed. The name RISmed is a portmanteau of
22755 RIS (for Research Information Systems, a common tag format for
22756 bibliographic data) and PubMed.")
22757 (license license:gpl2+)))
22759 (define-public r-semver
22766 (uri (cran-uri "semver" version))
22769 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22770 (properties `((upstream-name . "semver")))
22771 (build-system r-build-system)
22773 `(("r-assertthat" ,r-assertthat)
22774 ("r-rcpp" ,r-rcpp)))
22775 (native-inputs `(("r-knitr" ,r-knitr)))
22776 (home-page "https://github.com/johndharrison/semver")
22777 (synopsis "Parser for Semantic Versioning 2.0.0")
22779 "This package provides tools and functions for parsing, rendering and
22780 operating on semantic version strings. Semantic versioning is a simple set of
22781 rules and requirements that dictate how version numbers are assigned and
22782 incremented as outlined at @url{http://semver.org}.")
22783 (license license:expat)))
22785 (define-public r-binman
22792 (uri (cran-uri "binman" version))
22795 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22796 (properties `((upstream-name . "binman")))
22797 (build-system r-build-system)
22799 `(("r-assertthat" ,r-assertthat)
22801 ("r-jsonlite" ,r-jsonlite)
22802 ("r-rappdirs" ,r-rappdirs)
22803 ("r-semver" ,r-semver)
22805 ("r-yaml" ,r-yaml)))
22806 (native-inputs `(("r-knitr" ,r-knitr)))
22807 (home-page "https://github.com/ropensci/binman")
22808 (synopsis "Binary download manager")
22810 "This package provides tools and functions for managing the download of
22811 binary files. Binary repositories are defined in the YAML format. Defining
22812 new pre-download, download and post-download templates allow additional
22813 repositories to be added.")
22814 (license license:expat)))
22816 (define-public r-wdman
22823 (uri (cran-uri "wdman" version))
22826 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22827 (properties `((upstream-name . "wdman")))
22828 (build-system r-build-system)
22830 `(("r-assertthat" ,r-assertthat)
22831 ("r-binman" ,r-binman)
22832 ("r-processx" ,r-processx)
22833 ("r-semver" ,r-semver)
22834 ("r-yaml" ,r-yaml)))
22835 (native-inputs `(("r-knitr" ,r-knitr)))
22836 (home-page "https://docs.ropensci.org/wdman/")
22837 (synopsis "Webdriver/Selenium binary manager")
22839 "There are a number of binary files associated with the
22840 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22841 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22842 @url{https://github.com/mozilla/geckodriver},
22843 @url{http://phantomjs.org/download.html}, and
22844 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22845 more information). This package provides functions to download these binaries
22846 and to manage processes involving them.")
22847 (license license:expat)))
22849 (define-public r-rselenium
22851 (name "r-rselenium")
22856 (uri (cran-uri "RSelenium" version))
22859 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22860 (properties `((upstream-name . "RSelenium")))
22861 (build-system r-build-system)
22863 `(("r-binman" ,r-binman)
22864 ("r-catools" ,r-catools)
22866 ("r-openssl" ,r-openssl)
22867 ("r-wdman" ,r-wdman)
22869 (native-inputs `(("r-knitr" ,r-knitr)))
22870 (home-page "https://docs.ropensci.org/RSelenium/")
22871 (synopsis "R bindings for Selenium WebDriver")
22873 "This package provides a set of R bindings for the Selenium 2.0
22874 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22875 information) using the @code{JsonWireProtocol} (see
22876 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22877 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22878 a user would either locally or on a remote machine using the Selenium server
22879 it marks a leap forward in terms of web browser automation. Selenium
22880 automates web browsers (commonly referred to as browsers). Using RSelenium
22881 you can automate browsers locally or remotely.")
22882 (license license:agpl3+)))
22884 (define-public r-conquer
22891 (uri (cran-uri "conquer" version))
22894 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
22895 (properties `((upstream-name . "conquer")))
22896 (build-system r-build-system)
22898 `(("r-matrix" ,r-matrix)
22899 ("r-matrixstats" ,r-matrixstats)
22901 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22902 (home-page "https://github.com/XiaoouPan/conquer")
22903 (synopsis "Convolution-type smoothed quantile regression")
22905 "This package provides fast and accurate convolution-type smoothed
22906 quantile regression, implemented using Barzilai-Borwein gradient descent with
22907 a Huber regression warm start. Confidence intervals for regression
22908 coefficients are constructed using multiplier bootstrap.")
22909 (license license:gpl3)))
22911 (define-public r-fastshap
22913 (name "r-fastshap")
22918 (uri (cran-uri "fastshap" version))
22921 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22922 (properties `((upstream-name . "fastshap")))
22923 (build-system r-build-system)
22925 `(("r-abind" ,r-abind)
22926 ("r-ggplot2" ,r-ggplot2)
22927 ("r-gridextra" ,r-gridextra)
22928 ("r-matrixstats" ,r-matrixstats)
22931 ("r-rcpparmadillo" ,r-rcpparmadillo)
22932 ("r-tibble" ,r-tibble)))
22933 (home-page "https://github.com/bgreenwell/fastshap")
22934 (synopsis "Fast approximate Shapley values")
22936 "This package computes fast (relative to other implementations)
22937 approximate Shapley values for any supervised learning model. Shapley values
22938 help to explain the predictions from any black box model using ideas from game
22939 theory; see @url{Strumbel and Kononenko (2014),
22940 doi.org/10.1007/s10115-013-0679-x} for details.")
22941 (license license:gpl2+)))
22943 (define-public r-metrics
22950 (uri (cran-uri "Metrics" version))
22953 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22954 (properties `((upstream-name . "Metrics")))
22955 (build-system r-build-system)
22956 (home-page "https://github.com/mfrasco/Metrics")
22957 (synopsis "Evaluation metrics for machine learning")
22959 "This package provides an implementation of evaluation metrics in R that
22960 are commonly used in supervised machine learning. It implements metrics for
22961 regression, time series, binary classification, classification, and
22962 information retrieval problems. It has zero dependencies and a consistent,
22963 simple interface for all functions.")
22964 (license license:bsd-3)))
22966 (define-public r-iml
22973 (uri (cran-uri "iml" version))
22976 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22977 (properties `((upstream-name . "iml")))
22978 (build-system r-build-system)
22980 `(("r-checkmate" ,r-checkmate)
22981 ("r-data-table" ,r-data-table)
22982 ("r-formula" ,r-formula)
22983 ("r-future" ,r-future)
22984 ("r-future-apply" ,r-future-apply)
22985 ("r-ggplot2" ,r-ggplot2)
22986 ("r-gridextra" ,r-gridextra)
22987 ("r-metrics" ,r-metrics)
22988 ("r-prediction" ,r-prediction)
22990 (native-inputs `(("r-knitr" ,r-knitr)))
22991 (home-page "https://github.com/christophM/iml")
22992 (synopsis "Interpretable machine learning")
22994 "This package provides interpretability methods to analyze the behavior
22995 and predictions of any machine learning model. Implemented methods are:
22998 @item Feature importance described by Fisher et al. (2018),
22999 @item accumulated local effects plots described by Apley (2018),
23000 @item partial dependence plots described by Friedman (2001),
23001 @item individual conditional expectation ('ice') plots described by Goldstein
23002 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
23003 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
23004 @item the Shapley Value described by Strumbelj et. al (2014)
23005 @url{https://doi.org/10.1007/s10115-013-0679-x},
23006 @item feature interactions described by Friedman et. al
23007 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
23010 (license license:expat)))
23012 (define-public r-goftest
23019 (uri (cran-uri "goftest" version))
23022 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
23023 (properties `((upstream-name . "goftest")))
23024 (build-system r-build-system)
23025 (home-page "https://github.com/baddstats/goftest")
23026 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
23028 "This package provides Cramer-Von Mises and Anderson-Darling tests of
23029 goodness-of-fit for continuous univariate distributions, using efficient
23031 (license license:gpl2+)))
23033 (define-public r-tensor
23040 (uri (cran-uri "tensor" version))
23043 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
23044 (properties `((upstream-name . "tensor")))
23045 (build-system r-build-system)
23046 (home-page "https://cran.r-project.org/web/packages/tensor/")
23047 (synopsis "Tensor product of arrays")
23049 "The tensor product of two arrays is notionally an outer product of the
23050 arrays collapsed in specific extents by summing along the appropriate
23051 diagonals. This package allows you to compute the tensor product of arrays.")
23052 (license license:gpl2+)))
23054 (define-public r-spatstat-utils
23056 (name "r-spatstat-utils")
23061 (uri (cran-uri "spatstat.utils" version))
23064 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
23066 `((upstream-name . "spatstat.utils")))
23067 (build-system r-build-system)
23068 (home-page "http://www.spatstat.org")
23069 (synopsis "Utility functions for spatstat")
23071 "This package contains utility functions for the @code{spatstat} package
23072 which may also be useful for other purposes.")
23073 (license license:gpl2+)))
23075 (define-public r-spatstat-data
23077 (name "r-spatstat-data")
23082 (uri (cran-uri "spatstat.data" version))
23085 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
23086 (properties `((upstream-name . "spatstat.data")))
23087 (build-system r-build-system)
23089 `(("r-matrix" ,r-matrix)
23090 ("r-spatstat-utils" ,r-spatstat-utils)))
23091 (home-page "http://www.spatstat.org")
23092 (synopsis "Datasets for spatstat")
23094 "This package contains all the datasets for the @code{spatstat}
23096 (license license:gpl2+)))
23098 (define-public r-spatstat
23100 (name "r-spatstat")
23105 (uri (cran-uri "spatstat" version))
23108 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
23109 (properties `((upstream-name . "spatstat")))
23110 (build-system r-build-system)
23112 `(("r-abind" ,r-abind)
23113 ("r-deldir" ,r-deldir)
23114 ("r-goftest" ,r-goftest)
23115 ("r-matrix" ,r-matrix)
23118 ("r-polyclip" ,r-polyclip)
23119 ("r-rpart" ,r-rpart)
23120 ("r-spatstat-data" ,r-spatstat-data)
23121 ("r-spatstat-utils" ,r-spatstat-utils)
23122 ("r-tensor" ,r-tensor)))
23123 (home-page "http://www.spatstat.org")
23124 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
23126 "This package provides a comprehensive toolbox for analysing Spatial
23127 Point Patterns. It is focused mainly on two-dimensional point patterns,
23128 including multitype/marked points, in any spatial region. It also supports
23129 three-dimensional point patterns, space-time point patterns in any number of
23130 dimensions, point patterns on a linear network, and patterns of other
23131 geometrical objects. It supports spatial covariate data such as pixel images
23132 and contains over 2000 functions for plotting spatial data, exploratory data
23133 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
23134 formal inference.")
23135 (license license:gpl2+)))
23137 (define-public r-gaston
23144 (uri (cran-uri "gaston" version))
23147 "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg"))))
23148 (properties `((upstream-name . "gaston")))
23149 (build-system r-build-system)
23150 (inputs `(("zlib" ,zlib)))
23152 `(("r-rcpp" ,r-rcpp)
23153 ("r-rcppeigen" ,r-rcppeigen)
23154 ("r-rcppparallel" ,r-rcppparallel)))
23155 (native-inputs `(("r-knitr" ,r-knitr)))
23156 (home-page "https://cran.r-project.org/web/packages/gaston/")
23157 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
23159 "This is a package for the manipulation of genetic data (SNPs).
23160 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
23161 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
23162 for linear mixed models (AIREML).")
23163 (license license:gpl3)))
23165 (define-public r-cpp11
23172 (uri (cran-uri "cpp11" version))
23175 "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda"))))
23176 (properties `((upstream-name . "cpp11")))
23177 (build-system r-build-system)
23178 (native-inputs `(("r-knitr" ,r-knitr)))
23179 (home-page "https://github.com/r-lib/cpp11")
23180 (synopsis "C++11 Interface for R's C Interface")
23182 "This package provides a header only, C++11 interface to R's C interface.
23183 Compared to other approaches @code{cpp11} strives to be safe against long
23184 jumps from the C API as well as C++ exceptions, conform to normal R function
23185 semantics and supports interaction with @code{ALTREP} vectors.")
23186 (license license:expat)))
23188 (define-public r-rcppziggurat
23190 (name "r-rcppziggurat")
23195 (uri (cran-uri "RcppZiggurat" version))
23198 "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv"))))
23199 (properties `((upstream-name . "RcppZiggurat")))
23200 (build-system r-build-system)
23202 `(("r-rcpp" ,r-rcpp)
23203 ("r-rcppgsl" ,r-rcppgsl)))
23204 (native-inputs `(("r-knitr" ,r-knitr)))
23205 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
23206 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
23208 "The Ziggurat generator for normally distributed random numbers,
23209 originally proposed by Marsaglia and Tsang (2000,
23210 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
23211 times starting with Leong et al (2005,
23212 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
23213 aggregation for comparing different implementations in order to provide a
23214 'faster but good enough' alternative for use with R and C++ code.")
23215 (license license:gpl2+)))
23217 (define-public r-rfast
23224 (uri (cran-uri "Rfast" version))
23227 "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
23228 (properties `((upstream-name . "Rfast")))
23229 (build-system r-build-system)
23231 `(("r-rcpp" ,r-rcpp)
23232 ("r-rcpparmadillo" ,r-rcpparmadillo)
23233 ("r-rcppziggurat" ,r-rcppziggurat)))
23234 (home-page "https://github.com/RfastOfficial/Rfast")
23235 (synopsis "Collection of efficient and fast R functions")
23237 "This package provides a collection of fast (utility) functions for data
23238 analysis. Column- and row- wise means, medians, variances, minimums,
23239 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23240 Poisson), are some of the many fast functions.")
23241 (license license:gpl2+)))
23243 (define-public r-clusterr
23245 (name "r-clusterr")
23250 (uri (cran-uri "ClusterR" version))
23253 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23254 (properties `((upstream-name . "ClusterR")))
23255 (build-system r-build-system)
23257 `(("r-ggplot2" ,r-ggplot2)
23259 ("r-gtools" ,r-gtools)
23261 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23262 (native-inputs `(("r-knitr" ,r-knitr)))
23263 (home-page "https://github.com/mlampros/ClusterR")
23264 (synopsis "Clustering")
23266 "This package provides Gaussian mixture models, k-means,
23267 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23268 option to plot, validate, predict (new data) and estimate the optimal number
23269 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23270 the computationally intensive parts of the functions. For more information,
23274 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23275 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23276 @url{https://doi.org/10.18637/jss.v001.i04};
23277 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23278 Library, @url{https://doi.org/10.1145/1772690.1772862};
23279 @item \"Armadillo: a template-based C++ library
23280 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23281 Software, @url{https://doi.org/10.21105/joss.00026};
23282 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23283 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23284 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23287 (license license:gpl3)))
23289 (define-public r-spectrum
23291 (name "r-spectrum")
23296 (uri (cran-uri "Spectrum" version))
23299 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23300 (properties `((upstream-name . "Spectrum")))
23301 (build-system r-build-system)
23303 `(("r-clusterr" ,r-clusterr)
23304 ("r-diptest" ,r-diptest)
23305 ("r-ggplot2" ,r-ggplot2)
23306 ("r-rfast" ,r-rfast)))
23307 (native-inputs `(("r-knitr" ,r-knitr)))
23308 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23309 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23311 "This package provides a self-tuning spectral clustering method for
23312 single or multi-view data. Spectrum uses a new type of adaptive density aware
23313 kernel that strengthens connections in the graph based on common nearest
23314 neighbours. It uses a tensor product graph data integration and diffusion
23315 procedure to integrate different data sources and reduce noise. Spectrum uses
23316 either the eigengap or multimodality gap heuristics to determine the number of
23317 clusters. The method is sufficiently flexible so that a wide range of
23318 Gaussian and non-Gaussian structures can be clustered with automatic selection
23320 (license license:agpl3+)))
23322 (define-public r-nabor
23329 (uri (cran-uri "nabor" version))
23332 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23333 (properties `((upstream-name . "nabor")))
23334 (build-system r-build-system)
23338 ("r-rcppeigen" ,r-rcppeigen)))
23339 (home-page "https://cran.r-project.org/web/packages/nabor/")
23340 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23342 "This package provides an R wrapper for libnabo, an exact or approximate
23343 k nearest neighbour library which is optimised for low dimensional
23344 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23345 designed as a drop-in replacement for the RANN function @code{nn2}. In
23346 addition, objects which include the k-d tree search structure can be returned
23347 to speed up repeated queries of the same set of target points.")
23348 (license license:bsd-3)))
23350 (define-public r-muhaz
23353 (version "1.2.6.1")
23357 (uri (cran-uri "muhaz" version))
23360 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
23361 (properties `((upstream-name . "muhaz")))
23362 (build-system r-build-system)
23364 `(("r-survival" ,r-survival)))
23366 `(("gfortran" ,gfortran)))
23367 (home-page "https://cran.r-project.org/web/packages/muhaz/")
23368 (synopsis "Hazard function estimation in survival analysis")
23370 "This package produces a smooth estimate of the hazard function for
23372 ;; Any version of the GPL.
23373 (license license:gpl3+)))
23375 (define-public r-flexsurv
23377 (name "r-flexsurv")
23382 (uri (cran-uri "flexsurv" version))
23385 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
23386 (properties `((upstream-name . "flexsurv")))
23387 (build-system r-build-system)
23389 `(("r-desolve" ,r-desolve)
23390 ("r-mstate" ,r-mstate)
23391 ("r-muhaz" ,r-muhaz)
23392 ("r-mvtnorm" ,r-mvtnorm)
23393 ("r-quadprog" ,r-quadprog)
23395 ("r-survival" ,r-survival)
23396 ("r-tibble" ,r-tibble)
23397 ("r-tidyr" ,r-tidyr)))
23399 `(("r-knitr" ,r-knitr)))
23400 (home-page "https://github.com/chjackson/flexsurv-dev")
23401 (synopsis "Flexible parametric survival and multi-state models")
23403 "This package provides flexible parametric models for time-to-event data,
23404 including the Royston-Parmar spline model, generalized gamma and generalized F
23405 distributions. Any user-defined parametric distribution can be fitted, given
23406 at least an R function defining the probability density or hazard. There are
23407 also tools for fitting and predicting from fully parametric multi-state
23409 (license license:gpl2+)))
23411 (define-public r-transphylo
23413 (name "r-transphylo")
23418 (uri (cran-uri "TransPhylo" version))
23421 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
23422 (properties `((upstream-name . "TransPhylo")))
23423 (build-system r-build-system)
23426 ("r-rcpp" ,r-rcpp)))
23428 `(("r-knitr" ,r-knitr)))
23429 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
23430 (synopsis "Inference of transmission tree from a dated phylogeny")
23432 "This is a package to infer transmission trees from a dated phylogeny.
23433 It includes methods to simulate and analyze outbreaks. The methodology is
23434 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
23435 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
23436 (license license:gpl2+)))
23438 (define-public r-km-ci
23445 (uri (cran-uri "km.ci" version))
23448 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
23449 (properties `((upstream-name . "km.ci")))
23450 (build-system r-build-system)
23452 `(("r-survival" ,r-survival)))
23453 (home-page "https://cran.r-project.org/web/packages/km.ci/")
23454 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
23456 "This package computes various @dfn{confidence intervals} (CI) for the
23457 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
23458 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
23459 Nair and Hall and Wellner.")
23460 (license license:gpl2+)))
23462 (define-public r-kmsurv
23469 (uri (cran-uri "KMsurv" version))
23472 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
23473 (properties `((upstream-name . "KMsurv")))
23474 (build-system r-build-system)
23475 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
23476 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
23478 "This package provides data sets and functions for Klein and Moeschberger
23479 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
23481 (license license:gpl3+)))
23483 (define-public r-survmisc
23485 (name "r-survmisc")
23490 (uri (cran-uri "survMisc" version))
23493 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
23494 (properties `((upstream-name . "survMisc")))
23495 (build-system r-build-system)
23497 `(("r-data-table" ,r-data-table)
23498 ("r-ggplot2" ,r-ggplot2)
23499 ("r-gridextra" ,r-gridextra)
23500 ("r-km-ci" ,r-km-ci)
23501 ("r-kmsurv" ,r-kmsurv)
23502 ("r-knitr" ,r-knitr)
23503 ("r-survival" ,r-survival)
23504 ("r-xtable" ,r-xtable)
23507 `(("r-knitr" ,r-knitr)))
23508 (home-page "https://cran.r-project.org/web/packages/survMisc/")
23509 (synopsis "Miscellaneous functions for survival data")
23511 "This package provides a collection of functions to help in the analysis
23512 of right-censored survival data. These extend the methods available in
23513 the @code{survival} package.")
23514 (license license:gpl2)))
23516 (define-public r-exactranktests
23518 (name "r-exactranktests")
23523 (uri (cran-uri "exactRankTests" version))
23526 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
23528 `((upstream-name . "exactRankTests")))
23529 (build-system r-build-system)
23530 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
23531 (synopsis "Exact distributions for rank and permutation tests")
23533 "This package computes exact conditional p-values and quantiles using an
23534 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
23535 (license license:gpl2+)))
23537 (define-public r-maxstat
23544 (uri (cran-uri "maxstat" version))
23547 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
23548 (properties `((upstream-name . "maxstat")))
23549 (build-system r-build-system)
23551 `(("r-exactranktests" ,r-exactranktests)
23552 ("r-mvtnorm" ,r-mvtnorm)))
23553 (home-page "https://cran.r-project.org/web/packages/maxstat/")
23554 (synopsis "Maximally selected rank statistics")
23556 "This package provides maximally selected rank statistics with several
23557 p-value approximations.")
23558 (license license:gpl2+)))
23560 (define-public r-survminer
23562 (name "r-survminer")
23567 (uri (cran-uri "survminer" version))
23570 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
23571 (properties `((upstream-name . "survminer")))
23572 (build-system r-build-system)
23574 `(("r-broom" ,r-broom)
23575 ("r-dplyr" ,r-dplyr)
23576 ("r-ggplot2" ,r-ggplot2)
23577 ("r-ggpubr" ,r-ggpubr)
23578 ("r-gridextra" ,r-gridextra)
23579 ("r-magrittr" ,r-magrittr)
23580 ("r-maxstat" ,r-maxstat)
23581 ("r-purrr" ,r-purrr)
23582 ("r-rlang" ,r-rlang)
23583 ("r-scales" ,r-scales)
23584 ("r-survival" ,r-survival)
23585 ("r-survmisc" ,r-survmisc)
23586 ("r-tibble" ,r-tibble)
23587 ("r-tidyr" ,r-tidyr)))
23589 `(("r-knitr" ,r-knitr)))
23590 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
23591 (synopsis "Drawing survival curves using ggplot2")
23593 "This package contains the function @code{ggsurvplot()} for easily
23594 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
23595 risk' table and 'censoring count plot'. Other functions are also available to
23596 plot adjusted curves for Cox model and to visually examine Cox model
23598 (license license:gpl2)))
23600 (define-public r-forge
23607 (uri (cran-uri "forge" version))
23610 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
23611 (properties `((upstream-name . "forge")))
23612 (build-system r-build-system)
23614 `(("r-magrittr" ,r-magrittr)
23615 ("r-rlang" ,r-rlang)))
23616 (home-page "https://cran.r-project.org/web/packages/forge/")
23617 (synopsis "Cast values into shape")
23619 "This package provides helper functions with a consistent interface to
23620 coerce and verify the types and shapes of values for input checking.")
23621 (license license:asl2.0)))
23623 (define-public r-config
23630 (uri (cran-uri "config" version))
23633 "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
23634 (properties `((upstream-name . "config")))
23635 (build-system r-build-system)
23637 `(("r-yaml" ,r-yaml)))
23639 `(("r-knitr" ,r-knitr)))
23640 (home-page "https://github.com/rstudio/config")
23641 (synopsis "Manage environment specific configuration values")
23643 "This package lets you manage configuration values across multiple
23644 environments (e.g. development, test, production). It reads values using a
23645 function that determines the current environment and returns the appropriate
23647 (license license:gpl3)))
23649 (define-public r-adaptivesparsity
23651 (name "r-adaptivesparsity")
23655 (uri (cran-uri "AdaptiveSparsity" version))
23658 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
23660 `((upstream-name . "AdaptiveSparsity")))
23661 (build-system r-build-system)
23664 (modify-phases %standard-phases
23665 (add-after 'unpack 'link-against-armadillo
23667 (substitute* "src/Makevars"
23668 (("PKG_LIBS=" prefix)
23669 (string-append prefix "-larmadillo")))
23672 `(("r-mass" ,r-mass)
23673 ("r-matrix" ,r-matrix)
23675 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23677 `(("armadillo" ,armadillo)))
23678 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
23679 (synopsis "Adaptive sparsity models")
23681 "This package implements the Figueiredo machine learning algorithm for
23682 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
23683 geometric models.")
23684 (license license:lgpl3+)))
23686 (define-public r-diffusionmap
23688 (name "r-diffusionmap")
23693 (uri (cran-uri "diffusionMap" version))
23696 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
23697 (properties `((upstream-name . "diffusionMap")))
23698 (build-system r-build-system)
23700 `(("r-igraph" ,r-igraph)
23701 ("r-matrix" ,r-matrix)
23702 ("r-scatterplot3d" ,r-scatterplot3d)))
23703 (home-page "https://www.r-project.org")
23704 (synopsis "Diffusion map")
23705 (description "This package implements the diffusion map method of data
23706 parametrization, including creation and visualization of diffusion maps,
23707 clustering with diffusion K-means and regression using the adaptive regression
23709 (license license:gpl2)))
23711 (define-public r-igraph
23718 (uri (cran-uri "igraph" version))
23721 "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
23722 (build-system r-build-system)
23724 `(("gfortran" ,gfortran)))
23728 ("libxml2" ,libxml2)
23731 `(("r-magrittr" ,r-magrittr)
23732 ("r-matrix" ,r-matrix)
23733 ("r-pkgconfig" ,r-pkgconfig)))
23734 (home-page "https://igraph.org")
23735 (synopsis "Network analysis and visualization")
23737 "This package provides routines for simple graphs and network analysis.
23738 It can handle large graphs very well and provides functions for generating
23739 random and regular graphs, graph visualization, centrality methods and much
23741 (license license:gpl2+)))
23743 (define-public r-workflows
23745 (name "r-workflows")
23750 (uri (cran-uri "workflows" version))
23753 "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m"))))
23754 (properties `((upstream-name . "workflows")))
23755 (build-system r-build-system)
23758 ("r-ellipsis" ,r-ellipsis)
23759 ("r-generics" ,r-generics)
23761 ("r-hardhat" ,r-hardhat)
23762 ("r-parsnip" ,r-parsnip)
23763 ("r-rlang" ,r-rlang)))
23765 `(("r-knitr" ,r-knitr)))
23766 (home-page "https://github.com/tidymodels/workflows")
23767 (synopsis "Modeling workflows")
23769 "A workflow is an object that can bundle together your pre-processing,
23770 modeling, and post-processing requests. For example, if you have a
23771 @code{recipe} and @code{parsnip} model, these can be combined into a
23772 workflow. The advantages are:
23775 @item You don’t have to keep track of separate objects in your workspace.
23776 @item The recipe prepping and model fitting can be executed using a single
23777 call to @code{fit()}.
23778 @item If you have custom tuning parameter settings, these can be defined using
23779 a simpler interface when combined with @code{tune}.
23780 @item In the future, workflows will be able to add post-processing operations,
23781 such as modifying the probability cutoff for two-class models.
23784 (license license:expat)))
23786 (define-public r-gpfit
23793 (uri (cran-uri "GPfit" version))
23796 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
23797 (properties `((upstream-name . "GPfit")))
23798 (build-system r-build-system)
23800 `(("r-lattice" ,r-lattice)
23802 (home-page "https://cran.r-project.org/web/packages/GPfit/")
23803 (synopsis "Gaussian Processes modeling")
23805 "This package provides a computationally stable approach of fitting a
23806 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
23807 (license license:gpl2)))
23809 (define-public r-yardstick
23811 (name "r-yardstick")
23816 (uri (cran-uri "yardstick" version))
23819 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
23820 (properties `((upstream-name . "yardstick")))
23821 (build-system r-build-system)
23823 `(("r-dplyr" ,r-dplyr)
23824 ("r-generics" ,r-generics)
23826 ("r-rlang" ,r-rlang)
23827 ("r-tidyselect" ,r-tidyselect)))
23829 `(("r-knitr" ,r-knitr)))
23830 (home-page "https://github.com/tidymodels/yardstick")
23831 (synopsis "Tidy characterizations of model performance")
23833 "This package provides tidy tools for quantifying how well a model fits
23834 to a data set such as confusion matrices, class probability curve summaries,
23835 and regression metrics (e.g., RMSE).")
23836 (license license:gpl2)))
23838 (define-public r-rsample
23845 (uri (cran-uri "rsample" version))
23848 "0s6hgq0rcv3ianyidq3n9z34y5ww51gaggqkwmwns9yyxmwfjcm8"))))
23849 (properties `((upstream-name . "rsample")))
23850 (build-system r-build-system)
23852 `(("r-dplyr" ,r-dplyr)
23853 ("r-furrr" ,r-furrr)
23854 ("r-generics" ,r-generics)
23855 ("r-purrr" ,r-purrr)
23856 ("r-rlang" ,r-rlang)
23857 ("r-tibble" ,r-tibble)
23858 ("r-tidyr" ,r-tidyr)
23859 ("r-tidyselect" ,r-tidyselect)
23860 ("r-vctrs" ,r-vctrs)))
23862 `(("r-knitr" ,r-knitr)))
23863 (home-page "https://rsample.tidymodels.org")
23864 (synopsis "General resampling infrastructure")
23866 "This package provides classes and functions to create and summarize
23867 different types of resampling objects (e.g. bootstrap, cross-validation).")
23868 (license license:gpl2)))
23870 (define-public r-dicedesign
23872 (name "r-dicedesign")
23877 (uri (cran-uri "DiceDesign" version))
23880 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
23881 (properties `((upstream-name . "DiceDesign")))
23882 (build-system r-build-system)
23883 (home-page "http://dice.emse.fr/")
23884 (synopsis "Designs of computer experiments")
23886 "This package provides tools to create some specific @code{Space-Filling
23887 Design} (SFD) and to test their quality.")
23888 (license license:gpl3)))
23890 (define-public r-dials
23897 (uri (cran-uri "dials" version))
23900 "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p"))))
23901 (properties `((upstream-name . "dials")))
23902 (build-system r-build-system)
23904 `(("r-dicedesign" ,r-dicedesign)
23905 ("r-dplyr" ,r-dplyr)
23907 ("r-purrr" ,r-purrr)
23908 ("r-rlang" ,r-rlang)
23909 ("r-scales" ,r-scales)
23910 ("r-tibble" ,r-tibble)
23911 ("r-vctrs" ,r-vctrs)
23912 ("r-withr" ,r-withr)))
23913 (native-inputs `(("r-knitr" ,r-knitr)))
23914 (home-page "https://dials.tidymodels.org/")
23915 (synopsis "Tools for creating tuning parameter values")
23917 "Many models contain tuning parameters (i.e. parameters that cannot be
23918 directly estimated from the data). These tools can be used to define objects
23919 for creating, simulating, or validating values for such parameters.")
23920 (license license:gpl2)))
23922 (define-public r-tune
23929 (uri (cran-uri "tune" version))
23932 "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
23933 (properties `((upstream-name . "tune")))
23934 (build-system r-build-system)
23937 ("r-crayon" ,r-crayon)
23938 ("r-dials" ,r-dials)
23939 ("r-dplyr" ,r-dplyr)
23940 ("r-foreach" ,r-foreach)
23941 ("r-ggplot2" ,r-ggplot2)
23943 ("r-gpfit" ,r-gpfit)
23944 ("r-hardhat" ,r-hardhat)
23945 ("r-lifecycle" ,r-lifecycle)
23946 ("r-parsnip" ,r-parsnip)
23947 ("r-purrr" ,r-purrr)
23948 ("r-recipes" ,r-recipes)
23949 ("r-rlang" ,r-rlang)
23950 ("r-rsample" ,r-rsample)
23951 ("r-tibble" ,r-tibble)
23952 ("r-tidyr" ,r-tidyr)
23953 ("r-vctrs" ,r-vctrs)
23954 ("r-workflows" ,r-workflows)
23955 ("r-yardstick" ,r-yardstick)))
23956 (home-page "https://github.com/tidymodels/tune")
23957 (synopsis "Tidy tuning tools")
23959 "The ability to tune models is important. @code{tune} contains functions
23960 and classes to be used in conjunction with other @code{tidymodels} packages
23961 for finding reasonable values of hyper-parameters in models, pre-processing
23962 methods, and post-processing steps.")
23963 (license license:expat)))
23965 (define-public r-tidyposterior
23967 (name "r-tidyposterior")
23972 (uri (cran-uri "tidyposterior" version))
23975 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
23976 (properties `((upstream-name . "tidyposterior")))
23977 (build-system r-build-system)
23979 `(("r-dplyr" ,r-dplyr)
23980 ("r-generics" ,r-generics)
23981 ("r-ggplot2" ,r-ggplot2)
23982 ("r-lifecycle" ,r-lifecycle)
23983 ("r-purrr" ,r-purrr)
23984 ("r-rlang" ,r-rlang)
23985 ("r-rsample" ,r-rsample)
23986 ("r-rstanarm" ,r-rstanarm)
23987 ("r-tibble" ,r-tibble)
23988 ("r-tidyr" ,r-tidyr)
23989 ("r-vctrs" ,r-vctrs)))
23991 `(("r-knitr" ,r-knitr)))
23992 (home-page "https://tidyposterior.tidymodels.org")
23993 (synopsis "Bayesian analysis to compare models using resampling statistics")
23995 "This package can be used to conduct post hoc analyses of resampling
23996 results generated by models. For example, if two models are evaluated with
23997 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
23998 are 10 paired statistics. These can be used to make comparisons between
23999 models without involving a test set.")
24000 (license license:gpl2)))
24002 (define-public r-tidypredict
24004 (name "r-tidypredict")
24009 (uri (cran-uri "tidypredict" version))
24012 "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
24013 (properties `((upstream-name . "tidypredict")))
24014 (build-system r-build-system)
24016 `(("r-dplyr" ,r-dplyr)
24017 ("r-generics" ,r-generics)
24018 ("r-knitr" ,r-knitr)
24019 ("r-purrr" ,r-purrr)
24020 ("r-rlang" ,r-rlang)
24021 ("r-tibble" ,r-tibble)))
24023 `(("r-knitr" ,r-knitr)))
24024 (home-page "https://tidypredict.tidymodels.org")
24025 (synopsis "Run predictions inside the database")
24027 "This package parses a fitted R model object, and returns a formula in
24028 Tidy Eval code that calculates the predictions. It works with several
24029 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
24030 final SQL translation of the algorithm. It currently supports @code{lm()},
24031 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
24032 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
24033 (license license:gpl3)))
24035 (define-public r-janeaustenr
24037 (name "r-janeaustenr")
24042 (uri (cran-uri "janeaustenr" version))
24045 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
24046 (properties `((upstream-name . "janeaustenr")))
24047 (build-system r-build-system)
24048 (home-page "https://github.com/juliasilge/janeaustenr")
24049 (synopsis "Jane Austen's complete novels")
24051 "This package provides the full texts for Jane Austen's six completed
24052 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
24053 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
24054 and \"Persuasion\".")
24055 (license license:expat)))
24057 (define-public r-tokenizers
24059 (name "r-tokenizers")
24064 (uri (cran-uri "tokenizers" version))
24067 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
24068 (properties `((upstream-name . "tokenizers")))
24069 (build-system r-build-system)
24071 `(("r-rcpp" ,r-rcpp)
24072 ("r-snowballc" ,r-snowballc)
24073 ("r-stringi" ,r-stringi)))
24075 `(("r-knitr" ,r-knitr)))
24076 (home-page "https://lincolnmullen.com/software/tokenizers/")
24077 (synopsis "Fast, consistent tokenization of natural language text")
24079 "This is a package for converting natural language text into tokens.
24080 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
24081 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
24082 Treebank, regular expressions, as well as functions for counting characters,
24083 words, and sentences, and a function for splitting longer texts into separate
24084 documents, each with the same number of words. The tokenizers have a
24085 consistent interface, and the package is built on the @code{stringi} and
24086 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
24087 (license license:expat)))
24089 (define-public r-hunspell
24091 (name "r-hunspell")
24096 (uri (cran-uri "hunspell" version))
24099 "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
24100 (properties `((upstream-name . "hunspell")))
24101 (build-system r-build-system)
24103 `(("r-digest" ,r-digest)
24104 ("r-rcpp" ,r-rcpp)))
24106 `(("r-knitr" ,r-knitr)))
24107 (home-page "https://github.com/ropensci/hunspell#readme")
24108 (synopsis "High-performance stemmer, tokenizer, and spell checker")
24110 "This package provides a low-level spell checker and morphological
24111 analyzer based on the famous @code{hunspell} library. The package can analyze
24112 or check individual words as well as parse text, LaTeX, HTML or XML documents.
24113 For a more user-friendly interface use the @code{spelling} package which
24114 builds on this package to automate checking of files, documentation and
24115 vignettes in all common formats.")
24116 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
24117 ;; MPL; in addition to these licenses the rest of the R wrapper is also
24118 ;; available under the Expat license.
24119 (license (list license:gpl2
24124 (define-public r-tidytext
24126 (name "r-tidytext")
24131 (uri (cran-uri "tidytext" version))
24134 "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
24135 (properties `((upstream-name . "tidytext")))
24136 (build-system r-build-system)
24138 `(("r-dplyr" ,r-dplyr)
24139 ("r-generics" ,r-generics)
24140 ("r-hunspell" ,r-hunspell)
24141 ("r-janeaustenr" ,r-janeaustenr)
24142 ("r-matrix" ,r-matrix)
24143 ("r-purrr" ,r-purrr)
24144 ("r-rlang" ,r-rlang)
24145 ("r-stringr" ,r-stringr)
24146 ("r-tibble" ,r-tibble)
24147 ("r-tokenizers" ,r-tokenizers)))
24149 `(("r-knitr" ,r-knitr)))
24150 (home-page "https://github.com/juliasilge/tidytext")
24151 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
24153 "This is a package for text mining for word processing and sentiment
24154 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
24155 (license license:expat)))
24157 (define-public r-parsnip
24164 (uri (cran-uri "parsnip" version))
24167 "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
24168 (properties `((upstream-name . "parsnip")))
24169 (build-system r-build-system)
24171 `(("r-dplyr" ,r-dplyr)
24172 ("r-generics" ,r-generics)
24173 ("r-globals" ,r-globals)
24175 ("r-magrittr" ,r-magrittr)
24176 ("r-prettyunits" ,r-prettyunits)
24177 ("r-purrr" ,r-purrr)
24178 ("r-rlang" ,r-rlang)
24179 ("r-tibble" ,r-tibble)
24180 ("r-tidyr" ,r-tidyr)
24181 ("r-vctrs" ,r-vctrs)))
24183 `(("r-knitr" ,r-knitr)))
24184 (home-page "https://parsnip.tidymodels.org")
24185 (synopsis "Common API to modeling and analysis functions")
24187 "This package provides a common interface to allow users to specify a
24188 model without having to remember the different argument names across different
24189 functions or computational engines (e.g. R, Spark, Stan, etc).")
24190 (license license:gpl2)))
24192 (define-public r-infer
24199 (uri (cran-uri "infer" version))
24202 "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
24203 (properties `((upstream-name . "infer")))
24204 (build-system r-build-system)
24206 `(("r-dplyr" ,r-dplyr)
24207 ("r-ggplot2" ,r-ggplot2)
24209 ("r-magrittr" ,r-magrittr)
24210 ("r-purrr" ,r-purrr)
24211 ("r-rlang" ,r-rlang)
24212 ("r-tibble" ,r-tibble)))
24214 `(("r-knitr" ,r-knitr)))
24215 (home-page "https://github.com/tidymodels/infer")
24216 (synopsis "Tidy statistical inference")
24218 "The objective of this package is to perform inference using an
24219 expressive statistical grammar that coheres with the Tidy design framework.")
24220 (license license:cc0)))
24222 (define-public r-modeldata
24224 (name "r-modeldata")
24229 (uri (cran-uri "modeldata" version))
24232 "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
24233 (properties `((upstream-name . "modeldata")))
24234 (build-system r-build-system)
24235 (home-page "https://modeldata.tidymodels.org")
24236 (synopsis "Data sets useful for modeling packages")
24238 "This package provides data sets used for demonstrating or testing
24239 model-related packages.")
24240 (license license:expat)))
24242 (define-public r-tidymodels
24244 (name "r-tidymodels")
24249 (uri (cran-uri "tidymodels" version))
24252 "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
24253 (properties `((upstream-name . "tidymodels")))
24254 (build-system r-build-system)
24256 `(("r-broom" ,r-broom)
24258 ("r-crayon" ,r-crayon)
24259 ("r-dials" ,r-dials)
24260 ("r-dplyr" ,r-dplyr)
24261 ("r-ggplot2" ,r-ggplot2)
24262 ("r-infer" ,r-infer)
24263 ("r-magrittr" ,r-magrittr)
24264 ("r-modeldata" ,r-modeldata)
24265 ("r-parsnip" ,r-parsnip)
24266 ("r-purrr" ,r-purrr)
24267 ("r-recipes" ,r-recipes)
24268 ("r-rlang" ,r-rlang)
24269 ("r-rsample" ,r-rsample)
24270 ("r-rstudioapi" ,r-rstudioapi)
24271 ("r-tibble" ,r-tibble)
24272 ("r-tidyr" ,r-tidyr)
24274 ("r-workflows" ,r-workflows)
24275 ("r-yardstick" ,r-yardstick)))
24277 `(("r-knitr" ,r-knitr)
24278 ("r-rmarkdown" ,r-rmarkdown)
24280 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
24281 (home-page "https://github.com/tidymodels/tidymodels")
24282 (synopsis "Tidy collection for modeling and statistical analysis")
24284 "The tidy modeling \"verse\" is a collection of packages for modeling and
24285 statistical analysis that share the underlying design philosophy, grammar, and
24286 data structures of the tidyverse.")
24287 (license license:gpl3)))
24289 (define-public r-mlecens
24296 (uri (cran-uri "MLEcens" version))
24299 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
24300 (properties `((upstream-name . "MLEcens")))
24301 (build-system r-build-system)
24302 (home-page "http://stat.ethz.ch/~maathuis/")
24303 (synopsis "Computation of the MLE for bivariate (interval) censored data")
24305 "This package contains functions to compute the nonparametric
24306 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
24307 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
24308 To be more precise, we consider the situation where we observe a set of
24309 rectangles that are known to contain the unobservable realizations of (X,Y).
24310 We compute the MLE based on such a set of rectangles. The methods can also be
24311 used for univariate censored data (see data set @code{cosmesis}), and for
24312 censored data with competing risks (see data set @code{menopause}). The
24313 package also provides functions to visualize the observed data and the MLE.")
24314 (license license:gpl2+)))
24316 (define-public r-perm
24319 (version "1.0-0.0")
24323 (uri (cran-uri "perm" version))
24326 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
24327 (properties `((upstream-name . "perm")))
24328 (build-system r-build-system)
24329 (home-page "https://cran.r-project.org/web/packages/perm/")
24330 (synopsis "Exact or asymptotic permutation tests")
24332 "This package provides several methods for performing permutation tests.
24333 It has three main functions, to perform linear permutation tests. These tests
24334 are tests where the test statistic is the sum of the product of a
24335 covariate (usually group indicator) and the scores.")
24336 ;; Any version of the GPL
24337 (license license:gpl2+)))
24339 (define-public r-qtl
24346 (uri (cran-uri "qtl" version))
24349 "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
24350 (build-system r-build-system)
24351 (home-page "https://rqtl.org/")
24352 (synopsis "R package for analyzing QTL experiments in genetics")
24353 (description "R/qtl is an extension library for the R statistics system.
24354 It is used to analyze experimental crosses for identifying genes contributing
24355 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
24357 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
24358 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
24360 (license license:gpl3)))
24362 (define-public r-qtl2
24365 (version "0.22-11")
24368 (uri (cran-uri "qtl2" version))
24370 (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
24371 (build-system r-build-system)
24373 `(("r-data-table" ,r-data-table)
24374 ("r-jsonlite" ,r-jsonlite)
24376 ("r-rcppeigen" ,r-rcppeigen)
24377 ("r-rsqlite" ,r-rsqlite)
24378 ("r-yaml" ,r-yaml)))
24379 (home-page "https://kbroman.org/qtl2/")
24380 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
24382 "This package provides a set of tools to perform @dfn{Quantitative Trait
24383 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
24384 @code{R/qtl} package to better handle high-dimensional data and complex cross
24385 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
24386 (license license:gpl3)))
24388 (define-public r-seqminer
24390 (name "r-seqminer")
24395 (uri (cran-uri "seqminer" version))
24398 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
24399 (build-system r-build-system)
24402 (home-page "http://seqminer.genomic.codes")
24403 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
24405 "This package provides tools to integrate nucleotide sequencing
24406 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
24407 ;; Any version of the GPL is acceptable
24408 (license (list license:gpl2+ license:gpl3+))))
24410 (define-public r-maldiquant
24412 (name "r-maldiquant")
24417 (uri (cran-uri "MALDIquant" version))
24420 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
24421 (properties `((upstream-name . "MALDIquant")))
24422 (build-system r-build-system)
24423 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
24424 (synopsis "Quantitative analysis of mass spectrometry data")
24426 "This package provides a complete analysis pipeline for matrix-assisted
24427 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
24428 two-dimensional mass spectrometry data. In addition to commonly used plotting
24429 and processing methods it includes distinctive features, namely baseline
24430 subtraction methods such as morphological filters (TopHat) or the
24431 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
24432 alignment using warping functions, handling of replicated measurements as well
24433 as allowing spectra with different resolutions.")
24434 (license license:gpl3+)))
24436 (define-public r-seurat
24442 (uri (cran-uri "Seurat" version))
24445 "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
24446 (properties `((upstream-name . "Seurat")))
24447 (build-system r-build-system)
24450 ("r-cluster" ,r-cluster)
24451 ("r-cowplot" ,r-cowplot)
24452 ("r-fitdistrplus" ,r-fitdistrplus)
24453 ("r-future" ,r-future)
24454 ("r-future-apply" ,r-future-apply)
24455 ("r-ggplot2" ,r-ggplot2)
24456 ("r-ggrepel" ,r-ggrepel)
24457 ("r-ggridges" ,r-ggridges)
24460 ("r-igraph" ,r-igraph)
24461 ("r-irlba" ,r-irlba)
24462 ("r-jsonlite" ,r-jsonlite)
24463 ("r-kernsmooth" ,r-kernsmooth)
24464 ("r-leiden" ,r-leiden)
24465 ("r-lmtest" ,r-lmtest)
24467 ("r-matrix" ,r-matrix)
24468 ("r-miniui" ,r-miniui)
24469 ("r-patchwork" ,r-patchwork)
24470 ("r-pbapply" ,r-pbapply)
24471 ("r-plotly" ,r-plotly)
24474 ("r-rcolorbrewer" ,r-rcolorbrewer)
24476 ("r-rcppannoy" ,r-rcppannoy)
24477 ("r-rcppeigen" ,r-rcppeigen)
24478 ("r-rcppprogress" ,r-rcppprogress)
24479 ("r-reticulate" ,r-reticulate)
24480 ("r-rlang" ,r-rlang)
24483 ("r-rtsne" ,r-rtsne)
24484 ("r-scales" ,r-scales)
24485 ("r-sctransform" ,r-sctransform)
24486 ("r-shiny" ,r-shiny)
24487 ("r-spatstat" ,r-spatstat)
24488 ("r-tibble" ,r-tibble)
24489 ("r-uwot" ,r-uwot)))
24490 (home-page "http://www.satijalab.org/seurat")
24491 (synopsis "Seurat is an R toolkit for single cell genomics")
24493 "This package is an R package designed for QC, analysis, and
24494 exploration of single cell RNA-seq data. It easily enables widely-used
24495 analytical techniques, including the identification of highly variable genes,
24496 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
24497 algorithms; density clustering, hierarchical clustering, k-means, and the
24498 discovery of differentially expressed genes and markers.")
24499 (license license:gpl3)))
24501 (define-public r-phangorn
24503 (name "r-phangorn")
24508 (uri (cran-uri "phangorn" version))
24511 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
24512 (build-system r-build-system)
24515 ("r-fastmatch" ,r-fastmatch)
24516 ("r-igraph" ,r-igraph)
24517 ("r-magrittr" ,r-magrittr)
24518 ("r-matrix" ,r-matrix)
24519 ("r-quadprog" ,r-quadprog)
24520 ("r-rcpp" ,r-rcpp)))
24521 (home-page "https://github.com/KlausVigo/phangorn")
24522 (synopsis "Phylogenetic analysis in R")
24524 "Phangorn is a package for phylogenetic analysis in R. It supports
24525 estimation of phylogenetic trees and networks using Maximum Likelihood,
24526 Maximum Parsimony, distance methods and Hadamard conjugation.")
24527 (license license:gpl2+)))
24529 (define-public r-diversitree
24531 (name "r-diversitree")
24536 (uri (cran-uri "diversitree" version))
24539 "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
24540 (build-system r-build-system)
24542 `(("gfortran" ,gfortran)))
24543 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
24546 ("r-desolve" ,r-desolve)
24548 ("r-subplex" ,r-subplex)))
24549 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
24550 (synopsis "Comparative 'phylogenetic' analyses of diversification")
24551 (description "This package contains a number of comparative \"phylogenetic\"
24552 methods, mostly focusing on analysing diversification and character evolution.
24553 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
24554 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
24555 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
24556 include Markov models of discrete and continuous trait evolution and constant
24557 rate speciation and extinction.")
24558 (license license:gpl2+)))
24560 (define-public r-absfiltergsea
24562 (name "r-absfiltergsea")
24567 (uri (cran-uri "AbsFilterGSEA" version))
24569 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
24570 (properties `((upstream-name . "AbsFilterGSEA")))
24571 (build-system r-build-system)
24573 `(("r-biobase" ,r-biobase)
24574 ("r-deseq" ,r-deseq)
24575 ("r-limma" ,r-limma)
24577 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24578 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
24579 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
24581 "This package provides a function that performs gene-permuting of a gene-set
24582 enrichment analysis (GSEA) calculation with or without the absolute filtering.
24583 Without filtering, users can perform (original) two-tailed or one-tailed
24585 (license license:gpl2)))