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 "0853kq4j8kic8z2gh5mxfqkwxjs4bdphlajzyvxka7af4r04bfmi"))))
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 "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4"))))
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 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj"))))
7925 (properties `((upstream-name . "mosaicCore")))
7926 (build-system r-build-system)
7928 `(("r-dplyr" ,r-dplyr)
7930 ("r-rlang" ,r-rlang)
7931 ("r-tidyr" ,r-tidyr)))
7932 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7933 (synopsis "Common utilities for mosaic family packages")
7935 "Common utilities used in other Mosaic family packages are collected here.")
7936 (license license:gpl2+)))
7938 (define-public r-ggformula
7940 (name "r-ggformula")
7945 (uri (cran-uri "ggformula" version))
7947 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7948 (build-system r-build-system)
7950 `(("r-ggforce" ,r-ggforce)
7951 ("r-ggplot2" ,r-ggplot2)
7952 ("r-ggstance" ,r-ggstance)
7953 ("r-magrittr" ,r-magrittr)
7954 ("r-mosaiccore" ,r-mosaiccore)
7955 ("r-rlang" ,r-rlang)
7956 ("r-stringr" ,r-stringr)
7957 ("r-tibble" ,r-tibble)))
7958 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7959 (synopsis "Formula interface for the @code{r-ggplot2}")
7961 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7962 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7963 and extends the excellent simplicity of the lattice-graphics formula interface,
7964 while providing the intuitive capabilities of @code{r-ggplot2}.")
7965 (license license:expat)))
7967 (define-public r-mosaicdata
7969 (name "r-mosaicdata")
7974 (uri (cran-uri "mosaicData" version))
7976 (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji"))))
7977 (properties `((upstream-name . "mosaicData")))
7978 (build-system r-build-system)
7979 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7980 (synopsis "Data sets for project Mosaic")
7982 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7983 used to teach mathematics, statistics, computation and modeling.")
7984 (license license:gpl2+)))
7986 (define-public r-raster
7993 (uri (cran-uri "raster" version))
7996 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
7997 (build-system r-build-system)
7999 `(("r-rcpp" ,r-rcpp)
8001 (home-page "https://www.rspatial.org/")
8002 (synopsis "Geographic data analysis and modeling")
8004 "The package implements basic and high-level functions for reading,
8005 writing, manipulating, analyzing and modeling of gridded spatial data.
8006 Processing of very large files is supported.")
8007 (license license:gpl3+)))
8009 (define-public r-mosaic
8016 (uri (cran-uri "mosaic" version))
8018 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8019 (build-system r-build-system)
8021 `(("r-broom" ,r-broom)
8022 ("r-dplyr" ,r-dplyr)
8023 ("r-ggdendro" ,r-ggdendro)
8024 ("r-ggformula" ,r-ggformula)
8025 ("r-ggplot2" ,r-ggplot2)
8026 ("r-ggrepel" ,r-ggrepel)
8028 ("r-gridextra" ,r-gridextra)
8029 ("r-lattice" ,r-lattice)
8030 ("r-latticeextra" ,r-latticeextra)
8031 ("r-lazyeval" ,r-lazyeval)
8033 ("r-matrix" ,r-matrix)
8034 ("r-mosaiccore" ,r-mosaiccore)
8035 ("r-mosaicdata" ,r-mosaicdata)
8036 ("r-readr" ,r-readr)
8037 ("r-tidyr" ,r-tidyr)))
8039 `(("r-knitr" ,r-knitr)))
8040 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8041 (synopsis "Mathematics, statistics, and computation teaching utilities")
8043 "This package contain data sets and utilities from
8044 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8045 statistics, computation and modeling. Project MOSAIC is a community of
8046 educators working to tie together aspects of quantitative work that students
8047 in science, technology, engineering and mathematics will need in their
8048 professional lives, but which are usually taught in isolation, if at all.")
8049 (license license:gpl2+)))
8051 (define-public r-abd
8058 (uri (cran-uri "abd" version))
8060 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8061 (build-system r-build-system)
8063 `(("r-lattice" ,r-lattice)
8064 ("r-mosaic" ,r-mosaic)
8065 ("r-nlme" ,r-nlme)))
8066 (home-page "https://cran.r-project.org/web/packages/abd/")
8067 (synopsis "Analysis of biological data")
8069 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8070 biological data by Michael Whitlock and Dolph Schluter.")
8071 (license license:gpl2)))
8073 (define-public r-svgui
8080 (uri (cran-uri "svGUI" version))
8082 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8083 (properties `((upstream-name . "svGUI")))
8084 (build-system r-build-system)
8085 (home-page "https://github.com/SciViews/svGUI/")
8086 (synopsis "Functions for managing GUI clients in R")
8088 "The SciViews @code{svGUI} package eases the management of Graphical User
8089 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8090 centralizes info about GUI elements currently used, and it dispatches GUI
8091 calls to the particular toolkits in use in function of the context.")
8092 (license license:gpl2)))
8094 (define-public r-svdialogs
8096 (name "r-svdialogs")
8101 (uri (cran-uri "svDialogs" version))
8103 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8104 (properties `((upstream-name . "svDialogs")))
8105 (build-system r-build-system)
8108 ("zenity" ,zenity)))
8110 `(("r-rstudioapi" ,r-rstudioapi)
8111 ("r-svgui" ,r-svgui)))
8112 (home-page "https://github.com/SciViews/svDialogs/")
8113 (synopsis "Portable dialog boxes")
8115 "This package helps to construct standard dialog boxes for your GUI, including
8116 message boxes, input boxes, list, file or directory selection, and others. In
8117 case R cannot display GUI dialog boxes, a simpler command line version of these
8118 interactive elements is also provided as a fallback solution.")
8119 (license license:gpl2)))
8121 (define-public r-abe
8128 (uri (cran-uri "abe" version))
8131 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8132 (build-system r-build-system)
8133 (home-page "https://cran.r-project.org/web/packages/abe/")
8134 (synopsis "Augmented backward elimination")
8136 "This package performs augmented backward elimination and checks the
8137 stability of the obtained model. Augmented backward elimination combines
8138 significance or information based criteria with the change in estimate to
8139 either select the optimal model for prediction purposes or to serve as a tool
8140 to obtain a practically sound, highly interpretable model.")
8141 (license license:gpl2+)))
8143 (define-public r-abf2
8150 (uri (cran-uri "abf2" version))
8152 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8153 (build-system r-build-system)
8154 (home-page "https://cran.r-project.org/web/packages/abf2/")
8155 (synopsis "Load gap-free axon @code{r-abf2} files")
8157 "This package loads electrophysiology data from ABF2 files, as created by
8158 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8159 mode are currently supported.")
8160 (license license:artistic2.0)))
8162 (define-public r-abhgenotyper
8164 (name "r-abhgenotyper")
8169 (uri (cran-uri "ABHgenotypeR" version))
8171 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8172 (properties `((upstream-name . "ABHgenotypeR")))
8173 (build-system r-build-system)
8175 `(("r-ggplot2" ,r-ggplot2)
8176 ("r-reshape2" ,r-reshape2)))
8177 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8178 (synopsis "Visualize and manipulate ABH genotypes")
8180 "The @code{r-abhgenotyper} package provides simple imputation,
8181 error-correction and plotting capacities for genotype data. The package is
8182 supposed to serve as an intermediate but independent analysis tool between the
8183 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8184 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8185 genotypes as \"graphical genotypes\".")
8186 (license license:gpl3)))
8188 (define-public r-furrr
8195 (uri (cran-uri "furrr" version))
8198 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8199 (build-system r-build-system)
8201 `(("r-future" ,r-future)
8202 ("r-globals" ,r-globals)
8203 ("r-purrr" ,r-purrr)
8204 ("r-rlang" ,r-rlang)))
8205 (home-page "https://github.com/DavisVaughan/furrr")
8206 (synopsis "Apply mapping functions in parallel using futures")
8208 "This package provides implementations of the family of @code{map()}
8209 functions from the @code{purrr} package that can be resolved using any
8210 @code{future}-supported backend, e.g. parallel on the local machine or
8211 distributed on a compute cluster.")
8212 (license license:lgpl2.1+)))
8214 (define-public r-abjutils
8221 (uri (cran-uri "abjutils" version))
8223 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8224 (build-system r-build-system)
8226 `(("r-dplyr" ,r-dplyr)
8227 ("r-magrittr" ,r-magrittr)
8228 ("r-purrr" ,r-purrr)
8229 ("r-rlang" ,r-rlang)
8230 ("r-rstudioapi" ,r-rstudioapi)
8231 ("r-stringi" ,r-stringi)
8232 ("r-stringr" ,r-stringr)
8233 ("r-tidyr" ,r-tidyr)))
8234 (home-page "https://github.com/abjur/abjutils/")
8235 (synopsis "Collection of tools for jurimetrical analysis")
8237 "This package implements general purpose tools, such as functions for
8238 sampling and basic manipulation of Brazilian lawsuits identification number.
8239 It also implements functions for text cleaning, such as accentuation
8241 (license license:expat)))
8243 (define-public r-abnormality
8245 (name "r-abnormality")
8250 (uri (cran-uri "abnormality" version))
8252 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8253 (build-system r-build-system)
8255 `(("r-mass" ,r-mass)
8256 ("r-matrix" ,r-matrix)))
8257 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8258 (synopsis "Measure a subject's abnormality with respect to a reference population")
8260 "This package contains functions to implement the methodology and
8261 considerations laid out by Marks et al. in the article \"Measuring abnormality
8262 in high dimensional spaces: applications in biomechanical gait analysis\".
8263 Using high-dimensional datasets to measure a subject's overall level of
8264 abnormality as compared to a reference population is often needed in outcomes
8266 (license license:expat)))
8268 (define-public r-abodoutlier
8270 (name "r-abodoutlier")
8275 (uri (cran-uri "abodOutlier" version))
8277 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8278 (properties `((upstream-name . "abodOutlier")))
8279 (build-system r-build-system)
8281 `(("r-cluster" ,r-cluster)))
8282 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8283 (synopsis "Angle-based outlier detection")
8285 "This package performs angle-based outlier detection on a given data
8286 frame. It offers three methods to process data:
8288 @item full but slow implementation using all the data that has cubic
8290 @item a fully randomized method;
8291 @item a method using k-nearest neighbours.
8293 These algorithms are well suited for high dimensional data outlier
8295 (license license:expat)))
8297 (define-public r-abps
8304 (uri (cran-uri "ABPS" version))
8306 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8307 (properties `((upstream-name . "ABPS")))
8308 (build-system r-build-system)
8309 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8310 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8311 (synopsis "Abnormal blood profile score to detect blood doping")
8313 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8314 The ABPS is a part of the Athlete biological passport program of the World
8315 anti-doping agency, which combines several blood parameters into a single
8316 score in order to detect blood doping. The package also contains functions to
8317 calculate other scores used in anti-doping programs, such as the ratio of
8318 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8319 (license license:gpl2+)))
8321 (define-public r-parmigene
8323 (name "r-parmigene")
8328 (uri (cran-uri "parmigene" version))
8331 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8332 (build-system r-build-system)
8333 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8334 (synopsis "Mutual information estimation for gene network reconstruction")
8336 "This package provides a parallel estimation of the mutual information
8337 based on entropy estimates from k-nearest neighbors distances and algorithms
8338 for the reconstruction of gene regulatory networks.")
8339 (license license:agpl3+)))
8341 (define-public r-pscl
8348 (uri (cran-uri "pscl" version))
8350 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8351 (build-system r-build-system)
8353 `(("r-mass" ,r-mass)))
8354 (home-page "https://github.com/atahk/pscl/")
8355 (synopsis "Political science computational laboratory")
8357 "The @code{pscl} is an R package providing classes and methods for:
8359 @item Bayesian analysis of roll call data (item-response models);
8360 @item elementary Bayesian statistics;
8361 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8363 @item utility functions.
8365 (license license:gpl2)))
8367 (define-public r-accelmissing
8369 (name "r-accelmissing")
8374 (uri (cran-uri "accelmissing" version))
8376 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8377 (build-system r-build-system)
8379 `(("r-mice" ,r-mice)
8380 ("r-pscl" ,r-pscl)))
8381 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8382 (synopsis "Missing value imputation for accelerometer data")
8384 "This package provides a statistical method to impute the missing values in
8385 accelerometer data. The methodology includes both parametric and
8386 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8387 model. It also provides multiple functions to preprocess the accelerometer data
8388 previous to the missing data imputation. These include detecting the wearing
8389 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8390 (license license:gpl2+)))
8392 (define-public r-mhsmm
8399 (uri (cran-uri "mhsmm" version))
8401 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8402 (build-system r-build-system)
8403 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8404 (home-page "https://github.com/jaredo/mhsmm/")
8405 (synopsis "Inference for hidden Markov and semi-Markov models")
8407 "The @code{r-mhsmm} package implements estimation and prediction methods for
8408 hidden Markov and semi-Markov models for multiple observation sequences. Such
8409 techniques are of interest when observed data is thought to be dependent on some
8410 unobserved (or hidden) state. Also, this package is suitable for equidistant
8411 time series data, with multivariate and/or missing data. Allows user defined
8412 emission distributions.")
8413 (license license:gpl2+)))
8415 (define-public r-nleqslv
8422 (uri (cran-uri "nleqslv" version))
8424 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8425 (build-system r-build-system)
8426 (native-inputs `(("gfortran" ,gfortran)))
8427 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8428 (synopsis "Solve systems of nonlinear equations")
8430 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8431 Broyden or a Newton method with a choice of global strategies such as line
8432 search and trust region. There are options for using a numerical or user
8433 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8434 singular or ill-conditioned Jacobian.")
8435 (license license:gpl2+)))
8437 (define-public r-physicalactivity
8439 (name "r-physicalactivity")
8444 (uri (cran-uri "PhysicalActivity" version))
8446 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8448 `((upstream-name . "PhysicalActivity")))
8449 (build-system r-build-system)
8450 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8451 (synopsis "Procesing accelerometer data for physical activity measurement")
8453 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8454 for classification of monitor wear and nonwear time intervals in accelerometer
8455 data collected to assess physical activity. The package also contains functions
8456 for making plots of accelerometer data and obtaining the summary of various
8457 information including daily monitor wear time and the mean monitor wear time
8458 during valid days. The revised package version 0.2-1 improved the functions
8459 regarding speed, robustness and add better support for time zones and daylight
8460 saving. In addition, several functions were added:
8462 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8463 @item the @code{markPAI} can categorize physical activity intensity level based
8464 on user-defined cut-points of accelerometer counts.
8466 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8467 @code{queryActigraph} functions.")
8468 (license license:gpl3+)))
8470 (define-public r-acc
8477 (uri (cran-uri "acc" version))
8479 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8480 (build-system r-build-system)
8482 `(("r-circlize" ,r-circlize)
8484 ("r-ggplot2" ,r-ggplot2)
8485 ("r-iterators" ,r-iterators)
8486 ("r-mhsmm" ,r-mhsmm)
8487 ("r-nleqslv" ,r-nleqslv)
8488 ("r-physicalactivity" ,r-physicalactivity)
8490 ("r-r-utils" ,r-r-utils)
8492 ("r-rcpparmadillo" ,r-rcpparmadillo)
8493 ("r-rsqlite" ,r-rsqlite)
8495 (home-page "https://cran.r-project.org/web/packages/acc/")
8496 (synopsis "Exploring accelerometer data")
8498 "This package processes accelerometer data from uni-axial and tri-axial devices
8499 and generates data summaries. Also, includes functions to plot, analyze, and
8500 simulate accelerometer data.")
8501 (license license:gpl2+)))
8503 (define-public r-rbenchmark
8505 (name "r-rbenchmark")
8510 (uri (cran-uri "rbenchmark" version))
8512 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8513 (build-system r-build-system)
8514 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8515 (synopsis "Benchmarking routine for R")
8517 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8518 and is intended to facilitate benchmarking of arbitrary R code. The library
8519 consists of just one function, benchmark, which is a simple wrapper around
8520 system.time. Given a specification of the benchmarking process (counts of
8521 replications, evaluation environment) and an arbitrary number of expressions,
8522 benchmark evaluates each of the expressions in the specified environment,
8523 replicating the evaluation as many times as specified, and returning the results
8524 conveniently wrapped into a data frame.")
8525 (license license:gpl2+)))
8527 (define-public r-mitools
8534 (uri (cran-uri "mitools" version))
8537 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8538 (build-system r-build-system)
8539 (propagated-inputs `(("r-dbi" ,r-dbi)))
8540 (home-page "https://cran.r-project.org/web/packages/mitools/")
8541 (synopsis "Tools for multiple imputation of missing data")
8543 "This package provides tools to perform analyses and combine results from
8544 multiple-imputation datasets.")
8545 (license license:gpl2)))
8547 (define-public r-magick
8554 (uri (cran-uri "magick" version))
8557 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8558 (build-system r-build-system)
8560 `(("imagemagick" ,imagemagick)
8563 `(("r-curl" ,r-curl)
8564 ("r-magrittr" ,r-magrittr)
8565 ("r-rcpp" ,r-rcpp)))
8567 `(("pkg-config" ,pkg-config)
8568 ("r-knitr" ,r-knitr)))
8569 (home-page "https://github.com/ropensci/magick")
8570 (synopsis "Advanced graphics and image-processing in R")
8572 "This package provides bindings to ImageMagick, a comprehensive image
8573 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8574 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8575 operations are vectorized via the Magick++ STL meaning they operate either on
8576 a single frame or a series of frames for working with layers, collages, or
8577 animation. In RStudio, images are automatically previewed when printed to the
8578 console, resulting in an interactive editing environment.")
8579 (license license:expat)))
8581 (define-public r-survey
8588 (uri (cran-uri "survey" version))
8591 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8592 (build-system r-build-system)
8594 `(("r-lattice" ,r-lattice)
8595 ("r-matrix" ,r-matrix)
8596 ("r-minqa" ,r-minqa)
8597 ("r-mitools" ,r-mitools)
8598 ("r-numderiv" ,r-numderiv)
8599 ("r-survival" ,r-survival)))
8600 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8601 (synopsis "Analysis of complex survey samples")
8603 "This package provides tools for the analysis of complex survey samples.
8604 The provided features include: summary statistics, two-sample tests, rank
8605 tests, generalised linear models, cumulative link models, Cox models,
8606 loglinear models, and general maximum pseudolikelihood estimation for
8607 multistage stratified, cluster-sampled, unequally weighted survey samples;
8608 variances by Taylor series linearisation or replicate weights;
8609 post-stratification, calibration, and raking; two-phase subsampling designs;
8610 graphics; PPS sampling without replacement; principal components, and factor
8612 ;; Either version of the GPL.
8613 (license (list license:gpl2 license:gpl3))))
8615 (define-public r-gee
8622 (uri (cran-uri "gee" version))
8625 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8626 (properties `((upstream-name . "gee")))
8627 (build-system r-build-system)
8629 `(("gfortran" ,gfortran)))
8630 (home-page "https://cran.r-project.org/web/packages/gee/")
8631 (synopsis "Generalized estimation equation solver")
8633 "This package provides a solver for generalized estimation equations.")
8634 (license license:gpl2)))
8636 (define-public r-tab
8643 (uri (cran-uri "tab" version))
8646 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8647 (properties `((upstream-name . "tab")))
8648 (build-system r-build-system)
8650 `(("r-dplyr" ,r-dplyr)
8652 ("r-knitr" ,r-knitr)
8654 ("r-survey" ,r-survey)
8655 ("r-survival" ,r-survival)
8656 ("r-xtable" ,r-xtable)))
8657 (home-page "https://cran.r-project.org/web/packages/tab/")
8658 (synopsis "Create summary tables for statistical reports")
8660 "This package contains functions for creating various types of summary
8661 tables, e.g. comparing characteristics across levels of a categorical variable
8662 and summarizing fitted generalized linear models, generalized estimating
8663 equations, and Cox proportional hazards models. Functions are available to
8664 handle data from simple random samples as well as complex surveys.")
8665 (license license:gpl3+)))
8667 (define-public r-dvmisc
8674 (uri (cran-uri "dvmisc" version))
8676 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8677 (build-system r-build-system)
8679 `(("r-cubature" ,r-cubature)
8680 ("r-data-table" ,r-data-table)
8681 ("r-dplyr" ,r-dplyr)
8682 ("r-ggplot2" ,r-ggplot2)
8684 ("r-mvtnorm" ,r-mvtnorm)
8685 ("r-pracma" ,r-pracma)
8686 ("r-rbenchmark" ,r-rbenchmark)
8688 ("r-survey" ,r-survey)
8690 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8691 (synopsis "Faster computation of common statistics and miscellaneous functions")
8693 "This package implements faster versions of base R functions (e.g. mean, standard
8694 deviation, covariance, weighted mean), mostly written in C++, along with
8695 miscellaneous functions for various purposes (e.g. create the histogram with
8696 fitted probability density function or probability mass function curve, create
8697 the body mass index groups, assess the linearity assumption in logistic
8699 (license license:gpl2)))
8701 (define-public r-accelerometry
8703 (name "r-accelerometry")
8708 (uri (cran-uri "accelerometry" version))
8710 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8711 (build-system r-build-system)
8713 `(("r-dvmisc" ,r-dvmisc)
8714 ("r-rcpp" ,r-rcpp)))
8715 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8716 (synopsis "Functions for processing accelerometer data")
8718 "This package provides a collection of functions that perform operations on
8719 time-series accelerometer data, such as identify the non-wear time, flag minutes
8720 that are part of an activity bout, and find the maximum 10-minute average count
8721 value. The functions are generally very flexible, allowing for a variety of
8722 algorithms to be implemented.")
8723 (license license:gpl3)))
8725 (define-public r-absim
8732 (uri (cran-uri "AbSim" version))
8734 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8735 (properties `((upstream-name . "AbSim")))
8736 (build-system r-build-system)
8739 ("r-powerlaw" ,r-powerlaw)))
8740 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8741 (synopsis "Time resolved simulations of antibody repertoires")
8743 "This package provides simulation methods for the evolution of antibody repertoires.
8744 The heavy and light chain variable region of both human and C57BL/6 mice can
8745 be simulated in a time-dependent fashion. Both single lineages using one set of
8746 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8747 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8748 Upon completion, the main loop of the algorithm begins, with each iteration
8749 representing one simulated time step. Various mutation events are possible at
8750 each time step, contributing to a diverse final repertoire.")
8751 (license license:gpl2)))
8753 (define-public r-quic
8760 (uri (cran-uri "QUIC" version))
8762 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8763 (properties `((upstream-name . "QUIC")))
8764 (build-system r-build-system)
8765 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8766 (synopsis "Regularized sparse inverse covariance matrix estimation")
8768 "This package implements the regularized Gaussian maximum likelihood
8769 estimation of the inverse of a covariance matrix. It uses Newton's method and
8770 coordinate descent to solve the regularized inverse covariance matrix
8771 estimation problem.")
8772 ;; The project home page states that the release is under GPLv3 or later.
8773 ;; The CRAN page only says GPL-3.
8774 (license license:gpl3+)))
8776 (define-public r-abundant
8783 (uri (cran-uri "abundant" version))
8785 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8786 (build-system r-build-system)
8788 `(("r-quic" ,r-quic)))
8789 (home-page "https://cran.r-project.org/web/packages/abundant/")
8790 (synopsis "Abundant regression and high-dimensional principal fitted components")
8792 "This package provides tools to fit and predict with the high-dimensional
8793 principal fitted components model. This model is described by Cook, Forzani,
8794 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8795 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8796 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8797 (license license:gpl2+)))
8799 (define-public r-ac3net
8806 (uri (cran-uri "Ac3net" version))
8808 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8809 (properties `((upstream-name . "Ac3net")))
8810 (build-system r-build-system)
8812 `(("r-data-table" ,r-data-table)))
8813 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8814 (synopsis "Inferring directional conservative causal core gene networks")
8815 (description "This package infers directional Conservative causal core
8816 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8817 directional network.")
8818 (license license:gpl3+)))
8820 (define-public r-aca
8827 (uri (cran-uri "ACA" version))
8829 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8830 (properties `((upstream-name . "ACA")))
8831 (build-system r-build-system)
8832 (home-page "https://cran.r-project.org/web/packages/ACA/")
8833 (synopsis "Abrupt change-point or aberration detection in point series")
8835 "This package offers an interactive function for the detection of breakpoints in
8837 ;; Any version of the GPL
8838 (license (list license:gpl2+ license:gpl3+))))
8840 (define-public r-acceptancesampling
8842 (name "r-acceptancesampling")
8847 (uri (cran-uri "AcceptanceSampling" version))
8849 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8851 `((upstream-name . "AcceptanceSampling")))
8852 (build-system r-build-system)
8853 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8854 (synopsis "Creation and evaluation of acceptance sampling plans")
8856 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8857 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8858 in quality control and improvement. International standards of acceptance
8859 sampling provide sampling plans for specific circumstances. The aim of this
8860 package is to provide an easy-to-use interface to visualize single, double or
8861 multiple sampling plans. In addition, methods have been provided to enable the
8862 user to assess sampling plans against pre-specified levels of performance, as
8863 measured by the probability of acceptance for a given level of quality in the
8865 (license license:gpl3+)))
8867 (define-public r-acclma
8874 (uri (cran-uri "ACCLMA" version))
8876 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8877 (properties `((upstream-name . "ACCLMA")))
8878 (build-system r-build-system)
8879 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8880 (synopsis "ACC & LMA graph plotting")
8882 "This package contains a function that imports data from a @acronym{CSV,
8883 Comma-Separated Values} file, or uses manually entered data from the format (x,
8884 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8885 Curve} vs @acronym{LOI, Line of Independence} graph and
8886 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8887 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8888 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8889 string) was passed, a manual data entry window is opened. The header parameter
8890 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8891 a header row or not. The dataset should contain only one independent variable
8892 (x) and one dependent variable (y) and can contain a weight for each
8894 (license license:gpl2)))
8896 (define-public r-aspi
8903 (uri (cran-uri "aspi" version))
8905 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8906 (build-system r-build-system)
8908 "https://cran.r-project.org/web/packages/aspi/")
8910 "Analysis of symmetry of parasitic infections")
8912 "This package provides tools for the analysis and visualization of bilateral
8913 asymmetry in parasitic infections.")
8914 (license license:gpl3+)))
8916 (define-public r-sandwich
8923 (uri (cran-uri "sandwich" version))
8926 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8927 (build-system r-build-system)
8929 `(("r-zoo" ,r-zoo)))
8930 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8931 (synopsis "Robust Covariance Matrix Estimators")
8933 "This package provides model-robust standard error estimators for
8934 cross-sectional, time series, clustered, panel, and longitudinal data.")
8935 ;; Either version of the license.
8936 (license (list license:gpl2 license:gpl3))))
8938 (define-public r-th-data
8945 (uri (cran-uri "TH.data" version))
8948 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8949 (properties `((upstream-name . "TH.data")))
8950 (build-system r-build-system)
8952 `(("r-mass" ,r-mass)
8953 ("r-survival" ,r-survival)))
8954 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8955 (synopsis "Shared data sets")
8957 "This package contains supporting data sets that are used in other
8958 packages maintained by Torsten Hothorn.")
8959 (license license:gpl3)))
8961 (define-public r-multcomp
8968 (uri (cran-uri "multcomp" version))
8971 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8972 (build-system r-build-system)
8974 `(("r-codetools" ,r-codetools)
8975 ("r-mvtnorm" ,r-mvtnorm)
8976 ("r-sandwich" ,r-sandwich)
8977 ("r-survival" ,r-survival)
8978 ("r-th-data" ,r-th-data)))
8979 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8980 (synopsis "Simultaneous inference in general parametric models")
8982 "Simultaneous tests and confidence intervals for general linear
8983 hypotheses in parametric models, including linear, generalized linear, linear
8984 mixed effects, and survival models. The package includes demos reproducing
8985 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8986 Hothorn, Westfall, 2010, CRC Press).")
8987 (license license:gpl2)))
8989 (define-public r-emmeans
8996 (uri (cran-uri "emmeans" version))
8999 "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k"))))
9000 (build-system r-build-system)
9002 `(("r-estimability" ,r-estimability)
9003 ("r-mvtnorm" ,r-mvtnorm)
9004 ("r-numderiv" ,r-numderiv)
9006 ("r-xtable" ,r-xtable)))
9008 `(("r-knitr" ,r-knitr)))
9009 (home-page "https://github.com/rvlenth/emmeans")
9010 (synopsis "Estimated marginal means, aka least-squares means")
9012 "This package provides tools to obtain @dfn{estimated marginal
9013 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9014 be used to compute contrasts or linear functions of EMMs, trends, and
9015 comparisons of slopes.")
9016 ;; Either version of the license.
9017 (license (list license:gpl2 license:gpl3))))
9019 (define-public r-pwr
9026 (uri (cran-uri "pwr" version))
9029 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9030 (build-system r-build-system)
9032 `(("r-knitr" ,r-knitr)))
9033 (home-page "https://github.com/heliosdrm/pwr")
9034 (synopsis "Basic functions for power analysis")
9036 "This package provides power analysis functions along the lines of
9038 (license license:gpl3+)))
9040 (define-public r-libcoin
9047 (uri (cran-uri "libcoin" version))
9049 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
9050 (build-system r-build-system)
9051 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9052 (home-page "https://cran.r-project.org/web/packages/libcoin")
9053 (synopsis "Linear test statistics for permutation inference")
9055 "This package provides basic infrastructure for linear test statistics
9056 and permutation inference in the framework of Strasser and Weber (1999).")
9057 (license license:gpl2)))
9059 (define-public r-coin
9066 (uri (cran-uri "coin" version))
9069 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
9070 (build-system r-build-system)
9072 `(("r-libcoin" ,r-libcoin)
9073 ("r-matrixstats" ,r-matrixstats)
9074 ("r-modeltools" ,r-modeltools)
9075 ("r-multcomp" ,r-multcomp)
9076 ("r-mvtnorm" ,r-mvtnorm)
9077 ("r-survival" ,r-survival)))
9078 (home-page "http://coin.r-forge.r-project.org")
9079 (synopsis "Conditional inference procedures in a permutation test framework")
9081 "This package provides conditional inference procedures for the general
9082 independence problem including two-sample, K-sample (non-parametric ANOVA),
9083 correlation, censored, ordered and multivariate problems.")
9084 (license license:gpl2)))
9086 (define-public r-bayesplot
9088 (name "r-bayesplot")
9093 (uri (cran-uri "bayesplot" version))
9096 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
9097 (build-system r-build-system)
9099 `(("pandoc" ,pandoc)
9100 ("pandoc-citeproc" ,pandoc-citeproc)))
9102 `(("r-knitr" ,r-knitr)))
9104 `(("r-dplyr" ,r-dplyr)
9105 ("r-ggplot2" ,r-ggplot2)
9106 ("r-ggridges" ,r-ggridges)
9108 ("r-reshape2" ,r-reshape2)
9109 ("r-rlang" ,r-rlang)
9110 ("r-tibble" ,r-tibble)
9111 ("r-tidyselect" ,r-tidyselect)))
9112 (home-page "https://mc-stan.org/bayesplot")
9113 (synopsis "Plotting for Bayesian models")
9115 "This package provides plotting functions for posterior analysis, model
9116 checking, and MCMC diagnostics. The package is designed not only to provide
9117 convenient functionality for users, but also a common set of functions that
9118 can be easily used by developers working on a variety of R packages for
9119 Bayesian modeling.")
9120 (license license:gpl3+)))
9122 (define-public r-tmb
9129 (uri (cran-uri "TMB" version))
9132 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
9133 (properties `((upstream-name . "TMB")))
9134 (build-system r-build-system)
9136 `(("r-matrix" ,r-matrix)
9137 ("r-rcppeigen" ,r-rcppeigen)))
9138 (home-page "http://tmb-project.org")
9139 (synopsis "Template model builder: a general random effect tool")
9141 "With this tool, a user should be able to quickly implement complex
9142 random effect models through simple C++ templates. The package combines
9143 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9144 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9145 from R) to obtain an efficient implementation of the applied Laplace
9146 approximation with exact derivatives. Key features are: Automatic sparseness
9147 detection, parallelism through BLAS and parallel user templates.")
9148 (license license:gpl2)))
9150 (define-public r-sjstats
9157 (uri (cran-uri "sjstats" version))
9159 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
9160 (build-system r-build-system)
9162 `(("r-bayestestr" ,r-bayestestr)
9163 ("r-broom" ,r-broom)
9164 ("r-dplyr" ,r-dplyr)
9165 ("r-effectsize" ,r-effectsize)
9166 ("r-emmeans" ,r-emmeans)
9167 ("r-insight" ,r-insight)
9169 ("r-magrittr" ,r-magrittr)
9171 ("r-modelr" ,r-modelr)
9172 ("r-parameters" ,r-parameters)
9173 ("r-performance" ,r-performance)
9174 ("r-purrr" ,r-purrr)
9175 ("r-rlang" ,r-rlang)
9176 ("r-sjlabelled" ,r-sjlabelled)
9177 ("r-sjmisc" ,r-sjmisc)
9178 ("r-tidyr" ,r-tidyr)))
9179 (home-page "https://github.com/strengejacke/sjstats")
9180 (synopsis "Functions for common statistical computations")
9182 "This package provides a collection of convenient functions for common
9183 statistical computations, which are not directly provided by R's @code{base}
9184 or @code{stats} packages. This package aims at providing, first, shortcuts
9185 for statistical measures, which otherwise could only be calculated with
9186 additional effort. Second, these shortcut functions are generic, and can be
9187 applied not only to vectors, but also to other objects as well. The focus of
9188 most functions lies on summary statistics or fit measures for regression
9189 models, including generalized linear models, mixed effects models and Bayesian
9191 (license license:gpl3)))
9193 (define-public r-glmmtmb
9200 (uri (cran-uri "glmmTMB" version))
9203 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9204 (properties `((upstream-name . "glmmTMB")))
9205 (build-system r-build-system)
9207 `(("r-lme4" ,r-lme4)
9208 ("r-matrix" ,r-matrix)
9210 ("r-rcppeigen" ,r-rcppeigen)
9213 `(("r-knitr" ,r-knitr))) ; for vignettes
9214 (home-page "https://github.com/glmmTMB")
9215 (synopsis "Generalized linear mixed models")
9217 "Fit linear and generalized linear mixed models with various extensions,
9218 including zero-inflation. The models are fitted using maximum likelihood
9219 estimation via the Template Model Builder. Random effects are assumed to be
9220 Gaussian on the scale of the linear predictor and are integrated out using the
9221 Laplace approximation. Gradients are calculated using automatic
9223 (license license:agpl3+)))
9225 (define-public r-bayestestr
9227 (name "r-bayestestr")
9232 (uri (cran-uri "bayestestR" version))
9235 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2"))))
9236 (properties `((upstream-name . "bayestestR")))
9237 (build-system r-build-system)
9239 `(("r-insight" ,r-insight)))
9241 `(("r-knitr" ,r-knitr)))
9242 (home-page "https://github.com/easystats/bayestestR")
9243 (synopsis "Describe Bayesian models and posterior distributions")
9245 "This package provides utilities to understand and describe posterior
9246 distributions and Bayesian models. It includes point-estimates such as
9247 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9248 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9249 ROPE percentage and pd).")
9250 (license license:gpl3)))
9252 (define-public r-performance
9254 (name "r-performance")
9259 (uri (cran-uri "performance" version))
9262 "01csmn52d6rhlmcj7gi6ckc6v6a8pymnrpx9l729h13igxsnaf28"))))
9263 (build-system r-build-system)
9265 `(("r-bayestestr" ,r-bayestestr)
9266 ("r-insight" ,r-insight)))
9267 (home-page "https://easystats.github.io/performance/")
9268 (synopsis "Assessment of regression models performance")
9270 "This package provides utilities for computing measures to assess model
9271 quality, which are not directly provided by R's @code{base} or @code{stats}
9272 packages. These include e.g. measures like r-squared, intraclass correlation
9273 coefficient, root mean squared error or functions to check models for
9274 overdispersion, singularity or zero-inflation and more. Functions apply to a
9275 large variety of regression models, including generalized linear models, mixed
9276 effects models and Bayesian models.")
9277 (license license:gpl3)))
9279 (define-public r-ggeffects
9281 (name "r-ggeffects")
9286 (uri (cran-uri "ggeffects" version))
9289 "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5"))))
9290 (build-system r-build-system)
9292 `(("r-insight" ,r-insight)
9294 ("r-sjlabelled" ,r-sjlabelled)))
9296 `(("r-knitr" ,r-knitr)))
9297 (home-page "https://github.com/strengejacke/ggeffects")
9298 (synopsis "Create tidy data frames of marginal effects for ggplot")
9300 "This package provides tools to compute marginal effects from statistical
9301 models and return the result as tidy data frames. These data frames are ready
9302 to use with the @code{ggplot2} package. Marginal effects can be calculated
9303 for many different models. Interaction terms, splines and polynomial terms
9304 are also supported. The two main functions are @code{ggpredict()} and
9305 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9306 results using @code{ggplot2}.")
9307 (license license:gpl3)))
9309 (define-public r-effectsize
9311 (name "r-effectsize")
9316 (uri (cran-uri "effectsize" version))
9319 "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9"))))
9320 (properties `((upstream-name . "effectsize")))
9321 (build-system r-build-system)
9323 `(("r-bayestestr" ,r-bayestestr)
9324 ("r-insight" ,r-insight)
9325 ("r-parameters" ,r-parameters)))
9327 `(("r-knitr" ,r-knitr)))
9328 (home-page "https://github.com/easystats/effectsize")
9329 (synopsis "Indices of effect size and standardized parameters")
9331 "This package provides utilities to work with indices of effect size and
9332 standardized parameters for a wide variety of models, allowing computation and
9333 conversion of indices such as Cohen's d, r, odds, etc.")
9334 (license license:gpl3)))
9336 (define-public r-sjplot
9343 (uri (cran-uri "sjPlot" version))
9345 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9346 (properties `((upstream-name . "sjPlot")))
9347 (build-system r-build-system)
9349 `(("r-bayestestr" ,r-bayestestr)
9350 ("r-dplyr" ,r-dplyr)
9351 ("r-effectsize" ,r-effectsize)
9352 ("r-ggeffects" ,r-ggeffects)
9353 ("r-ggplot2" ,r-ggplot2)
9354 ("r-insight" ,r-insight)
9355 ("r-knitr" ,r-knitr)
9357 ("r-parameters" ,r-parameters)
9358 ("r-performance" ,r-performance)
9359 ("r-purrr" ,r-purrr)
9360 ("r-rlang" ,r-rlang)
9361 ("r-scales" ,r-scales)
9362 ("r-sjlabelled" ,r-sjlabelled)
9363 ("r-sjmisc" ,r-sjmisc)
9364 ("r-sjstats" ,r-sjstats)
9365 ("r-tidyr" ,r-tidyr)))
9367 `(("r-knitr" ,r-knitr)))
9368 (home-page "https://strengejacke.github.io/sjPlot/")
9369 (synopsis "Data visualization for statistics in social science")
9371 "This package represents a collection of plotting and table output
9372 functions for data visualization. Results of various statistical
9373 analyses (that are commonly used in social sciences) can be visualized using
9374 this package, including simple and cross tabulated frequencies, histograms,
9375 box plots, (generalized) linear models, mixed effects models, principal
9376 component analysis and correlation matrices, cluster analyses, scatter plots,
9377 stacked scales, effects plots of regression models (including interaction
9378 terms) and much more. This package supports labelled data.")
9379 (license license:gpl3)))
9381 (define-public r-ini
9388 (uri (cran-uri "ini" version))
9391 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9392 (build-system r-build-system)
9393 (home-page "https://github.com/dvdscripter/ini")
9394 (synopsis "Read and write configuration files")
9396 "This package provides tools to parse simple @code{.ini} configuration
9397 files to an structured list. Users can manipulate this resulting list with
9398 @code{lapply()} functions. This same structured list can be used to write
9399 back to file after modifications.")
9400 (license license:gpl3)))
9409 (uri (cran-uri "gh" version))
9412 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9413 (build-system r-build-system)
9418 ("r-jsonlite" ,r-jsonlite)))
9419 (home-page "https://github.com/r-lib/gh#readme")
9420 (synopsis "Access the GitHub API via R")
9422 "This package provides a minimal R client to access the GitHub API.")
9423 (license license:expat)))
9432 (uri (cran-uri "fs" version))
9435 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9436 (build-system r-build-system)
9438 `(("r-knitr" ,r-knitr)))
9439 (home-page "https://fs.r-lib.org")
9440 (synopsis "Cross-platform file system operations based on libuv")
9442 "This package provides a cross-platform interface to file system
9443 operations, built on top of the libuv C library.")
9444 (license license:gpl3)))
9446 (define-public r-clisymbols
9448 (name "r-clisymbols")
9453 (uri (cran-uri "clisymbols" version))
9456 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9457 (build-system r-build-system)
9458 (home-page "https://github.com/gaborcsardi/clisymbols")
9459 (synopsis "Unicode symbols at the R prompt")
9461 "This package provides a small subset of Unicode symbols, that are useful
9462 when building command line applications. They fall back to alternatives on
9463 terminals that do not support Unicode.")
9464 (license license:expat)))
9466 (define-public r-usethis
9473 (uri (cran-uri "usethis" version))
9476 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9477 (build-system r-build-system)
9480 ("r-clipr" ,r-clipr)
9481 ("r-crayon" ,r-crayon)
9486 ("r-git2r" ,r-git2r)
9488 ("r-purrr" ,r-purrr)
9489 ("r-rematch2" ,r-rematch2)
9490 ("r-rlang" ,r-rlang)
9491 ("r-rprojroot" ,r-rprojroot)
9492 ("r-rstudioapi" ,r-rstudioapi)
9493 ("r-whisker" ,r-whisker)
9494 ("r-withr" ,r-withr)
9495 ("r-yaml" ,r-yaml)))
9496 (home-page "https://github.com/r-lib/usethis")
9497 (synopsis "Automate R package and project setup")
9499 "This package helps you to automate R package and project setup tasks
9500 that are otherwise performed manually. This includes setting up unit testing,
9501 test coverage, continuous integration, Git, GitHub integration, licenses,
9502 Rcpp, RStudio projects, and more.")
9503 (license license:gpl3)))
9505 (define-public r-sessioninfo
9507 (name "r-sessioninfo")
9512 (uri (cran-uri "sessioninfo" version))
9515 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9516 (build-system r-build-system)
9519 ("r-withr" ,r-withr)))
9520 (home-page "https://github.com/r-lib/sessioninfo#readme")
9521 (synopsis "R session information")
9523 "This package provides tools to query and print information about the
9524 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9525 more information about packages, and where they were installed from.")
9526 (license license:gpl2)))
9528 (define-public r-remotes
9535 (uri (cran-uri "remotes" version))
9538 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9539 (build-system r-build-system)
9541 `(("r-knitr" ,r-knitr)))
9542 (home-page "https://github.com/r-lib/remotes#readme")
9543 (synopsis "R package installation from remote repositories")
9545 "Download and install R packages stored in GitHub, BitBucket, or plain
9546 subversion or git repositories. This package is a lightweight replacement of
9547 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9548 the code was copied over from @code{devtools}.")
9549 (license license:gpl2+)))
9551 (define-public r-xopen
9558 (uri (cran-uri "xopen" version))
9561 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9562 (build-system r-build-system)
9564 `(("r-processx" ,r-processx)))
9565 (home-page "https://github.com/r-lib/xopen#readme")
9566 (synopsis "Open system files, URLs, anything")
9568 "This package provides a cross-platform solution to open files,
9569 directories or URLs with their associated programs.")
9570 (license license:expat)))
9572 (define-public r-rcmdcheck
9574 (name "r-rcmdcheck")
9579 (uri (cran-uri "rcmdcheck" version))
9582 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9583 (build-system r-build-system)
9585 `(("r-callr" ,r-callr)
9587 ("r-crayon" ,r-crayon)
9589 ("r-digest" ,r-digest)
9590 ("r-pkgbuild" ,r-pkgbuild)
9591 ("r-prettyunits" ,r-prettyunits)
9593 ("r-rprojroot" ,r-rprojroot)
9594 ("r-sessioninfo" ,r-sessioninfo)
9595 ("r-withr" ,r-withr)
9596 ("r-xopen" ,r-xopen)))
9597 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9598 (synopsis "Run R CMD check from R and capture results")
9600 "Run @code{R CMD check} from R programmatically, and capture the results
9601 of the individual checks.")
9602 (license license:expat)))
9604 (define-public r-rapportools
9606 (name "r-rapportools")
9611 (uri (cran-uri "rapportools" version))
9614 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9615 (build-system r-build-system)
9617 `(("r-pander" ,r-pander)
9619 ("r-reshape" ,r-reshape)))
9620 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9621 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9623 "This package provides helper functions that act as wrappers to more
9624 advanced statistical methods with the advantage of having sane defaults for
9626 (license license:agpl3+)))
9628 (define-public r-pander
9635 (uri (cran-uri "pander" version))
9638 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9639 (build-system r-build-system)
9641 `(("r-digest" ,r-digest)
9642 ("r-rcpp" ,r-rcpp)))
9643 (home-page "https://rapporter.github.io/pander")
9644 (synopsis "Render R objects into Pandoc's markdown")
9646 "The main aim of the pander R package is to provide a minimal and easy
9647 tool for rendering R objects into Pandoc's markdown. The package is also
9648 capable of exporting/converting complex Pandoc documents (reports) in various
9650 ;; This package is licensed under either the AGPLv3+ or the very rarely
9652 (license license:agpl3+)))
9654 (define-public r-summarytools
9656 (name "r-summarytools")
9661 (uri (cran-uri "summarytools" version))
9664 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9665 (build-system r-build-system)
9667 `(("r-base64enc" ,r-base64enc)
9668 ("r-checkmate" ,r-checkmate)
9669 ("r-dplyr" ,r-dplyr)
9670 ("r-htmltools" ,r-htmltools)
9671 ("r-lubridate" ,r-lubridate)
9672 ("r-magick" ,r-magick)
9673 ("r-matrixstats" ,r-matrixstats)
9674 ("r-pander" ,r-pander)
9676 ("r-rapportools" ,r-rapportools)
9677 ("r-tibble" ,r-tibble)
9678 ("r-tidyr" ,r-tidyr)))
9679 (home-page "https://github.com/dcomtois/summarytools")
9680 (synopsis "Tools to quickly and neatly summarize data")
9682 "This package provides tools for data frame summaries, cross-tabulations,
9683 weight-enabled frequency tables and common univariate statistics in concise
9684 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9685 good point-of-entry for exploring data, both for experienced and new R
9687 (license license:gpl2)))
9689 (define-public r-lsei
9696 (uri (cran-uri "lsei" version))
9699 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9700 (build-system r-build-system)
9702 `(("gfortran" ,gfortran)))
9703 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9704 (synopsis "Solve regression problems under equality/inequality constraints")
9706 "It contains functions that solve least squares linear regression
9707 problems under linear equality/inequality constraints. Functions for solving
9708 quadratic programming problems are also available, which transform such
9709 problems into least squares ones first.")
9710 (license license:gpl2+)))
9712 (define-public r-npsurv
9719 (uri (cran-uri "npsurv" version))
9722 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9723 (build-system r-build-system)
9725 `(("r-lsei" ,r-lsei)))
9726 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9727 (synopsis "Nonparametric survival analysis")
9729 "This package contains functions for non-parametric survival analysis of
9730 exact and interval-censored observations.")
9731 (license license:gpl2+)))
9733 (define-public r-clusteval
9735 (name "r-clusteval")
9740 (uri (cran-uri "clusteval" version))
9743 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9744 (build-system r-build-system)
9746 `(("r-mvtnorm" ,r-mvtnorm)
9747 ("r-rcpp" ,r-rcpp)))
9748 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9749 (synopsis "Evaluation of clustering algorithms")
9751 "This R package provides a suite of tools to evaluate clustering
9752 algorithms, clusterings, and individual clusters.")
9753 (license license:expat)))
9755 (define-public r-tweedie
9762 (uri (cran-uri "tweedie" version))
9765 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9766 (build-system r-build-system)
9767 (native-inputs `(("gfortran" ,gfortran)))
9768 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9769 (synopsis "Evaluation of Tweedie exponential family models")
9771 "Maximum likelihood computations for Tweedie families, including the
9772 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9773 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9774 and related methods.")
9775 (license license:gpl2+)))
9777 (define-public r-rcppgsl
9784 (uri (cran-uri "RcppGSL" version))
9786 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9787 (properties `((upstream-name . "RcppGSL")))
9788 (build-system r-build-system)
9790 `(("r-rcpp" ,r-rcpp)
9792 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9793 (synopsis "Rcpp integration for GSL vectors and matrices")
9795 "The GNU Scientific Library (or GSL) is a collection of numerical
9796 routines for scientific computing. It is particularly useful for C and C++
9797 programs as it provides a standard C interface to a wide range of mathematical
9798 routines. There are over 1000 functions in total with an extensive test
9799 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9800 structures and R using concepts from Rcpp which is itself a package that eases
9801 the interfaces between R and C++.")
9802 (license license:gpl2+)))
9804 (define-public r-mvabund
9811 (uri (cran-uri "mvabund" version))
9814 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9815 (build-system r-build-system)
9817 `(("r-mass" ,r-mass)
9819 ("r-rcppgsl" ,r-rcppgsl)
9820 ("r-statmod" ,r-statmod)
9821 ("r-tweedie" ,r-tweedie)))
9822 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9823 (synopsis "Statistical methods for analysing multivariate abundance data")
9825 "This package provides a set of tools for displaying, modeling and
9826 analysing multivariate abundance data in community ecology.")
9827 (license license:lgpl2.1+)))
9829 (define-public r-afex
9836 (uri (cran-uri "afex" version))
9839 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9840 (build-system r-build-system)
9844 ("r-lmertest" ,r-lmertest)
9845 ("r-pbkrtest" ,r-pbkrtest)
9846 ("r-reshape2" ,r-reshape2)))
9848 `(("r-knitr" ,r-knitr)))
9849 (home-page "https://afex.singmann.science/")
9850 (synopsis "Analysis of factorial experiments")
9852 "This package provides convenience functions for analyzing factorial
9853 experiments using ANOVA or mixed models.")
9854 (license license:gpl2+)))
9856 (define-public r-lmertest
9863 (uri (cran-uri "lmerTest" version))
9866 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9867 (properties `((upstream-name . "lmerTest")))
9868 (build-system r-build-system)
9870 `(("r-ggplot2" ,r-ggplot2)
9873 ("r-numderiv" ,r-numderiv)))
9874 (home-page "https://github.com/runehaubo/lmerTestR")
9875 (synopsis "Tests in linear mixed effects models")
9877 "This package provides p-values in type I, II or III anova and summary
9878 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9879 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9880 package. Model selection methods include step, drop1 and anova-like tables
9881 for random effects (ranova). Methods for Least-Square means (LS-means) and
9882 tests of linear contrasts of fixed effects are also available.")
9883 (license license:gpl2+)))
9885 (define-public r-r2glmm
9892 (uri (cran-uri "r2glmm" version))
9895 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9896 (build-system r-build-system)
9898 `(("r-afex" ,r-afex)
9899 ("r-data-table" ,r-data-table)
9900 ("r-dplyr" ,r-dplyr)
9901 ("r-ggplot2" ,r-ggplot2)
9902 ("r-gridextra" ,r-gridextra)
9903 ("r-lmertest" ,r-lmertest)
9905 ("r-matrix" ,r-matrix)
9907 ("r-pbkrtest" ,r-pbkrtest)))
9908 (home-page "https://github.com/bcjaeger/r2glmm")
9909 (synopsis "Compute R squared for mixed (multilevel) models")
9911 "This package computes model and semi partial R squared with confidence
9912 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9913 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9914 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9916 (license license:gpl2)))
9918 (define-public r-weights
9925 (uri (cran-uri "weights" version))
9928 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9929 (build-system r-build-system)
9931 `(("r-gdata" ,r-gdata)
9932 ("r-hmisc" ,r-hmisc)
9933 ("r-mice" ,r-mice)))
9935 "https://cran.r-project.org/web/packages/weights/")
9936 (synopsis "Weighting and weighted statistics")
9937 (description "This package Provides a variety of functions for producing
9938 simple weighted statistics, such as weighted Pearson's correlations, partial
9939 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9940 includes some software for quickly recoding survey data and plotting point
9941 estimates from interaction terms in regressions (and multiply imputed
9942 regressions). NOTE: Weighted partial correlation calculations pulled to
9944 (license license:gpl2+)))
9946 (define-public r-rcppannoy
9948 (name "r-rcppannoy")
9953 (uri (cran-uri "RcppAnnoy" version))
9956 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9957 (properties `((upstream-name . "RcppAnnoy")))
9958 (build-system r-build-system)
9960 `(("r-rcpp" ,r-rcpp)))
9961 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9962 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9964 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9965 for efficient memory usage as well an ability to load from and save to disk.
9966 This package provides an R interface.")
9967 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9969 (license (list license:gpl2+ license:asl2.0))))
9971 (define-public r-rcpphnsw
9978 (uri (cran-uri "RcppHNSW" version))
9981 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
9982 (properties `((upstream-name . "RcppHNSW")))
9983 (build-system r-build-system)
9984 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9985 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9986 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9988 "Hnswlib is a C++ library for approximate nearest neighbors. This
9989 package provides a minimal R interface by relying on the Rcpp package.")
9990 ;; hnswlib is released under Version 2.0 of the Apache License.
9991 (license (list license:gpl3 license:asl2.0))))
9993 (define-public r-rcppparallel
9995 (name "r-rcppparallel")
10000 (uri (cran-uri "RcppParallel" version))
10003 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10004 (properties `((upstream-name . "RcppParallel")))
10005 (build-system r-build-system)
10006 (home-page "https://rcppcore.github.io/RcppParallel/")
10007 (synopsis "Parallel programming tools for Rcpp")
10009 "This package provides high level functions for parallel programming with
10010 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10011 the work of a standard serial @code{for} loop into a parallel one and the
10012 @code{parallelReduce()} function can be used for accumulating aggregates or
10014 (license license:gpl2)))
10016 (define-public r-ncdf4
10023 (uri (cran-uri "ncdf4" version))
10026 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10027 (build-system r-build-system)
10029 `(("netcdf" ,netcdf)
10031 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10032 (synopsis "R interface to Unidata netCDF format data files")
10034 "This package provides a high-level R interface to data files written
10035 using Unidata's netCDF library (version 4 or earlier), which are binary data
10036 files that are portable across platforms and include metadata information in
10037 addition to the data sets. Using this package, netCDF files can be opened and
10038 data sets read in easily. It is also easy to create new netCDF dimensions,
10039 variables, and files, in either version 3 or 4 format, and manipulate existing
10041 (license license:gpl3+)))
10043 (define-public r-biocmanager
10045 (name "r-biocmanager")
10046 (version "1.30.10")
10050 (uri (cran-uri "BiocManager" version))
10052 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10053 (properties `((upstream-name . "BiocManager")))
10054 (build-system r-build-system)
10055 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10056 (synopsis "Access the Bioconductor project package repository")
10058 "This package provides a convenient tool to install and update
10059 Bioconductor packages.")
10060 (license license:artistic2.0)))
10062 (define-public r-rgl
10065 (version "0.100.54")
10069 (uri (cran-uri "rgl" version))
10072 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
10073 (build-system r-build-system)
10075 `(("pkg-config" ,pkg-config)))
10077 `(("freetype" ,freetype)
10084 `(("r-crosstalk" ,r-crosstalk)
10085 ("r-htmltools" ,r-htmltools)
10086 ("r-htmlwidgets" ,r-htmlwidgets)
10087 ("r-jsonlite" ,r-jsonlite)
10088 ("r-knitr" ,r-knitr)
10089 ("r-magrittr" ,r-magrittr)
10090 ("r-manipulatewidget" ,r-manipulatewidget)
10091 ("r-shiny" ,r-shiny)))
10092 (home-page "https://r-forge.r-project.org/projects/rgl/")
10093 (synopsis "3D visualization using OpenGL")
10095 "This package provides medium to high level functions for 3D interactive graphics,
10096 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
10097 as functions for constructing representations of geometric
10098 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
10099 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
10100 image formats, including PNG, Postscript, SVG, PGF.")
10101 ;; Any version of the GPL.
10102 (license (list license:gpl2+ license:gpl3+))))
10104 (define-public r-multicool
10106 (name "r-multicool")
10111 (uri (cran-uri "multicool" version))
10114 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
10115 (build-system r-build-system)
10116 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10117 (home-page "https://cran.r-project.org/web/packages/multicool/")
10118 (synopsis "Permutations of multisets in cool-lex order")
10120 "This package provides a set of tools to permute multisets without loops
10121 or hash tables and to generate integer partitions. Cool-lex order is similar
10122 to colexicographical order.")
10123 (license license:gpl2)))
10125 (define-public r-misc3d
10132 (uri (cran-uri "misc3d" version))
10135 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
10136 (build-system r-build-system)
10137 (home-page "https://cran.r-project.org/web/packages/misc3d/")
10138 (synopsis "Miscellaneous 3D Plots")
10140 "This package provides a collection of miscellaneous 3d plots, including
10142 ;; Any version of the GPL.
10143 (license (list license:gpl2+ license:gpl3+))))
10145 (define-public r-ks
10152 (uri (cran-uri "ks" version))
10154 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
10155 (build-system r-build-system)
10158 ("r-kernlab" ,r-kernlab)
10159 ("r-kernsmooth" ,r-kernsmooth)
10160 ("r-matrix" ,r-matrix)
10161 ("r-mclust" ,r-mclust)
10163 ("r-multicool" ,r-multicool)
10164 ("r-mvtnorm" ,r-mvtnorm)))
10165 (home-page "http://www.mvstat.net/tduong/")
10166 (synopsis "Kernel smoothing")
10168 "This package provides kernel smoothers for univariate and multivariate
10169 data, including density functions, density derivatives, cumulative
10170 distributions, modal clustering, discriminant analysis, and two-sample
10171 hypothesis testing.")
10172 ;; Either version of the GPL.
10173 (license (list license:gpl2 license:gpl3))))
10175 (define-public r-feature
10182 (uri (cran-uri "feature" version))
10185 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
10186 (build-system r-build-system)
10189 ("r-misc3d" ,r-misc3d)
10191 (home-page "http://www.mvstat.net/tduong/")
10192 (synopsis "Inferential feature significance for kernel density estimation")
10194 "The feature package contains functions to display and compute kernel
10195 density estimates, significant gradient and significant curvature regions.
10196 Significant gradient and/or curvature regions often correspond to significant
10197 features (e.g. local modes).")
10198 ;; Either version of the GPL.
10199 (license (list license:gpl2 license:gpl3))))
10201 (define-public r-arm
10208 (uri (cran-uri "arm" version))
10211 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10212 (build-system r-build-system)
10214 `(("r-abind" ,r-abind)
10216 ("r-hmisc" ,r-hmisc)
10219 ("r-matrix" ,r-matrix)
10220 ("r-nlme" ,r-nlme)))
10221 (home-page "https://cran.r-project.org/web/packages/arm/")
10222 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10224 "This package provides functions to accompany A. Gelman and J. Hill,
10225 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10226 University Press, 2007.")
10227 (license license:gpl3+)))
10229 (define-public r-circular
10231 (name "r-circular")
10236 (uri (cran-uri "circular" version))
10239 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10240 (build-system r-build-system)
10242 `(("r-boot" ,r-boot)
10243 ("r-mvtnorm" ,r-mvtnorm)))
10245 `(("gfortran" ,gfortran)))
10246 (home-page "https://cran.r-project.org/web/packages/circular/")
10247 (synopsis "Circular statistics")
10249 "This package provides tools for circular statistics, from \"Topics in
10250 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10252 (license license:gpl2+)))
10254 (define-public r-activity
10256 (name "r-activity")
10261 (uri (cran-uri "activity" version))
10264 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10265 (build-system r-build-system)
10267 `(("r-circular" ,r-circular)
10268 ("r-insol" ,r-insol)
10269 ("r-pbapply" ,r-pbapply)))
10270 (home-page "https://cran.r-project.org/web/packages/activity/")
10271 (synopsis "Animal activity statistics")
10273 "This package provides functions to fit kernel density functions to
10274 animal activity time data; plot activity distributions; quantify overall
10275 levels of activity; statistically compare activity metrics through
10276 bootstrapping; and evaluate variation in linear variables with time (or other
10277 circular variables).")
10278 (license license:gpl3)))
10280 (define-public r-ouch
10287 (uri (cran-uri "ouch" version))
10290 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10291 (build-system r-build-system)
10292 (propagated-inputs `(("r-subplex" ,r-subplex)))
10293 (home-page "https://kingaa.github.io/ouch/")
10294 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10296 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10297 for evolution along a phylogenetic tree.")
10298 (license license:gpl2+)))
10300 (define-public r-fmsb
10307 (uri (cran-uri "fmsb" version))
10310 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10311 (build-system r-build-system)
10312 (home-page "http://minato.sip21c.org/msb/")
10313 (synopsis "Functions for medical statistics book with demographic data")
10315 "This package provides several utility functions for the book entitled
10316 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10317 Japan, 2007) with Japanese demographic data and some demographic analysis
10318 related functions.")
10319 (license license:gpl2+)))
10321 (define-public r-stabledist
10323 (name "r-stabledist")
10328 (uri (cran-uri "stabledist" version))
10331 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10332 (build-system r-build-system)
10333 (home-page "https://www.rmetrics.org")
10334 (synopsis "Stable distribution functions")
10336 "This package provides density, probability and quantile functions, and
10337 random number generation for (skew) stable distributions, using the
10338 parametrizations of Nolan.")
10339 (license license:gpl2+)))
10341 (define-public r-gsl
10348 (uri (cran-uri "gsl" version))
10351 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10352 (build-system r-build-system)
10355 (home-page "https://cran.r-project.org/web/packages/gsl")
10356 (synopsis "Wrapper for the GNU Scientific Library")
10358 "This package provides an R wrapper for the special functions and quasi
10359 random number generators of the GNU Scientific Library.")
10360 (license license:gpl2+)))
10362 (define-public r-adgoftest
10364 (name "r-adgoftest")
10369 (uri (cran-uri "ADGofTest" version))
10372 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10373 (properties `((upstream-name . "ADGofTest")))
10374 (build-system r-build-system)
10375 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10376 (synopsis "Anderson-Darling GoF test")
10378 "This package provides an implementation of the Anderson-Darling GoF test
10379 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10380 Anderson-Darling Distribution\".")
10381 ;; Any version of the GPL.
10382 (license license:gpl3+)))
10384 (define-public r-softimpute
10386 (name "r-softimpute")
10391 (uri (cran-uri "softImpute" version))
10394 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10395 (properties `((upstream-name . "softImpute")))
10396 (build-system r-build-system)
10398 `(("r-matrix" ,r-matrix)))
10400 `(("gfortran" ,gfortran)))
10401 (home-page "https://cran.r-project.org/web/packages/softImpute")
10402 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10404 "This package provides iterative methods for matrix completion that use
10405 nuclear-norm regularization. The package includes procedures for centering
10406 and scaling rows, columns or both, and for computing low-rank @dfn{single
10407 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10409 (license license:gpl2)))
10411 (define-public r-fftwtools
10413 (name "r-fftwtools")
10418 (uri (cran-uri "fftwtools" version))
10421 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10422 (build-system r-build-system)
10423 (inputs `(("fftw" ,fftw)))
10424 (home-page "https://github.com/krahim/fftwtools")
10425 (synopsis "Wrapper for FFTW3")
10427 "This package provides a wrapper for several FFTW functions. It provides
10428 access to the two-dimensional FFT, the multivariate FFT, and the
10429 one-dimensional real to complex FFT using the FFTW3 library. The package
10430 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10431 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10432 The FFT functions have a parameter that allows them to not return the
10433 redundant complex conjugate when the input is real data.")
10434 (license license:gpl2+)))
10436 (define-public r-tiff
10443 (uri (cran-uri "tiff" version))
10446 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10447 (build-system r-build-system)
10449 `(("libtiff" ,libtiff)
10450 ("libjpeg" ,libjpeg-turbo)
10452 (home-page "https://www.rforge.net/tiff/")
10453 (synopsis "Read and write TIFF images")
10455 "This package provides an easy and simple way to read, write and display
10456 bitmap images stored in the TIFF format. It can read and write both files and
10457 in-memory raw vectors.")
10458 ;; Either of these two license versions.
10459 (license (list license:gpl2 license:gpl3))))
10461 (define-public r-nlp
10468 (uri (cran-uri "NLP" version))
10471 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10472 (properties `((upstream-name . "NLP")))
10473 (build-system r-build-system)
10474 (home-page "https://cran.r-project.org/web/packages/NLP/")
10475 (synopsis "Natural language processing infrastructure")
10477 "This package provides basic classes and methods for Natural Language
10479 (license license:gpl3)))
10481 (define-public r-tm
10488 (uri (cran-uri "tm" version))
10491 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10492 (properties `((upstream-name . "tm")))
10493 (build-system r-build-system)
10499 ("r-xml2" ,r-xml2)))
10500 (home-page "http://tm.r-forge.r-project.org/")
10501 (synopsis "Text mining package")
10503 "This package provides a framework for text mining applications within R.")
10504 (license license:gpl3)))
10506 (define-public r-waveslim
10508 (name "r-waveslim")
10513 (uri (cran-uri "waveslim" version))
10516 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10517 (build-system r-build-system)
10519 `(("gfortran" ,gfortran)))
10520 (home-page "http://waveslim.blogspot.com")
10521 (synopsis "Basic wavelet routines for signal processing")
10523 "This package provides basic wavelet routines for time series (1D),
10524 image (2D) and array (3D) analysis. The code provided here is based on
10525 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10526 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10527 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10528 pairs (Selesnick 2001, 2002).")
10529 (license license:bsd-3)))
10531 (define-public r-wordcloud
10533 (name "r-wordcloud")
10538 (uri (cran-uri "wordcloud" version))
10541 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10542 (build-system r-build-system)
10544 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10546 ;; The "tm" package is only "suggested" according to CRAN, but the
10547 ;; wordcloud package cannot be loaded without it.
10549 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10550 (synopsis "Word clouds")
10552 "This package provides functionality to create pretty word clouds,
10553 visualize differences and similarity between documents, and avoid
10554 over-plotting in scatter plots with text.")
10555 (license license:lgpl2.1)))
10557 (define-public r-colorramps
10559 (name "r-colorramps")
10564 (uri (cran-uri "colorRamps" version))
10567 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10568 (properties `((upstream-name . "colorRamps")))
10569 (build-system r-build-system)
10570 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10571 (synopsis "Build color tables")
10572 (description "This package provides features to build gradient color
10574 ;; Any version of the GPL
10575 (license license:gpl3+)))
10577 (define-public r-tidytree
10579 (name "r-tidytree")
10584 (uri (cran-uri "tidytree" version))
10586 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10587 (build-system r-build-system)
10590 ("r-dplyr" ,r-dplyr)
10591 ("r-lazyeval" ,r-lazyeval)
10592 ("r-magrittr" ,r-magrittr)
10593 ("r-rlang" ,r-rlang)
10594 ("r-tibble" ,r-tibble)))
10596 `(("r-knitr" ,r-knitr)))
10597 (home-page "https://github.com/GuangchuangYu/tidytree")
10598 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10600 "Phylogenetic trees generally contain multiple components including nodes,
10601 edges, branches and associated data. This package provides an approach to
10602 convert tree objects to tidy data frames. It also provides tidy interfaces to
10603 manipulate tree data.")
10604 (license license:artistic2.0)))
10606 (define-public r-rvcheck
10613 (uri (cran-uri "rvcheck" version))
10615 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10616 (build-system r-build-system)
10618 `(("r-biocmanager" ,r-biocmanager)
10619 ("r-rlang" ,r-rlang)))
10620 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10621 (synopsis "R package version check")
10623 "This package provides tools to check the latest release version of R and
10624 R packages (on CRAN, Bioconductor or Github).")
10625 (license license:artistic2.0)))
10627 (define-public r-docopt
10634 (uri (cran-uri "docopt" version))
10637 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10638 (build-system r-build-system)
10639 (home-page "https://github.com/docopt/docopt.R")
10640 (synopsis "Command-line interface specification language")
10642 "This package enables you to define a command-line interface by just
10643 giving it a description in the specific format.")
10644 (license license:expat)))
10646 (define-public r-sparsesvd
10648 (name "r-sparsesvd")
10653 (uri (cran-uri "sparsesvd" version))
10656 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10657 (build-system r-build-system)
10658 (propagated-inputs `(("r-matrix" ,r-matrix)))
10659 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10660 (synopsis "Sparse truncated singular value decomposition")
10662 "This package provides a Wrapper around the SVDLIBC library
10663 for (truncated) singular value decomposition of a sparse matrix. Currently,
10664 only sparse real matrices in Matrix package format are supported.")
10665 ;; SVDLIBC is released under BSD-2. The R interface is released under
10667 (license (list license:bsd-3 license:bsd-2))))
10669 (define-public r-speedglm
10671 (name "r-speedglm")
10676 (uri (cran-uri "speedglm" version))
10679 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10680 (build-system r-build-system)
10682 `(("r-mass" ,r-mass)
10683 ("r-matrix" ,r-matrix)))
10684 (home-page "https://cran.r-project.org/web/packages/speedglm")
10685 (synopsis "Fit linear and generalized linear models to large data sets")
10687 "This package provides tools for fitting linear models and generalized
10688 linear models to large data sets by updating algorithms.")
10689 ;; Any version of the GPL
10690 (license license:gpl2+)))
10692 (define-public r-densityclust
10694 (name "r-densityclust")
10699 (uri (cran-uri "densityClust" version))
10702 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10703 (properties `((upstream-name . "densityClust")))
10704 (build-system r-build-system)
10707 ("r-ggplot2" ,r-ggplot2)
10708 ("r-ggrepel" ,r-ggrepel)
10709 ("r-gridextra" ,r-gridextra)
10710 ("r-rcolorbrewer" ,r-rcolorbrewer)
10712 ("r-rtsne" ,r-rtsne)))
10713 (home-page "https://cran.r-project.org/web/packages/densityClust")
10714 (synopsis "Clustering by fast search and find of density peaks")
10716 "This package provides an improved implementation (based on k-nearest
10717 neighbors) of the density peak clustering algorithm, originally described by
10718 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10719 large datasets (> 100,000 samples) very efficiently.")
10720 (license license:gpl2+)))
10722 (define-public r-combinat
10724 (name "r-combinat")
10729 (uri (cran-uri "combinat" version))
10732 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10733 (build-system r-build-system)
10734 (home-page "https://cran.r-project.org/web/packages/combinat")
10735 (synopsis "Combinatorics utilities")
10736 (description "This package provides assorted routines for combinatorics.")
10737 (license license:gpl2)))
10739 (define-public r-qlcmatrix
10741 (name "r-qlcmatrix")
10746 (uri (cran-uri "qlcMatrix" version))
10749 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10750 (properties `((upstream-name . "qlcMatrix")))
10751 (build-system r-build-system)
10753 `(("r-docopt" ,r-docopt)
10754 ("r-matrix" ,r-matrix)
10756 ("r-sparsesvd" ,r-sparsesvd)))
10757 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10758 (synopsis "Sparse matrix functions for quantitative language comparison")
10760 "This package provides an extension of the functionality of the Matrix
10761 package for using sparse matrices. Some of the functions are very general,
10762 while other are highly specific for the special data format used for
10763 @dfn{quantitative language comparison} (QLC).")
10764 (license license:gpl3)))
10766 (define-public r-ddrtree
10773 (uri (cran-uri "DDRTree" version))
10776 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10777 (properties `((upstream-name . "DDRTree")))
10778 (build-system r-build-system)
10781 ("r-irlba" ,r-irlba)
10783 ("r-rcppeigen" ,r-rcppeigen)))
10784 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10785 (synopsis "Learning principal graphs with DDRTree")
10787 "This package provides an implementation of the framework of
10788 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10789 dimensional space while constructs a principal tree which passes through the
10790 middle of the data simultaneously. DDRTree shows superiority to
10791 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10792 intrinsic structure of single cell genomics data. In general, it could be
10793 used to reconstruct the temporal progression as well as the bifurcation
10794 structure of any data type.")
10795 (license license:asl2.0)))
10797 (define-public r-corpcor
10804 (uri (cran-uri "corpcor" version))
10807 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10808 (build-system r-build-system)
10809 (home-page "http://strimmerlab.org/software/corpcor/")
10810 (synopsis "Efficient estimation of covariance and (partial) correlation")
10812 "This package implements a James-Stein-type shrinkage estimator for the
10813 covariance matrix, with separate shrinkage for variances and correlations.
10814 Furthermore, functions are available for fast singular value decomposition,
10815 for computing the pseudoinverse, and for checking the rank and positive
10816 definiteness of a matrix.")
10817 (license license:gpl3+)))
10819 (define-public r-rspectra
10821 (name "r-rspectra")
10826 (uri (cran-uri "RSpectra" version))
10829 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10830 (properties `((upstream-name . "RSpectra")))
10831 (build-system r-build-system)
10833 `(("r-matrix" ,r-matrix)
10835 ("r-rcppeigen" ,r-rcppeigen)))
10836 (home-page "https://github.com/yixuan/RSpectra")
10837 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10839 "This package provides an R interface to the Spectra library for
10840 large-scale eigenvalue and SVD problems. It is typically used to compute a
10841 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10842 which is usually more efficient than @code{eigen()} if k << n.")
10844 (license license:mpl2.0)))
10846 (define-public r-vbsr
10853 (uri (cran-uri "vbsr" version))
10856 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10857 (build-system r-build-system)
10858 (home-page "https://cran.r-project.org/web/packages/vbsr")
10859 (synopsis "Variational Bayes spike regression regularized linear models")
10861 "This package provides an efficient algorithm for solving ultra-sparse
10862 regularized regression models using a variational Bayes algorithm with a spike
10863 prior. The algorithm is solved on a path, with coordinate updates, and is
10864 capable of generating very sparse models. Very general model
10865 diagnostics for controlling type-1 errors are also provided.")
10866 (license license:gpl2)))
10868 (define-public r-flare
10871 (version "1.6.0.2")
10875 (uri (cran-uri "flare" version))
10878 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10879 (build-system r-build-system)
10881 `(("r-igraph" ,r-igraph)
10882 ("r-lattice" ,r-lattice)
10884 ("r-matrix" ,r-matrix)))
10885 (home-page "https://cran.r-project.org/web/packages/flare")
10886 (synopsis "Family of Lasso regression implementations")
10888 "This package provides implementations of a family of Lasso variants
10889 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10890 high dimensional sparse linear models.")
10891 (license license:gpl2)))
10893 (define-public r-lassopv
10900 (uri (cran-uri "lassopv" version))
10903 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10904 (build-system r-build-system)
10905 (propagated-inputs `(("r-lars" ,r-lars)))
10906 (home-page "https://github.com/lingfeiwang/lassopv")
10907 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10909 "This package enables you to estimate the p-values for predictors x
10910 against target variable y in Lasso regression, using the regularization
10911 strength when each predictor enters the active set of regularization path for
10912 the first time as the statistic.")
10913 (license license:gpl3)))
10915 (define-public r-splitstackshape
10917 (name "r-splitstackshape")
10922 (uri (cran-uri "splitstackshape" version))
10925 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10926 (build-system r-build-system)
10928 `(("r-data-table" ,r-data-table)))
10929 (home-page "https://github.com/mrdwab/splitstackshape")
10930 (synopsis "Stack and reshape datasets after splitting concatenated values")
10932 "Online data collection tools like Google Forms often export
10933 multiple-response questions with data concatenated in cells. The
10934 @code{concat.split} (cSplit) family of functions provided by this package
10935 splits such data into separate cells. This package also includes functions to
10936 stack groups of columns and to reshape wide data, even when the data are
10937 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10938 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10940 (license license:gpl3)))
10942 (define-public r-tfmpvalue
10944 (name "r-tfmpvalue")
10949 (uri (cran-uri "TFMPvalue" version))
10952 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10953 (properties `((upstream-name . "TFMPvalue")))
10954 (build-system r-build-system)
10955 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10956 (home-page "https://github.com/ge11232002/TFMPvalue")
10957 (synopsis "P-value computation for position weight matrices")
10959 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10960 identification from sequence/alignments, we are interested in the significance
10961 of certain match scores. TFMPvalue provides the accurate calculation of a
10962 p-value with a score threshold for position weight matrices, or the score with
10963 a given p-value. It is an interface to code originally made available by
10964 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10965 Touzet and Varre (2007).")
10966 (license license:gpl2)))
10968 (define-public r-rnifti
10975 (uri (cran-uri "RNifti" version))
10978 "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg"))))
10979 (properties `((upstream-name . "RNifti")))
10980 (build-system r-build-system)
10981 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10982 (home-page "https://github.com/jonclayden/RNifti")
10983 (synopsis "Fast R and C++ access to NIfTI images")
10985 "This package provides very fast read and write access to images stored
10986 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10987 compiled C and interpreted R code. It also provides a C/C++ API that can be
10988 used by other packages.")
10989 (license license:gpl2)))
10991 (define-public r-shades
10998 (uri (cran-uri "shades" version))
11001 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
11002 (build-system r-build-system)
11003 (home-page "https://github.com/jonclayden/shades")
11004 (synopsis "Simple color manipulation")
11006 "This package provides functions for easily manipulating colors,
11007 creating color scales and calculating color distances.")
11008 (license license:bsd-3)))
11010 (define-public r-ore
11017 (uri (cran-uri "ore" version))
11019 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11020 (build-system r-build-system)
11021 (home-page "https://github.com/jonclayden/ore")
11022 (synopsis "R interface to the Onigmo regular expression library")
11024 "This package provides an alternative to R's built-in functionality for
11025 handling regular expressions, based on the Onigmo library. It offers
11026 first-class compiled regex objects, partial matching and function-based
11027 substitutions, amongst other features.")
11028 (license license:bsd-3)))
11030 (define-public r-reportr
11037 (uri (cran-uri "reportr" version))
11040 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11041 (build-system r-build-system)
11042 (propagated-inputs `(("r-ore" ,r-ore)))
11043 (home-page "https://github.com/jonclayden/reportr")
11044 (synopsis "General message and error reporting system")
11046 "This package provides a system for reporting messages, which offers
11047 certain useful features over the standard R system, such as the incorporation
11048 of output consolidation, message filtering, assertions, expression
11049 substitution, automatic generation of stack traces for debugging, and
11050 conditional reporting based on the current \"output level\".")
11051 (license license:gpl2)))
11053 (define-public r-tractor-base
11055 (name "r-tractor-base")
11060 (uri (cran-uri "tractor.base" version))
11063 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
11064 (properties `((upstream-name . "tractor.base")))
11065 (build-system r-build-system)
11068 ("r-reportr" ,r-reportr)
11069 ("r-rnifti" ,r-rnifti)
11070 ("r-shades" ,r-shades)))
11071 (home-page "https://www.tractor-mri.org.uk")
11072 (synopsis "Read, manipulate and visualize magnetic resonance images")
11074 "This package provides functions for working with magnetic resonance
11075 images. It supports reading and writing of popular file formats (DICOM,
11076 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
11077 visualization; flexible image manipulation; metadata and sparse image
11079 (license license:gpl2)))
11081 (define-public r-grimport
11083 (name "r-grimport")
11088 (uri (cran-uri "grImport" version))
11091 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
11092 (properties `((upstream-name . "grImport")))
11093 (build-system r-build-system)
11095 `(("ghostscript" ,ghostscript)))
11097 `(("r-xml" ,r-xml)))
11098 (home-page "https://cran.r-project.org/web/packages/grImport")
11099 (synopsis "Convert, import, and draw PostScript pictures")
11101 "This package provides functions for converting, importing, and drawing
11102 PostScript pictures in R plots.")
11103 (license license:gpl2+)))
11105 (define-public r-grimport2
11107 (name "r-grimport2")
11112 (uri (cran-uri "grImport2" version))
11115 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
11116 (properties `((upstream-name . "grImport2")))
11117 (build-system r-build-system)
11119 `(("r-base64enc" ,r-base64enc)
11123 (home-page "https://cran.r-project.org/web/packages/grImport2/")
11124 (synopsis "Import SVG graphics")
11126 "This package provides functions for importing external vector images and
11127 drawing them as part of R plots. This package is different from the
11128 @code{grImport} package because, where that package imports PostScript format
11129 images, this package imports SVG format images. Furthermore, this package
11130 imports a specific subset of SVG, so external images must be preprocessed
11131 using a package like @code{rsvg} to produce SVG that this package can import.
11132 SVG features that are not supported by R graphics, such as gradient fills, can
11133 be imported and then exported via the @code{gridSVG} package.")
11134 (license license:gpl2+)))
11136 (define-public r-kohonen
11143 (uri (cran-uri "kohonen" version))
11146 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
11147 (build-system r-build-system)
11149 `(("r-rcpp" ,r-rcpp)))
11150 (home-page "https://cran.r-project.org/web/packages/kohonen")
11151 (synopsis "Supervised and unsupervised self-organising maps")
11153 "This package provides functions to train @dfn{self-organising
11154 maps} (SOMs). Also interrogation of the maps and prediction using trained
11155 maps are supported. The name of the package refers to Teuvo Kohonen, the
11156 inventor of the SOM.")
11157 (license license:gpl2+)))
11159 (define-public r-nnls
11166 (uri (cran-uri "nnls" version))
11169 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
11170 (build-system r-build-system)
11171 (native-inputs `(("gfortran" ,gfortran)))
11172 (home-page "https://cran.r-project.org/web/packages/nnls")
11173 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
11175 "This package provides an R interface to the Lawson-Hanson implementation
11176 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
11177 the combination of non-negative and non-positive constraints.")
11178 (license license:gpl2+)))
11180 (define-public r-iso
11183 (version "0.0-18.1")
11187 (uri (cran-uri "Iso" version))
11190 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11191 (properties `((upstream-name . "Iso")))
11192 (build-system r-build-system)
11193 (native-inputs `(("gfortran" ,gfortran)))
11194 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11195 (synopsis "Functions to perform isotonic regression")
11197 "This package provides support for linear order and unimodal
11198 order (univariate) isotonic regression and bivariate isotonic regression with
11199 linear order on both variables.")
11200 (license license:gpl2+)))
11202 (define-public r-chemometricswithr
11204 (name "r-chemometricswithr")
11209 (uri (cran-uri "ChemometricsWithR" version))
11212 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11214 `((upstream-name . "ChemometricsWithR")))
11215 (build-system r-build-system)
11217 `(("r-devtools" ,r-devtools)
11218 ("r-kohonen" ,r-kohonen)
11221 (home-page "https://github.com/rwehrens/CWR")
11222 (synopsis "Chemometrics with R")
11224 "This package provides functions and scripts used in the book
11225 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11226 Life Sciences\" by Ron Wehrens, Springer (2011).")
11227 (license license:gpl2+)))
11229 (define-public r-als
11236 (uri (cran-uri "ALS" version))
11239 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11240 (properties `((upstream-name . "ALS")))
11241 (build-system r-build-system)
11244 ("r-nnls" ,r-nnls)))
11245 (home-page "https://cran.r-project.org/web/packages/ALS")
11246 (synopsis "Multivariate curve resolution alternating least squares")
11248 "Alternating least squares is often used to resolve components
11249 contributing to data with a bilinear structure; the basic technique may be
11250 extended to alternating constrained least squares. This package provides an
11251 implementation of @dfn{multivariate curve resolution alternating least
11252 squares} (MCR-ALS).
11254 Commonly applied constraints include unimodality, non-negativity, and
11255 normalization of components. Several data matrices may be decomposed
11256 simultaneously by assuming that one of the two matrices in the bilinear
11257 decomposition is shared between datasets.")
11258 (license license:gpl2+)))
11260 (define-public r-strucchange
11262 (name "r-strucchange")
11267 (uri (cran-uri "strucchange" version))
11270 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11271 (build-system r-build-system)
11273 `(("r-sandwich" ,r-sandwich)
11275 (home-page "https://cran.r-project.org/web/packages/strucchange")
11276 (synopsis "Testing, monitoring, and dating structural changes")
11278 "This package provides tools for testing, monitoring and dating
11279 structural changes in (linear) regression models. It features tests/methods
11280 from the generalized fluctuation test framework as well as from the F
11281 test (Chow test) framework. This includes methods to fit, plot and test
11282 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11283 statistics, respectively. It is possible to monitor incoming data online
11284 using fluctuation processes. Finally, the breakpoints in regression models
11285 with structural changes can be estimated together with confidence intervals.
11286 Emphasis is always given to methods for visualizing the data.")
11287 ;; Either of these two GPL versions
11288 (license (list license:gpl2 license:gpl3))))
11290 (define-public r-pixmap
11297 (uri (cran-uri "pixmap" version))
11300 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11301 (build-system r-build-system)
11302 (home-page "https://cran.r-project.org/web/packages/pixmap")
11303 (synopsis "Tools for bitmap images")
11305 "This package provides functions for importing, exporting, plotting and
11306 other manipulations of bitmapped images.")
11307 (license license:gpl2)))
11309 (define-public r-rapidjsonr
11311 (name "r-rapidjsonr")
11316 (uri (cran-uri "rapidjsonr" version))
11319 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11320 (build-system r-build-system)
11321 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11322 (synopsis "JSON parser")
11324 "This package provides JSON parsing capability through the Rapidjson
11326 (license license:expat)))
11328 (define-public r-ontologyindex
11330 (name "r-ontologyindex")
11335 (uri (cran-uri "ontologyIndex" version))
11338 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11339 (properties `((upstream-name . "ontologyIndex")))
11340 (build-system r-build-system)
11341 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11342 (synopsis "Functions for processing ontologies in R")
11344 "This package provides functions for reading ontologies into R as lists
11345 and manipulating sets of ontological terms.")
11346 (license license:gpl2+)))
11348 (define-public r-gargle
11355 (uri (cran-uri "gargle" version))
11358 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11359 (build-system r-build-system)
11364 ("r-jsonlite" ,r-jsonlite)
11365 ("r-rlang" ,r-rlang)
11366 ("r-withr" ,r-withr)))
11368 `(("r-knitr" ,r-knitr)))
11369 (home-page "https://gargle.r-lib.org")
11370 (synopsis "Utilities for working with Google APIs")
11372 "This package provides utilities for working with Google APIs. This
11373 includes functions and classes for handling common credential types and for
11374 preparing, executing, and processing HTTP requests.")
11375 (license license:expat)))
11377 (define-public r-bigrquery
11379 (name "r-bigrquery")
11384 (uri (cran-uri "bigrquery" version))
11387 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11388 (build-system r-build-system)
11390 `(("r-assertthat" ,r-assertthat)
11391 ("r-bit64" ,r-bit64)
11394 ("r-gargle" ,r-gargle)
11397 ("r-jsonlite" ,r-jsonlite)
11398 ("r-prettyunits" ,r-prettyunits)
11399 ("r-progress" ,r-progress)
11400 ("r-rapidjsonr" ,r-rapidjsonr)
11402 ("r-rlang" ,r-rlang)
11403 ("r-tibble" ,r-tibble)))
11404 (home-page "https://github.com/rstats-db/bigrquery")
11405 (synopsis "R interface to Google's BigQuery API")
11407 "This package provides an R interface to Google's BigQuery database.")
11408 (license license:gpl3)))
11410 (define-public r-gmp
11417 (uri (cran-uri "gmp" version))
11420 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11421 (build-system r-build-system)
11424 (modify-phases %standard-phases
11425 (add-after 'unpack 'set-CC
11426 (lambda _ (setenv "CC" "gcc") #t)))))
11427 (inputs `(("gmp" ,gmp)))
11428 (home-page "https://cran.r-project.org/web/packages/gmp")
11429 (synopsis "Multiple precision arithmetic")
11431 "This package supports multiple precision arithmetic (big integers and
11432 rationals, prime number tests, matrix computation), \"arithmetic without
11433 limitations\" using the GNU Multiple Precision library.")
11434 ;; Any version of the GPL.
11435 (license license:gpl3+)))
11437 (define-public r-rmpfr
11444 (uri (cran-uri "Rmpfr" version))
11447 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11448 (properties `((upstream-name . "Rmpfr")))
11449 (build-system r-build-system)
11454 `(("r-gmp" ,r-gmp)))
11456 `(("pkg-config" ,pkg-config)))
11457 (home-page "http://rmpfr.r-forge.r-project.org/")
11458 (synopsis "R bindings to the MPFR library")
11460 "This package supports arithmetic (via S4 classes and methods) for
11461 arbitrary precision floating point numbers, including transcendental
11462 functions. To this end, the package interfaces with the @dfn{Multiple
11463 Precision Floating-Point Reliable} (MPFR) library.")
11464 (license license:gpl2+)))
11466 (define-public r-assertive-base
11468 (name "r-assertive-base")
11473 (uri (cran-uri "assertive.base" version))
11476 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11478 `((upstream-name . "assertive.base")))
11479 (build-system r-build-system)
11480 (home-page "https://bitbucket.org/richierocks/assertive.base")
11481 (synopsis "Core of the assertive package")
11483 "This package provides a minimal set of predicates and assertions used by
11484 the assertive package. This is mainly for use by other package developers who
11485 want to include run-time testing features in their own packages.")
11486 (license license:gpl3+)))
11488 (define-public r-assertive-properties
11490 (name "r-assertive-properties")
11495 (uri (cran-uri "assertive.properties" version))
11498 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11500 `((upstream-name . "assertive.properties")))
11501 (build-system r-build-system)
11503 `(("r-assertive-base" ,r-assertive-base)))
11504 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11505 (synopsis "Assertions to check properties of variables")
11507 "This package provides a set of predicates and assertions for checking
11508 the properties of variables, such as length, names and attributes. This is
11509 mainly for use by other package developers who want to include run-time
11510 testing features in their own packages.")
11511 (license license:gpl3+)))
11513 (define-public r-assertive-numbers
11515 (name "r-assertive-numbers")
11520 (uri (cran-uri "assertive.numbers" version))
11523 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11525 `((upstream-name . "assertive.numbers")))
11526 (build-system r-build-system)
11528 `(("r-assertive-base" ,r-assertive-base)))
11529 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11530 (synopsis "Assertions to check properties of numbers")
11532 "This package provides a set of predicates and assertions for checking
11533 the properties of numbers. This is mainly for use by other package developers
11534 who want to include run-time testing features in their own packages.")
11535 (license license:gpl3+)))
11537 (define-public r-assertive-sets
11539 (name "r-assertive-sets")
11544 (uri (cran-uri "assertive.sets" version))
11547 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11549 `((upstream-name . "assertive.sets")))
11550 (build-system r-build-system)
11552 `(("r-assertive-base" ,r-assertive-base)))
11553 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11554 (synopsis "Assertions to check properties of sets")
11556 "This package provides a set of predicates and assertions for checking
11557 the properties of sets. This is mainly for use by other package developers
11558 who want to include run-time testing features in their own packages.")
11559 (license license:gpl3+)))
11561 (define-public r-assertive-matrices
11563 (name "r-assertive-matrices")
11568 (uri (cran-uri "assertive.matrices" version))
11571 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11573 `((upstream-name . "assertive.matrices")))
11574 (build-system r-build-system)
11576 `(("r-assertive-base" ,r-assertive-base)))
11577 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11578 (synopsis "Assertions to check properties of matrices")
11580 "This package provides a set of predicates and assertions for checking
11581 the properties of matrices. This is mainly for use by other package
11582 developers who want to include run-time testing features in their own
11584 (license license:gpl3+)))
11586 (define-public r-assertive-models
11588 (name "r-assertive-models")
11593 (uri (cran-uri "assertive.models" version))
11596 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11598 `((upstream-name . "assertive.models")))
11599 (build-system r-build-system)
11601 `(("r-assertive-base" ,r-assertive-base)))
11602 (home-page "https://bitbucket.org/richierocks/assertive.models")
11603 (synopsis "Assertions to check properties of models")
11605 "This package provides a set of predicates and assertions for checking
11606 the properties of models. This is mainly for use by other package developers
11607 who want to include run-time testing features in their own packages.")
11608 (license license:gpl3+)))
11610 (define-public r-assertive-reflection
11612 (name "r-assertive-reflection")
11617 (uri (cran-uri "assertive.reflection" version))
11620 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11622 `((upstream-name . "assertive.reflection")))
11623 (build-system r-build-system)
11625 `(("r-assertive-base" ,r-assertive-base)))
11626 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11627 (synopsis "Assertions for checking the state of R")
11629 "This package provides a set of predicates and assertions for checking
11630 the state and capabilities of R, the operating system it is running on, and
11631 the IDE being used. This is mainly for use by other package developers who
11632 want to include run-time testing features in their own packages.")
11633 (license license:gpl3+)))
11635 (define-public r-assertive-types
11637 (name "r-assertive-types")
11642 (uri (cran-uri "assertive.types" version))
11645 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11647 `((upstream-name . "assertive.types")))
11648 (build-system r-build-system)
11650 `(("r-assertive-base" ,r-assertive-base)
11651 ("r-assertive-properties" ,r-assertive-properties)
11652 ("r-codetools" ,r-codetools)))
11653 (home-page "https://bitbucket.org/richierocks/assertive.types")
11654 (synopsis "Assertions to check types of variables")
11656 "This package provides a set of predicates and assertions for checking
11657 the types of variables. This is mainly for use by other package developers
11658 who want to include run-time testing features in their own packages.")
11659 (license license:gpl3+)))
11661 (define-public r-assertive-files
11663 (name "r-assertive-files")
11668 (uri (cran-uri "assertive.files" version))
11671 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11673 `((upstream-name . "assertive.files")))
11674 (build-system r-build-system)
11676 `(("r-assertive-base" ,r-assertive-base)
11677 ("r-assertive-numbers" ,r-assertive-numbers)))
11678 (home-page "https://bitbucket.org/richierocks/assertive.files")
11679 (synopsis "Assertions to check properties of files")
11681 "This package provides a set of predicates and assertions for checking
11682 the properties of files and connections. This is mainly for use by other
11683 package developers who want to include run-time testing features in their own
11685 (license license:gpl3+)))
11687 (define-public r-assertive-code
11689 (name "r-assertive-code")
11694 (uri (cran-uri "assertive.code" version))
11697 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11699 `((upstream-name . "assertive.code")))
11700 (build-system r-build-system)
11702 `(("r-assertive-base" ,r-assertive-base)
11703 ("r-assertive-properties" ,r-assertive-properties)
11704 ("r-assertive-types" ,r-assertive-types)))
11705 (home-page "https://bitbucket.org/richierocks/assertive.code")
11706 (synopsis "Assertions to check properties of code")
11708 "This package provides a set of predicates and assertions for checking
11709 the properties of code. This is mainly for use by other package developers
11710 who want to include run-time testing features in their own packages.")
11711 (license license:gpl3+)))
11713 (define-public r-assertive-datetimes
11715 (name "r-assertive-datetimes")
11720 (uri (cran-uri "assertive.datetimes" version))
11723 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11725 `((upstream-name . "assertive.datetimes")))
11726 (build-system r-build-system)
11728 `(("r-assertive-base" ,r-assertive-base)
11729 ("r-assertive-types" ,r-assertive-types)))
11730 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11731 (synopsis "Assertions to check properties of dates and times")
11733 "This package provides a set of predicates and assertions for checking
11734 the properties of dates and times. This is mainly for use by other package
11735 developers who want to include run-time testing features in their own
11737 (license license:gpl3+)))
11739 (define-public r-assertive-strings
11741 (name "r-assertive-strings")
11746 (uri (cran-uri "assertive.strings" version))
11749 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11751 `((upstream-name . "assertive.strings")))
11752 (build-system r-build-system)
11754 `(("r-assertive-base" ,r-assertive-base)
11755 ("r-assertive-types" ,r-assertive-types)
11756 ("r-stringi" ,r-stringi)))
11757 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11758 (synopsis "Assertions to check properties of strings")
11760 "This package provides a set of predicates and assertions for checking
11761 the properties of strings. This is mainly for use by other package developers
11762 who want to include run-time testing features in their own packages.")
11763 (license license:gpl3+)))
11765 (define-public r-assertive-data-us
11767 (name "r-assertive-data-us")
11772 (uri (cran-uri "assertive.data.us" version))
11775 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11777 `((upstream-name . "assertive.data.us")))
11778 (build-system r-build-system)
11780 `(("r-assertive-base" ,r-assertive-base)
11781 ("r-assertive-strings" ,r-assertive-strings)))
11782 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11783 (synopsis "Assertions to check properties of strings")
11785 "This package provides a set of predicates and assertions for checking
11786 the properties of US-specific complex data types. This is mainly for use by
11787 other package developers who want to include run-time testing features in
11788 their own packages.")
11789 (license license:gpl3+)))
11791 (define-public r-assertive-data-uk
11793 (name "r-assertive-data-uk")
11798 (uri (cran-uri "assertive.data.uk" version))
11801 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11803 `((upstream-name . "assertive.data.uk")))
11804 (build-system r-build-system)
11806 `(("r-assertive-base" ,r-assertive-base)
11807 ("r-assertive-strings" ,r-assertive-strings)))
11808 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11809 (synopsis "Assertions to check properties of strings")
11811 "This package provides a set of predicates and assertions for checking
11812 the properties of UK-specific complex data types. This is mainly for use by
11813 other package developers who want to include run-time testing features in
11814 their own packages.")
11815 (license license:gpl3+)))
11817 (define-public r-assertive-data
11819 (name "r-assertive-data")
11824 (uri (cran-uri "assertive.data" version))
11827 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11829 `((upstream-name . "assertive.data")))
11830 (build-system r-build-system)
11832 `(("r-assertive-base" ,r-assertive-base)
11833 ("r-assertive-strings" ,r-assertive-strings)))
11834 (home-page "https://bitbucket.org/richierocks/assertive.data")
11835 (synopsis "Assertions to check properties of data")
11837 "This package provides a set of predicates and assertions for checking
11838 the properties of (country independent) complex data types. This is mainly
11839 for use by other package developers who want to include run-time testing
11840 features in their own packages.")
11841 (license license:gpl3+)))
11843 (define-public r-assertive
11845 (name "r-assertive")
11850 (uri (cran-uri "assertive" version))
11853 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11854 (build-system r-build-system)
11856 `(("r-assertive-base" ,r-assertive-base)
11857 ("r-assertive-code" ,r-assertive-code)
11858 ("r-assertive-data" ,r-assertive-data)
11859 ("r-assertive-data-uk" ,r-assertive-data-uk)
11860 ("r-assertive-data-us" ,r-assertive-data-us)
11861 ("r-assertive-datetimes" ,r-assertive-datetimes)
11862 ("r-assertive-files" ,r-assertive-files)
11863 ("r-assertive-matrices" ,r-assertive-matrices)
11864 ("r-assertive-models" ,r-assertive-models)
11865 ("r-assertive-numbers" ,r-assertive-numbers)
11866 ("r-assertive-properties" ,r-assertive-properties)
11867 ("r-assertive-reflection" ,r-assertive-reflection)
11868 ("r-assertive-sets" ,r-assertive-sets)
11869 ("r-assertive-strings" ,r-assertive-strings)
11870 ("r-assertive-types" ,r-assertive-types)
11871 ("r-knitr" ,r-knitr)))
11873 `(("r-knitr" ,r-knitr)))
11874 (home-page "https://bitbucket.org/richierocks/assertive")
11875 (synopsis "Readable check functions to ensure code integrity")
11877 "This package provides lots of predicates (@code{is_*} functions) to
11878 check the state of your variables, and assertions (@code{assert_*} functions)
11879 to throw errors if they aren't in the right form.")
11880 (license license:gpl3+)))
11882 (define-public r-dotcall64
11884 (name "r-dotcall64")
11889 (uri (cran-uri "dotCall64" version))
11892 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11893 (properties `((upstream-name . "dotCall64")))
11894 (build-system r-build-system)
11895 (native-inputs `(("gfortran" ,gfortran)))
11896 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11897 (synopsis "Enhanced foreign function interface supporting long vectors")
11899 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11900 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11901 supports long vectors, arguments of type 64-bit integer, and provides a
11902 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11903 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11904 (license license:gpl2+)))
11906 (define-public r-spam
11913 (uri (cran-uri "spam" version))
11915 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11916 (build-system r-build-system)
11918 `(("r-dotcall64" ,r-dotcall64)))
11919 (native-inputs `(("gfortran" ,gfortran)))
11920 (home-page "https://www.math.uzh.ch/pages/spam/")
11921 (synopsis "Sparse matrix algebra")
11923 "This package provides a set of functions for sparse matrix algebra.
11924 Differences with other sparse matrix packages are:
11927 @item it only supports (essentially) one sparse matrix format;
11928 @item it is based on transparent and simple structure(s);
11929 @item it is tailored for MCMC calculations within G(M)RF;
11930 @item and it is fast and scalable (with the extension package @code{spam64}).
11932 ;; Either of these licenses
11933 (license (list license:bsd-3 license:lgpl2.0))))
11935 (define-public r-fields
11942 (uri (cran-uri "fields" version))
11944 (base32 "0x8hbl0rn7gnhn7w45wd757g9in27884qr6vy30xrk150qaq941y"))))
11945 (build-system r-build-system)
11947 `(("r-maps" ,r-maps)
11948 ("r-spam" ,r-spam)))
11950 `(("gfortran" ,gfortran)))
11951 (home-page "https://www.image.ucar.edu/fields")
11952 (synopsis "Tools for spatial data")
11954 "This is a package for curve, surface and function fitting with an
11955 emphasis on splines, spatial data and spatial statistics. The major methods
11956 include cubic, and thin plate splines, Kriging, and compactly supported
11957 covariance functions for large data sets.")
11958 (license license:gpl2+)))
11960 (define-public r-spatialextremes
11962 (name "r-spatialextremes")
11967 (uri (cran-uri "SpatialExtremes" version))
11970 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11972 `((upstream-name . "SpatialExtremes")))
11973 (build-system r-build-system)
11975 `(("r-fields" ,r-fields)
11976 ("r-maps" ,r-maps)))
11977 (home-page "http://spatialextremes.r-forge.r-project.org/")
11978 (synopsis "Modelling spatial extremes")
11980 "This package provides tools for the statistical modelling of spatial
11981 extremes using max-stable processes, copula or Bayesian hierarchical models.
11982 More precisely, this package allows (conditional) simulations from various
11983 parametric max-stable models, analysis of the extremal spatial dependence, the
11984 fitting of such processes using composite likelihoods or least square (simple
11985 max-stable processes only), model checking and selection and prediction.")
11986 (license license:gpl2+)))
11988 (define-public r-drc
11995 (uri (cran-uri "drc" version))
11998 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11999 (build-system r-build-system)
12002 ("r-gtools" ,r-gtools)
12004 ("r-multcomp" ,r-multcomp)
12005 ("r-plotrix" ,r-plotrix)
12006 ("r-scales" ,r-scales)))
12007 (home-page "https://cran.r-project.org/web/packages/drc")
12008 (synopsis "Analysis of dose-response curves")
12010 "This package provides a suite of flexible and versatile model fitting
12011 and after-fitting functions for the analysis of dose-response data.")
12012 (license license:gpl2+)))
12014 (define-public r-rmeta
12021 (uri (cran-uri "rmeta" version))
12024 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12025 (build-system r-build-system)
12026 (home-page "https://cran.r-project.org/web/packages/rmeta")
12027 (synopsis "Tools for meta-analysis")
12029 "This package provides functions for simple fixed and random effects
12030 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12031 draws standard summary plots, funnel plots, and computes summaries and tests
12032 for association and heterogeneity.")
12033 (license license:gpl2)))
12035 (define-public r-bootstrap
12037 (name "r-bootstrap")
12042 (uri (cran-uri "bootstrap" version))
12045 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
12046 (build-system r-build-system)
12047 (native-inputs `(("gfortran" ,gfortran)))
12048 (home-page "https://cran.r-project.org/web/packages/bootstrap")
12049 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
12051 "This package provides software and data for the book \"An Introduction
12052 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
12053 This package is primarily provided for projects already based on it, and for
12054 support of the book. New projects should preferentially use the recommended
12055 package \"boot\".")
12056 (license license:bsd-3)))
12058 (define-public r-survivalroc
12060 (name "r-survivalroc")
12065 (uri (cran-uri "survivalROC" version))
12068 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
12069 (properties `((upstream-name . "survivalROC")))
12070 (build-system r-build-system)
12071 (home-page "https://cran.r-project.org/web/packages/survivalROC")
12072 (synopsis "Time-dependent ROC curve estimation from censored survival data")
12074 "Compute time-dependent ROC curve from censored survival data using
12075 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
12076 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
12077 (license license:gpl2+)))
12079 (define-public r-longitudinal
12081 (name "r-longitudinal")
12086 (uri (cran-uri "longitudinal" version))
12089 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
12090 (build-system r-build-system)
12091 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
12092 (home-page "http://strimmerlab.org/software/longitudinal/")
12093 (synopsis "Analysis of multiple time course data")
12095 "This package contains general data structures and functions for
12096 longitudinal data with multiple variables, repeated measurements, and
12097 irregularly spaced time points. It also implements a shrinkage estimator of
12098 dynamical correlation and dynamical covariance.")
12099 (license license:gpl3+)))
12101 (define-public r-genenet
12108 (uri (cran-uri "GeneNet" version))
12111 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
12112 (properties `((upstream-name . "GeneNet")))
12113 (build-system r-build-system)
12115 `(("r-corpcor" ,r-corpcor)
12116 ("r-fdrtool" ,r-fdrtool)
12117 ("r-longitudinal" ,r-longitudinal)))
12118 (home-page "http://strimmerlab.org/software/genenet/")
12119 (synopsis "Modeling and inferring gene networks")
12121 "This package analyzes gene expression (time series) data with focus on
12122 the inference of gene networks. In particular, GeneNet implements the methods
12123 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
12124 for learning large-scale gene association networks (including assignment of
12125 putative directions).")
12126 (license license:gpl3+)))
12128 (define-public r-rbamtools
12130 (name "r-rbamtools")
12131 (version "2.16.17")
12135 (uri (cran-uri "rbamtools" version))
12138 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
12139 (build-system r-build-system)
12140 (inputs `(("zlib" ,zlib)))
12142 `(("r-refgenome" ,r-refgenome)))
12143 (home-page "https://cran.r-project.org/web/packages/rbamtools")
12144 (synopsis "Read and write BAM (binary alignment) files")
12146 "This package provides an R interface to functions of the SAMtools
12148 (license license:artistic2.0)))
12150 (define-public r-protviz
12157 (uri (cran-uri "protViz" version))
12160 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
12161 (properties `((upstream-name . "protViz")))
12162 (build-system r-build-system)
12163 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12164 (home-page "https://github.com/protViz/protViz/")
12165 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
12167 "This package helps with quality checks, visualizations and analysis of
12168 mass spectrometry data, coming from proteomics experiments. The package is
12169 developed, tested and used at the Functional Genomics Center Zurich, where it
12170 is used mainly for prototyping, teaching, and having fun with proteomics data.
12171 But it can also be used to do data analysis for small scale data sets.")
12172 (license license:gpl3)))
12174 (define-public r-cmprsk
12181 (uri (cran-uri "cmprsk" version))
12183 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
12184 (build-system r-build-system)
12186 `(("r-survival" ,r-survival)))
12188 `(("gfortran" ,gfortran)))
12189 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12190 (synopsis "Subdistribution analysis of competing risks")
12192 "This package provides tool for estimation, testing and regression
12193 modeling of subdistribution functions in competing risks, as described in
12194 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12195 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12196 A proportional hazards model for the subdistribution of a competing risk,
12197 JASA, 94:496-509.")
12198 (license license:gpl2+)))
12200 (define-public r-etm
12207 (uri (cran-uri "etm" version))
12210 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
12211 (build-system r-build-system)
12213 `(("r-data-table" ,r-data-table)
12214 ("r-lattice" ,r-lattice)
12216 ("r-rcpparmadillo" ,r-rcpparmadillo)
12217 ("r-survival" ,r-survival)))
12218 (home-page "https://cran.r-project.org/web/packages/etm")
12219 (synopsis "Empirical transition matrix")
12221 "The @dfn{empirical transition matrix} (etm) package estimates
12222 the matrix of transition probabilities for any time-inhomogeneous multistate
12223 model with finite state space using the Aalen-Johansen estimator.")
12224 (license license:expat)))
12226 (define-public r-epi
12233 (uri (cran-uri "Epi" version))
12236 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12237 (properties `((upstream-name . "Epi")))
12238 (build-system r-build-system)
12240 `(("r-cmprsk" ,r-cmprsk)
12241 ("r-data-table" ,r-data-table)
12244 ("r-matrix" ,r-matrix)
12246 ("r-numderiv" ,r-numderiv)
12248 ("r-survival" ,r-survival)
12250 (home-page "https://BendixCarstensen.com/Epi/")
12251 (synopsis "Statistical analysis in epidemiology")
12253 "This package provides functions for demographic and epidemiological
12254 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12255 particular representation, manipulation and simulation of multistate data -
12256 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12257 @code{etm} and @code{cmprsk} packages. It also contains functions for
12258 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12259 data and some useful functions for tabulation and plotting, as well as a
12260 number of epidemiological data sets.")
12261 (license license:gpl2)))
12263 (define-public r-ppls
12266 (version "1.6-1.1")
12270 (uri (cran-uri "ppls" version))
12273 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12274 (build-system r-build-system)
12275 (propagated-inputs `(("r-mass" ,r-mass)))
12276 (home-page "https://cran.r-project.org/web/packages/ppls")
12277 (synopsis "Penalized partial least squares")
12279 "This package contains linear and nonlinear regression methods based on
12280 partial least squares and penalization techniques. Model parameters are
12281 selected via cross-validation, and confidence intervals ans tests for the
12282 regression coefficients can be conducted via jackknifing.")
12283 (license license:gpl2+)))
12285 (define-public r-huge
12288 (version "1.3.4.1")
12292 (uri (cran-uri "huge" version))
12294 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12295 (build-system r-build-system)
12297 `(("r-igraph" ,r-igraph)
12299 ("r-matrix" ,r-matrix)
12301 ("r-rcppeigen" ,r-rcppeigen)))
12302 (home-page "https://cran.r-project.org/web/packages/huge")
12303 (synopsis "High-dimensional undirected graph estimation")
12305 "This package provides a general framework for high-dimensional
12306 undirected graph estimation. It integrates data preprocessing, neighborhood
12307 screening, graph estimation, and model selection techniques into a pipeline.")
12308 (license license:gpl2)))
12310 (define-public r-parcor
12317 (uri (cran-uri "parcor" version))
12320 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12321 (build-system r-build-system)
12324 ("r-genenet" ,r-genenet)
12325 ("r-glmnet" ,r-glmnet)
12327 ("r-ppls" ,r-ppls)))
12328 (home-page "https://cran.r-project.org/web/packages/parcor")
12329 (synopsis "Regularized estimation of partial correlation matrices")
12331 "This package estimates the matrix of partial correlations based on
12332 different regularized regression methods: lasso, adaptive lasso, PLS, and
12333 Ridge Regression. In addition, the package provides model selection for
12334 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12335 (license license:gpl2+)))
12337 (define-public r-mcmc
12344 (uri (cran-uri "mcmc" version))
12347 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12348 (build-system r-build-system)
12349 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12350 (synopsis "Markov chain Monte Carlo")
12352 "This package simulates continuous distributions of random vectors using
12353 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12354 function that evaluates the log unnormalized density. Algorithms are random
12355 walk Metropolis algorithm (function @code{metrop}), simulated
12356 tempering (function @code{temper}), and morphometric random walk
12357 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12358 by change of variable.")
12359 (license license:expat)))
12361 (define-public r-listenv
12368 (uri (cran-uri "listenv" version))
12371 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12372 (build-system r-build-system)
12374 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12375 (home-page "https://github.com/HenrikBengtsson/listenv")
12376 (synopsis "Environments behaving (almost) as lists")
12378 "This package implements list environments. List environments are
12379 environments that have list-like properties. For instance, the elements of a
12380 list environment are ordered and can be accessed and iterated over using index
12382 (license license:lgpl2.1+)))
12384 (define-public r-globals
12391 (uri (cran-uri "globals" version))
12394 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12395 (build-system r-build-system)
12397 `(("r-codetools" ,r-codetools)))
12398 (home-page "https://github.com/HenrikBengtsson/globals")
12399 (synopsis "Identify global objects in R expressions")
12401 "This package provides tools to identify global (\"unknown\" or \"free\")
12402 objects in R expressions by code inspection using various strategies, e.g.
12403 conservative or liberal. The objective of this package is to make it as
12404 simple as possible to identify global objects for the purpose of exporting
12405 them in distributed compute environments.")
12406 (license license:lgpl2.1+)))
12408 (define-public r-future
12415 (uri (cran-uri "future" version))
12418 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12419 (build-system r-build-system)
12421 `(("r-digest" ,r-digest)
12422 ("r-globals" ,r-globals)
12423 ("r-listenv" ,r-listenv)))
12425 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12426 (home-page "https://github.com/HenrikBengtsson/future")
12427 (synopsis "Unified parallel and distributed processing in R")
12429 "The purpose of this package is to provide a lightweight and unified
12430 Future API for sequential and parallel processing of R expression via futures.
12431 This package implements sequential, multicore, multisession, and cluster
12432 futures. With these, R expressions can be evaluated on the local machine, in
12433 parallel a set of local machines, or distributed on a mix of local and remote
12434 machines. Extensions to this package implement additional backends for
12435 processing futures via compute cluster schedulers etc. Because of its unified
12436 API, there is no need to modify any code in order to switch from sequential on
12437 the local machine to, say, distributed processing on a remote compute cluster.")
12438 (license license:lgpl2.1+)))
12440 (define-public r-future-apply
12442 (name "r-future-apply")
12447 (uri (cran-uri "future.apply" version))
12450 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12451 (properties `((upstream-name . "future.apply")))
12452 (build-system r-build-system)
12454 `(("r-future" ,r-future)
12455 ("r-globals" ,r-globals)))
12457 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12458 (home-page "https://github.com/HenrikBengtsson/future.apply")
12459 (synopsis "Apply function to elements in parallel using futures")
12461 "This package provides implementations of @code{apply()},
12462 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12463 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12464 can be resolved using any future-supported backend, e.g. parallel on the local
12465 machine or distributed on a compute cluster.")
12466 (license license:gpl2+)))
12468 (define-public r-rsvd
12475 (uri (cran-uri "rsvd" version))
12478 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12479 (build-system r-build-system)
12481 `(("r-matrix" ,r-matrix)))
12482 (home-page "https://github.com/erichson/rSVD")
12483 (synopsis "Randomized singular value decomposition")
12485 "Low-rank matrix decompositions are fundamental tools and widely used for
12486 data analysis, dimension reduction, and data compression. Classically, highly
12487 accurate deterministic matrix algorithms are used for this task. However, the
12488 emergence of large-scale data has severely challenged our computational
12489 ability to analyze big data. The concept of randomness has been demonstrated
12490 as an effective strategy to quickly produce approximate answers to familiar
12491 problems such as the @dfn{singular value decomposition} (SVD). This package
12492 provides several randomized matrix algorithms such as the randomized singular
12493 value decomposition (@code{rsvd}), randomized principal component
12494 analysis (@code{rpca}), randomized robust principal component
12495 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12496 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12497 functions are provided.")
12498 (license license:gpl3+)))
12500 (define-public r-sloop
12507 (uri (cran-uri "sloop" version))
12510 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12511 (build-system r-build-system)
12513 `(("r-codetools" ,r-codetools)
12514 ("r-crayon" ,r-crayon)
12515 ("r-purrr" ,r-purrr)
12516 ("r-rlang" ,r-rlang)
12517 ("r-tibble" ,r-tibble)))
12518 (home-page "https://github.com/r-lib/sloop")
12519 (synopsis "Helpers for object-oriented programming in R")
12521 "This package provides a collection of helper functions designed to
12522 help you to better understand object oriented programming in R, particularly
12524 (license license:gpl3)))
12526 (define-public r-capushe
12533 (uri (cran-uri "capushe" version))
12536 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12537 (build-system r-build-system)
12538 (propagated-inputs `(("r-mass" ,r-mass)))
12539 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12540 (synopsis "Calibrating penalties using slope heuristics")
12542 "This package provides tools for the calibration of penalized criteria
12543 for model selection. The calibration methods available are based on the slope
12545 (license license:gpl2+)))
12547 (define-public r-dorng
12554 (uri (cran-uri "doRNG" version))
12557 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12558 (properties `((upstream-name . "doRNG")))
12559 (build-system r-build-system)
12561 `(("r-foreach" ,r-foreach)
12562 ("r-iterators" ,r-iterators)
12563 ("r-rngtools" ,r-rngtools)))
12564 (home-page "https://renozao.github.io/doRNG/")
12565 (synopsis "Generic reproducible parallel backend for foreach loops")
12567 "This package provides functions to perform reproducible parallel
12568 @code{foreach} loops, using independent random streams as generated by
12569 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12570 convert standard @code{%dopar%} loops into fully reproducible loops,
12571 independently of the number of workers, the task scheduling strategy, or the
12572 chosen parallel environment and associated foreach backend.")
12573 (license license:gpl2+)))
12575 (define-public r-blockmodeling
12577 (name "r-blockmodeling")
12582 (uri (cran-uri "blockmodeling" version))
12585 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12586 (build-system r-build-system)
12588 `(("r-matrix" ,r-matrix)))
12589 (native-inputs `(("gfortran" ,gfortran)))
12590 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12591 (synopsis "Generalized and classical blockmodeling of valued networks")
12593 "This package is primarily meant as an implementation of generalized
12594 blockmodeling for valued networks. In addition, measures of similarity or
12595 dissimilarity based on structural equivalence and regular equivalence (REGE
12596 algorithms) can be computed and partitioned matrices can be plotted.")
12597 (license license:gpl2+)))
12599 (define-public r-upsetr
12606 (uri (cran-uri "UpSetR" version))
12609 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12610 (properties `((upstream-name . "UpSetR")))
12611 (build-system r-build-system)
12613 `(("r-ggplot2" ,r-ggplot2)
12614 ("r-gridextra" ,r-gridextra)
12616 ("r-scales" ,r-scales)))
12617 (home-page "https://github.com/hms-dbmi/UpSetR")
12618 (synopsis "Visualize intersecting sets")
12620 "This package provides a more scalable alternative to Venn and Euler
12621 diagrams for visualizing intersecting sets. Create visualizations of
12622 intersecting sets using a novel matrix design, along with visualizations of
12623 several common set, element and attribute related tasks.")
12624 (license license:expat)))
12626 ;; This package includes a JavaScript file, which is not minified. When
12627 ;; upgrading please check that there are no new minified JavaScript files.
12628 (define-public r-shinybs
12635 (uri (cran-uri "shinyBS" version))
12638 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12639 (properties `((upstream-name . "shinyBS")))
12640 (build-system r-build-system)
12641 ;; The tests spawn Shiny browser apps. They cannot be run
12642 ;; non-interactively.
12643 (arguments '(#:tests? #f))
12645 `(("r-htmltools" ,r-htmltools)
12646 ("r-shiny" ,r-shiny)))
12647 (home-page "https://ebailey78.github.io/shinyBS/")
12648 (synopsis "Twitter Bootstrap components for Shiny")
12650 "This package adds additional Twitter Bootstrap components to Shiny.")
12651 (license license:gpl3)))
12653 (define-public r-outliers
12655 (name "r-outliers")
12660 (uri (cran-uri "outliers" version))
12663 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12664 (build-system r-build-system)
12665 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12666 (synopsis "Tests for outliers")
12668 "This package provides a collection of some tests commonly used for
12669 identifying outliers.")
12670 (license license:gpl2+)))
12672 (define-public r-bayesm
12679 (uri (cran-uri "bayesm" version))
12681 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12682 (build-system r-build-system)
12684 `(("r-rcpp" ,r-rcpp)
12685 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12686 (home-page "http://www.perossi.org/home/bsm-1")
12687 (synopsis "Bayesian inference for marketing/micro-econometrics")
12689 "This package covers many important models used in marketing and
12690 micro-econometrics applications, including Bayes Regression (univariate or
12691 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12692 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12693 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12694 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12695 Estimation with normal base, Hierarchical Linear Models with normal prior and
12696 covariates, Hierarchical Linear Models with a mixture of normals prior and
12697 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12698 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12699 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12700 analysis of choice-based conjoint data, Bayesian treatment of linear
12701 instrumental variables models, Analysis of Multivariate Ordinal survey data
12702 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12703 Coefficient Logit Models.")
12704 (license license:gpl2+)))
12706 (define-public r-tensora
12713 (uri (cran-uri "tensorA" version))
12716 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12717 (properties `((upstream-name . "tensorA")))
12718 (build-system r-build-system)
12719 (home-page "http://www.stat.boogaart.de/tensorA")
12720 (synopsis "Advanced tensor arithmetic with named indices")
12722 "This package provides convenience functions for advanced linear algebra
12723 with tensors and computation with datasets of tensors on a higher level
12724 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12725 co- and contravariate indices, and parallel computations on sequences of
12727 (license license:gpl2+)))
12729 (define-public r-rarpack
12736 (uri (cran-uri "rARPACK" version))
12739 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12740 (properties `((upstream-name . "rARPACK")))
12741 (build-system r-build-system)
12742 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12743 (home-page "https://github.com/yixuan/rARPACK")
12744 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12746 "This package was previously an R wrapper of the ARPACK library, and now
12747 a shell of the R package RSpectra, an R interface to the Spectra library for
12748 solving large scale eigenvalue/vector problems. The current version of
12749 rARPACK simply imports and exports the functions provided by RSpectra. New
12750 users of rARPACK are advised to switch to the RSpectra package.")
12751 (license license:bsd-3)))
12753 (define-public r-compositions
12755 (name "r-compositions")
12760 (uri (cran-uri "compositions" version))
12763 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12764 (build-system r-build-system)
12766 `(("r-bayesm" ,r-bayesm)
12768 ("r-robustbase" ,r-robustbase)
12769 ("r-tensora" ,r-tensora)))
12771 `(("r-knitr" ,r-knitr)))
12772 (home-page "http://www.stat.boogaart.de/compositions")
12773 (synopsis "Compositional data analysis")
12775 "This package provides functions for the consistent analysis of
12776 compositional data (e.g. portions of substances) and positive
12777 numbers (e.g. concentrations).")
12778 (license license:gpl2+)))
12780 (define-public r-cobs
12787 (uri (cran-uri "cobs" version))
12790 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12791 (build-system r-build-system)
12793 `(("r-quantreg" ,r-quantreg)
12794 ("r-sparsem" ,r-sparsem)))
12795 (home-page "https://cran.r-project.org/web/packages/cobs")
12796 (synopsis "Constrained B-Splines (sparse matrix based)")
12798 "This package provides qualitatively constrained (regression) smoothing
12799 splines via linear programming and sparse matrices.")
12800 (license license:gpl2+)))
12802 (define-public r-drimpute
12804 (name "r-drimpute")
12809 (uri (cran-uri "DrImpute" version))
12812 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12813 (properties `((upstream-name . "DrImpute")))
12814 (build-system r-build-system)
12816 `(("r-rcpp" ,r-rcpp)
12817 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12818 (home-page "https://github.com/ikwak2/DrImpute")
12819 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12821 "This is an R package for imputing dropout events. Many statistical
12822 methods in cell type identification, visualization and lineage reconstruction
12823 do not account for dropout events. DrImpute can improve the performance of
12824 such software by imputing dropout events.")
12825 (license license:gpl3)))
12827 (define-public r-gamlss-dist
12829 (name "r-gamlss-dist")
12834 (uri (cran-uri "gamlss.dist" version))
12836 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12837 (properties `((upstream-name . "gamlss.dist")))
12838 (build-system r-build-system)
12839 (propagated-inputs `(("r-mass" ,r-mass)))
12840 (home-page "http://www.gamlss.org/")
12841 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12843 "This package provides a set of distributions which can be used for
12844 modelling the response variables in Generalized Additive Models for Location
12845 Scale and Shape. The distributions can be continuous, discrete or mixed
12846 distributions. Extra distributions can be created, by transforming, any
12847 continuous distribution defined on the real line, to a distribution defined on
12848 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12849 transformation, respectively.")
12850 ;; Either version of the GPL.
12851 (license (list license:gpl2 license:gpl3))))
12853 ;; This package includes JavaScript files, which are not minified. When
12854 ;; upgrading please check that there are no new minified JavaScript files.
12855 (define-public r-shinyjs
12862 (uri (cran-uri "shinyjs" version))
12865 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
12866 (build-system r-build-system)
12868 `(("r-digest" ,r-digest)
12869 ("r-htmltools" ,r-htmltools)
12870 ("r-jsonlite" ,r-jsonlite)
12871 ("r-shiny" ,r-shiny)))
12873 `(("r-knitr" ,r-knitr)))
12874 (home-page "https://deanattali.com/shinyjs")
12875 (synopsis "Improve the user experience of your Shiny apps")
12877 "Perform common useful JavaScript operations in Shiny apps that will
12878 greatly improve your apps without having to know any JavaScript. Examples
12879 include: hiding an element, disabling an input, resetting an input back to its
12880 original value, delaying code execution by a few seconds, and many more useful
12881 functions for both the end user and the developer. Shinyjs can also be used
12882 to easily call your own custom JavaScript functions from R.")
12883 (license license:agpl3+)))
12885 ;; This package includes minified JavaScript files. When upgrading please
12886 ;; check that there are no new minified JavaScript files.
12887 (define-public r-colourpicker
12889 (name "r-colourpicker")
12894 (uri (cran-uri "colourpicker" version))
12897 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12898 (build-system r-build-system)
12900 `(#:modules ((guix build utils)
12901 (guix build r-build-system)
12905 (modify-phases %standard-phases
12906 (add-after 'unpack 'process-javascript
12907 (lambda* (#:key inputs #:allow-other-keys)
12908 (with-directory-excursion "inst"
12912 `((,(assoc-ref inputs "js-salvattore")
12913 "examples/colourInput/www/salvattore.min.js")
12914 (,(assoc-ref inputs "js-jquery")
12915 "htmlwidgets/lib/jquery/jquery.min.js")
12916 ("www/shared/colourpicker/js/colourpicker.js"
12917 "www/shared/colourpicker/js/colourpicker.min.js"))))
12918 (lambda (sources targets)
12919 (for-each (lambda (source target)
12920 (format #t "Processing ~a --> ~a~%"
12922 (delete-file target)
12923 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12924 (call-with-output-file target
12926 (dump-port minified port)))))
12927 sources targets))))
12930 `(("r-ggplot2" ,r-ggplot2)
12931 ("r-htmltools" ,r-htmltools)
12932 ("r-htmlwidgets" ,r-htmlwidgets)
12933 ("r-jsonlite" ,r-jsonlite)
12934 ("r-miniui" ,r-miniui)
12935 ("r-shiny" ,r-shiny)
12936 ("r-shinyjs" ,r-shinyjs)))
12938 `(("uglify-js" ,uglify-js)
12942 (uri "https://code.jquery.com/jquery-3.3.1.js")
12945 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12949 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12952 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12953 (home-page "https://github.com/daattali/colourpicker")
12954 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12956 "This package provides a color picker that can be used as an input in
12957 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12958 custom color palettes, and many more options. A plot color helper tool is
12959 available as an RStudio Addin, which helps you pick colors to use in your
12960 plots. A more generic color picker RStudio Addin is also provided to let you
12961 select colors to use in your R code.")
12962 (license license:expat)))
12964 (define-public r-ggextra
12971 (uri (cran-uri "ggExtra" version))
12974 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12975 (properties `((upstream-name . "ggExtra")))
12976 (build-system r-build-system)
12978 `(("r-colourpicker" ,r-colourpicker)
12979 ("r-ggplot2" ,r-ggplot2)
12980 ("r-gtable" ,r-gtable)
12981 ("r-miniui" ,r-miniui)
12983 ("r-scales" ,r-scales)
12984 ("r-shiny" ,r-shiny)
12985 ("r-shinyjs" ,r-shinyjs)))
12987 `(("r-knitr" ,r-knitr)))
12988 (home-page "https://github.com/daattali/ggExtra")
12989 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12991 "This package is a collection of functions and layers to enhance ggplot2.
12992 The flagship function is @code{ggMarginal()}, which can be used to add
12993 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12994 (license license:expat)))
12996 (define-public r-minpack-lm
12998 (name "r-minpack-lm")
13003 (uri (cran-uri "minpack.lm" version))
13006 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
13007 (properties `((upstream-name . "minpack.lm")))
13008 (build-system r-build-system)
13009 (native-inputs `(("gfortran" ,gfortran)))
13010 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
13011 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
13013 "The @code{nls.lm} function provides an R interface to @code{lmder} and
13014 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
13015 problems by a modification of the Levenberg-Marquardt algorithm, with support
13016 for lower and upper parameter bounds. The implementation can be used via
13017 @code{nls}-like calls using the @code{nlsLM} function.")
13018 (license license:gpl3)))
13020 (define-public r-moments
13027 (uri (cran-uri "moments" version))
13030 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
13031 (build-system r-build-system)
13032 (home-page "https://cran.r-project.org/web/packages/moments")
13033 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
13035 "This package provides functions to calculate: moments, Pearson's
13036 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
13037 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
13038 (license license:gpl2+)))
13040 (define-public r-msir
13047 (uri (cran-uri "msir" version))
13050 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
13051 (build-system r-build-system)
13053 `(("r-mclust" ,r-mclust)))
13054 (home-page "https://cran.r-project.org/web/packages/msir")
13055 (synopsis "Model-based sliced inverse regression")
13057 "This is an R package for dimension reduction based on finite Gaussian
13058 mixture modeling of inverse regression.")
13059 (license license:gpl2+)))
13061 (define-public r-pbivnorm
13063 (name "r-pbivnorm")
13068 (uri (cran-uri "pbivnorm" version))
13071 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
13072 (build-system r-build-system)
13073 (native-inputs `(("gfortran" ,gfortran)))
13074 (home-page "https://github.com/brentonk/pbivnorm")
13075 (synopsis "Vectorized bivariate normal CDF")
13077 "This package provides a vectorized R function for calculating
13078 probabilities from a standard bivariate normal CDF.")
13079 (license license:gpl2+)))
13081 (define-public r-lavaan
13088 (uri (cran-uri "lavaan" version))
13091 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
13092 (build-system r-build-system)
13094 `(("r-mass" ,r-mass)
13095 ("r-mnormt" ,r-mnormt)
13096 ("r-numderiv" ,r-numderiv)
13097 ("r-pbivnorm" ,r-pbivnorm)))
13098 (home-page "http://lavaan.ugent.be")
13099 (synopsis "Latent variable analysis")
13101 "This package provides tools to fit a variety of latent variable models,
13102 including confirmatory factor analysis, structural equation modeling and
13103 latent growth curve models.")
13104 (license license:gpl2+)))
13106 (define-public r-nonnest2
13108 (name "r-nonnest2")
13113 (uri (cran-uri "nonnest2" version))
13116 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
13117 (build-system r-build-system)
13119 `(("r-compquadform" ,r-compquadform)
13120 ("r-lavaan" ,r-lavaan)
13121 ("r-mvtnorm" ,r-mvtnorm)
13122 ("r-sandwich" ,r-sandwich)))
13124 `(("r-knitr" ,r-knitr)))
13125 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
13126 (synopsis "Tests of non-nested models")
13128 "This package allows for testing of non-nested models. It includes tests
13129 of model distinguishability and of model fit that can be applied to both
13130 nested and non-nested models. The package also includes functionality to
13131 obtain confidence intervals associated with AIC and BIC.")
13132 ;; Either version of the GPL.
13133 (license (list license:gpl2 license:gpl3))))
13135 (define-public r-penalized
13137 (name "r-penalized")
13142 (uri (cran-uri "penalized" version))
13145 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
13146 (build-system r-build-system)
13148 `(("r-rcpp" ,r-rcpp)
13149 ("r-rcpparmadillo" ,r-rcpparmadillo)
13150 ("r-survival" ,r-survival)))
13151 (home-page "https://cran.r-project.org/web/packages/penalized/")
13152 (synopsis "Penalized estimation in GLMs and in the Cox model")
13154 "This package provides tools for fitting possibly high dimensional
13155 penalized regression models. The penalty structure can be any combination of
13156 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
13157 constraint on the regression coefficients. The supported regression models
13158 are linear, logistic and Poisson regression and the Cox Proportional Hazards
13159 model. Cross-validation routines allow optimization of the tuning
13161 (license license:gpl2+)))
13163 (define-public r-zim
13170 (uri (cran-uri "ZIM" version))
13173 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
13174 (properties `((upstream-name . "ZIM")))
13175 (build-system r-build-system)
13176 (propagated-inputs `(("r-mass" ,r-mass)))
13177 (home-page "https://github.com/biostatstudio/ZIM")
13178 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
13180 "Analyze count time series with excess zeros. Two types of statistical
13181 models are supported: Markov regression and state-space models. They are also
13182 known as observation-driven and parameter-driven models respectively in the
13183 time series literature. The functions used for Markov regression or
13184 observation-driven models can also be used to fit ordinary regression models
13185 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
13186 negative binomial (ZINB) assumption. The package also contains miscellaneous
13187 functions to compute density, distribution, quantile, and generate random
13188 numbers from ZIP and ZINB distributions.")
13189 (license license:gpl3)))
13191 (define-public r-nor1mix
13198 (uri (cran-uri "nor1mix" version))
13201 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13202 (build-system r-build-system)
13203 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13204 (synopsis "Normal (1-d) mixture models")
13206 "This package provides S3 classes and methods for one-dimensional normal
13207 mixture models, for, e.g., density estimation or clustering algorithms
13208 research and teaching; it provides the widely used Marron-Wand densities. It
13209 also provides tools for efficient random number generation and graphics.")
13210 (license license:gpl2+)))
13212 (define-public r-beanplot
13214 (name "r-beanplot")
13219 (uri (cran-uri "beanplot" version))
13222 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13223 (build-system r-build-system)
13224 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13225 (synopsis "Visualization via beanplots")
13227 "This package provides beanplots, an alternative to
13228 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13230 (license license:gpl2)))
13232 (define-public r-pbdzmq
13239 (uri (cran-uri "pbdZMQ" version))
13242 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13243 (properties `((upstream-name . "pbdZMQ")))
13244 (build-system r-build-system)
13246 `(("zeromq" ,zeromq)
13249 `(("pkg-config" ,pkg-config)))
13250 (home-page "https://pbdr.org/")
13251 (synopsis "R interface to ZeroMQ")
13253 "ZeroMQ is a well-known library for high-performance asynchronous
13254 messaging in scalable, distributed applications. This package provides high
13255 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13256 interactive client/server programming frameworks. A few wrapper functions
13257 compatible with @code{rzmq} are also provided.")
13258 (license license:gpl3)))
13260 (define-public r-repr
13267 (uri (cran-uri "repr" version))
13270 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13271 (build-system r-build-system)
13273 `(("r-base64enc" ,r-base64enc)
13274 ("r-htmltools" ,r-htmltools)
13275 ("r-jsonlite" ,r-jsonlite)
13276 ("r-pillar" ,r-pillar)))
13277 (home-page "https://cran.r-project.org/web/packages/repr/")
13278 (synopsis "Serializable representations")
13280 "This package provides string and binary representations of objects for
13281 several formats and MIME types.")
13282 (license license:gpl3)))
13284 (define-public r-irdisplay
13286 (name "r-irdisplay")
13291 (uri (cran-uri "IRdisplay" version))
13294 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13295 (properties `((upstream-name . "IRdisplay")))
13296 (build-system r-build-system)
13298 `(("r-repr" ,r-repr)))
13299 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13300 (synopsis "Jupyter display machinery")
13302 "This package provides an interface to the rich display capabilities of
13303 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13304 running IRkernel session.")
13305 (license license:expat)))
13307 (define-public r-irkernel
13309 (name "r-irkernel")
13314 (uri (cran-uri "IRkernel" version))
13317 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13318 (properties `((upstream-name . "IRkernel")))
13319 (build-system r-build-system)
13322 (modify-phases %standard-phases
13323 (add-after 'install 'install-kernelspec
13324 (lambda* (#:key outputs #:allow-other-keys)
13325 (let ((out (assoc-ref outputs "out")))
13326 (setenv "HOME" "/tmp")
13327 (invoke "jupyter" "kernelspec" "install"
13330 (string-append out "/site-library/IRkernel/kernelspec"))
13331 ;; Record the absolute file name of the 'R' executable in
13333 (substitute* (string-append out "/share/jupyter"
13334 "/kernels/ir/kernel.json")
13336 (string-append "[\"" (which "R") "\",")))
13339 `(("jupyter" ,jupyter)))
13341 `(("r-crayon" ,r-crayon)
13342 ("r-digest" ,r-digest)
13343 ("r-evaluate" ,r-evaluate)
13344 ("r-irdisplay" ,r-irdisplay)
13345 ("r-jsonlite" ,r-jsonlite)
13346 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13347 ("r-minimal" ,r-minimal)
13348 ("r-pbdzmq" ,r-pbdzmq)
13350 ("r-uuid" ,r-uuid)))
13351 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13352 (synopsis "Native R kernel for Jupyter")
13354 "The R kernel for the Jupyter environment executes R code which the
13355 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13357 (license license:expat)))
13359 (define-public r-gmodels
13366 (uri (cran-uri "gmodels" version))
13369 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13370 (build-system r-build-system)
13372 `(("r-gdata" ,r-gdata)
13373 ("r-mass" ,r-mass)))
13374 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13375 (synopsis "Various R programming tools for model fitting")
13377 "This package provides various R programming tools for model fitting.")
13378 (license license:gpl2)))
13380 (define-public r-apcluster
13382 (name "r-apcluster")
13387 (uri (cran-uri "apcluster" version))
13390 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13391 (build-system r-build-system)
13393 `(("r-matrix" ,r-matrix)
13394 ("r-rcpp" ,r-rcpp)))
13395 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13396 (synopsis "Affinity propagation clustering")
13398 "This package implements affinity propagation clustering introduced by
13399 Frey and Dueck (2007). The package further provides leveraged affinity
13400 propagation and an algorithm for exemplar-based agglomerative clustering that
13401 can also be used to join clusters obtained from affinity propagation. Various
13402 plotting functions are available for analyzing clustering results.")
13403 (license license:gpl2+)))
13405 (define-public r-valr
13412 (uri (cran-uri "valr" version))
13415 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13416 (build-system r-build-system)
13418 `(("r-broom" ,r-broom)
13419 ("r-dplyr" ,r-dplyr)
13420 ("r-ggplot2" ,r-ggplot2)
13422 ("r-readr" ,r-readr)
13423 ("r-rlang" ,r-rlang)
13424 ("r-stringr" ,r-stringr)
13425 ("r-tibble" ,r-tibble)))
13427 `(("r-knitr" ,r-knitr)))
13428 (home-page "https://github.com/rnabioco/valr")
13429 (synopsis "Genome interval arithmetic in R")
13431 "This package enables you to read and manipulate genome intervals and
13432 signals. It provides functionality similar to command-line tool suites within
13433 R, enabling interactive analysis and visualization of genome-scale data.")
13434 (license license:expat)))
13436 (define-public r-rematch2
13438 (name "r-rematch2")
13443 (uri (cran-uri "rematch2" version))
13446 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13447 (build-system r-build-system)
13449 `(("r-tibble" ,r-tibble)))
13450 (home-page "https://github.com/r-lib/rematch2")
13451 (synopsis "Tidy output from regular expression matching")
13453 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13454 return the match results in tidy data frames.")
13455 (license license:expat)))
13457 (define-public r-picante
13464 (uri (cran-uri "picante" version))
13467 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13468 (build-system r-build-system)
13472 ("r-vegan" ,r-vegan)))
13473 (home-page "https://cran.r-project.org/web/packages/picante/")
13474 (synopsis "Integrating phylogenies and ecology")
13476 "This package provides functions for phylocom integration, community
13477 analyses, null-models, traits and evolution. It implements numerous
13478 ecophylogenetic approaches including measures of community phylogenetic and
13479 trait diversity, phylogenetic signal, estimation of trait values for
13480 unobserved taxa, null models for community and phylogeny randomizations, and
13481 utility functions for data input/output and phylogeny plotting. A full
13482 description of package functionality and methods are provided by Kembel et
13484 (license license:gpl2)))
13486 (define-public r-reinforcelearn
13488 (name "r-reinforcelearn")
13493 (uri (cran-uri "reinforcelearn" version))
13496 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13497 (build-system r-build-system)
13499 `(("r-checkmate" ,r-checkmate)
13501 ("r-purrr" ,r-purrr)
13503 (home-page "https://markusdumke.github.io/reinforcelearn")
13504 (synopsis "Reinforcement learning")
13506 "This package implements reinforcement learning environments and
13507 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13508 can be used with function approximation, eligibility traces (Singh & Sutton,
13509 1996) and experience replay (Mnih et al., 2013).")
13510 (license license:expat)))
13512 (define-public r-lemon
13519 (uri (cran-uri "lemon" version))
13522 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13523 (build-system r-build-system)
13525 `(("r-ggplot2" ,r-ggplot2)
13526 ("r-gridextra" ,r-gridextra)
13527 ("r-gtable" ,r-gtable)
13528 ("r-knitr" ,r-knitr)
13529 ("r-lattice" ,r-lattice)
13531 ("r-rlang" ,r-rlang)
13532 ("r-scales" ,r-scales)))
13534 `(("r-knitr" ,r-knitr)))
13535 (home-page "https://github.com/stefanedwards/lemon")
13536 (synopsis "Freshen up your ggplot2 plots")
13538 "This package provides functions for working with legends and axis lines
13539 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13541 (license license:gpl3)))
13543 (define-public r-wgaim
13550 (uri (cran-uri "wgaim" version))
13552 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13553 (build-system r-build-system)
13555 `(("r-ggplot2" ,r-ggplot2)
13557 (home-page "https://cran.r-project.org/web/packages/wgaim")
13558 (synopsis "Whole genome average interval mapping for QTL detection")
13560 "This package integrates sophisticated mixed modelling methods with a
13561 whole genome approach to detecting significant QTL in linkage maps.")
13562 (license license:gpl2+)))
13564 (define-public r-bedr
13571 (uri (cran-uri "bedr" version))
13574 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13575 (build-system r-build-system)
13577 `(("r-data-table" ,r-data-table)
13578 ("r-r-utils" ,r-r-utils)
13579 ("r-testthat" ,r-testthat)
13580 ("r-venndiagram" ,r-venndiagram)
13583 ("bedtools" ,bedtools)
13584 ("htslib" ,htslib))) ; for tabix
13586 `(("r-knitr" ,r-knitr))) ; for vignettes
13587 (home-page "https://cran.r-project.org/web/packages/bedr")
13588 (synopsis "Genomic region processing")
13590 "This package is for genomic regions processing using command line tools
13591 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13592 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13593 The bedr package's API enhances access to these tools as well as offers
13594 additional utilities for genomic regions processing.")
13595 (license license:gpl2)))
13597 (define-public r-sets
13604 (uri (cran-uri "sets" version))
13607 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13608 (properties `((upstream-name . "sets")))
13609 (build-system r-build-system)
13610 (home-page "https://cran.r-project.org/web/packages/sets")
13611 (synopsis "Sets, generalized sets, customizable sets and intervals")
13613 "This package provides data structures and basic operations for ordinary
13614 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13615 customizable sets, and intervals.")
13616 (license license:gpl2)))
13618 (define-public r-partitions
13620 (name "r-partitions")
13625 (uri (cran-uri "partitions" version))
13628 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13629 (build-system r-build-system)
13632 ("r-polynom" ,r-polynom)
13633 ("r-sets" ,r-sets)))
13634 (home-page "https://cran.r-project.org/web/packages/partitions")
13635 (synopsis "Additive partitions of integers")
13637 "This package provides tools to enumerates the partitions, unequal
13638 partitions, and restricted partitions of an integer; the three corresponding
13639 partition functions are also given.")
13640 ;; Any version of the GPL
13641 (license license:gpl2+)))
13643 (define-public r-brobdingnag
13645 (name "r-brobdingnag")
13650 (uri (cran-uri "Brobdingnag" version))
13653 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13654 (properties `((upstream-name . "Brobdingnag")))
13655 (build-system r-build-system)
13656 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13657 (synopsis "Very large numbers in R")
13659 "This package handles very large numbers in R. Real numbers are held
13660 using their natural logarithms, plus a logical flag indicating sign. The
13661 package includes a vignette that gives a step-by-step introduction to using S4
13663 ;; Any version of the GPL
13664 (license license:gpl2+)))
13666 (define-public r-untb
13673 (uri (cran-uri "untb" version))
13676 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13677 (build-system r-build-system)
13679 `(("r-brobdingnag" ,r-brobdingnag)
13680 ("r-partitions" ,r-partitions)
13681 ("r-polynom" ,r-polynom)))
13682 (home-page "https://github.com/RobinHankin/untb.git")
13683 (synopsis "Ecological drift under the UNTB")
13685 "This package provides numerical simulations, and visualizations, of
13686 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13687 (license license:gpl2+)))
13689 (define-public r-stepwise
13691 (name "r-stepwise")
13696 (uri (cran-uri "stepwise" version))
13699 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13700 (build-system r-build-system)
13701 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13702 (synopsis "Stepwise detection of recombination breakpoints")
13704 "This package provides a stepwise approach to identifying recombination
13705 breakpoints in a genomic sequence alignment.")
13706 (license license:gpl2+)))
13708 (define-public r-snpmaxsel
13710 (name "r-snpmaxsel")
13715 (uri (cran-uri "SNPmaxsel" version))
13718 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13719 (properties `((upstream-name . "SNPmaxsel")))
13720 (build-system r-build-system)
13722 `(("r-combinat" ,r-combinat)
13723 ("r-mvtnorm" ,r-mvtnorm)))
13724 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13725 (synopsis "Maximally selected statistics for SNP data")
13727 "This package implements asymptotic methods related to maximally selected
13728 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13730 (license license:gpl2+)))
13732 (define-public r-acsnminer
13734 (name "r-acsnminer")
13735 (version "0.16.8.25")
13738 (uri (cran-uri "ACSNMineR" version))
13741 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13742 (properties `((upstream-name . "ACSNMineR")))
13743 (build-system r-build-system)
13745 `(("r-ggplot2" ,r-ggplot2)
13746 ("r-gridextra" ,r-gridextra)))
13747 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13748 (synopsis "Gene enrichment analysis")
13750 "This package provides tools to compute and represent gene set enrichment
13751 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13752 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13753 enrichment can be run with hypergeometric test or Fisher exact test, and can
13754 use multiple corrections. Visualization of data can be done either by
13755 barplots or heatmaps.")
13756 (license license:gpl2+)))
13758 (define-public r-seqinr
13765 (uri (cran-uri "seqinr" version))
13768 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13769 (build-system r-build-system)
13771 `(("r-ade4" ,r-ade4)
13772 ("r-segmented" ,r-segmented)))
13775 (home-page "http://seqinr.r-forge.r-project.org/")
13776 (synopsis "Biological sequences retrieval and analysis")
13778 "This package provides tools for exploratory data analysis and data
13779 visualization of biological sequence (DNA and protein) data. It also includes
13780 utilities for sequence data management under the ACNUC system.")
13781 (license license:gpl2+)))
13783 (define-public r-units
13790 (uri (cran-uri "units" version))
13793 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13794 (build-system r-build-system)
13796 `(("udunits" ,udunits)))
13798 `(("r-rcpp" ,r-rcpp)))
13800 `(("r-knitr" ,r-knitr)))
13801 (home-page "https://github.com/r-quantities/units/")
13802 (synopsis "Measurement Units for R Vectors")
13804 "This package provides support for measurement units in R vectors,
13805 matrices and arrays: automatic propagation, conversion, derivation and
13806 simplification of units; raising errors in case of unit incompatibility. It
13807 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13809 (license license:gpl2)))
13811 (define-public r-classint
13813 (name "r-classint")
13818 (uri (cran-uri "classInt" version))
13821 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13822 (properties `((upstream-name . "classInt")))
13823 (build-system r-build-system)
13825 `(("r-class" ,r-class)
13826 ("r-e1071" ,r-e1071)
13827 ("r-kernsmooth" ,r-kernsmooth)))
13829 `(("gfortran" ,gfortran)
13830 ("r-knitr" ,r-knitr)))
13831 (home-page "https://github.com/r-spatial/classInt/")
13832 (synopsis "Choose univariate class intervals")
13834 "This package provides selected commonly used methods for choosing
13835 univariate class intervals for mapping or other graphics purposes.")
13836 (license license:gpl2+)))
13838 (define-public r-spdata
13845 (uri (cran-uri "spData" version))
13848 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13849 (properties `((upstream-name . "spData")))
13850 (build-system r-build-system)
13852 `(("r-raster" ,r-raster)
13854 (home-page "https://github.com/Nowosad/spData")
13855 (synopsis "Datasets for spatial analysis")
13857 "This a package containing diverse spatial datasets for demonstrating,
13858 benchmarking and teaching spatial data analysis. It includes R data of class
13859 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13860 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13861 of the datasets are designed to illustrate specific analysis techniques.
13862 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13863 illustrate point pattern analysis techniques.")
13864 (license license:cc0)))
13866 (define-public r-learnbayes
13868 (name "r-learnbayes")
13873 (uri (cran-uri "LearnBayes" version))
13876 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13877 (properties `((upstream-name . "LearnBayes")))
13878 (build-system r-build-system)
13879 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13880 (synopsis "Functions for learning Bayesian inference")
13882 "This package provides a collection of functions helpful in learning the
13883 basic tenets of Bayesian statistical inference. It contains functions for
13884 summarizing basic one and two parameter posterior distributions and predictive
13885 distributions. It contains MCMC algorithms for summarizing posterior
13886 distributions defined by the user. It also contains functions for regression
13887 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13889 (license license:gpl2+)))
13891 (define-public r-deldir
13898 (uri (cran-uri "deldir" version))
13901 "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
13902 (build-system r-build-system)
13903 (native-inputs `(("gfortran" ,gfortran)))
13904 (home-page "https://cran.r-project.org/web/packages/deldir")
13905 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13907 "This package provides tools for calculating the Delaunay triangulation
13908 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13909 of a planar point set. It plots triangulations and tessellations in various
13910 ways, clips tessellations to sub-windows, calculates perimeters of
13911 tessellations, and summarizes information about the tiles of the
13913 (license license:gpl2+)))
13915 (define-public r-sf
13922 (uri (cran-uri "sf" version))
13925 "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9"))))
13926 (build-system r-build-system)
13933 `(("r-classint" ,r-classint)
13935 ("r-magrittr" ,r-magrittr)
13937 ("r-units" ,r-units)))
13939 `(("pkg-config" ,pkg-config)
13940 ("r-knitr" ,r-knitr)))
13941 (home-page "https://github.com/r-spatial/sf/")
13942 (synopsis "Simple features for R")
13944 "This package provides support for simple features, a standardized way to
13945 encode spatial vector data. It binds to GDAL for reading and writing data, to
13946 GEOS for geometrical operations, and to PROJ for projection conversions and
13947 datum transformations.")
13948 ;; Either of these licenses
13949 (license (list license:gpl2 license:expat))))
13951 (define-public r-spdep
13958 (uri (cran-uri "spdep" version))
13961 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13962 (build-system r-build-system)
13964 `(("r-boot" ,r-boot)
13966 ("r-deldir" ,r-deldir)
13968 ("r-gmodels" ,r-gmodels)
13969 ("r-learnbayes" ,r-learnbayes)
13971 ("r-matrix" ,r-matrix)
13975 ("r-spdata" ,r-spdata)))
13977 `(("r-knitr" ,r-knitr)))
13978 (home-page "https://github.com/r-spatial/spdep/")
13979 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13981 "This package provides a collection of functions to create spatial
13982 weights matrix objects from polygon contiguities, from point patterns by
13983 distance and tessellations, for summarizing these objects, and for permitting
13984 their use in spatial data analysis, including regional aggregation by minimum
13986 (license license:gpl2+)))
13988 (define-public r-adegenet
13990 (name "r-adegenet")
13995 (uri (cran-uri "adegenet" version))
13998 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13999 (build-system r-build-system)
14001 `(("r-ade4" ,r-ade4)
14004 ("r-dplyr" ,r-dplyr)
14005 ("r-ggplot2" ,r-ggplot2)
14006 ("r-igraph" ,r-igraph)
14008 ("r-reshape2" ,r-reshape2)
14009 ("r-seqinr" ,r-seqinr)
14010 ("r-shiny" ,r-shiny)
14011 ("r-spdep" ,r-spdep)
14012 ("r-vegan" ,r-vegan)))
14013 (home-page "https://github.com/thibautjombart/adegenet")
14014 (synopsis "Exploratory analysis of genetic and genomic data")
14016 "This package provides a toolset for the exploration of genetic and
14017 genomic data. Adegenet provides formal (S4) classes for storing and handling
14018 various genetic data, including genetic markers with varying ploidy and
14019 hierarchical population structure (@code{genind} class), alleles counts by
14020 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
14021 also implements original multivariate methods (DAPC, sPCA), graphics,
14022 statistical tests, simulation tools, distance and similarity measures, and
14023 several spatial methods. A range of both empirical and simulated datasets is
14024 also provided to illustrate various methods.")
14025 (license license:gpl2+)))
14027 (define-public r-pegas
14034 (uri (cran-uri "pegas" version))
14036 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
14037 (build-system r-build-system)
14039 `(("r-adegenet" ,r-adegenet)
14041 (home-page "http://ape-package.ird.fr/pegas.html")
14042 (synopsis "Population and evolutionary genetics analysis system")
14044 "This package provides functions for reading, writing, plotting,
14045 analysing, and manipulating allelic and haplotypic data, including from VCF
14046 files, and for the analysis of population nucleotide sequences and
14047 micro-satellites including coalescent analyses, linkage disequilibrium,
14048 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
14049 minimum spanning tree and network, and median-joining networks.")
14050 (license license:gpl2+)))
14052 (define-public r-rmetasim
14054 (name "r-rmetasim")
14059 (uri (cran-uri "rmetasim" version))
14062 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
14063 (build-system r-build-system)
14065 `(("r-ade4" ,r-ade4)
14066 ("r-adegenet" ,r-adegenet)
14067 ("r-gtools" ,r-gtools)
14068 ("r-pegas" ,r-pegas)))
14069 (home-page "https://cran.r-project.org/web/packages/rmetasim")
14070 (synopsis "Individual-based population genetic simulation environment")
14072 "This package provides an interface between R and the metasim simulation
14073 engine. The simulation environment is documented in: Strand, A.(2002),
14074 Metasim 1.0: an individual-based environment for simulating population
14075 genetics of complex population dynamics.")
14077 (license license:gpl2+)))
14079 (define-public r-genetics
14081 (name "r-genetics")
14082 (version "1.3.8.1.2")
14086 (uri (cran-uri "genetics" version))
14089 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
14090 (build-system r-build-system)
14092 `(("r-combinat" ,r-combinat)
14093 ("r-gdata" ,r-gdata)
14094 ("r-gtools" ,r-gtools)
14096 ("r-mvtnorm" ,r-mvtnorm)))
14097 (home-page "https://cran.r-project.org/web/packages/genetics/")
14098 (synopsis "Population genetics")
14100 "This package provides classes and methods for handling genetic data.
14101 It includes classes to represent genotypes and haplotypes at single markers up
14102 to multiple markers on multiple chromosomes. Function include allele
14103 frequencies, flagging homo/heterozygotes, flagging carriers of certain
14104 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
14105 and testing for linkage disequilibrium, ...")
14106 ;; Any GPL version.
14107 (license license:gpl2+)))
14109 (define-public r-snp-plotter
14111 (name "r-snp-plotter")
14116 (uri (cran-uri "snp.plotter" version))
14119 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
14120 (properties `((upstream-name . "snp.plotter")))
14121 (build-system r-build-system)
14122 (propagated-inputs `(("r-genetics" ,r-genetics)))
14123 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
14124 (synopsis "Plot p-values using single SNP and/or haplotype data")
14126 "This package helps you create plots of p-values using single SNP and/or
14127 haplotype data. Main features of the package include options to display a
14128 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
14129 datasets simultaneously. Plots can be created using global and/or individual
14130 haplotype p-values along with single SNP p-values. Images are created as
14131 either PDF/EPS files.")
14132 (license license:gpl2+)))
14134 (define-public r-polspline
14136 (name "r-polspline")
14141 (uri (cran-uri "polspline" version))
14143 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
14144 (build-system r-build-system)
14145 (native-inputs `(("gfortran" ,gfortran)))
14146 (home-page "https://cran.r-project.org/web/packages/polspline/")
14147 (synopsis "Polynomial spline routines")
14149 "This package provides routines for the polynomial spline fitting
14150 routines hazard regression, hazard estimation with flexible tails, logspline,
14151 lspec, polyclass, and polymars.")
14152 (license license:gpl2+)))
14154 (define-public r-rms
14161 (uri (cran-uri "rms" version))
14163 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
14164 (build-system r-build-system)
14166 `(("r-cluster" ,r-cluster)
14167 ("r-digest" ,r-digest)
14168 ("r-ggplot2" ,r-ggplot2)
14169 ("r-hmisc" ,r-hmisc)
14170 ("r-htmltable" ,r-htmltable)
14171 ("r-htmltools" ,r-htmltools)
14172 ("r-lattice" ,r-lattice)
14174 ("r-multcomp" ,r-multcomp)
14176 ("r-polspline" ,r-polspline)
14177 ("r-quantreg" ,r-quantreg)
14178 ("r-rpart" ,r-rpart)
14179 ("r-sparsem" ,r-sparsem)
14180 ("r-survival" ,r-survival)))
14181 (native-inputs `(("gfortran" ,gfortran)))
14182 (home-page "http://biostat.mc.vanderbilt.edu/rms")
14183 (synopsis "Regression modeling strategies")
14185 "This is a package for regression modeling, testing, estimation,
14186 validation, graphics, prediction, and typesetting by storing enhanced model
14187 design attributes in the fit. The rms package is a collection of functions
14188 that assist with and streamline modeling. It also contains functions for
14189 binary and ordinal logistic regression models, ordinal models for continuous Y
14190 with a variety of distribution families, and the Buckley-James multiple
14191 regression model for right-censored responses, and implements penalized
14192 maximum likelihood estimation for logistic and ordinary linear models. The
14193 package works with almost any regression model, but it was especially written
14194 to work with binary or ordinal regression models, Cox regression, accelerated
14195 failure time models, ordinary linear models, the Buckley-James model,
14196 generalized least squares for serially or spatially correlated observations,
14197 generalized linear models, and quantile regression.")
14198 (license license:gpl2+)))
14200 (define-public r-arsenal
14207 (uri (cran-uri "arsenal" version))
14210 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14211 (properties `((upstream-name . "arsenal")))
14212 (build-system r-build-system)
14213 (propagated-inputs `(("r-knitr" ,r-knitr)))
14214 (native-inputs `(("r-knitr" ,r-knitr)))
14215 (home-page "https://github.com/mayoverse/arsenal")
14216 (synopsis "Functions for large-scale statistical summaries")
14218 "This package provides an arsenal of R functions for large-scale
14219 statistical summaries, which are streamlined to work within the latest
14220 reporting tools in R and RStudio and which use formulas and versatile
14221 summary statistics for summary tables and models. The primary functions
14225 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14226 levels of one or more categorical variables;
14227 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14228 across two time points;
14229 @item @code{modelsum}, which performs simple model fits on one or more
14230 endpoints for many variables (univariate or adjusted for covariates);
14231 @item @code{freqlist}, a powerful frequency table across many categorical
14233 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14234 @item @code{write2}, a function to output tables to a document.
14237 (license license:gpl2+)))
14239 (define-public r-haplo-stats
14241 (name "r-haplo-stats")
14246 (uri (cran-uri "haplo.stats" version))
14249 "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9"))))
14250 (properties `((upstream-name . "haplo.stats")))
14251 (build-system r-build-system)
14253 `(("r-arsenal" ,r-arsenal)
14256 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14257 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14258 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14260 "This package provides routines for the analysis of indirectly measured
14261 haplotypes. The statistical methods assume that all subjects are unrelated
14262 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14263 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14264 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14265 examples in the vignette.")
14266 (license license:gpl2+)))
14268 (define-public r-bqtl
14275 (uri (cran-uri "bqtl" version))
14278 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14279 (build-system r-build-system)
14280 (native-inputs `(("gfortran" ,gfortran)))
14281 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14282 (synopsis "Bayesian QTL mapping toolkit")
14284 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14285 lines. It includes maximum likelihood and Bayesian tools.")
14286 (license license:gpl2+)))
14288 (define-public r-ibdreg
14295 (uri (cran-uri "ibdreg" version))
14298 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14299 (build-system r-build-system)
14300 (home-page "https://www.mayo.edu/research/labs/\
14301 statistical-genetics-genetic-epidemiology/software")
14302 (synopsis "Regression methods for IBD linkage with covariates")
14304 "This package provides a method to test genetic linkage with covariates
14305 by regression methods with response IBD sharing for relative pairs. Account
14306 for correlations of IBD statistics and covariates for relative pairs within
14307 the same pedigree.")
14308 (license license:gpl2+)))
14310 (define-public r-dlmap
14317 (uri (cran-uri "dlmap" version))
14320 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14321 (build-system r-build-system)
14323 `(("r-ibdreg" ,r-ibdreg)
14327 ("r-wgaim" ,r-wgaim)))
14328 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14329 (synopsis "Detection localization mapping for QTL")
14331 "This is package for QTL mapping in a mixed model framework with separate
14332 detection and localization stages. The first stage detects the number of QTL
14333 on each chromosome based on the genetic variation due to grouped markers on
14334 the chromosome; the second stage uses this information to determine the most
14335 likely QTL positions. The mixed model can accommodate general fixed and
14336 random effects, including spatial effects in field trials and pedigree
14337 effects. It is applicable to backcrosses, doubled haploids, recombinant
14338 inbred lines, F2 intercrosses, and association mapping populations.")
14339 (license license:gpl2)))
14341 (define-public r-ldheatmap
14343 (name "r-ldheatmap")
14348 (uri (cran-uri "LDheatmap" version))
14351 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14352 (properties `((upstream-name . "LDheatmap")))
14353 (build-system r-build-system)
14355 `(("r-genetics" ,r-genetics)
14357 ("r-snpstats" ,r-snpstats)))
14358 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14359 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14361 "This package provides tools to produce a graphical display, as a heat
14362 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14363 optionally include the physical locations or genetic map distances of each SNP
14365 (license license:gpl3)))
14367 (define-public r-hwde
14374 (uri (cran-uri "hwde" version))
14377 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14378 (build-system r-build-system)
14379 (home-page "https://cran.r-project.org/web/packages/hwde/")
14380 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14382 "This package fits models for genotypic disequilibria, as described in
14383 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14384 terms are available that account for first order interactions between loci.
14385 It also implements, for a single locus in a single population, a conditional
14386 exact test for Hardy-Weinberg equilibrium.")
14387 (license license:gpl2+)))
14389 (define-public r-tdthap
14396 (uri (cran-uri "tdthap" version))
14399 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14400 (build-system r-build-system)
14401 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14402 (synopsis "TDT tests for extended haplotypes")
14404 "Functions and examples are provided for transmission/disequilibrium
14405 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14406 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14407 (license license:artistic2.0)))
14409 (define-public r-sparql
14415 (uri (cran-uri "SPARQL" version))
14418 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14419 (properties `((upstream-name . "SPARQL")))
14420 (build-system r-build-system)
14422 `(("r-rcurl" ,r-rcurl)
14424 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14425 (synopsis "SPARQL client for R")
14426 (description "This package provides an interface to use SPARQL to pose
14427 SELECT or UPDATE queries to an end-point.")
14428 ;; The only license indication is found in the DESCRIPTION file,
14429 ;; which states GPL-3. So we cannot assume GPLv3+.
14430 (license license:gpl3)))
14432 (define-public r-bookdown
14434 (name "r-bookdown")
14438 (uri (cran-uri "bookdown" version))
14441 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14442 (build-system r-build-system)
14444 `(("r-htmltools" ,r-htmltools)
14445 ("r-knitr" ,r-knitr)
14446 ("r-rmarkdown" ,r-rmarkdown)
14447 ("r-tinytex" ,r-tinytex)
14449 ("pandoc" ,pandoc)))
14450 (home-page "https://github.com/rstudio/bookdown")
14451 (synopsis "Authoring books and technical documents with R markdown")
14452 (description "This package provides output formats and utilities for
14453 authoring books and technical documents with R Markdown.")
14454 (license license:gpl3)))
14456 (define-public r-optparse
14458 (name "r-optparse")
14463 (uri (cran-uri "optparse" version))
14466 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14467 (build-system r-build-system)
14469 `(("r-getopt" ,r-getopt)))
14471 `(("r-knitr" ,r-knitr)))
14472 (home-page "https://github.com/trevorld/optparse")
14473 (synopsis "Command line option parser")
14475 "This package provides a command line parser inspired by Python's
14476 @code{optparse} library to be used with Rscript to write shebang scripts
14477 that accept short and long options.")
14478 (license license:gpl2+)))
14480 (define-public r-wgcna
14487 (uri (cran-uri "WGCNA" version))
14490 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14491 (properties `((upstream-name . "WGCNA")))
14492 (build-system r-build-system)
14494 `(("r-annotationdbi" ,r-annotationdbi)
14495 ("r-doparallel" ,r-doparallel)
14496 ("r-dynamictreecut" ,r-dynamictreecut)
14497 ("r-fastcluster" ,r-fastcluster)
14498 ("r-foreach" ,r-foreach)
14499 ("r-go-db" ,r-go-db)
14500 ("r-hmisc" ,r-hmisc)
14501 ("r-impute" ,r-impute)
14503 ("r-survival" ,r-survival)
14504 ("r-matrixstats" ,r-matrixstats)
14505 ("r-preprocesscore" ,r-preprocesscore)))
14507 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14508 (synopsis "Weighted correlation network analysis")
14510 "This package provides functions necessary to perform Weighted
14511 Correlation Network Analysis on high-dimensional data. It includes functions
14512 for rudimentary data cleaning, construction and summarization of correlation
14513 networks, module identification and functions for relating both variables and
14514 modules to sample traits. It also includes a number of utility functions for
14515 data manipulation and visualization.")
14516 (license license:gpl2+)))
14518 (define-public r-kernlab
14525 (uri (cran-uri "kernlab" version))
14527 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14528 (build-system r-build-system)
14529 (home-page "https://cran.r-project.org/web/packages/kernlab")
14530 (synopsis "Kernel-based machine learning tools")
14532 "This package provides kernel-based machine learning methods for
14533 classification, regression, clustering, novelty detection, quantile regression
14534 and dimensionality reduction. Among other methods @code{kernlab} includes
14535 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14537 (license license:gpl2)))
14539 (define-public r-hierfstat
14541 (name "r-hierfstat")
14546 (uri (cran-uri "hierfstat" version))
14549 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14550 (build-system r-build-system)
14552 `(("r-ade4" ,r-ade4)
14553 ("r-adegenet" ,r-adegenet)
14554 ("r-gaston" ,r-gaston)
14555 ("r-gtools" ,r-gtools)))
14557 `(("r-knitr" ,r-knitr)))
14558 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14559 (synopsis "Estimation and tests of hierarchical F-statistics")
14561 "This package allows the estimation of hierarchical F-statistics from
14562 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14563 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14564 are also given to test via randomisations the significance of each F and
14565 variance components, using the likelihood-ratio statistics G.")
14566 (license license:gpl2+)))
14568 (define-public r-hapassoc
14570 (name "r-hapassoc")
14575 (uri (cran-uri "hapassoc" version))
14578 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14579 (build-system r-build-system)
14580 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14581 (synopsis "Inference of trait associations with SNP haplotypes")
14583 "Hapassoc performs likelihood inference of trait associations with
14584 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14585 functions are developed primarily for data collected in cohort or
14586 cross-sectional studies. They can accommodate uncertain haplotype phase and
14587 handle missing genotypes at some SNPs.")
14588 (license license:gpl2)))
14590 (define-public r-sampling
14592 (name "r-sampling")
14597 (uri (cran-uri "sampling" version))
14600 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14601 (build-system r-build-system)
14603 `(("r-lpsolve" ,r-lpsolve)
14604 ("r-mass" ,r-mass)))
14605 (home-page "https://cran.r-project.org/web/packages/sampling/")
14606 (synopsis "Survey sampling")
14608 "This package provides functions for drawing and calibrating samples.")
14609 (license license:gpl2+)))
14611 (define-public r-r2html
14618 (uri (cran-uri "R2HTML" version))
14621 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14622 (properties `((upstream-name . "R2HTML")))
14623 (build-system r-build-system)
14624 (home-page "https://github.com/nalimilan/R2HTML")
14625 (synopsis "HTML export for R objects")
14627 "This package includes HTML functions and methods to write in an HTML
14628 file. Thus, making HTML reports is easy. It includes a function that allows
14629 redirection on the fly, which appears to be very useful for teaching purposes,
14630 as the student can keep a copy of the produced output to keep all that they
14631 did during the course. The package comes with a vignette describing how to
14632 write HTML reports for statistical analysis. Finally, a driver for Sweave
14633 parses HTML flat files containing R code and to automatically write
14634 the corresponding outputs (tables and graphs).")
14635 (license license:gpl2+)))
14637 (define-public r-rjava
14644 (uri (cran-uri "rJava" version))
14647 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14648 (properties `((upstream-name . "rJava")))
14649 (build-system r-build-system)
14651 `(#:modules ((guix build utils)
14652 (guix build r-build-system)
14655 (modify-phases %standard-phases
14656 (add-after 'unpack 'set-JAVA_HOME
14657 (lambda* (#:key inputs #:allow-other-keys)
14658 (let ((jdk (assoc-ref inputs "jdk")))
14659 (setenv "JAVA_HOME" jdk)
14660 (setenv "JAVA" (which "java"))
14661 (setenv "JAR" (which "jar"))
14662 (setenv "JAVAC" (which "javac"))
14663 (setenv "JAVAH" (which "javah"))
14664 (setenv "JAVA_CPPFLAGS"
14665 (string-append "-I" jdk "/include "
14666 "-I" jdk "/include/linux"))
14667 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14668 ((lib) (setenv "JAVA_LIBS" lib))
14669 (_ (error "Could not find libjvm.so"))))
14673 ("jdk" ,icedtea-8 "jdk")
14676 (home-page "https://www.rforge.net/rJava/")
14677 (synopsis "Low-Level R to Java interface")
14679 "This package provides a low-level interface to the Java VM very much
14680 like .C/.Call and friends. It allows the creation of objects, calling methods
14681 and accessing fields.")
14682 (license license:gpl2)))
14684 (define-public r-svmisc
14691 (uri (cran-uri "svMisc" version))
14694 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14695 (properties `((upstream-name . "svMisc")))
14696 (build-system r-build-system)
14697 (home-page "https://github.com/SciViews/svMisc")
14698 (synopsis "Miscellaneous functions for SciViews")
14700 "This package provides miscellaneous functions for SciViews or general
14701 use, including tools to manage a temporary environment attached to the search
14702 path for temporary variables you do not want to @code{save()} or
14703 @code{load()}; test the current platform; showing progress bars, etc.")
14704 (license license:gpl2)))
14706 (define-public r-xyz
14713 (uri (cran-uri "xyz" version))
14716 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14717 (build-system r-build-system)
14719 `(("r-rcpp" ,r-rcpp)))
14720 (home-page "https://cran.r-project.org/web/packages/xyz/")
14721 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14723 "High dimensional interaction search by brute force requires a quadratic
14724 computational cost in the number of variables. The xyz algorithm provably
14725 finds strong interactions in almost linear time. For details of the algorithm
14726 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14727 interaction search in high-dimensional data.")
14728 ;; Any version of the GPL.
14729 (license license:gpl2+)))
14731 (define-public r-rttf2pt1
14733 (name "r-rttf2pt1")
14738 (uri (cran-uri "Rttf2pt1" version))
14741 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14742 (properties `((upstream-name . "Rttf2pt1")))
14743 (build-system r-build-system)
14744 (home-page "https://github.com/wch/Rttf2pt1")
14745 (synopsis "Font conversion utility")
14747 "This package contains the program @code{ttf2pt1}, for use with the
14748 @code{extrafont} package.")
14749 ;; Most of the files are covered under the Expat license. Some files are
14750 ;; covered under BSD-3. Deviations for individual files are recorded in
14751 ;; the LICENSE file.
14752 (license (list license:bsd-3 license:expat
14753 (license:non-copyleft "file://LICENSE")))))
14755 (define-public r-extrafontdb
14757 (name "r-extrafontdb")
14762 (uri (cran-uri "extrafontdb" version))
14765 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14766 (build-system r-build-system)
14767 (home-page "https://github.com/wch/extrafontdb")
14768 (synopsis "Database for the extrafont package")
14770 "This package holds the database for the @code{extrafont} package.")
14771 (license license:gpl2)))
14773 (define-public r-extrafont
14775 (name "r-extrafont")
14780 (uri (cran-uri "extrafont" version))
14783 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14784 (build-system r-build-system)
14786 `(("r-extrafontdb" ,r-extrafontdb)
14787 ("r-rttf2pt1" ,r-rttf2pt1)))
14788 (home-page "https://github.com/wch/extrafont")
14789 (synopsis "Tools for using fonts in R")
14791 "The extrafont package makes it easier to use fonts other than the basic
14792 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14793 used with PDF or PostScript output files. There are two hurdles for using
14794 fonts in PDF (or Postscript) output files:
14797 @item Making R aware of the font and the dimensions of the characters.
14798 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14799 properly on a device that doesn't have the font. This is usually needed if
14800 you want to print the PDF file or share it with others.
14803 The extrafont package makes both of these things easier.")
14804 (license license:gpl2)))
14806 (define-public r-xkcd
14813 (uri (cran-uri "xkcd" version))
14816 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14817 (build-system r-build-system)
14819 `(("r-extrafont" ,r-extrafont)
14820 ("r-ggplot2" ,r-ggplot2)
14821 ("r-hmisc" ,r-hmisc)))
14822 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14823 (synopsis "Plot ggplot2 graphics in the XKCD style")
14825 "This package provides the means to plot ggplot2 graphs in the style of
14826 the XKCD web comic.")
14827 (license license:gpl3)))
14829 (define-public r-msigdbr
14836 (uri (cran-uri "msigdbr" version))
14839 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14840 (build-system r-build-system)
14842 `(("r-dplyr" ,r-dplyr)
14843 ("r-magrittr" ,r-magrittr)
14844 ("r-rlang" ,r-rlang)
14845 ("r-tibble" ,r-tibble)))
14847 `(("r-knitr" ,r-knitr)))
14848 (home-page "https://github.com/igordot/msigdbr")
14849 (synopsis "MSigDB gene sets for multiple organisms")
14851 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14852 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14853 software in a standard R data frame with key-value pairs. Included are the
14854 original human gene symbols and Entrez IDs as well as the equivalents for
14855 various frequently studied model organisms such as mouse, rat, pig, fly, and
14857 ;; The package is covered under the Expat license, but the upstream MSigDB
14858 ;; files are made available under the Creative Commons Attribution 4.0
14859 ;; International license.
14860 (license (list license:expat license:cc-by4.0))))
14862 (define-public r-gridgraphics
14864 (name "r-gridgraphics")
14869 (uri (cran-uri "gridGraphics" version))
14872 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14873 (properties `((upstream-name . "gridGraphics")))
14874 (build-system r-build-system)
14875 (home-page "https://github.com/pmur002/gridgraphics")
14876 (synopsis "Redraw base graphics using @code{grid} graphics")
14878 "This package provides functions to convert a page of plots drawn with
14879 the @code{graphics} package into identical output drawn with the @code{grid}
14880 package. The result looks like the original @code{graphics}-based plot, but
14881 consists of @code{grid} grobs and viewports that can then be manipulated with
14882 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14883 (license license:gpl2+)))
14885 (define-public r-farver
14892 (uri (cran-uri "farver" version))
14895 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14896 (build-system r-build-system)
14897 (home-page "https://github.com/thomasp85/farver")
14898 (synopsis "Vectorized color conversion and comparison")
14900 "The encoding of color can be handled in many different ways, using
14901 different color spaces. As different color spaces have different uses,
14902 efficient conversion between these representations are important. This
14903 package provides a set of functions that gives access to very fast color space
14904 conversion and comparisons implemented in C++, and offers 100-fold speed
14905 improvements over the @code{convertColor} function in the @code{grDevices}
14907 (license license:expat)))
14909 (define-public r-ggplotify
14911 (name "r-ggplotify")
14916 (uri (cran-uri "ggplotify" version))
14919 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14920 (build-system r-build-system)
14922 `(("r-ggplot2" ,r-ggplot2)
14923 ("r-gridgraphics" ,r-gridgraphics)
14924 ("r-rvcheck" ,r-rvcheck)))
14926 `(("r-knitr" ,r-knitr)))
14927 (home-page "https://github.com/GuangchuangYu/ggplotify")
14928 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14930 "This package provides tools to convert plot function calls (using
14931 expression or formula) to @code{grob} or @code{ggplot} objects that are
14932 compatible with the @code{grid} and @code{ggplot2} environment. With this
14933 package, we are able to e.g. use @code{cowplot} to align plots produced by
14934 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14935 converting them to @code{ggplot} objects.")
14936 (license license:artistic2.0)))
14938 (define-public r-triebeard
14940 (name "r-triebeard")
14945 (uri (cran-uri "triebeard" version))
14948 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14949 (build-system r-build-system)
14950 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14951 (home-page "https://github.com/Ironholds/triebeard/")
14952 (synopsis "Radix trees in Rcpp")
14954 "Radix trees, or tries, are key-value data structures optimized for
14955 efficient lookups, similar in purpose to hash tables. This package provides
14956 an implementation of radix trees for use in R programming and in developing
14957 packages with Rcpp.")
14958 (license license:expat)))
14960 (define-public r-tweenr
14967 (uri (cran-uri "tweenr" version))
14970 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14971 (build-system r-build-system)
14973 `(("r-farver" ,r-farver)
14974 ("r-magrittr" ,r-magrittr)
14976 ("r-rlang" ,r-rlang)))
14977 (home-page "https://github.com/thomasp85/tweenr")
14978 (synopsis "Interpolate data for smooth animations")
14980 "In order to create smooth animation between states of data, tweening is
14981 necessary. This package provides a range of functions for creating tweened
14982 data that can be used as basis for animation. Furthermore it adds a number of
14983 vectorized interpolaters for common R data types such as numeric, date and
14985 (license license:expat)))
14987 (define-public r-polyclip
14989 (name "r-polyclip")
14994 (uri (cran-uri "polyclip" version))
14997 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14998 (build-system r-build-system)
14999 (native-inputs `(("pkg-config" ,pkg-config)))
15000 (home-page "http://www.angusj.com/delphi/clipper.php")
15001 (synopsis "Polygon clipping")
15003 "This package provides an R port of the library Clipper. It performs
15004 polygon clipping operations (intersection, union, set minus, set difference)
15005 for polygonal regions of arbitrary complexity, including holes. It computes
15006 offset polygons (spatial buffer zones, morphological dilations, Minkowski
15007 dilations) for polygonal regions and polygonal lines. It computes the
15008 Minkowski Sum of general polygons. There is a function for removing
15009 self-intersections from polygon data.")
15010 (license license:boost1.0)))
15012 (define-public r-urltools
15014 (name "r-urltools")
15019 (uri (cran-uri "urltools" version))
15022 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
15023 (build-system r-build-system)
15025 `(("r-rcpp" ,r-rcpp)
15026 ("r-triebeard" ,r-triebeard)))
15027 (home-page "https://github.com/Ironholds/urltools/")
15028 (synopsis "Vectorized tools for URL handling and parsing")
15030 "This package provides a toolkit for all URL-handling needs, including
15031 encoding and decoding, parsing, parameter extraction and modification. All
15032 functions are designed to be both fast and entirely vectorized. It is
15033 intended to be useful for people dealing with web-related datasets, such as
15034 server-side logs, although may be useful for other situations involving large
15036 (license license:expat)))
15038 (define-public r-ggforce
15045 (uri (cran-uri "ggforce" version))
15048 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
15049 (build-system r-build-system)
15051 `(("r-ggplot2" ,r-ggplot2)
15052 ("r-gtable" ,r-gtable)
15054 ("r-polyclip" ,r-polyclip)
15056 ("r-rcppeigen" ,r-rcppeigen)
15057 ("r-rlang" ,r-rlang)
15058 ("r-scales" ,r-scales)
15059 ("r-tidyselect" ,r-tidyselect)
15060 ("r-tweenr" ,r-tweenr)
15061 ("r-withr" ,r-withr)))
15062 (home-page "https://ggforce.data-imaginist.com")
15063 (synopsis "Accelerating ggplot2")
15065 "The aim of the ggplot2 package is to aid in visual data investigations.
15066 This focus has led to a lack of facilities for composing specialized plots.
15067 Thi package aims to be a collection of mainly new statistics and geometries
15068 that fills this gap.")
15069 (license license:expat)))
15071 (define-public r-europepmc
15073 (name "r-europepmc")
15078 (uri (cran-uri "europepmc" version))
15081 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
15082 (build-system r-build-system)
15084 `(("r-dplyr" ,r-dplyr)
15086 ("r-jsonlite" ,r-jsonlite)
15088 ("r-progress" ,r-progress)
15089 ("r-purrr" ,r-purrr)
15090 ("r-rlang" ,r-rlang)
15091 ("r-tibble" ,r-tibble)
15092 ("r-tidyr" ,r-tidyr)
15093 ("r-urltools" ,r-urltools)
15094 ("r-xml2" ,r-xml2)))
15096 `(("r-knitr" ,r-knitr)))
15097 (home-page "https://github.com/ropensci/europepmc/")
15098 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
15100 "This package provides an R Client for the
15101 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
15102 Service}. It gives access to both metadata on life science literature and
15103 open access full texts. Europe PMC indexes all PubMed content and other
15104 literature sources including Agricola, a bibliographic database of citations
15105 to the agricultural literature, or Biological Patents. In addition to
15106 bibliographic metadata, the client allows users to fetch citations and
15107 reference lists. Links between life-science literature and other EBI
15108 databases, including ENA, PDB or ChEMBL are also accessible.")
15109 (license license:gpl3)))
15111 (define-public r-ggraph
15118 (uri (cran-uri "ggraph" version))
15121 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
15122 (build-system r-build-system)
15124 `(("r-digest" ,r-digest)
15125 ("r-dplyr" ,r-dplyr)
15126 ("r-ggforce" ,r-ggforce)
15127 ("r-ggplot2" ,r-ggplot2)
15128 ("r-ggrepel" ,r-ggrepel)
15129 ("r-graphlayouts" ,r-graphlayouts)
15130 ("r-gtable" ,r-gtable)
15131 ("r-igraph" ,r-igraph)
15134 ("r-rlang" ,r-rlang)
15135 ("r-scales" ,r-scales)
15136 ("r-tidygraph" ,r-tidygraph)
15137 ("r-viridis" ,r-viridis)))
15139 `(("r-knitr" ,r-knitr)))
15140 (home-page "https://cran.r-project.org/web/packages/ggraph/")
15141 (synopsis "Implementation of grammar of graphics for graphs and networks")
15143 "The grammar of graphics as implemented in ggplot2 is a poor fit for
15144 graph and network visualizations due to its reliance on tabular data input.
15145 The ggraph package is an extension of the ggplot2 API tailored to graph
15146 visualizations and provides the same flexible approach to building up plots
15148 (license license:gpl3)))
15150 (define-public r-varselrf
15152 (name "r-varselrf")
15157 (uri (cran-uri "varSelRF" version))
15160 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
15161 (properties `((upstream-name . "varSelRF")))
15162 (build-system r-build-system)
15164 `(("r-randomforest" ,r-randomforest)))
15165 (home-page "https://www.ligarto.org/rdiaz/software/software")
15166 (synopsis "Variable selection using random forests")
15168 "This package provides tools for the variable selection from random
15169 forests using both backwards variable elimination (for the selection of small
15170 sets of non-redundant variables) and selection based on the importance
15171 spectrum (somewhat similar to scree plots; for the selection of large,
15172 potentially highly-correlated variables). The main applications are in
15173 high-dimensional data (e.g., microarray data, and other genomics and
15174 proteomics applications).")
15175 (license license:gpl2+)))
15177 (define-public r-pamr
15184 (uri (cran-uri "pamr" version))
15187 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
15188 (build-system r-build-system)
15190 `(("r-cluster" ,r-cluster)
15191 ("r-survival" ,r-survival)))
15192 (native-inputs `(("gfortran" ,gfortran)))
15193 (home-page "https://cran.r-project.org/web/packages/pamr/")
15194 (synopsis "Prediction Analysis for Microarrays")
15196 "This package provides some functions for sample classification in
15198 (license license:gpl2)))
15200 (define-public r-rda
15203 (version "1.0.2-2.1")
15207 (uri (cran-uri "rda" version))
15210 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15211 (build-system r-build-system)
15212 (home-page "https://cran.r-project.org/web/packages/rda/")
15213 (synopsis "Shrunken centroids regularized discriminant analysis")
15215 "This package provides tools for shrunken centroids regularized
15216 discriminant analysis for the purpose of classifying high dimensional data.")
15217 (license license:gpl2+)))
15219 (define-public r-ggvis
15226 (uri (cran-uri "ggvis" version))
15229 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
15230 (build-system r-build-system)
15232 `(("r-assertthat" ,r-assertthat)
15233 ("r-dplyr" ,r-dplyr)
15234 ("r-htmltools" ,r-htmltools)
15235 ("r-jsonlite" ,r-jsonlite)
15236 ("r-lazyeval" ,r-lazyeval)
15237 ("r-magrittr" ,r-magrittr)
15238 ("r-shiny" ,r-shiny)))
15239 (home-page "https://ggvis.rstudio.com/")
15240 (synopsis "Interactive grammar of graphics")
15242 "This package is a data visualization package for R providing an
15243 implementation of an interactive grammar of graphics, taking the best parts of
15244 ggplot2, combining them with the reactive framework of Shiny and drawing web
15245 graphics using Vega.")
15246 (license license:gpl2)))
15248 (define-public r-gbm
15255 (uri (cran-uri "gbm" version))
15258 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15259 (build-system r-build-system)
15261 `(("r-lattice" ,r-lattice)
15262 ("r-survival" ,r-survival)))
15264 `(("r-knitr" ,r-knitr)))
15265 (home-page "https://github.com/gbm-developers/gbm")
15266 (synopsis "Generalized boosted regression models")
15268 "This package is an implementation of extensions to Freund and Schapire's
15269 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15270 regression methods for least squares, absolute loss, t-distribution loss,
15271 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15272 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15273 and Learning to Rank measures (LambdaMart).")
15274 (license license:gpl2+)))
15276 (define-public r-threejs
15283 (uri (cran-uri "threejs" version))
15286 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15287 (build-system r-build-system)
15289 `(#:modules ((guix build utils)
15290 (guix build r-build-system)
15294 (modify-phases %standard-phases
15295 (add-after 'unpack 'process-javascript
15296 (lambda* (#:key inputs #:allow-other-keys)
15297 (with-directory-excursion "inst"
15301 `((,(assoc-ref inputs "js-jquery")
15302 "htmlwidgets/lib/jquery/jquery.min.js")
15303 (,(assoc-ref inputs "js-threejs-111")
15304 "htmlwidgets/lib/threejs-111/three.min.js"))))
15305 (lambda (sources targets)
15306 (for-each (lambda (source target)
15307 (format #t "Processing ~a --> ~a~%"
15309 (delete-file target)
15310 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15311 (call-with-output-file target
15313 (dump-port minified port)))))
15314 sources targets))))
15317 `(("r-base64enc" ,r-base64enc)
15318 ("r-crosstalk" ,r-crosstalk)
15319 ("r-htmlwidgets" ,r-htmlwidgets)
15320 ("r-igraph" ,r-igraph)))
15322 `(("uglify-js" ,uglify-js)
15326 (uri "https://code.jquery.com/jquery-1.12.4.js")
15329 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15333 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15336 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15337 (home-page "https://bwlewis.github.io/rthreejs")
15338 (synopsis "Interactive 3D scatter plots, networks and globes")
15340 "Create interactive 3D scatter plots, network plots, and globes in R
15341 using the three.js visualization library.")
15342 (license license:expat)))
15344 (define-public r-mlbench
15351 (uri (cran-uri "mlbench" version))
15354 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15355 (build-system r-build-system)
15356 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15357 (synopsis "Machine learning benchmark problems")
15359 "This package provides a collection of artificial and real-world machine
15360 learning benchmark problems, including, e.g., several data sets from the UCI
15362 (license license:gpl2)))
15364 (define-public r-mpm
15371 (uri (cran-uri "mpm" version))
15374 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15375 (build-system r-build-system)
15377 `(("r-kernsmooth" ,r-kernsmooth)
15378 ("r-mass" ,r-mass)))
15379 (home-page "http://mpm.r-forge.r-project.org")
15380 (synopsis "Multivariate projection methods")
15382 "This is a package for exploratory graphical analysis of multivariate
15383 data, specifically gene expression data with different projection methods:
15384 principal component analysis, correspondence analysis, spectral map
15386 (license license:gpl2+)))
15388 (define-public r-png
15394 (uri (cran-uri "png" version))
15397 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15398 (build-system r-build-system)
15400 `(("libpng" ,libpng)
15402 (home-page "https://www.rforge.net/png/")
15403 (synopsis "Read and write PNG images")
15405 "This package provides an easy and simple way to read, write and display
15406 bitmap images stored in the PNG format. It can read and write both files and
15407 in-memory raw vectors.")
15408 ;; Any of these GPL versions.
15409 (license (list license:gpl2 license:gpl3))))
15411 (define-public r-ggcorrplot
15413 (name "r-ggcorrplot")
15418 (uri (cran-uri "ggcorrplot" version))
15421 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15422 (build-system r-build-system)
15424 `(("r-ggplot2" ,r-ggplot2)
15425 ("r-reshape2" ,r-reshape2)))
15426 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15427 (synopsis "Visualization of a correlation matrix using ggplot2")
15429 "The ggcorrplot package can be used to visualize easily a correlation
15430 matrix using ggplot2. It provides a solution for reordering the correlation
15431 matrix and displays the significance level on the plot. It also includes a
15432 function for computing a matrix of correlation p-values.")
15433 (license license:gpl2)))
15435 ;; This package includes minified JavaScript files. When upgrading please
15436 ;; check that there are no new minified JavaScript files.
15437 (define-public r-flexdashboard
15439 (name "r-flexdashboard")
15444 (uri (cran-uri "flexdashboard" version))
15447 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15448 (modules '((guix build utils)))
15451 ;; Delete bundled minified JavaScript files
15452 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15453 (delete-file "inst/www/sly/sly.min.js")
15454 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15455 (delete-file "inst/www/prism/prism.js")
15457 (build-system r-build-system)
15459 `(#:modules ((guix build utils)
15460 (guix build r-build-system)
15464 (ice-9 textual-ports))
15466 (modify-phases %standard-phases
15467 (add-after 'unpack 'process-javascript
15468 (lambda* (#:key inputs #:allow-other-keys)
15469 (with-directory-excursion "inst"
15470 ;; Concatenate all components of prism.js
15471 (let ((contents (string-join
15472 (map (lambda (name)
15473 (call-with-input-file
15474 (assoc-ref inputs name)
15478 "js-prism-line-numbers"))
15480 (call-with-output-file "prism-src.js"
15481 (cut display contents <>)))
15485 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15486 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15488 "www/sly/sly.min.js")
15490 "www/prism/prism.js")
15491 (,(assoc-ref inputs "js-raphael")
15492 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15493 (,(assoc-ref inputs "js-featherlight")
15494 "www/featherlight/featherlight.min.js"))))
15495 (lambda (sources targets)
15496 (for-each (lambda (source target)
15497 (format #t "Processing ~a --> ~a~%"
15499 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15500 (call-with-output-file target
15502 (dump-port minified port)))))
15503 sources targets))))
15506 `(("r-htmltools" ,r-htmltools)
15507 ("r-htmlwidgets" ,r-htmlwidgets)
15508 ("r-jsonlite" ,r-jsonlite)
15509 ("r-knitr" ,r-knitr)
15510 ("r-rmarkdown" ,r-rmarkdown)
15511 ("r-shiny" ,r-shiny)))
15513 `(("uglify-js" ,uglify-js)
15517 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15520 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15524 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15527 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15531 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15534 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15535 ("js-prism-line-numbers"
15538 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15541 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15545 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15548 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15549 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15550 (synopsis "R Markdown format for flexible dashboards")
15552 "This package provides an R Markdown format for converting an R Markdown
15553 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15554 of its components to the containing web page.")
15555 (license license:expat)))
15557 (define-public r-preseqr
15564 (uri (cran-uri "preseqR" version))
15567 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15568 (properties `((upstream-name . "preseqR")))
15569 (build-system r-build-system)
15571 `(("r-polynom" ,r-polynom)))
15572 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15573 (synopsis "Predicting species accumulation curves")
15575 "This package can be used to predict the r-species accumulation
15576 curve (r-SAC), which is the number of species represented at least r times as
15577 a function of the sampling effort. When r = 1, the curve is known as the
15578 species accumulation curve, or the library complexity curve in high-throughput
15579 genomic sequencing. The package includes both parametric and nonparametric
15580 methods, as described by Deng C, et al. (2018).")
15581 (license license:gpl3)))
15583 (define-public r-mapplots
15585 (name "r-mapplots")
15590 (uri (cran-uri "mapplots" version))
15593 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15594 (build-system r-build-system)
15595 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15596 (synopsis "Data visualization on maps")
15598 "This package helps you create simple maps; add sub-plots like pie plots
15599 to a map or any other plot; format, plot and export gridded data. The package
15600 was developed for displaying fisheries data but most functions can be used for
15601 more generic data visualisation.")
15602 (license license:gpl2+)))
15604 (define-public r-pmcmr
15611 (uri (cran-uri "PMCMR" version))
15614 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15615 (properties `((upstream-name . "PMCMR")))
15616 (build-system r-build-system)
15617 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15618 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15620 "This is a deprecated package for calculating pairwise multiple
15621 comparisons of mean rank sums. This package is superseded by the novel
15622 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15623 compatibility of dependent packages for some time.")
15624 (license license:gpl3+)))
15626 (define-public r-downloader
15628 (name "r-downloader")
15633 (uri (cran-uri "downloader" version))
15636 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15637 (build-system r-build-system)
15639 `(("r-digest" ,r-digest)))
15640 (home-page "https://github.com/wch/downloader")
15641 (synopsis "Download files over HTTP and HTTPS")
15643 "This package provides a wrapper for the @code{download.file} function,
15644 making it possible to download files over HTTPS across platforms. The
15645 @code{RCurl} package provides this functionality (and much more) but has
15646 external dependencies. This package has is implemented purely in R.")
15647 (license license:gpl2)))
15649 (define-public r-rex
15656 (uri (cran-uri "rex" version))
15659 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15660 (build-system r-build-system)
15662 `(("r-lazyeval" ,r-lazyeval)))
15664 `(("r-knitr" ,r-knitr)))
15665 (home-page "https://github.com/kevinushey/rex")
15666 (synopsis "Friendly regular expressions")
15668 "This package provides a friendly interface for the construction of
15669 regular expressions. Regular expressions are a very powerful feature, however
15670 they are often difficult to interpret. Rex allows you to build complex
15671 regular expressions from human readable expressions")
15672 (license license:expat)))
15674 (define-public r-xmlparsedata
15676 (name "r-xmlparsedata")
15681 (uri (cran-uri "xmlparsedata" version))
15684 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
15685 (properties `((upstream-name . "xmlparsedata")))
15686 (build-system r-build-system)
15687 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15688 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15690 "This package provides tools to convert the output of
15691 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15692 @code{XPath}, and is easier to manipulate in general.")
15693 (license license:expat)))
15695 (define-public r-cyclocomp
15697 (name "r-cyclocomp")
15702 (uri (cran-uri "cyclocomp" version))
15705 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15706 (properties `((upstream-name . "cyclocomp")))
15707 (build-system r-build-system)
15709 `(("r-callr" ,r-callr)
15710 ("r-crayon" ,r-crayon)
15712 ("r-remotes" ,r-remotes)
15713 ("r-withr" ,r-withr)))
15714 (home-page "https://github.com/MangoTheCat/cyclocomp")
15715 (synopsis "Cyclomatic complexity of R code")
15717 "Cyclomatic complexity is a software metric, used to indicate the
15718 complexity of a program. It is a quantitative measure of the number of
15719 linearly independent paths through a program's source code. This package
15720 provides tools to compute this metric.")
15721 (license license:expat)))
15723 (define-public r-lintr
15730 (uri (cran-uri "lintr" version))
15733 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15734 (properties `((upstream-name . "lintr")))
15735 (build-system r-build-system)
15737 `(("r-codetools" ,r-codetools)
15738 ("r-crayon" ,r-crayon)
15739 ("r-cyclocomp" ,r-cyclocomp)
15740 ("r-digest" ,r-digest)
15742 ("r-jsonlite" ,r-jsonlite)
15743 ("r-knitr" ,r-knitr)
15745 ("r-rstudioapi" ,r-rstudioapi)
15746 ("r-testthat" ,r-testthat)
15748 ("r-xmlparsedata" ,r-xmlparsedata)))
15749 (home-page "https://github.com/jimhester/lintr")
15750 (synopsis "Linter for R code")
15751 (description "This package checks adherence to a given style, syntax
15752 errors and possible semantic issues. It supports on the fly checking of R
15753 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15754 (license license:expat)))
15756 (define-public r-sctransform
15758 (name "r-sctransform")
15763 (uri (cran-uri "sctransform" version))
15766 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15767 (build-system r-build-system)
15769 `(("r-future-apply" ,r-future-apply)
15770 ("r-ggplot2" ,r-ggplot2)
15771 ("r-gridextra" ,r-gridextra)
15773 ("r-matrix" ,r-matrix)
15775 ("r-rcppeigen" ,r-rcppeigen)
15776 ("r-reshape2" ,r-reshape2)))
15777 (home-page "https://github.com/ChristophH/sctransform")
15778 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15780 "This package provides a normalization method for single-cell UMI count
15781 data using a variance stabilizing transformation. The transformation is based
15782 on a negative binomial regression model with regularized parameters. As part
15783 of the same regression framework, this package also provides functions for
15784 batch correction, and data correction.")
15785 (license license:gpl3)))
15787 (define-public r-styler
15794 (uri (cran-uri "styler" version))
15797 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15798 (build-system r-build-system)
15800 `(("r-backports" ,r-backports)
15802 ("r-magrittr" ,r-magrittr)
15803 ("r-purrr" ,r-purrr)
15804 ("r-r-cache" ,r-r-cache)
15805 ("r-rematch2" ,r-rematch2)
15806 ("r-rlang" ,r-rlang)
15807 ("r-rprojroot" ,r-rprojroot)
15808 ("r-tibble" ,r-tibble)
15809 ("r-withr" ,r-withr)
15810 ("r-xfun" ,r-xfun)))
15811 (home-page "https://github.com/r-lib/styler")
15812 (synopsis "Non-invasive pretty printing of R code")
15814 "This is a package for pretty-printing R code without changing the user's
15815 formatting intent.")
15816 (license license:gpl3)))
15818 (define-public r-scrime
15825 (uri (cran-uri "scrime" version))
15828 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15829 (build-system r-build-system)
15830 (home-page "https://cran.r-project.org/web/packages/scrime/")
15831 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15833 "This package provides tools for the analysis of high-dimensional data
15834 developed/implemented at the group \"Statistical Complexity Reduction In
15835 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15836 the functions can also be applied to other types of categorical data.")
15837 (license license:gpl2)))
15839 (define-public r-pbmcapply
15841 (name "r-pbmcapply")
15846 (uri (cran-uri "pbmcapply" version))
15849 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15850 (build-system r-build-system)
15851 (home-page "https://github.com/kvnkuang/pbmcapply")
15852 (synopsis "Track the progress of apply procedures with a progress bar")
15854 "This light-weight package helps you track and visualize the progress of
15855 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15856 (license license:expat)))
15858 (define-public r-blme
15865 (uri (cran-uri "blme" version))
15868 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15869 (build-system r-build-system)
15870 (propagated-inputs `(("r-lme4" ,r-lme4)))
15871 (home-page "https://github.com/vdorie/blme")
15872 (synopsis "Bayesian linear mixed-effects models")
15874 "This package provides tools for maximum a posteriori estimation for
15875 linear and generalized linear mixed-effects models in a Bayesian setting. It
15876 extends the lme4 package.")
15877 (license license:gpl2+)))
15879 (define-public r-batchtools
15881 (name "r-batchtools")
15886 (uri (cran-uri "batchtools" version))
15889 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15890 (build-system r-build-system)
15892 `(("r-backports" ,r-backports)
15893 ("r-base64url" ,r-base64url)
15895 ("r-checkmate" ,r-checkmate)
15896 ("r-data-table" ,r-data-table)
15897 ("r-digest" ,r-digest)
15899 ("r-progress" ,r-progress)
15901 ("r-rappdirs" ,r-rappdirs)
15902 ("r-stringi" ,r-stringi)
15903 ("r-withr" ,r-withr)))
15905 `(("r-knitr" ,r-knitr)))
15906 (home-page "https://github.com/mllg/batchtools")
15907 (synopsis "Tools for computation on batch systems")
15909 "As a successor of the packages BatchJobs and BatchExperiments, this
15910 package provides a parallel implementation of the Map function for high
15911 performance computing systems managed by various schedulers. A multicore and
15912 socket mode allow the parallelization on a local machines, and multiple
15913 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15914 the package provides an abstraction mechanism to define large-scale computer
15915 experiments in a well-organized and reproducible way.")
15916 (license license:lgpl3)))
15918 (define-public r-clue
15925 (uri (cran-uri "clue" version))
15928 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15929 (build-system r-build-system)
15930 (propagated-inputs `(("r-cluster" ,r-cluster)))
15931 (home-page "https://cran.r-project.org/web/packages/clue/")
15932 (synopsis "Tools for analyzing cluster ensembles")
15933 (description "Cluster ensembles are collections of individual solutions to
15934 a given clustering problem which are useful or necessary to consider in a wide
15935 range of applications. This R package provides an extensible computational
15936 environment for creating and analyzing cluster ensembles, with basic data
15937 structures for representing partitions and hierarchies, and facilities for
15938 computing on them, including methods for measuring proximity and obtaining
15939 consensus and secondary clusterings.")
15940 (license license:gpl2)))
15942 (define-public r-sitmo
15949 (uri (cran-uri "sitmo" version))
15952 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15953 (build-system r-build-system)
15954 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15955 (home-page "https://github.com/coatless/sitmo/")
15956 (synopsis "Parallel pseudo random number generator header files")
15958 "This package provides two high quality and fast PPRNGs that may be used
15959 in an OpenMP parallel environment. In addition, there is a generator for one
15960 dimensional low-discrepancy sequence.")
15961 (license license:expat)))
15963 (define-public r-dqrng
15970 (uri (cran-uri "dqrng" version))
15973 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15974 (build-system r-build-system)
15978 ("r-sitmo" ,r-sitmo)))
15979 (home-page "https://www.daqana.org/dqrng")
15980 (synopsis "Fast pseudo random number generators")
15982 "Several fast random number generators are provided as C++ header-only
15983 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15984 Additionally, fast functions for generating random numbers according to a
15985 uniform, normal and exponential distribution are included. The latter two use
15986 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15987 functions are exported to R and as a C++ interface and are enabled for use
15988 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15989 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15990 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15991 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15992 ;; whole is distributed under the terms of the AGPL 3.
15993 (license license:agpl3)))
15995 (define-public r-ingredients
15997 (name "r-ingredients")
16002 (uri (cran-uri "ingredients" version))
16005 "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
16006 (properties `((upstream-name . "ingredients")))
16007 (build-system r-build-system)
16009 `(("r-ggplot2" ,r-ggplot2)
16010 ("r-gridextra" ,r-gridextra)
16011 ("r-scales" ,r-scales)))
16012 (native-inputs `(("r-knitr" ,r-knitr)))
16013 (home-page "https://ModelOriented.github.io/ingredients/")
16014 (synopsis "Effects and importances of model ingredients")
16016 "This is a collection of tools for assessment of feature importance and
16017 feature effects. Key functions are:
16020 @item @code{feature_importance()} for assessment of global level feature
16022 @item @code{ceteris_paribus()} for calculation of the what-if plots,
16023 @item @code{partial_dependence()} for partial dependence plots,
16024 @item @code{conditional_dependence()} for conditional dependence plots,
16025 @item @code{accumulated_dependence()} for accumulated local effects plots,
16026 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
16027 aggregation of ceteris paribus profiles,
16028 @item generic @code{print()} and @code{plot()} for better usability of
16029 selected explainers,
16030 @item generic @code{plotD3()} for interactive, D3 based explanations, and
16031 @item generic @code{describe()} for explanations in natural language.
16033 (license license:gpl3)))
16035 (define-public r-ibreakdown
16037 (name "r-ibreakdown")
16042 (uri (cran-uri "iBreakDown" version))
16045 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
16046 (properties `((upstream-name . "iBreakDown")))
16047 (build-system r-build-system)
16048 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
16049 (native-inputs `(("r-knitr" ,r-knitr)))
16050 (home-page "https://ModelOriented.github.io/iBreakDown/")
16051 (synopsis "Model agnostic instance level variable attributions")
16053 "This package provides a model agnostic tool for decomposition of
16054 predictions from black boxes. It supports additive attributions and
16055 attributions with interactions. The Break Down Table shows contributions of
16056 every variable to a final prediction. The Break Down Plot presents variable
16057 contributions in a concise graphical way. This package works for
16058 classification and regression models.")
16059 (license license:gpl3)))
16061 (define-public r-dae
16068 (uri (cran-uri "dae" version))
16071 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
16072 (build-system r-build-system)
16074 `(("r-ggplot2" ,r-ggplot2)
16075 ("r-plyr" ,r-plyr)))
16077 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
16078 (home-page "http://chris.brien.name")
16079 (synopsis "Functions useful in the design and ANOVA of experiments")
16081 "This package provides functions useful in the design and ANOVA of
16082 experiments. The content falls into the following groupings:
16086 @item factor manipulation functions,
16087 @item design functions,
16088 @item ANOVA functions,
16089 @item matrix functions,
16090 @item projector and canonical efficiency functions, and
16091 @item miscellaneous functions.
16094 There is a vignette called @code{DesignNotes} describing how to use the design
16095 functions for randomizing and assessing designs. The ANOVA functions
16096 facilitate the extraction of information when the @code{Error} function has
16097 been used in the call to @code{aov}.")
16098 (license license:gpl2)))
16100 (define-public r-dalex
16107 (uri (cran-uri "DALEX" version))
16110 "1yn61cbqvyycn617pzhd7kgd34xsnmqvj3s10inn2ywycybk7byi"))))
16111 (properties `((upstream-name . "DALEX")))
16112 (build-system r-build-system)
16114 `(("r-ggplot2" ,r-ggplot2)
16115 ("r-ibreakdown" ,r-ibreakdown)
16116 ("r-ingredients" ,r-ingredients)))
16117 (home-page "https://pbiecek.github.io/DALEX/")
16118 (synopsis "Descriptive machine learning explanations")
16120 "Machine Learning models are widely used and have various applications in
16121 classification or regression. Models created with boosting, bagging, stacking
16122 or similar techniques are often used due to their high performance, but such
16123 black-box models usually lack interpretability. The DALEX package contains
16124 various explainers that help to understand the link between input variables
16125 and model output.")
16126 ;; Any version of the GPL
16127 (license license:gpl3+)))
16129 (define-public r-enrichr
16136 (uri (cran-uri "enrichR" version))
16139 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
16140 (properties `((upstream-name . "enrichR")))
16141 (build-system r-build-system)
16143 `(("r-httr" ,r-httr)
16144 ("r-rjson" ,r-rjson)))
16145 (home-page "https://cran.r-project.org/web/packages/enrichR/")
16146 (synopsis "R Interface to Enrichr database for analyzing gene sets")
16148 "This package provides an R interface to all Enrichr databases, a
16149 web-based tool for analyzing gene sets and returns any enrichment of common
16150 annotated biological functions.")
16151 (license license:gpl2+)))
16153 (define-public r-plot3d
16160 (uri (cran-uri "plot3D" version))
16163 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
16164 (properties `((upstream-name . "plot3D")))
16165 (build-system r-build-system)
16166 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
16167 (home-page "https://cran.r-project.org/web/packages/plot3D")
16168 (synopsis "Plot multi-dimensional data")
16170 "This package provides functions for viewing 2D and 3D data, including
16171 perspective plots, slice plots, surface plots, scatter plots, etc. It
16172 includes data sets from oceanography.")
16173 (license license:gpl3+)))
16175 (define-public r-ggfortify
16177 (name "r-ggfortify")
16182 (uri (cran-uri "ggfortify" version))
16185 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
16186 (build-system r-build-system)
16188 `(("r-dplyr" ,r-dplyr)
16189 ("r-ggplot2" ,r-ggplot2)
16190 ("r-gridextra" ,r-gridextra)
16191 ("r-scales" ,r-scales)
16192 ("r-stringr" ,r-stringr)
16193 ("r-tibble" ,r-tibble)
16194 ("r-tidyr" ,r-tidyr)))
16196 `(("r-knitr" ,r-knitr)))
16197 (home-page "https://github.com/sinhrks/ggfortify")
16198 (synopsis "Data visualization tools for statistical analysis results")
16200 "This package provides unified plotting tools for statistics commonly
16201 used, such as GLM, time series, PCA families, clustering and survival
16202 analysis. The package offers a single plotting interface for these analysis
16203 results and plots in a unified style using the @code{ggplot2} package.")
16204 (license license:gpl2)))
16206 (define-public r-refmanager
16208 (name "r-refmanager")
16213 (uri (cran-uri "RefManageR" version))
16216 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16217 (properties `((upstream-name . "RefManageR")))
16218 (build-system r-build-system)
16220 `(("r-bibtex" ,r-bibtex)
16222 ("r-jsonlite" ,r-jsonlite)
16223 ("r-lubridate" ,r-lubridate)
16225 ("r-stringr" ,r-stringr)
16226 ("r-xml2" ,r-xml2)))
16227 (home-page "https://github.com/ropensci/RefManageR/")
16228 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16230 "This package provides tools for importing and working with bibliographic
16231 references. It greatly enhances the @code{bibentry} class by providing a
16232 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16233 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16234 by various formats for name lists (author by last names, translator by full
16235 names, etc.). Entries can be updated, combined, sorted, printed in a number
16236 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16237 into R and converted to @code{BibEntry} objects.")
16238 ;; Any of these licenses may be picked.
16239 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16241 (define-public r-citr
16248 (uri (cran-uri "citr" version))
16251 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16252 (build-system r-build-system)
16254 `(("r-assertthat" ,r-assertthat)
16257 ("r-miniui" ,r-miniui)
16258 ("r-refmanager" ,r-refmanager)
16259 ("r-rstudioapi" ,r-rstudioapi)
16260 ("r-shiny" ,r-shiny)
16261 ("r-shinyjs" ,r-shinyjs)
16262 ("r-yaml" ,r-yaml)))
16263 (home-page "https://github.com/crsh/citr")
16264 (synopsis "RStudio add-in to insert Markdown citations")
16266 "This package provides functions and an RStudio add-in that search a
16267 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16268 the current document.")
16269 (license license:expat)))
16271 (define-public r-xgboost
16274 (version "1.2.0.1")
16278 (uri (cran-uri "xgboost" version))
16281 "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
16282 (build-system r-build-system)
16284 `(("r-data-table" ,r-data-table)
16285 ("r-magrittr" ,r-magrittr)
16286 ("r-matrix" ,r-matrix)
16287 ("r-stringi" ,r-stringi)))
16289 `(("r-knitr" ,r-knitr)))
16290 (home-page "https://github.com/dmlc/xgboost")
16291 (synopsis "Extreme gradient boosting")
16293 "This package provides an R interface to Extreme Gradient Boosting, which
16294 is an efficient implementation of the gradient boosting framework from Chen
16295 and Guestrin (2016). The package includes efficient linear model solver and
16296 tree learning algorithms. The package can automatically do parallel
16297 computation on a single machine. It supports various objective functions,
16298 including regression, classification and ranking. The package is made to be
16299 extensible, so that users are also allowed to define their own objectives
16301 (license license:asl2.0)))
16303 (define-public r-umap
16306 (version "0.2.6.0")
16310 (uri (cran-uri "umap" version))
16313 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16314 (build-system r-build-system)
16316 `(("r-openssl" ,r-openssl)
16318 ("r-reticulate" ,r-reticulate)
16319 ("r-rspectra" ,r-rspectra)))
16321 `(("r-knitr" ,r-knitr)))
16322 (home-page "https://github.com/tkonopka/umap")
16323 (synopsis "Uniform manifold approximation and projection")
16325 "Uniform manifold approximation and projection is a technique for
16326 dimension reduction. This package provides an interface to the UMAP algorithm
16327 in R, including a translation of the original algorithm into R.")
16328 (license license:expat)))
16330 (define-public r-uwot
16337 (uri (cran-uri "uwot" version))
16340 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16341 (build-system r-build-system)
16343 `(("r-dqrng" ,r-dqrng)
16345 ("r-irlba" ,r-irlba)
16346 ("r-matrix" ,r-matrix)
16348 ("r-rcppannoy" ,r-rcppannoy)
16349 ("r-rcppprogress" ,r-rcppprogress)
16350 ("r-rspectra" ,r-rspectra)))
16351 (home-page "https://github.com/jlmelville/uwot")
16352 (synopsis "Uniform manifold approximation and projection")
16354 "This package provides an implementation of the Uniform Manifold
16355 Approximation and Projection dimensionality reduction by McInnes et
16356 al. (2018). It also provides means to transform new data and to carry out
16357 supervised dimensionality reduction. An implementation of the related
16358 LargeVis method of Tang et al. (2016) is also provided.")
16359 (license license:gpl3)))
16361 (define-public r-kableextra
16363 (name "r-kableextra")
16368 (uri (cran-uri "kableExtra" version))
16371 "0n25y7zwpspvkd62rd6x8c22dg2ys27smlpdz5brqs5ddv7x9dis"))))
16372 (properties `((upstream-name . "kableExtra")))
16373 (build-system r-build-system)
16375 `(("r-digest" ,r-digest)
16377 ("r-htmltools" ,r-htmltools)
16378 ("r-knitr" ,r-knitr)
16379 ("r-magrittr" ,r-magrittr)
16380 ("r-rmarkdown" ,r-rmarkdown)
16381 ("r-rstudioapi" ,r-rstudioapi)
16382 ("r-rvest" ,r-rvest)
16383 ("r-scales" ,r-scales)
16384 ("r-stringr" ,r-stringr)
16385 ("r-viridislite" ,r-viridislite)
16386 ("r-webshot" ,r-webshot)
16387 ("r-xml2" ,r-xml2)))
16389 `(("r-knitr" ,r-knitr)))
16390 (home-page "https://haozhu233.github.io/kableExtra/")
16391 (synopsis "Construct complex tables with pipe syntax")
16393 "Build complex HTML or LaTeX tables using @code{kable()} from
16394 @code{knitr} and the piping syntax from @code{magrittr}. The function
16395 @code{kable()} is a light weight table generator coming from @code{knitr}.
16396 This package simplifies the way to manipulate the HTML or LaTeX codes
16397 generated by @code{kable()} and allows users to construct complex tables and
16398 customize styles using a readable syntax.")
16399 (license license:expat)))
16401 (define-public r-glasso
16408 (uri (cran-uri "glasso" version))
16410 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16411 (build-system r-build-system)
16412 (native-inputs `(("gfortran" ,gfortran)))
16413 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16414 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16416 "This is a package for estimation of a sparse inverse covariance matrix
16417 using a lasso (L1) penalty. Facilities are provided for estimates along a
16418 path of values for the regularization parameter.")
16419 (license license:gpl2)))
16421 (define-public r-rhpcblasctl
16423 (name "r-rhpcblasctl")
16424 (version "0.20-137")
16428 (uri (cran-uri "RhpcBLASctl" version))
16431 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16432 (properties `((upstream-name . "RhpcBLASctl")))
16433 (build-system r-build-system)
16434 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16435 (synopsis "Control the number of threads on BLAS")
16437 "This package allows you to control the number of threads the BLAS
16438 library uses. It is also possible to control the number of threads in
16440 (license license:agpl3+)))
16442 (define-public r-lda
16449 (uri (cran-uri "lda" version))
16452 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16453 (build-system r-build-system)
16454 (home-page "https://cran.r-project.org/web/packages/lda/")
16455 (synopsis "Collapsed Gibbs sampling methods for topic models")
16457 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16458 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16459 mixed-membership stochastic blockmodel. Inference for all of these models is
16460 implemented via a fast collapsed Gibbs sampler written in C. Utility
16461 functions for reading/writing data typically used in topic models, as well as
16462 tools for examining posterior distributions are also included.")
16463 ;; Any version of the LGPL
16464 (license license:lgpl3+)))
16466 (define-public r-rann-l1
16473 (uri (cran-uri "RANN.L1" version))
16476 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16477 (properties `((upstream-name . "RANN.L1")))
16478 (build-system r-build-system)
16479 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16480 (synopsis "Fast nearest neighbour search using L1 metric")
16482 "This package provides tools to find the k nearest neighbours for every
16483 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16484 library. There is support for approximate as well as exact searches, fixed
16485 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16486 computed using the L1 (Manhattan, taxicab) metric.")
16487 (license license:gpl3+)))
16489 (define-public r-leiden
16496 (uri (cran-uri "leiden" version))
16499 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16500 (properties `((upstream-name . "leiden")))
16501 (build-system r-build-system)
16503 `(("r-igraph" ,r-igraph)
16504 ("r-matrix" ,r-matrix)
16505 ("r-reticulate" ,r-reticulate)))
16506 (home-page "https://github.com/TomKellyGenetics/leiden")
16507 (synopsis "R implementation of Leiden clustering algorithm")
16509 "This package implements the Python @code{leidenalg} module to be called
16510 in R. It enables clustering using the Leiden algorithm for partitioning a
16511 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16512 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16513 (license license:gpl3)))
16515 (define-public r-patchwork
16517 (name "r-patchwork")
16522 (uri (cran-uri "patchwork" version))
16525 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16526 (build-system r-build-system)
16528 `(("r-ggplot2" ,r-ggplot2)
16529 ("r-gtable" ,r-gtable)))
16531 `(("r-knitr" ,r-knitr)))
16532 (home-page "https://github.com/thomasp85/patchwork")
16533 (synopsis "Compose ggplot2 plots")
16535 "The @code{ggplot2} package provides a strong API for sequentially
16536 building up a plot, but does not concern itself with composition of multiple
16537 plots. Patchwork is a package that expands the API to allow for arbitrarily
16538 complex composition of plots by providing mathmatical operators for combining
16540 (license license:expat)))
16542 (define-public r-liger
16549 (uri (git-reference
16550 (url "https://github.com/MacoskoLab/liger")
16551 (commit (string-append "v" version))))
16552 (file-name (git-file-name name version))
16555 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16556 (modules '((guix build utils)))
16559 (delete-file "inst/java/ModularityOptimizer.jar")
16561 (build-system r-build-system)
16564 (modify-phases %standard-phases
16565 (add-after 'unpack 'build-java-part
16566 (lambda* (#:key inputs #:allow-other-keys)
16567 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16568 (for-each (lambda (file) (invoke "javac" file))
16569 (find-files "." "\\.java$"))
16570 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16571 (find-files "." "\\.class$"))
16574 `(("r-cowplot" ,r-cowplot)
16575 ("r-dosnow" ,r-dosnow)
16576 ("r-dplyr" ,r-dplyr)
16578 ("r-foreach" ,r-foreach)
16579 ("r-ggplot2" ,r-ggplot2)
16580 ("r-ggrepel" ,r-ggrepel)
16581 ("r-hmisc" ,r-hmisc)
16583 ("r-irlba" ,r-irlba)
16584 ("r-matrix" ,r-matrix)
16585 ("r-mclust" ,r-mclust)
16586 ("r-patchwork" ,r-patchwork)
16588 ("r-rann-l1" ,r-rann-l1)
16590 ("r-rcpparmadillo" ,r-rcpparmadillo)
16591 ("r-riverplot" ,r-riverplot)
16592 ("r-rtsne" ,r-rtsne)
16593 ("r-snow" ,r-snow)))
16595 `(("jdk" ,icedtea "jdk")
16596 ;; See https://github.com/MacoskoLab/liger/issues/96
16597 ;; The optimizer is released under the Expat license.
16601 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16604 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16606 ("r-knitr" ,r-knitr))) ; for vignettes
16607 (home-page "https://github.com/MacoskoLab/liger")
16608 (synopsis "Integrate and analyze multiple single-cell datasets")
16610 "LIGER is a package for integrating and analyzing multiple single-cell
16611 datasets, developed and maintained by the Macosko lab. It relies on
16612 integrative non-negative matrix factorization to identify shared and
16613 dataset-specific factors.")
16614 (license license:gpl3)))
16616 (define-public r-harmony
16623 (uri (git-reference
16624 (url "https://github.com/immunogenomics/harmony")
16626 (file-name (git-file-name name version))
16629 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16630 (modules '((guix build utils)))
16633 (for-each delete-file '("config.status" "configure"))
16635 (build-system r-build-system)
16637 `(("r-cowplot" ,r-cowplot)
16638 ("r-dplyr" ,r-dplyr)
16639 ("r-ggplot2" ,r-ggplot2)
16640 ("r-irlba" ,r-irlba)
16641 ("r-matrix" ,r-matrix)
16643 ("r-rcpparmadillo" ,r-rcpparmadillo)
16644 ("r-rcppprogress" ,r-rcppprogress)
16645 ("r-rlang" ,r-rlang)
16646 ("r-tibble" ,r-tibble)
16647 ("r-tidyr" ,r-tidyr)))
16649 `(("autoconf" ,autoconf)))
16650 (home-page "https://github.com/immunogenomics/harmony")
16651 (synopsis "Integration of single cell sequencing data")
16653 "This package provides an implementation of the Harmony algorithm for
16654 single cell integration, described in Korsunsky et al
16655 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16656 function and interfaces to external frameworks.")
16657 (license license:gpl3)))
16659 (define-public r-covr
16666 (uri (cran-uri "covr" version))
16668 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16669 (properties `((upstream-name . "covr")))
16670 (build-system r-build-system)
16672 `(("r-crayon" ,r-crayon)
16673 ("r-digest" ,r-digest)
16675 ("r-jsonlite" ,r-jsonlite)
16677 ("r-withr" ,r-withr)
16678 ("r-yaml" ,r-yaml)))
16680 `(("r-knitr" ,r-knitr))) ; for vignettes
16681 (home-page "https://github.com/r-lib/covr")
16682 (synopsis "Test coverage for R packages")
16684 "Thisp package enables you to track and report code coverage for your
16685 package and (optionally) upload the results to a coverage service. Code
16686 coverage is a measure of the amount of code being exercised by a set of tests.
16687 It is an indirect measure of test quality and completeness. This package is
16688 compatible with any testing methodology or framework and tracks coverage of
16689 both R code and compiled C/C++/FORTRAN code.")
16690 (license license:gpl3)))
16692 (define-public r-systemfonts
16694 (name "r-systemfonts")
16699 (uri (cran-uri "systemfonts" version))
16702 "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
16703 (properties `((upstream-name . "systemfonts")))
16704 (build-system r-build-system)
16706 `(("r-cpp11" ,r-cpp11)))
16708 `(("fontconfig" ,fontconfig)
16711 `(("pkg-config" ,pkg-config)
16712 ("r-knitr" ,r-knitr)))
16713 (home-page "https://github.com/r-lib/systemfonts")
16714 (synopsis "System native font finding")
16716 "This package provides system native access to the font catalogue. As
16717 font handling varies between systems it is difficult to correctly locate
16718 installed fonts across different operating systems. The 'systemfonts' package
16719 provides bindings to the native libraries for finding font files that can then
16720 be used further by e.g. graphic devices.")
16721 (license license:expat)))
16723 (define-public r-graphlayouts
16725 (name "r-graphlayouts")
16730 (uri (cran-uri "graphlayouts" version))
16733 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16734 (properties `((upstream-name . "graphlayouts")))
16735 (build-system r-build-system)
16737 `(("r-igraph" ,r-igraph)
16739 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16740 (home-page "https://github.com/schochastics/graphlayouts")
16741 (synopsis "Additional layout algorithms for network visualizations")
16743 "This package provides several layout algorithms to visualize networks
16744 which are not part of the igraph library. Most are based on the concept of
16745 stress majorization by Gansner et al. (2004)
16746 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16747 emphasize hidden group structures in networks or focus on specific nodes.")
16748 (license license:expat)))
16750 (define-public r-tidygraph
16752 (name "r-tidygraph")
16757 (uri (cran-uri "tidygraph" version))
16760 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16761 (properties `((upstream-name . "tidygraph")))
16762 (build-system r-build-system)
16764 `(("r-dplyr" ,r-dplyr)
16765 ("r-igraph" ,r-igraph)
16766 ("r-magrittr" ,r-magrittr)
16767 ("r-pillar" ,r-pillar)
16770 ("r-rlang" ,r-rlang)
16771 ("r-tibble" ,r-tibble)
16772 ("r-tidyr" ,r-tidyr)))
16773 (home-page "https://github.com/thomasp85/tidygraph")
16774 (synopsis "Tidy API for graph manipulation")
16776 "This package provides a graph implementation that can be thought of as
16777 two tidy data frames describing node and edge data respectively. It provides
16778 an approach to manipulate these two virtual data frames using the API defined
16779 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16780 common graph algorithms.")
16781 (license license:expat)))
16783 (define-public r-soupx
16784 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16788 (version (git-version "0.3.1" revision commit))
16792 (uri (git-reference
16793 (url "https://github.com/constantAmateur/SoupX")
16795 (file-name (git-file-name name version))
16798 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16799 (properties `((upstream-name . "SoupX")))
16800 (build-system r-build-system)
16802 `(("r-ggplot2" ,r-ggplot2)
16803 ("r-matrix" ,r-matrix)
16804 ("r-seurat" ,r-seurat)))
16805 (home-page "https://github.com/constantAmateur/SoupX")
16806 (synopsis "Single cell mRNA Soup eXterminator")
16808 "This package provides a package for quantifying, profiling and
16809 removing cell free mRNA contamination (the \"soup\") from droplet based single
16810 cell RNA-seq experiments.")
16811 (license license:gpl2))))
16813 (define-public r-assertr
16820 (uri (cran-uri "assertr" version))
16823 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16824 (build-system r-build-system)
16826 `(("r-dplyr" ,r-dplyr)
16828 ("r-rlang" ,r-rlang)))
16830 `(("r-knitr" ,r-knitr))) ; needed for vignette
16831 (home-page "https://github.com/ropensci/assertr")
16832 (synopsis "Assertive programming for R analysis pipelines")
16834 "This package provides functionality to assert conditions that have to be
16835 met so that errors in data used in analysis pipelines can fail quickly. It is
16836 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16838 (license license:expat)))
16840 (define-public r-parameters
16842 (name "r-parameters")
16847 (uri (cran-uri "parameters" version))
16850 "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
16851 (properties `((upstream-name . "parameters")))
16852 (build-system r-build-system)
16854 `(("r-bayestestr" ,r-bayestestr)
16855 ("r-insight" ,r-insight)))
16857 `(("r-knitr" ,r-knitr)))
16858 (home-page "https://cran.r-project.org/web/packages/parameters")
16859 (synopsis "Processing of model parameters")
16861 "This package provides utilities for processing the parameters of various
16862 statistical models. Beyond computing p values, CIs, and other indices for a
16863 wide variety of models, this package implements features like standardization
16864 or bootstrapping of parameters and models, feature reduction (feature
16865 extraction and variable selection) as well as conversion between indices of
16867 (license license:gpl3)))
16869 (define-public r-rgdal
16876 (uri (cran-uri "rgdal" version))
16878 (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp"))))
16879 (properties `((upstream-name . "rgdal")))
16880 (build-system r-build-system)
16888 `(("pkg-config" ,pkg-config)
16889 ("r-knitr" ,r-knitr)))
16890 (home-page "http://rgdal.r-forge.r-project.org")
16891 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16893 "This package provides bindings to the Geospatial Data Abstraction
16894 Library (GDAL) and access to projection/transformation operations from the
16896 (license license:gpl2+)))
16898 (define-public r-insol
16905 (uri (cran-uri "insol" version))
16908 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16909 (properties `((upstream-name . "insol")))
16910 (build-system r-build-system)
16912 `(("r-raster" ,r-raster)))
16914 `(("gfortran" ,gfortran)))
16915 (home-page "https://meteoexploration.com/R/insol/index.html")
16916 (synopsis "Tools for calculating solar radiation")
16918 "This package provides functions to compute insolation on tilted
16919 surfaces, computes atmospheric transmittance and related parameters such as:
16920 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16921 time, vector in the direction of the sun, vector normal to surface, and some
16922 atmospheric physics.")
16923 (license license:gpl2+)))
16925 (define-public r-lifecycle
16927 (name "r-lifecycle")
16932 (uri (cran-uri "lifecycle" version))
16935 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16936 (properties `((upstream-name . "lifecycle")))
16937 (build-system r-build-system)
16939 `(("r-glue" ,r-glue)
16940 ("r-rlang" ,r-rlang)))
16942 `(("r-knitr" ,r-knitr))) ; for vignettes
16943 (home-page "https://github.com/r-lib/lifecycle")
16944 (synopsis "Manage the life cycle of your package functions")
16946 "Manage the life cycle of your exported functions with shared
16947 conventions, documentation badges, and non-invasive deprecation warnings. The
16948 lifecycle package defines four development stages (experimental, maturing,
16949 stable, and questioning) and three deprecation stages (soft-deprecated,
16950 deprecated, and defunct). It makes it easy to insert badges corresponding to
16951 these stages in your documentation. Usage of deprecated functions are
16952 signalled with increasing levels of non-invasive verbosity.")
16953 (license license:gpl3)))
16955 (define-public r-assertable
16957 (name "r-assertable")
16962 (uri (cran-uri "assertable" version))
16965 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16966 (build-system r-build-system)
16968 `(("r-data-table" ,r-data-table)))
16969 (home-page "https://cran.r-project.org/web/packages/assertable/")
16970 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16971 (description "This package provides simple, flexible assertions on
16972 data.frame or data.table objects with verbose output for vetting. While other
16973 assertion packages apply towards more general use-cases, @code{assertable} is
16974 tailored towards tabular data. It includes functions to check variable names
16975 and values, whether the dataset contains all combinations of a given set of
16976 unique identifiers, and whether it is a certain length. In addition,
16977 @code{assertable} includes utility functions to check the existence of target
16978 files and to efficiently import multiple tabular data files into one
16980 (license license:gpl3)))
16982 (define-public r-quadprog
16984 (name "r-quadprog")
16989 (uri (cran-uri "quadprog" version))
16991 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16992 (build-system r-build-system)
16994 `(("gfortran" ,gfortran)))
16995 (home-page "https://cran.r-project.org/web/packages/quadprog")
16996 (synopsis "Functions to solve quadratic programming problems")
16998 "This package contains routines and documentation for solving quadratic
16999 programming problems.")
17000 (license license:gpl3+)))
17002 (define-public r-desolve
17009 (uri (cran-uri "deSolve" version))
17011 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
17012 (properties `((upstream-name . "deSolve")))
17013 (build-system r-build-system)
17015 `(("gfortran" ,gfortran)))
17016 (home-page "https://desolve.r-forge.r-project.org/")
17017 (synopsis "Solvers for initial value problems of differential equations")
17018 (description "This package provides functions that solve initial value
17019 problems of a system of first-order @dfn{ordinary differential
17020 equations} (ODE), of @dfn{partial differential equations} (PDE), of
17021 @dfn{differential algebraic equations} (DAE), and of delay differential
17022 equations. The functions provide an interface to the FORTRAN functions
17023 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
17024 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
17025 C-implementation of solvers of the Runge-Kutta family with fixed or variable
17026 time steps. The package contains routines designed for solving ODEs resulting
17027 from 1-D, 2-D and 3-D partial differential equations that have been converted
17028 to ODEs by numerical differencing.")
17029 (license license:gpl2+)))
17031 (define-public r-pracma
17037 (uri (cran-uri "pracma" version))
17039 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
17040 (build-system r-build-system)
17041 (home-page "https://cran.r-project.org/web/packages/pracma/")
17042 (synopsis "Practical numerical math functions")
17043 (description "This package provides functions for numerical analysis and
17044 linear algebra, numerical optimization, differential equations, plus some
17045 special functions. It uses Matlab function names where appropriate to simplify
17047 (license license:gpl3+)))
17049 (define-public r-subplex
17056 (uri (cran-uri "subplex" version))
17059 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
17060 (build-system r-build-system)
17062 `(("gfortran" ,gfortran)))
17063 (home-page "https://cran.r-project.org/web/packages/subplex")
17064 (synopsis "Unconstrained optimization using the subplex algorithm")
17066 "This package implements the Subplex optimization algorithm.
17067 It solves unconstrained optimization problems using a simplex method on
17068 subspaces. The method is well suited for optimizing objective functions that
17069 are noisy or are discontinuous at the solution.")
17070 (license license:gpl3+)))
17072 (define-public r-txtplot
17079 (uri (cran-uri "txtplot" version))
17082 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
17083 (build-system r-build-system)
17084 (home-page "https://cran.r-project.org/web/packages/txtplot/")
17085 (synopsis "Text-based plotting")
17086 (description "This package provides functions to produce rudimentary ASCII
17087 graphics directly in the terminal window. This package provides a basic
17088 plotting function (and equivalents of curve, density, acf and barplot) as well
17089 as a boxplot function.")
17090 (license license:lgpl3+)))
17092 (define-public r-bio3d
17099 (uri (cran-uri "bio3d" version))
17102 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
17103 (properties `((upstream-name . "bio3d")))
17104 (build-system r-build-system)
17105 (inputs `(("zlib" ,zlib)))
17106 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17107 (home-page "http://thegrantlab.org/bio3d/")
17108 (synopsis "Biological structure analysis")
17110 "This package provides utilities to process, organize and explore protein
17111 structure, sequence and dynamics data. Features include the ability to read
17112 and write structure, sequence and dynamic trajectory data, perform sequence
17113 and structure database searches, data summaries, atom selection, alignment,
17114 superposition, rigid core identification, clustering, torsion analysis,
17115 distance matrix analysis, structure and sequence conservation analysis, normal
17116 mode analysis, principal component analysis of heterogeneous structure data,
17117 and correlation network analysis from normal mode and molecular dynamics data.
17118 In addition, various utility functions are provided to enable the statistical
17119 and graphical power of the R environment to work with biological sequence and
17121 (license license:gpl2+)))
17123 (define-public r-bios2cor
17125 (name "r-bios2cor")
17130 (uri (cran-uri "Bios2cor" version))
17133 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
17134 (properties `((upstream-name . "Bios2cor")))
17135 (build-system r-build-system)
17137 `(("r-bigmemory" ,r-bigmemory)
17138 ("r-bio3d" ,r-bio3d)
17139 ("r-circular" ,r-circular)
17140 ("r-igraph" ,r-igraph)))
17141 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
17142 (synopsis "From biological sequences and simulations to correlation analysis")
17144 "This package provides utilities for computation and analysis of
17145 correlation/covariation in multiple sequence alignments and in side chain
17146 motions during molecular dynamics simulations. Features include the
17147 computation of correlation/covariation scores using a variety of scoring
17148 functions between either sequence positions in alignments or side chain
17149 dihedral angles in molecular dynamics simulations and utilities to analyze the
17150 correlation/covariation matrix through a variety of tools including network
17151 representation and principal components analysis. In addition, several
17152 utility functions are based on the R graphical environment to provide friendly
17153 tools for help in data interpretation.")
17154 (license license:gpl2+)))
17156 ;; This package includes minified JavaScript files. When upgrading please
17157 ;; check that there are no new minified JavaScript files.
17158 (define-public r-networkd3
17160 (name "r-networkd3")
17165 (uri (cran-uri "networkD3" version))
17168 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
17171 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
17173 (properties `((upstream-name . "networkD3")))
17174 (build-system r-build-system)
17176 `(#:modules ((guix build utils)
17177 (guix build r-build-system)
17181 (modify-phases %standard-phases
17182 (add-after 'unpack 'process-javascript
17183 (lambda* (#:key inputs #:allow-other-keys)
17184 (with-directory-excursion "inst/htmlwidgets/lib/"
17188 `((,(assoc-ref inputs "d3.v4.js")
17189 "d3-4.5.0/d3.min.js"))))
17190 (lambda (sources targets)
17191 (for-each (lambda (source target)
17192 (format #t "Processing ~a --> ~a~%"
17194 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17195 (call-with-output-file target
17197 (dump-port minified port)))))
17198 sources targets))))
17201 `(("uglify-js" ,uglify-js)
17202 ;; NOTE: Make sure that this version of d3 is still valid when
17203 ;; upgrading the package.
17207 (uri "https://d3js.org/d3.v4.js")
17210 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17212 `(("r-htmlwidgets" ,r-htmlwidgets)
17213 ("r-igraph" ,r-igraph)
17214 ("r-magrittr" ,r-magrittr)))
17215 (home-page "https://cran.r-project.org/package=networkD3")
17216 (synopsis "D3 JavaScript network graphs from R")
17218 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17220 (license license:gpl3+)))
17222 (define-public r-aasea
17229 (uri (cran-uri "aaSEA" version))
17232 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17233 (properties `((upstream-name . "aaSEA")))
17234 (build-system r-build-system)
17236 `(("r-bios2cor" ,r-bios2cor)
17238 ("r-hmisc" ,r-hmisc)
17239 ("r-magrittr" ,r-magrittr)
17240 ("r-networkd3" ,r-networkd3)
17241 ("r-plotly" ,r-plotly)
17242 ("r-seqinr" ,r-seqinr)
17243 ("r-shiny" ,r-shiny)
17244 ("r-shinydashboard" ,r-shinydashboard)))
17245 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17246 (synopsis "Amino acid substitution effect analyzer")
17248 "Given a protein multiple sequence alignment, it is a daunting task to
17249 assess the effects of substitutions along sequence length. The aaSEA package
17250 is intended to help researchers to rapidly analyze property changes caused by
17251 single, multiple and correlated amino acid substitutions in proteins.")
17252 (license license:gpl3)))
17254 (define-public r-abacus
17261 (uri (cran-uri "ABACUS" version))
17264 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17265 (properties `((upstream-name . "ABACUS")))
17266 (build-system r-build-system)
17268 `(("r-ggplot2" ,r-ggplot2)
17269 ("r-shiny" ,r-shiny)))
17270 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17271 (synopsis "Apps-based activities for communicating and understanding statistics")
17273 "This package provides a set of Shiny apps for effective communication
17274 and understanding in statistics. The current version includes properties of
17275 normal distribution, properties of sampling distribution, one-sample z and t
17276 tests, two samples independent (unpaired) t test and analysis of variance.")
17277 (license license:gpl3)))
17279 (define-public r-abc-rap
17286 (uri (cran-uri "ABC.RAP" version))
17289 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17290 (properties `((upstream-name . "ABC.RAP")))
17291 (build-system r-build-system)
17292 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17293 (synopsis "Array-based CpG region analysis pipeline")
17295 "This package aims to identify candidate genes that are differentially
17296 methylated between cases and controls. It applies Student's t-test and delta
17297 beta analysis to identify candidate genes containing multiple CpG sites.")
17298 (license license:gpl3)))
17300 (define-public r-abcadm
17307 (uri (cran-uri "abcADM" version))
17310 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17311 (properties `((upstream-name . "abcADM")))
17312 (build-system r-build-system)
17315 ("r-rcpp" ,r-rcpp)))
17316 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17317 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17319 "This package provides tools to estimate parameters of accumulated
17320 damage (load duration) models based on failure time data under a Bayesian
17321 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17322 long-term reliability under stochastic load profiles.")
17323 (license license:gpl3)))
17325 (define-public r-rglpk
17332 (uri (cran-uri "Rglpk" version))
17335 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17336 (properties `((upstream-name . "Rglpk")))
17337 (build-system r-build-system)
17339 `(("r-slam" ,r-slam)))
17342 (home-page "https://r-forge.r-project.org/projects/rglp/")
17343 (synopsis "R interface to the GNU Linear Programming Kit")
17345 "This package provides an R interface to the GNU Linear Programming Kit,
17346 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17347 integer linear programming} (MILP) and other related problems.")
17349 (license (list license:gpl2 license:gpl3))))
17351 (define-public r-abcdefba
17353 (name "r-abcdefba")
17358 (uri (cran-uri "abcdeFBA" version))
17361 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17362 (properties `((upstream-name . "abcdeFBA")))
17363 (build-system r-build-system)
17365 `(("r-corrplot" ,r-corrplot)
17366 ("r-lattice" ,r-lattice)
17368 ("r-rglpk" ,r-rglpk)))
17369 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17370 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17372 "This package provides functions for Constraint Based Simulation using
17373 Flux Balance Analysis and informative analysis of the data generated during
17375 (license license:gpl2)))
17377 (define-public r-abcrlda
17384 (uri (cran-uri "abcrlda" version))
17387 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17388 (properties `((upstream-name . "abcrlda")))
17389 (build-system r-build-system)
17390 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17391 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17393 "This package offers methods to perform @dfn{asymptotically
17394 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17395 cost-sensitive binary classification. The bias-correction is an estimate of
17396 the bias term added to regularized discriminant analysis that minimizes the
17398 (license license:gpl3)))
17400 (define-public r-abemus
17407 (uri (cran-uri "abemus" version))
17410 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17411 (properties `((upstream-name . "abemus")))
17412 (build-system r-build-system)
17414 `(("r-data-table" ,r-data-table)))
17415 (home-page "https://cran.r-project.org/web/packages/abemus/")
17416 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17418 "This package provides an implementation of @dfn{Adaptive Base Error
17419 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17420 platform-specific genetic knowledge and empirical signal to readily detect and
17421 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17422 cell free DNA} (cfDNA).")
17423 (license license:gpl3)))
17425 ;; This package includes minified JavaScript files. When upgrading please
17426 ;; check that there are no new minified JavaScript files.
17427 (define-public r-rintrojs
17429 (name "r-rintrojs")
17434 (uri (cran-uri "rintrojs" version))
17437 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17438 (properties `((upstream-name . "rintrojs")))
17439 (build-system r-build-system)
17441 `(#:modules ((guix build utils)
17442 (guix build r-build-system)
17446 (modify-phases %standard-phases
17447 (add-after 'unpack 'process-javascript
17448 (lambda* (#:key inputs #:allow-other-keys)
17449 (with-directory-excursion "inst/javascript/introjs/"
17453 `((,(assoc-ref inputs "intro.js")
17455 (lambda (sources targets)
17456 (for-each (lambda (source target)
17457 (format #t "Processing ~a --> ~a~%"
17459 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17460 (call-with-output-file target
17462 (dump-port minified port)))))
17463 sources targets))))
17466 `(("uglify-js" ,uglify-js)
17470 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17473 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17475 `(("r-jsonlite" ,r-jsonlite)
17476 ("r-shiny" ,r-shiny)))
17477 (home-page "https://github.com/carlganz/rintrojs")
17478 (synopsis "Wrapper for the Intro.js library")
17480 "This package provides a wrapper for the @url{http://www.introjs.com,
17481 Intro.js} library. This package makes it easy to include step-by-step
17482 introductions, and clickable hints in a Shiny application. It supports both
17483 static introductions in the UI, and programmatic introductions from the
17485 (license license:agpl3+)))
17487 (define-public r-sysfonts
17489 (name "r-sysfonts")
17494 (uri (cran-uri "sysfonts" version))
17497 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17498 (properties `((upstream-name . "sysfonts")))
17499 (build-system r-build-system)
17501 `(("freetype" ,freetype)
17505 `(("pkg-config" ,pkg-config)))
17506 (home-page "https://github.com/yixuan/sysfonts")
17507 (synopsis "Loading fonts into R")
17509 "This is a package to simplify loading of system fonts and Google Fonts
17510 into R, in order to support other packages.")
17511 (license license:gpl2)))
17513 (define-public r-showtextdb
17515 (name "r-showtextdb")
17520 (uri (cran-uri "showtextdb" version))
17523 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17524 (properties `((upstream-name . "showtextdb")))
17525 (build-system r-build-system)
17527 `(("r-sysfonts" ,r-sysfonts)))
17528 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17529 (synopsis "Font files for the 'showtext' package")
17531 "This package provides font files that can be used by the @code{showtext}
17533 (license license:asl2.0)))
17535 (define-public r-showtext
17537 (name "r-showtext")
17542 (uri (cran-uri "showtext" version))
17545 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17546 (properties `((upstream-name . "showtext")))
17547 (build-system r-build-system)
17549 `(("freetype" ,freetype)
17553 `(("r-showtextdb" ,r-showtextdb)
17554 ("r-sysfonts" ,r-sysfonts)))
17556 `(("pkg-config" ,pkg-config)
17557 ("r-knitr" ,r-knitr)))
17558 (home-page "https://github.com/yixuan/showtext")
17559 (synopsis "Using fonts more easily in R graphs")
17561 "This package aims to make it easy to use various types of
17562 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17563 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17564 will be converted into polygons or raster images, hence after the plot has
17565 been created, it no longer relies on the font files. No external software
17566 such as Ghostscript is needed to use this package.")
17567 (license license:asl2.0)))
17569 (define-public r-emojifont
17571 (name "r-emojifont")
17576 (uri (cran-uri "emojifont" version))
17579 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17580 (properties `((upstream-name . "emojifont")))
17581 (build-system r-build-system)
17583 `(("r-ggplot2" ,r-ggplot2)
17584 ("r-proto" ,r-proto)
17585 ("r-showtext" ,r-showtext)
17586 ("r-sysfonts" ,r-sysfonts)))
17587 (home-page "https://guangchuangyu.github.io/emojifont")
17588 (synopsis "Emoji and Font Awesome in R graphics")
17590 "This package enables the use of emoji and the Font Awesome glyphs in
17591 both base and ggplot2 graphics.")
17592 (license license:artistic2.0)))
17594 (define-public r-abstractr
17596 (name "r-abstractr")
17601 (uri (cran-uri "abstractr" version))
17604 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17605 (properties `((upstream-name . "abstractr")))
17606 (build-system r-build-system)
17608 `(("r-colourpicker" ,r-colourpicker)
17609 ("r-emojifont" ,r-emojifont)
17610 ("r-ggplot2" ,r-ggplot2)
17611 ("r-gridextra" ,r-gridextra)
17612 ("r-rintrojs" ,r-rintrojs)
17613 ("r-shiny" ,r-shiny)
17614 ("r-shinythemes" ,r-shinythemes)))
17615 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17616 (synopsis "R-Shiny application for creating visual abstracts")
17618 "This package provides an R Shiny application to create visual abstracts
17619 for original research. A variety of user defined options and formatting are
17621 (license license:gpl3)))
17623 (define-public r-qgam
17630 (uri (cran-uri "qgam" version))
17633 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17634 (properties `((upstream-name . "qgam")))
17635 (build-system r-build-system)
17637 `(("r-doparallel" ,r-doparallel)
17640 ("r-shiny" ,r-shiny)))
17641 (native-inputs `(("r-knitr" ,r-knitr)))
17642 (home-page "https://cran.r-project.org/web/packages/qgam/")
17643 (synopsis "Smooth additive quantile regression models")
17645 "This package provides smooth additive quantile regression models, fitted
17646 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17647 the smoothing parameters are estimated automatically by marginal loss
17648 minimization, while the regression coefficients are estimated using either
17649 PIRLS or Newton algorithm. The learning rate is determined so that the
17650 Bayesian credible intervals of the estimated effects have approximately the
17651 correct coverage. The main function is @code{qgam()} which is similar to
17652 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17653 regression models.")
17654 (license license:gpl2+)))
17656 (define-public r-abtest
17663 (uri (cran-uri "abtest" version))
17666 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17667 (properties `((upstream-name . "abtest")))
17668 (build-system r-build-system)
17670 `(("r-matrix" ,r-matrix)
17671 ("r-mvtnorm" ,r-mvtnorm)
17672 ("r-plotrix" ,r-plotrix)
17674 ("r-rcolorbrewer" ,r-rcolorbrewer)
17677 ("r-truncnorm" ,r-truncnorm)))
17678 (home-page "https://cran.r-project.org/web/packages/abtest/")
17679 (synopsis "Bayesian A/B testing")
17681 "This package provides functions for Bayesian A/B testing including prior
17682 elicitation options based on Kass and Vaidyanathan (1992)
17683 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17684 (license license:gpl2+)))
17686 (define-public r-accept
17693 (uri (cran-uri "accept" version))
17696 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17697 (properties `((upstream-name . "accept")))
17698 (build-system r-build-system)
17700 `(("r-dplyr" ,r-dplyr)
17701 ("r-extrafont" ,r-extrafont)
17703 ("r-plotly" ,r-plotly)
17704 ("r-stringr" ,r-stringr)
17705 ("r-viridis" ,r-viridis)))
17706 (home-page "https://cran.r-project.org/web/packages/accept/")
17707 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17709 "This package allows clinicians to predict the rate and severity of
17710 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17711 Disease} (COPD) patients, based on the clinical prediction model published in
17712 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17713 (license license:gpl3)))
17715 (define-public r-smpracticals
17717 (name "r-smpracticals")
17722 (uri (cran-uri "SMPracticals" version))
17725 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17726 (properties `((upstream-name . "SMPracticals")))
17727 (build-system r-build-system)
17729 `(("r-ellipse" ,r-ellipse)
17732 ("r-survival" ,r-survival)))
17733 (home-page "http://statwww.epfl.ch/davison/SM/")
17734 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17736 "This package contains the datasets and a few functions for use with the
17737 practicals outlined in Appendix A of the book Statistical Models (Davison,
17738 2003, Cambridge University Press). The practicals themselves can be found at
17739 @url{http://statwww.epfl.ch/davison/SM/}.")
17740 (license license:gpl2+)))
17742 (define-public r-fgui
17749 (uri (cran-uri "fgui" version))
17752 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17753 (properties `((upstream-name . "fgui")))
17754 (build-system r-build-system)
17756 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17757 (synopsis "Create GUI for R functions")
17759 "Rapidly create a GUI for a function you created by automatically
17760 creating widgets for arguments of the function. This package automatically
17761 parses help routines for context-sensitive help to these arguments. The
17762 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17763 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17764 incorporated into the interface for greater customization for the more
17766 ;; Any version of the GPL.
17767 (license (list license:gpl2+ license:gpl3+))))
17769 (define-public r-tcltk2
17776 (uri (cran-uri "tcltk2" version))
17779 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17780 (properties `((upstream-name . "tcltk2")))
17781 (build-system r-build-system)
17785 (home-page "https://www.sciviews.org/SciViews-R")
17786 (synopsis "Tcl/Tk additions")
17788 "This package provides a series of additional Tcl commands and Tk widgets
17789 with style and various functions to supplement the tcltk package")
17790 (license license:lgpl3)))
17792 (define-public r-accrual
17799 (uri (cran-uri "accrual" version))
17802 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17803 (properties `((upstream-name . "accrual")))
17804 (build-system r-build-system)
17806 `(("r-fgui" ,r-fgui)
17807 ("r-smpracticals" ,r-smpracticals)
17808 ("r-tcltk2" ,r-tcltk2)))
17809 (home-page "https://cran.r-project.org/web/packages/accrual/")
17810 (synopsis "Bayesian accrual prediction")
17812 "Subject recruitment for medical research is challenging. Slow patient
17813 accrual leads to delay in research. Accrual monitoring during the process of
17814 recruitment is critical. Researchers need reliable tools to manage the
17815 accrual rate. This package provides an implementation of a Bayesian method
17816 that integrates researcher's experience on previous trials and data from the
17817 current study, providing reliable prediction on accrual rate for clinical
17818 studies. It provides functions for Bayesian accrual prediction which can be
17819 easily used by statisticians and clinical researchers.")
17820 (license license:gpl2)))
17822 (define-public r-accrued
17829 (uri (cran-uri "accrued" version))
17832 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17833 (properties `((upstream-name . "accrued")))
17834 (build-system r-build-system)
17835 (home-page "https://cran.r-project.org/web/packages/accrued/")
17836 (synopsis "Data quality visualization tools for partially accruing data")
17838 "This is a package for visualizing data quality of partially accruing
17840 (license license:gpl3)))
17842 (define-public r-mda
17849 (uri (cran-uri "mda" version))
17852 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17853 (properties `((upstream-name . "mda")))
17854 (build-system r-build-system)
17855 (propagated-inputs `(("r-class" ,r-class)))
17856 (native-inputs `(("gfortran" ,gfortran)))
17857 (home-page "https://cran.r-project.org/web/packages/mda/")
17858 (synopsis "Mixture and flexible discriminant analysis")
17860 "This is a package for mixture and flexible discriminant analysis,
17861 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17862 (license license:gpl2)))
17864 (define-public r-elasticnet
17866 (name "r-elasticnet")
17871 (uri (cran-uri "elasticnet" version))
17874 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17875 (properties `((upstream-name . "elasticnet")))
17876 (build-system r-build-system)
17878 `(("r-lars" ,r-lars)))
17879 (home-page "http://users.stat.umn.edu/~zouxx019/")
17880 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17882 "This package provides functions for fitting the entire solution path of
17883 the Elastic-Net and also provides functions for estimating sparse Principal
17884 Components. The Lasso solution paths can be computed by the same function.")
17885 (license license:gpl2+)))
17887 (define-public r-sparselda
17889 (name "r-sparselda")
17894 (uri (cran-uri "sparseLDA" version))
17897 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17898 (properties `((upstream-name . "sparseLDA")))
17899 (build-system r-build-system)
17901 `(("r-elasticnet" ,r-elasticnet)
17904 (home-page "https://www.imm.dtu.dk/~lkhc/")
17905 (synopsis "Sparse discriminant analysis")
17907 "This package performs sparse linear discriminant analysis for Gaussians
17908 and mixture of Gaussian models.")
17909 (license license:gpl2+)))
17911 (define-public r-accsda
17918 (uri (cran-uri "accSDA" version))
17921 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17922 (properties `((upstream-name . "accSDA")))
17923 (build-system r-build-system)
17925 `(("r-ggplot2" ,r-ggplot2)
17926 ("r-ggthemes" ,r-ggthemes)
17927 ("r-gridextra" ,r-gridextra)
17929 ("r-rarpack" ,r-rarpack)
17930 ("r-sparselda" ,r-sparselda)))
17931 (home-page "https://github.com/gumeo/accSDA/wiki")
17932 (synopsis "Accelerated sparse discriminant analysis")
17934 "This package provides an implementation of sparse linear discriminant
17935 analysis, which is a supervised classification method for multiple classes.
17936 Various novel optimization approaches to this problem are implemented
17937 including @dfn{alternating direction method of multipliers} (ADMM),
17938 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17939 Functions for performing cross validation are also supplied along with basic
17940 prediction and plotting functions. @dfn{Sparse zero variance
17941 discriminant} (SZVD) analysis is also included in the package.")
17942 (license license:gpl2+)))
17944 (define-public r-ace2fastq
17946 (name "r-ace2fastq")
17951 (uri (cran-uri "ace2fastq" version))
17954 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17955 (properties `((upstream-name . "ace2fastq")))
17956 (build-system r-build-system)
17958 `(("r-stringr" ,r-stringr)))
17959 (home-page "https://github.com/c5sire/ace2fastq")
17960 (synopsis "ACE file to FASTQ converter")
17962 "The ACE file format is used in genomics to store contigs from sequencing
17963 machines. This tools converts it into FASTQ format. Both formats contain the
17964 sequence characters and their corresponding quality information. Unlike the
17965 FASTQ file, the ACE file stores the quality values numerically. The
17966 conversion algorithm uses the standard Sanger formula. The package
17967 facilitates insertion into pipelines, and content inspection.")
17968 (license license:gpl3)))
17970 (define-public r-rngwell
17977 (uri (cran-uri "rngWELL" version))
17980 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17981 (properties `((upstream-name . "rngWELL")))
17982 (build-system r-build-system)
17983 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17984 (synopsis "Toolbox for WELL random number generators")
17986 "This is a dedicated package to WELL pseudo random generators, which were
17987 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17988 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17989 (license license:bsd-3)))
17991 (define-public r-randtoolbox
17993 (name "r-randtoolbox")
17998 (uri (cran-uri "randtoolbox" version))
18001 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
18002 (properties `((upstream-name . "randtoolbox")))
18003 (build-system r-build-system)
18005 `(("r-rngwell" ,r-rngwell)))
18007 `(("gfortran" ,gfortran)))
18008 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
18009 (synopsis "Toolbox for pseudo and quasi random number generation")
18011 "This package provides
18014 @item pseudo random generators, such as general linear
18015 congruential generators, multiple recursive generators and generalized
18016 feedback shift register (SF-Mersenne Twister algorithm and WELL
18019 @item quasi random generators, such as the Torus algorithm, the Sobol
18020 sequence, the Halton sequence (including the Van der Corput sequence), and
18022 @item some generator tests: the gap test, the serial test, the poker test.
18025 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
18026 (license license:bsd-3)))
18028 (define-public r-lhs
18035 (uri (cran-uri "lhs" version))
18038 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
18039 (properties `((upstream-name . "lhs")))
18040 (build-system r-build-system)
18041 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18043 `(("r-knitr" ,r-knitr)))
18044 (home-page "https://github.com/bertcarnell/lhs")
18045 (synopsis "Latin Hypercube Samples")
18047 "This package provides a number of methods for creating and augmenting
18048 Latin Hypercube Samples.")
18049 (license license:gpl3)))
18051 (define-public r-acebayes
18053 (name "r-acebayes")
18058 (uri (cran-uri "acebayes" version))
18061 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
18062 (properties `((upstream-name . "acebayes")))
18063 (build-system r-build-system)
18065 `(("r-compare" ,r-compare)
18067 ("r-randtoolbox" ,r-randtoolbox)
18069 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18070 (home-page "https://cran.r-project.org/web/packages/acebayes/")
18071 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
18073 "Finding an optimal Bayesian experimental design involves maximizing an
18074 objective function given by the expectation of some appropriately chosen
18075 utility function with respect to the joint distribution of unknown
18076 quantities (including responses). This objective function is usually not
18077 available in closed form and the design space can be continuous and of high
18078 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
18079 to maximise an approximation to the expectation of the utility function.")
18080 (license license:gpl2)))
18082 (define-public r-acet
18089 (uri (cran-uri "ACEt" version))
18092 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
18093 (properties `((upstream-name . "ACEt")))
18094 (build-system r-build-system)
18099 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18100 (home-page "https://cran.r-project.org/web/packages/ACEt/")
18101 (synopsis "Estimating dynamic heritability and twin model comparison")
18103 "This package supports twin models that are able to estimate the dynamic
18104 behaviour of the variance components in the classical twin models with respect
18105 to age using B-splines and P-splines.")
18106 (license license:gpl2+)))
18108 (define-public r-acfmperiod
18110 (name "r-acfmperiod")
18115 (uri (cran-uri "acfMPeriod" version))
18118 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
18119 (properties `((upstream-name . "acfMPeriod")))
18120 (build-system r-build-system)
18122 `(("r-mass" ,r-mass)))
18123 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
18124 (synopsis "Estimation of the ACF from the M-periodogram")
18126 "This package support non-robust and robust computations of the sample
18127 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
18128 univariate and multivariate processes. The methodology consists in reversing
18129 the diagonalization procedure involving the periodogram or the
18130 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
18131 ACOVF or the ACF as discussed in Fuller (1995)
18132 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
18133 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
18134 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
18135 (license license:gpl2+)))
18137 (define-public r-gamlss-data
18139 (name "r-gamlss-data")
18144 (uri (cran-uri "gamlss.data" version))
18147 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
18148 (properties `((upstream-name . "gamlss.data")))
18149 (build-system r-build-system)
18150 (home-page "http://www.gamlss.org/")
18151 (synopsis "GAMLSS data")
18153 "This package provides data used as examples to demonstrate GAMLSS
18155 ;; Either version of the license
18156 (license (list license:gpl2 license:gpl3))))
18158 (define-public r-gamlss
18165 (uri (cran-uri "gamlss" version))
18168 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
18169 (properties `((upstream-name . "gamlss")))
18170 (build-system r-build-system)
18172 `(("r-gamlss-data" ,r-gamlss-data)
18173 ("r-gamlss-dist" ,r-gamlss-dist)
18176 ("r-survival" ,r-survival)))
18177 (home-page "http://www.gamlss.org/")
18178 (synopsis "Generalized additive models for location scale and shape")
18180 "This package provides functions for fitting the generalized additive
18181 models for location scale and shape introduced by Rigby and
18182 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
18183 use a distributional regression approach where all the parameters of the
18184 conditional distribution of the response variable are modelled using
18185 explanatory variables.")
18186 ;; Either version of the license
18187 (license (list license:gpl2 license:gpl3))))
18189 (define-public r-acid
18196 (uri (cran-uri "acid" version))
18199 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18200 (properties `((upstream-name . "acid")))
18201 (build-system r-build-system)
18203 `(("r-gamlss" ,r-gamlss)
18204 ("r-gamlss-dist" ,r-gamlss-dist)
18205 ("r-hmisc" ,r-hmisc)))
18206 (home-page "https://cran.r-project.org/web/packages/acid/")
18207 (synopsis "Analysing conditional income distributions")
18209 "This package provides functions for the analysis of income distributions
18210 for subgroups of the population as defined by a set of variables like age,
18211 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18212 distribution as well as functions for moments, inequality measures, entropy
18213 measures and polarisation measures of income distributions. This package thus
18214 aides the analysis of income inequality by offering tools for the exploratory
18215 analysis of income distributions at the disaggregated level.")
18216 (license license:gpl3)))
18218 (define-public r-acm4r
18225 (uri (cran-uri "acm4r" version))
18228 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18229 (properties `((upstream-name . "acm4r")))
18230 (build-system r-build-system)
18231 (propagated-inputs `(("r-mass" ,r-mass)))
18232 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18233 (synopsis "Align-and-count method comparisons of RFLP data")
18235 "This is a package to compare sequence fragment lengths or molecular
18236 weights from pairs of lanes. The number of matching bands in the
18237 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18238 the align-and-count method.")
18239 ;; Any version of the GPL
18240 (license (list license:gpl2+ license:gpl3+))))
18242 (define-public r-filematrix
18244 (name "r-filematrix")
18249 (uri (cran-uri "filematrix" version))
18252 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18253 (properties `((upstream-name . "filematrix")))
18254 (build-system r-build-system)
18255 ;; These inputs are needed for vignettes
18257 `(("r-knitr" ,r-knitr)
18258 ("r-rmarkdown" ,r-rmarkdown)
18259 ("pandoc-citeproc" ,pandoc-citeproc)))
18260 (home-page "https://github.com/andreyshabalin/filematrix")
18261 (synopsis "File-backed matrix class with convenient read and write access")
18263 "This package provides an interface for working with large matrices
18264 stored in files, not in computer memory. It supports multiple non-character
18265 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18266 byte real values). Access to parts of the matrix is done by indexing, exactly
18267 as with usual R matrices. It supports very large matrices; the package has
18268 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18269 columns, ad allows for quick addition of extra columns to a filematrix.")
18270 (license license:lgpl3)))
18272 (define-public r-acmeeqtl
18274 (name "r-acmeeqtl")
18279 (uri (cran-uri "ACMEeqtl" version))
18282 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18283 (properties `((upstream-name . "ACMEeqtl")))
18284 (build-system r-build-system)
18286 `(("r-filematrix" ,r-filematrix)))
18287 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18288 (synopsis "Estimation of interpretable eQTL effect sizes")
18290 "This package provides a non-linear model, termed ACME, that reflects a
18291 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18292 With non-linear least-squares algorithm the maximum likelihood parameters can
18293 be estimated. The ACME model provides interpretable effect size estimates and
18294 p-values with well controlled Type-I error.")
18295 (license license:lgpl3)))
18297 (define-public r-acmer
18304 (uri (cran-uri "acmeR" version))
18307 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18308 (properties `((upstream-name . "acmeR")))
18309 (build-system r-build-system)
18310 (propagated-inputs `(("r-foreign" ,r-foreign)))
18311 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18312 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18314 "This package provides an implementation of the ACME estimator, described
18315 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18316 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18317 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18318 as carcasses age; variable bleed-through at successive searches; and interval
18319 mortality estimates. The package provides, based on search data, functions
18320 for estimating the mortality inflation factor in Frequentist and Bayesian
18322 (license license:expat)))
18324 (define-public r-r-huge
18331 (uri (cran-uri "R.huge" version))
18334 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18335 (properties `((upstream-name . "R.huge")))
18336 (build-system r-build-system)
18338 `(("r-r-methodss3" ,r-r-methodss3)
18340 ("r-r-utils" ,r-r-utils)))
18341 (home-page "https://github.com/HenrikBengtsson/R.huge")
18342 (synopsis "Methods for accessing huge amounts of data")
18344 "This is a deprecated package for accessing huge amounts of data.
18345 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18346 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18347 the @code{aroma.affymetrix} package.")
18348 (license license:lgpl2.1+)))
18350 (define-public r-r-filesets
18352 (name "r-r-filesets")
18357 (uri (cran-uri "R.filesets" version))
18360 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18361 (properties `((upstream-name . "R.filesets")))
18362 (build-system r-build-system)
18364 `(("r-digest" ,r-digest)
18365 ("r-r-cache" ,r-r-cache)
18366 ("r-r-methodss3" ,r-r-methodss3)
18368 ("r-r-utils" ,r-r-utils)))
18369 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18370 (synopsis "Easy handling of and access to files")
18372 "This package provides classes and methods to locate, setup, subset,
18373 navigate and iterate file sets, i.e. sets of files located in one or more
18374 directories on the file system. The API is designed such that these classes
18375 can be extended via inheritance to provide a richer API for special file
18376 formats. Moreover, a specific name format is defined such that filenames and
18377 directories can be considered to have full names which consists of a name
18378 followed by comma-separated tags. This adds additional flexibility to
18379 identify file sets and individual files.")
18380 (license license:lgpl2.1+)))
18382 (define-public r-r-devices
18384 (name "r-r-devices")
18389 (uri (cran-uri "R.devices" version))
18392 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18393 (properties `((upstream-name . "R.devices")))
18394 (build-system r-build-system)
18396 `(("r-base64enc" ,r-base64enc)
18397 ("r-r-methodss3" ,r-r-methodss3)
18399 ("r-r-utils" ,r-r-utils)))
18400 (home-page "https://github.com/HenrikBengtsson/R.devices")
18401 (synopsis "Unified handling of graphics devices")
18403 "This package provides functions for creating plots and image files in a
18404 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18405 Default device options as well as scales and aspect ratios are controlled in a
18406 uniform way across all device types. Switching output format requires minimal
18407 changes in code. This package is ideal for large-scale batch processing,
18408 because it will never leave open graphics devices or incomplete image files
18409 behind, even on errors or user interrupts.")
18410 (license license:lgpl2.1+)))
18412 (define-public r-acnr
18419 (uri (cran-uri "acnr" version))
18422 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18423 (properties `((upstream-name . "acnr")))
18424 (build-system r-build-system)
18425 (home-page "https://github.com/mpierrejean/acnr")
18426 (synopsis "Annotated copy-number regions")
18428 "This package provides SNP array data from different types of copy-number
18429 regions. These regions were identified manually by the authors of the package
18430 and may be used to generate realistic data sets with known truth.")
18431 (license license:lgpl2.1+)))
18433 (define-public r-acopula
18440 (uri (cran-uri "acopula" version))
18443 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18444 (properties `((upstream-name . "acopula")))
18445 (build-system r-build-system)
18446 (home-page "https://cran.r-project.org/web/packages/acopula/")
18447 (synopsis "Modelling dependence with multivariate Archimax copulas")
18449 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18450 package provides definitions of several parametric families of generator and
18451 dependence function, computes CDF and PDF, estimates parameters, tests for
18452 goodness of fit, generates random sample and checks copula properties for
18453 custom constructs. In the 2-dimensional case explicit formulas for density
18454 are used, contrary to higher dimensions when all derivatives are linearly
18455 approximated. Several non-archimax families (normal, FGM, Plackett) are
18456 provided as well.")
18457 (license license:gpl2)))
18459 (define-public r-tuner
18466 (uri (cran-uri "tuneR" version))
18469 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18470 (properties `((upstream-name . "tuneR")))
18471 (build-system r-build-system)
18472 (propagated-inputs `(("r-signal" ,r-signal)))
18473 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18474 (synopsis "Analysis of music and speech")
18476 "This is a package for the analysis of music and speech. Analyze music
18477 and speech, extract features like MFCCs, handle wave files and their
18478 representation in various ways, read MP3, read MIDI, perform steps of a
18479 transcription, ...")
18480 ;; Either of these versions.
18481 (license (list license:gpl2 license:gpl3))))
18483 (define-public r-seewave
18490 (uri (cran-uri "seewave" version))
18493 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18494 (properties `((upstream-name . "seewave")))
18495 (build-system r-build-system)
18497 `(("libsndfile" ,libsndfile)))
18499 `(("r-tuner" ,r-tuner)))
18500 (home-page "http://rug.mnhn.fr/seewave")
18501 (synopsis "Sound analysis and synthesis")
18503 "This package provides functions for analysing, manipulating, displaying,
18504 editing and synthesizing time waves (particularly sound). This package
18505 processes time analysis (oscillograms and envelopes), spectral content,
18506 resonance quality factor, entropy, cross correlation and autocorrelation,
18507 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18508 and 3D spectrograms and many other analyses.")
18509 (license license:gpl2+)))
18511 (define-public r-acousticndlcoder
18513 (name "r-acousticndlcoder")
18518 (uri (cran-uri "AcousticNDLCodeR" version))
18521 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18523 `((upstream-name . "AcousticNDLCodeR")))
18524 (build-system r-build-system)
18526 `(("r-seewave" ,r-seewave)
18527 ("r-tuner" ,r-tuner)
18529 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18530 (synopsis "Coding sound files for use with NDL")
18532 "Make acoustic cues to use with the R package @code{ndl}.
18533 The package implements functions used in the PLoS ONE paper \"Words from
18534 spontaneous conversational speech can be recognized with human-like accuracy
18535 by an error-driven learning algorithm that discriminates between meanings
18536 straight from smart acoustic features, bypassing the phoneme as recognition
18537 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18538 (license license:gpl2+)))
18540 (define-public r-acp
18547 (uri (cran-uri "acp" version))
18550 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18551 (properties `((upstream-name . "acp")))
18552 (build-system r-build-system)
18554 `(("r-quantmod" ,r-quantmod)
18555 ("r-tseries" ,r-tseries)))
18556 (home-page "https://cran.r-project.org/web/packages/acp/")
18557 (synopsis "Autoregressive conditional Poisson")
18559 "This package supports the analysis of count data exhibiting
18560 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18561 model (ACP(p,q)) proposed by Heinen (2003).")
18562 (license license:gpl2)))
18564 (define-public r-ada
18571 (uri (cran-uri "ada" version))
18574 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18575 (properties `((upstream-name . "ada")))
18576 (build-system r-build-system)
18577 (propagated-inputs `(("r-rpart" ,r-rpart)))
18578 (home-page "https://cran.r-project.org/web/packages/ada/")
18579 (synopsis "Stochastic boosting")
18581 "This package provides a straightforward, well-documented, and broad
18582 boosting routine for classification, ideally suited for small to
18583 moderate-sized data sets. It performs discrete, real, and gentle boost under
18584 both exponential and logistic loss on a given data set.")
18585 ;; Any version of the GPL.
18586 (license (list license:gpl2+ license:gpl3+))))
18588 (define-public r-genalg
18595 (uri (cran-uri "genalg" version))
18598 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18599 (properties `((upstream-name . "genalg")))
18600 (build-system r-build-system)
18601 (home-page "https://github.com/egonw/genalg")
18602 (synopsis "R based genetic algorithm")
18604 "This package provides an R based genetic algorithm for binary and
18605 floating point chromosomes.")
18606 (license license:gpl2)))
18608 (define-public r-kernelfactory
18610 (name "r-kernelfactory")
18615 (uri (cran-uri "kernelFactory" version))
18618 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18619 (properties `((upstream-name . "kernelFactory")))
18620 (build-system r-build-system)
18623 ("r-genalg" ,r-genalg)
18624 ("r-kernlab" ,r-kernlab)
18625 ("r-randomforest" ,r-randomforest)))
18626 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18627 (synopsis "Ensemble of kernel machines")
18629 "Kernel factory is an ensemble method where each base classifier (random
18630 forest) is fit on the kernel matrix of a subset of the training data.")
18631 (license license:gpl2+)))
18633 (define-public r-dummies
18640 (uri (cran-uri "dummies" version))
18643 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18644 (properties `((upstream-name . "dummies")))
18645 (build-system r-build-system)
18646 (home-page "https://decisionpatterns.com")
18647 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18649 "This package lets you expand factors, characters and other eligible
18650 classes into dummy/indicator variables.")
18651 (license license:gpl2+)))
18653 (define-public r-acrm
18660 (uri (cran-uri "aCRM" version))
18663 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18664 (properties `((upstream-name . "aCRM")))
18665 (build-system r-build-system)
18668 ("r-dummies" ,r-dummies)
18669 ("r-kernelfactory" ,r-kernelfactory)
18670 ("r-randomforest" ,r-randomforest)))
18671 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18672 (synopsis "Convenience functions for analytical customer relationship management")
18674 "This package provides convenience functions for data preparation and
18675 modeling often used in @dfn{analytical customer relationship
18676 management} (aCRM).")
18677 (license license:gpl2+)))
18679 (define-public r-treeclust
18681 (name "r-treeclust")
18686 (uri (cran-uri "treeClust" version))
18689 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18690 (properties `((upstream-name . "treeClust")))
18691 (build-system r-build-system)
18693 `(("r-cluster" ,r-cluster)
18694 ("r-rpart" ,r-rpart)))
18695 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18696 (synopsis "Cluster distances through trees")
18698 "This package provides tools to create a measure of inter-point
18699 dissimilarity useful for clustering mixed data, and, optionally, perform the
18701 (license license:gpl2+)))
18703 (define-public r-acrosstic
18705 (name "r-acrosstic")
18710 (uri (cran-uri "AcrossTic" version))
18713 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18714 (properties `((upstream-name . "AcrossTic")))
18715 (build-system r-build-system)
18717 `(("r-lpsolve" ,r-lpsolve)
18718 ("r-treeclust" ,r-treeclust)))
18719 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18720 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18722 "This is a package for constructing minimum-cost regular spanning
18723 subgraph as part of a non-parametric two-sample test for equality of
18725 (license license:gpl2+)))
18727 (define-public r-acrt
18734 (uri (cran-uri "acrt" version))
18737 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18738 (properties `((upstream-name . "acrt")))
18739 (build-system r-build-system)
18741 `(("r-rcpp" ,r-rcpp)
18742 ("r-rcppeigen" ,r-rcppeigen)
18743 ("r-sandwich" ,r-sandwich)))
18744 (home-page "https://cran.r-project.org/web/packages/acrt/")
18745 (synopsis "Autocorrelation robust testing")
18747 "This package provides functions for testing affine hypotheses on the
18748 regression coefficient vector in regression models with autocorrelated
18750 (license license:gpl2)))
18752 (define-public r-acs
18759 (uri (cran-uri "acs" version))
18762 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18763 (properties `((upstream-name . "acs")))
18764 (build-system r-build-system)
18766 `(("r-httr" ,r-httr)
18769 ("r-stringr" ,r-stringr)
18771 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18772 (synopsis "Work with data from the US Census")
18774 "This package provides a general toolkit for downloading, managing,
18775 analyzing, and presenting data from the
18776 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18777 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18778 American Community Survey (ACS). Confidence intervals provided with ACS data
18779 are converted to standard errors to be bundled with estimates in complex
18780 @code{acs} objects. The package provides new methods to conduct standard
18781 operations on @code{acs} objects and present/plot data in statistically
18782 appropriate ways.")
18783 (license license:gpl3)))
18785 (define-public r-acss-data
18787 (name "r-acss-data")
18792 (uri (cran-uri "acss.data" version))
18795 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18796 (properties `((upstream-name . "acss.data")))
18797 (build-system r-build-system)
18798 (home-page "http://complexitycalculator.com/methodology.html")
18799 (synopsis "Data for algorithmic complexity of short strings")
18801 "This is a data only package providing the algorithmic complexity of
18802 short strings, computed using the coding theorem method. For a given set of
18803 symbols in a string, all possible or a large number of random samples of
18804 Turing machines with a given number of states (e.g., 5) and number of symbols
18805 corresponding to the number of symbols in the strings were simulated until
18806 they reached a halting state or failed to end. This package contains data on
18807 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18808 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18809 distribution of the halting states.")
18810 (license license:gpl2+)))
18812 (define-public r-acss
18819 (uri (cran-uri "acss" version))
18822 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18823 (properties `((upstream-name . "acss")))
18824 (build-system r-build-system)
18826 `(("r-acss-data" ,r-acss-data)
18828 (home-page "http://complexitycalculator.com/methodology.html")
18829 (synopsis "Algorithmic complexity for short strings")
18831 "The main purpose of this package is to provide the algorithmic
18832 complexity for short strings, an approximation of the Kolmogorov Complexity of
18833 a short string using the coding theorem method. While the database containing
18834 the complexity is provided in the data only package @code{acss.data}, this
18835 package provides functions accessing the data such as @code{prob_random}
18836 returning the posterior probability that a given string was produced by a
18837 random process. In addition, two traditional (but problematic) measures of
18838 complexity are also provided: entropy and change complexity.")
18839 (license license:gpl2+)))
18841 (define-public r-acswr
18848 (uri (cran-uri "ACSWR" version))
18851 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18852 (properties `((upstream-name . "ACSWR")))
18853 (build-system r-build-system)
18855 `(("r-mass" ,r-mass)))
18856 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18857 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18859 "This is a companion package for the book \"A Course in Statistics with
18860 R\" (ISBN 978-1-119-15272-9.)")
18861 (license license:gpl2)))
18863 (define-public r-alabama
18866 (version "2015.3-1")
18870 (uri (cran-uri "alabama" version))
18873 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18874 (properties `((upstream-name . "alabama")))
18875 (build-system r-build-system)
18876 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18877 (home-page "https://cran.r-project.org/web/packages/alabama/")
18878 (synopsis "Constrained nonlinear optimization")
18880 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18881 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18882 constraints. Linear or nonlinear equality and inequality constraints are
18884 (license license:gpl2+)))
18886 (define-public r-gdina
18893 (uri (cran-uri "GDINA" version))
18896 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18897 (properties `((upstream-name . "GDINA")))
18898 (build-system r-build-system)
18900 `(("r-alabama" ,r-alabama)
18901 ("r-ggplot2" ,r-ggplot2)
18903 ("r-nloptr" ,r-nloptr)
18904 ("r-numderiv" ,r-numderiv)
18906 ("r-rcpparmadillo" ,r-rcpparmadillo)
18907 ("r-rsolnp" ,r-rsolnp)
18908 ("r-shiny" ,r-shiny)
18909 ("r-shinydashboard" ,r-shinydashboard)))
18911 `(("r-knitr" ,r-knitr)))
18912 (home-page "https://github.com/Wenchao-Ma/GDINA")
18913 (synopsis "Generalized DINA model framework")
18915 "This package provides a set of psychometric tools for cognitive
18916 diagnosis modeling based on the generalized deterministic inputs, noisy and
18917 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18918 and its extensions, including the sequential G-DINA model by Ma and de la
18919 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18920 polytomous G-DINA model by Chen and de la Torre
18921 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18922 distribution can be independent, saturated, higher-order, loglinear smoothed
18923 or structured. Q-matrix validation, item and model fit statistics, model
18924 comparison at test and item level and differential item functioning can also
18925 be conducted. A graphical user interface is also provided.")
18926 (license license:gpl3)))
18928 (define-public r-actcd
18935 (uri (cran-uri "ACTCD" version))
18938 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18939 (properties `((upstream-name . "ACTCD")))
18940 (build-system r-build-system)
18942 `(("r-gdina" ,r-gdina)
18943 ("r-r-methodss3" ,r-r-methodss3)))
18945 `(("gfortran" ,gfortran)))
18946 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18947 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18949 "This is a package supporting cluster analysis for cognitive diagnosis
18950 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18951 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18952 sum-scores, cluster analysis techniques can be used to classify examinees into
18953 latent classes based on their attribute patterns. In addition to the
18954 algorithms used to classify data, three labeling approaches are proposed to
18955 label clusters so that examinees' attribute profiles can be obtained.")
18956 (license license:gpl2+)))
18958 (define-public r-ineq
18965 (uri (cran-uri "ineq" version))
18968 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18969 (properties `((upstream-name . "ineq")))
18970 (build-system r-build-system)
18971 (home-page "https://cran.r-project.org/web/packages/ineq/")
18972 (synopsis "Measuring inequality, concentration, and poverty")
18974 "This package provides tools for measuring inequality, concentration, and
18975 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18976 ;; Either of these two versions.
18977 (license (list license:gpl2 license:gpl3))))
18979 (define-public r-actfrag
18986 (uri (cran-uri "ActFrag" version))
18989 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18990 (properties `((upstream-name . "ActFrag")))
18991 (build-system r-build-system)
18993 `(("r-accelerometry" ,r-accelerometry)
18994 ("r-dplyr" ,r-dplyr)
18996 ("r-survival" ,r-survival)
18997 ("r-tidyr" ,r-tidyr)))
18998 (home-page "https://github.com/junruidi/ActFrag")
18999 (synopsis "Activity fragmentation metrics extraction")
19001 "This package provides functions to extract commonly used fragmentation
19002 metrics to quantify time accumulation strategies based on minute level
19003 actigraphy-measured activity counts data.")
19004 (license license:gpl3)))
19006 (define-public r-fda
19009 (version "5.1.5.1")
19013 (uri (cran-uri "fda" version))
19016 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
19017 (properties `((upstream-name . "fda")))
19018 (build-system r-build-system)
19020 `(("r-matrix" ,r-matrix)))
19021 (home-page "https://www.functionaldata.org")
19022 (synopsis "Functional data analysis")
19024 "These functions were developed to support functional data analysis as
19025 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
19026 Analysis. The package includes data sets and script files working many
19028 (license license:gpl2+)))
19030 (define-public r-actigraphy
19032 (name "r-actigraphy")
19037 (uri (cran-uri "Actigraphy" version))
19040 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
19041 (properties `((upstream-name . "Actigraphy")))
19042 (build-system r-build-system)
19044 `(("r-fda" ,r-fda)))
19045 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
19046 (synopsis "Actigraphy data analysis")
19048 "This package provides tools for functional linear modeling and analysis
19049 of actigraphy data.")
19050 (license license:asl2.0)))
19052 (define-public r-activedriver
19054 (name "r-activedriver")
19059 (uri (cran-uri "ActiveDriver" version))
19062 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
19063 (properties `((upstream-name . "ActiveDriver")))
19064 (build-system r-build-system)
19066 `(("r-mass" ,r-mass)))
19067 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
19068 (synopsis "Tools for finding cancer driver proteins")
19070 "This package provides a mutation analysis tool that discovers cancer
19071 driver genes with frequent mutations in protein signalling sites such as
19072 post-translational modifications (phosphorylation, ubiquitination, etc). The
19073 Poisson generalized linear regression model identifies genes where cancer
19074 mutations in signalling sites are more frequent than expected from the
19075 sequence of the entire gene. Integration of mutations with signalling
19076 information helps find new driver genes and propose candidate mechanisms to
19078 (license license:gpl2+)))
19080 (define-public r-activitycounts
19082 (name "r-activitycounts")
19087 (uri (cran-uri "activityCounts" version))
19090 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
19092 `((upstream-name . "activityCounts")))
19093 (build-system r-build-system)
19095 `(("r-lubridate" ,r-lubridate)
19096 ("r-magrittr" ,r-magrittr)
19097 ("r-seewave" ,r-seewave)
19098 ("r-signal" ,r-signal)
19099 ("r-tibble" ,r-tibble)))
19100 (home-page "https://github.com/walkabillylab/activityCounts")
19101 (synopsis "Generate ActiLife counts")
19103 "ActiLife generates activity counts from data collected by Actigraph
19104 accelerometers. Actigraph is one of the most common research-grade
19105 accelerometers. There is considerable research validating and developing
19106 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
19107 counts are proprietary and difficult to implement if researchers use different
19108 accelerometer brands. The code creates ActiLife counts from raw acceleration
19109 data for different accelerometer brands.")
19110 (license license:gpl3)))
19112 (define-public r-activityindex
19114 (name "r-activityindex")
19119 (uri (cran-uri "ActivityIndex" version))
19122 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
19123 (properties `((upstream-name . "ActivityIndex")))
19124 (build-system r-build-system)
19126 `(("r-data-table" ,r-data-table)
19127 ("r-matrixstats" ,r-matrixstats)
19128 ("r-r-utils" ,r-r-utils)))
19129 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
19130 (synopsis "Activity Index calculation using raw accelerometry data")
19132 "This is a package to read raw accelerometry from GT3X+ accelerometry
19133 data and plain table data to calculate the Activity Index from Bai et
19134 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
19135 (license license:gpl3)))
19137 (define-public r-activpal
19139 (name "r-activpal")
19144 (uri (cran-uri "activPAL" version))
19147 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
19148 (properties `((upstream-name . "activPAL")))
19149 (build-system r-build-system)
19151 `(("r-devtools" ,r-devtools)
19152 ("r-dplyr" ,r-dplyr)
19153 ("r-ggplot2" ,r-ggplot2)
19154 ("r-lubridate" ,r-lubridate)
19155 ("r-magrittr" ,r-magrittr)
19156 ("r-tidyr" ,r-tidyr)))
19157 (home-page "https://cran.r-project.org/web/packages/activPAL")
19158 (synopsis "Processing and chart generation from activPAL events files")
19160 "This package contains functions to generate pre-defined summary
19161 statistics from activPAL events files. The package also contains functions to
19162 produce informative graphics that visualize physical activity behaviour and
19163 trends. This includes generating graphs that align physical activity
19164 behaviour with additional time based observations described by other data
19165 sets, such as sleep diaries and continuous glucose monitoring data.")
19166 (license license:gpl3)))
19168 (define-public r-activpalprocessing
19170 (name "r-activpalprocessing")
19175 (uri (cran-uri "activpalProcessing" version))
19178 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
19180 `((upstream-name . "activpalProcessing")))
19181 (build-system r-build-system)
19183 `(("r-chron" ,r-chron)))
19184 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
19185 (synopsis "Process activPAL events files")
19187 "This package performs estimation of physical activity and sedentary
19188 behavior variables from activPAL events files.")
19189 ;; Either version of the GPL.
19190 (license (list license:gpl2 license:gpl3))))
19192 (define-public r-actogrammr
19194 (name "r-actogrammr")
19199 (uri (cran-uri "actogrammr" version))
19202 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19203 (properties `((upstream-name . "actogrammr")))
19204 (build-system r-build-system)
19206 `(("r-dplyr" ,r-dplyr)
19207 ("r-ggplot2" ,r-ggplot2)
19208 ("r-lubridate" ,r-lubridate)
19209 ("r-readr" ,r-readr)
19210 ("r-tidyr" ,r-tidyr)))
19211 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19212 (synopsis "Read in activity data and plot actograms")
19214 "Read in activity measurements from standard file formats used by
19215 circadian rhythm researchers, currently only ClockLab format, and process and
19216 plot the data. The central type of plot is the actogram, as first described
19217 in \"Activity and distribution of certain wild mice in relation to biotic
19218 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19219 (license license:gpl3)))
19221 (define-public r-expint
19228 (uri (cran-uri "expint" version))
19231 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19232 (properties `((upstream-name . "expint")))
19233 (build-system r-build-system)
19234 (home-page "https://gitlab.com/vigou3/expint")
19235 (synopsis "Exponential integral and incomplete Gamma function")
19237 "This package provides the exponential integrals @code{E_1(x)},
19238 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19239 function @code{G(a, x)} defined for negative values of its first argument.
19240 The package also gives easy access to the underlying C routines through an
19241 API; see the package vignette for details.")
19242 (license license:gpl2+)))
19244 (define-public r-actuar
19251 (uri (cran-uri "actuar" version))
19254 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19255 (properties `((upstream-name . "actuar")))
19256 (build-system r-build-system)
19257 (propagated-inputs `(("r-expint" ,r-expint)))
19258 (home-page "https://gitlab.com/vigou3/actuar")
19259 (synopsis "Actuarial functions and heavy tailed distributions")
19261 "This package provides functions and data sets for actuarial science:
19262 modeling of loss distributions; risk theory and ruin theory; simulation of
19263 compound models, discrete mixtures and compound hierarchical models;
19264 credibility theory. It boasts support for many additional probability
19265 distributions to model insurance loss amounts and loss frequency: 19
19266 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19267 distribution; zero-truncated and zero-modified extensions of the standard
19268 discrete distributions. It also supports phase-type distributions commonly
19269 used to compute ruin probabilities.")
19270 (license license:gpl2+)))
19272 (define-public r-bmp
19279 (uri (cran-uri "bmp" version))
19282 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19283 (properties `((upstream-name . "bmp")))
19284 (build-system r-build-system)
19285 (home-page "https://cran.r-project.org/web/packages/bmp/")
19286 (synopsis "Read Bitmap (BMP) images")
19288 "This package provides pure R tools to read BMP format images. It is
19289 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19290 (license license:gpl2+)))
19292 (define-public r-readbitmap
19294 (name "r-readbitmap")
19299 (uri (cran-uri "readbitmap" version))
19302 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19303 (properties `((upstream-name . "readbitmap")))
19304 (build-system r-build-system)
19306 `(("libjpeg" ,libjpeg-turbo)
19307 ("libpng" ,libpng)))
19312 ("r-tiff" ,r-tiff)))
19313 (home-page "https://github.com/jefferis/readbitmap")
19314 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19316 "This package provides tools to identify and read BMP, JPEG, PNG, and
19317 TIFF format bitmap images. Identification defaults to the use of the magic
19318 number embedded in the file rather than the file extension.")
19319 (license license:gpl2+)))
19321 (define-public r-imager
19328 (uri (cran-uri "imager" version))
19331 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19332 (properties `((upstream-name . "imager")))
19333 (build-system r-build-system)
19336 ("libtiff" ,libtiff)
19340 `(("r-downloader" ,r-downloader)
19341 ("r-igraph" ,r-igraph)
19343 ("r-magrittr" ,r-magrittr)
19345 ("r-purrr" ,r-purrr)
19347 ("r-readbitmap" ,r-readbitmap)
19348 ("r-stringr" ,r-stringr)))
19350 `(("pkg-config" ,pkg-config)
19351 ("r-knitr" ,r-knitr)))
19352 (home-page "https://dahtah.github.io/imager/")
19353 (synopsis "Image processing library")
19355 "This is a package for fast image processing for images in up to 4
19356 dimensions (two spatial dimensions, one time/depth dimension, one color
19357 dimension). It provides most traditional image processing tools (filtering,
19358 morphology, transformations, etc.) as well as various functions for easily
19359 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19360 simple, modern C++ library for image processing.")
19361 (license license:lgpl3)))
19363 (define-public r-acuityview
19365 (name "r-acuityview")
19370 (uri (cran-uri "AcuityView" version))
19373 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19374 (properties `((upstream-name . "AcuityView")))
19375 (build-system r-build-system)
19377 `(("r-fftwtools" ,r-fftwtools)
19378 ("r-imager" ,r-imager)
19379 ("r-plotrix" ,r-plotrix)))
19380 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19381 (synopsis "Display scenes as seen by an animal with less acute vision")
19383 "This package provides a simple method for representing a visual scene as
19384 it may be seen by an animal with less acute vision.")
19385 (license license:gpl2+)))
19387 (define-public r-caret
19394 (uri (cran-uri "caret" version))
19397 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19398 (build-system r-build-system)
19400 `(("r-foreach" ,r-foreach)
19401 ("r-ggplot2" ,r-ggplot2)
19402 ("r-lattice" ,r-lattice)
19403 ("r-modelmetrics" ,r-modelmetrics)
19407 ("r-recipes" ,r-recipes)
19408 ("r-reshape2" ,r-reshape2)
19409 ("r-withr" ,r-withr)))
19411 `(("r-knitr" ,r-knitr)))
19412 (home-page "https://github.com/topepo/caret")
19413 (synopsis "Classification and regression training")
19415 "This package provides miscellaneous functions for training and plotting
19416 classification and regression models.")
19417 (license license:gpl2+)))
19419 (define-public r-adabag
19426 (uri (cran-uri "adabag" version))
19429 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19430 (properties `((upstream-name . "adabag")))
19431 (build-system r-build-system)
19433 `(("r-caret" ,r-caret)
19434 ("r-doparallel" ,r-doparallel)
19435 ("r-foreach" ,r-foreach)
19436 ("r-rpart" ,r-rpart)))
19437 (home-page "https://cran.r-project.org/web/packages/adabag/")
19438 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19440 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19441 Breiman's Bagging algorithm using classification trees as individual
19442 classifiers. Once these classifiers have been trained, they can be used to
19443 predict on new data. Also, cross validation estimation of the error can be
19445 (license license:gpl2+)))
19447 (define-public r-adagio
19454 (uri (cran-uri "adagio" version))
19457 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19458 (properties `((upstream-name . "adagio")))
19459 (build-system r-build-system)
19460 (native-inputs `(("gfortran" ,gfortran)))
19461 (home-page "https://cran.r-project.org/web/packages/adagio/")
19462 (synopsis "Discrete and global optimization routines")
19464 "This package provides methods and algorithms for discrete optimization,
19465 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19466 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19468 (license license:gpl3+)))
19470 (define-public r-univoutl
19472 (name "r-univoutl")
19477 (uri (cran-uri "univOutl" version))
19480 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19481 (properties `((upstream-name . "univOutl")))
19482 (build-system r-build-system)
19484 `(("r-hmisc" ,r-hmisc)
19485 ("r-robustbase" ,r-robustbase)))
19486 (home-page "https://github.com/marcellodo/univOutl")
19487 (synopsis "Detection of univariate outliers")
19489 "This package provides well-known outlier detection techniques in the
19490 univariate case. Methods to deal with skewed distribution are included too.
19491 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19492 historical data is implemented as well. When available, survey weights can be
19493 used in outliers detection.")
19494 (license license:gpl2+)))
19496 (define-public r-tolerance
19498 (name "r-tolerance")
19503 (uri (cran-uri "tolerance" version))
19506 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19507 (properties `((upstream-name . "tolerance")))
19508 (build-system r-build-system)
19510 `(("r-mass" ,r-mass)
19512 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19513 (synopsis "Statistical tolerance intervals and regions")
19515 "This package provides functions for estimating tolerance
19516 limits (intervals) for various univariate distributions (binomial, Cauchy,
19517 discrete Pareto, exponential, two-parameter exponential, extreme value,
19518 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19519 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19520 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19521 nonparametric tolerance intervals, tolerance bands for regression
19522 settings (linear regression, nonlinear regression, nonparametric regression,
19523 and multivariate regression), and analysis of variance tolerance intervals.
19524 Visualizations are also available for most of these settings.")
19525 (license license:gpl2+)))
19527 (define-public r-additivitytests
19529 (name "r-additivitytests")
19534 (uri (cran-uri "additivityTests" version))
19537 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19539 `((upstream-name . "additivityTests")))
19540 (build-system r-build-system)
19541 (home-page "https://github.com/simecek/additivityTests")
19542 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19544 "This package provides an implementation of the Tukey, Mandel,
19545 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19546 (license license:gpl3)))
19548 (define-public r-flexclust
19550 (name "r-flexclust")
19555 (uri (cran-uri "flexclust" version))
19558 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19559 (properties `((upstream-name . "flexclust")))
19560 (build-system r-build-system)
19562 `(("r-class" ,r-class)
19563 ("r-lattice" ,r-lattice)
19564 ("r-modeltools" ,r-modeltools)))
19565 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19566 (synopsis "Flexible cluster algorithms")
19568 "The main function @code{kcca} implements a general framework for
19569 k-centroids cluster analysis supporting arbitrary distance measures and
19570 centroid computation. Further cluster methods include hard competitive
19571 learning, neural gas, and QT clustering. There are numerous visualization
19572 methods for cluster results (neighborhood graphs, convex cluster hulls,
19573 barcharts of centroids, ...), and bootstrap methods for the analysis of
19574 cluster stability.")
19575 (license license:gpl2)))
19577 (define-public r-biclust
19584 (uri (cran-uri "biclust" version))
19587 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19588 (properties `((upstream-name . "biclust")))
19589 (build-system r-build-system)
19591 `(("r-additivitytests" ,r-additivitytests)
19592 ("r-colorspace" ,r-colorspace)
19593 ("r-flexclust" ,r-flexclust)
19594 ("r-ggplot2" ,r-ggplot2)
19595 ("r-lattice" ,r-lattice)
19597 ("r-tidyr" ,r-tidyr)))
19598 (home-page "https://cran.r-project.org/web/packages/biclust/")
19599 (synopsis "BiCluster algorithms")
19601 "The main function @code{biclust()} provides several algorithms to find
19602 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19603 In addition, the package provides methods for data
19604 preprocessing (normalization and discretization), visualization, and
19605 validation of bicluster solutions.")
19606 (license license:gpl3)))
19608 (define-public r-icge
19615 (uri (cran-uri "ICGE" version))
19618 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19619 (properties `((upstream-name . "ICGE")))
19620 (build-system r-build-system)
19622 `(("r-cluster" ,r-cluster)
19623 ("r-mass" ,r-mass)))
19624 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19625 (synopsis "Cluster estimation and identification of atypical units")
19627 "ICGE is a package that helps to estimate the number of real clusters in
19628 data as well as to identify atypical units. The underlying methods are based
19629 on distances rather than on unit x variables.")
19630 (license license:gpl2+)))
19632 (define-public r-depth
19635 (version "2.1-1.1")
19639 (uri (cran-uri "depth" version))
19642 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19643 (properties `((upstream-name . "depth")))
19644 (build-system r-build-system)
19646 `(("r-abind" ,r-abind)
19647 ("r-circular" ,r-circular)
19650 `(("gfortran" ,gfortran)))
19651 (home-page "https://cran.r-project.org/web/packages/depth/")
19652 (synopsis "Nonparametric depth functions for multivariate analysis")
19654 "This package provides tools for depth functions methodology applied to
19655 multivariate analysis. Besides allowing calculation of depth values and
19656 depth-based location estimators, the package includes functions or drawing
19657 contour plots and perspective plots of depth functions. Euclidian and
19658 spherical depths are supported.")
19659 (license license:gpl2)))
19661 (define-public r-archetypes
19663 (name "r-archetypes")
19664 (version "2.2-0.1")
19668 (uri (cran-uri "archetypes" version))
19671 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19672 (properties `((upstream-name . "archetypes")))
19673 (build-system r-build-system)
19675 `(("r-modeltools" ,r-modeltools)
19676 ("r-nnls" ,r-nnls)))
19677 (home-page "https://cran.r-project.org/web/packages/archetypes")
19678 (synopsis "Archetypal analysis")
19680 "The main function @code{archetypes} implements a framework for
19681 archetypal analysis supporting arbitrary problem solving mechanisms for the
19682 different conceptual parts of the algorithm.")
19683 (license license:gpl2+)))
19685 (define-public r-shapes
19692 (uri (cran-uri "shapes" version))
19695 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19696 (properties `((upstream-name . "shapes")))
19697 (build-system r-build-system)
19699 `(("r-mass" ,r-mass)
19700 ("r-minpack-lm" ,r-minpack-lm)
19702 ("r-scatterplot3d" ,r-scatterplot3d)))
19703 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19704 (synopsis "Statistical shape analysis")
19706 "This package provides routines for the statistical analysis of landmark
19707 shapes, including Procrustes analysis, graphical displays, principal
19708 components analysis, permutation and bootstrap tests, thin-plate spline
19709 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19710 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19711 Edition), John Wiley and Sons.")
19712 (license license:gpl2)))
19714 (define-public r-anthropometry
19716 (name "r-anthropometry")
19721 (uri (cran-uri "Anthropometry" version))
19724 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19725 (properties `((upstream-name . "Anthropometry")))
19726 (build-system r-build-system)
19728 `(("r-archetypes" ,r-archetypes)
19729 ("r-biclust" ,r-biclust)
19730 ("r-cluster" ,r-cluster)
19731 ("r-depth" ,r-depth)
19736 ("r-shapes" ,r-shapes)))
19738 `(("r-knitr" ,r-knitr)))
19739 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19740 (synopsis "Statistical methods for anthropometric data")
19742 "This package provides statistical methods especially developed to
19743 analyze anthropometric data. These methods are aimed at providing effective
19744 solutions to some commons problems related to Ergonomics and Anthropometry.
19745 They are based on clustering, the statistical concept of data depth,
19746 statistical shape analysis and archetypal analysis.")
19747 (license license:gpl2+)))
19749 (define-public r-adamethods
19751 (name "r-adamethods")
19756 (uri (cran-uri "adamethods" version))
19759 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19760 (properties `((upstream-name . "adamethods")))
19761 (build-system r-build-system)
19763 `(("r-anthropometry" ,r-anthropometry)
19764 ("r-archetypes" ,r-archetypes)
19766 ("r-foreach" ,r-foreach)
19768 ("r-tolerance" ,r-tolerance)
19769 ("r-univoutl" ,r-univoutl)))
19770 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19771 (synopsis "Archetypoid algorithms and anomaly detection")
19773 "This package is a collection of several algorithms to obtain
19774 archetypoids with small and large databases and with both classical
19775 multivariate data and functional data (univariate and multivariate). Some of
19776 these algorithms also allow to detect anomalies (outliers).")
19777 (license license:gpl2+)))
19779 (define-public r-idpmisc
19786 (uri (cran-uri "IDPmisc" version))
19789 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19790 (properties `((upstream-name . "IDPmisc")))
19791 (build-system r-build-system)
19793 `(("r-lattice" ,r-lattice)))
19794 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19795 (synopsis "Functions for data analyses and visualization")
19797 "This package provides different high-level graphics functions for
19798 displaying large datasets, displaying circular data in a very flexible way,
19799 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19800 2D-plots, creating figures with differently colored margin and plot region.
19801 In addition, the package contains auxiliary functions for data manipulation
19802 like omitting observations with irregular values or selecting data by logical
19803 vectors, which include NAs. Other functions are especially useful in
19804 spectroscopy and analyses of environmental data: robust baseline fitting,
19805 finding peaks in spectra, converting humidity measures.")
19806 (license license:gpl3+)))
19808 (define-public r-qqman
19815 (uri (cran-uri "qqman" version))
19818 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19819 (properties `((upstream-name . "qqman")))
19820 (build-system r-build-system)
19822 `(("r-calibrate" ,r-calibrate)))
19823 (home-page "https://cran.r-project.org/web/packages/qqman/")
19824 (synopsis "Q-Q and Manhattan plots for GWAS data")
19826 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19827 from PLINK results.")
19828 (license license:gpl3)))
19830 (define-public r-ggplot-multistats
19832 (name "r-ggplot-multistats")
19837 (uri (cran-uri "ggplot.multistats" version))
19840 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19842 `((upstream-name . "ggplot.multistats")))
19843 (build-system r-build-system)
19845 `(("r-ggplot2" ,r-ggplot2)
19846 ("r-hexbin" ,r-hexbin)
19847 ("r-rlang" ,r-rlang)
19848 ("r-scales" ,r-scales)))
19849 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19850 (synopsis "Multiple summary statistics for binned stats/geometries")
19852 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19853 which functions similar to its singular form, but allows the use of multiple
19854 statistics per bin. Those statistics can be mapped to multiple bin
19856 (license license:gpl3)))
19858 (define-public r-knn-covertree
19860 (name "r-knn-covertree")
19865 (uri (cran-uri "knn.covertree" version))
19868 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19869 (properties `((upstream-name . "knn.covertree")))
19870 (build-system r-build-system)
19872 `(("r-matrix" ,r-matrix)
19874 ("r-rcppeigen" ,r-rcppeigen)))
19875 (home-page "https://github.com/flying-sheep/knn.covertree")
19876 (synopsis "Accurate kNN Implementation with multiple distance measures")
19878 "Similarly to the FNN package, this package allows calculation of the k
19879 nearest neighbors (kNN) of a data matrix. The implementation is based on
19880 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19881 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19882 (license license:agpl3+)))
19884 (define-public r-poibin
19891 (uri (cran-uri "poibin" version))
19894 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19895 (properties `((upstream-name . "poibin")))
19896 (build-system r-build-system)
19897 (home-page "https://cran.r-project.org/web/packages/poibin/")
19898 (synopsis "Poisson binomial distribution")
19900 "This package provides an implementation of both the exact and
19901 approximation methods for computing the @dfn{cumulative distribution
19902 function} (CDF) of the Poisson binomial distribution. It also provides the
19903 @dfn{probability mass function} (PMF), quantile function, and random number
19904 generation for the Poisson binomial distribution.")
19905 (license license:gpl2)))
19907 (define-public r-diagram
19914 (uri (cran-uri "diagram" version))
19917 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19918 (properties `((upstream-name . "diagram")))
19919 (build-system r-build-system)
19921 `(("r-shape" ,r-shape)))
19922 (home-page "https://cran.r-project.org/web/packages/diagram/")
19923 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19925 "This package provides tools to visualize simple graphs (networks) based
19926 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19927 electrical networks, etc. It also includes supporting material for the book
19928 \"A practical guide to ecological modelling - using R as a simulation
19929 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19930 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19931 Francesca Mazzia (2012).")
19932 (license license:gpl2+)))
19934 (define-public r-lim
19941 (uri (cran-uri "LIM" version))
19944 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19945 (properties `((upstream-name . "LIM")))
19946 (build-system r-build-system)
19948 `(("r-diagram" ,r-diagram)
19949 ("r-limsolve" ,r-limsolve)))
19950 (home-page "https://cran.r-project.org/web/packages/LIM/")
19951 (synopsis "Linear inverse model examples and solution methods")
19953 "This package provides functions that read and solve linear inverse
19954 problems (food web problems, linear programming problems).")
19955 (license license:gpl2+)))
19957 (define-public r-shinycssloaders
19959 (name "r-shinycssloaders")
19964 (uri (cran-uri "shinycssloaders" version))
19967 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19969 `((upstream-name . "shinycssloaders")))
19970 (build-system r-build-system)
19972 `(("r-digest" ,r-digest)
19974 ("r-shiny" ,r-shiny)))
19975 (home-page "https://github.com/andrewsali/shinycssloaders")
19976 (synopsis "Add CSS loading animations to Shiny outputs")
19978 "This package provides tools to create a lightweight Shiny wrapper for
19979 the css-loaders created by Luke Hass
19980 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19981 automatically show a loader when the output is (re)calculating.")
19982 (license license:gpl3)))
19984 (define-public r-rsvg
19991 (uri (cran-uri "rsvg" version))
19994 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19995 (properties `((upstream-name . "rsvg")))
19996 (build-system r-build-system)
19998 `(("librsvg" ,librsvg)
20001 `(("pkg-config" ,pkg-config)
20002 ("r-knitr" ,r-knitr)))
20003 (home-page "https://github.com/jeroen/rsvg#readme")
20004 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
20006 "This package allows you to render vector-based SVG images into
20007 high-quality custom-size bitmap arrays using the librsvg2 library. The
20008 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
20009 addition, the package can convert images directly to various formats such as
20010 PDF or PostScript.")
20011 (license license:expat)))
20013 (define-public r-influencer
20015 (name "r-influencer")
20020 (uri (cran-uri "influenceR" version))
20023 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
20024 (properties `((upstream-name . "influenceR")))
20025 (build-system r-build-system)
20027 `(("r-igraph" ,r-igraph)
20028 ("r-matrix" ,r-matrix)))
20029 (home-page "https://github.com/rcc-uchicago/influenceR")
20030 (synopsis "Tools to quantify structural importance of nodes in a network")
20032 "This package provides functionality to compute various node centrality
20033 measures on networks. Included are functions to compute betweenness
20034 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
20035 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
20036 algorithm to identify key players, and Valente's bridging metric. The
20037 betweenness, Key Players, and bridging implementations are parallelized with
20039 (license license:gpl2)))
20041 (define-public r-emplik
20048 (uri (cran-uri "emplik" version))
20051 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
20052 (properties `((upstream-name . "emplik")))
20053 (build-system r-build-system)
20055 `(("r-quantreg" ,r-quantreg)))
20056 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
20057 (synopsis "Empirical likelihood ratio for censored/truncated data")
20059 "This package provides empirical likelihood ratio tests for
20060 means/quantiles/hazards from possibly censored and/or truncated data. It also
20062 (license license:gpl2+)))
20064 (define-public r-imputeyn
20066 (name "r-imputeyn")
20071 (uri (cran-uri "imputeYn" version))
20074 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
20075 (properties `((upstream-name . "imputeYn")))
20076 (build-system r-build-system)
20078 `(("r-boot" ,r-boot)
20079 ("r-emplik" ,r-emplik)
20080 ("r-mvtnorm" ,r-mvtnorm)
20081 ("r-quadprog" ,r-quadprog)
20082 ("r-survival" ,r-survival)))
20083 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
20084 (synopsis "Impute last largest censored observation under weighted least squares")
20086 "This package allows for the imputation of the last largest censored
20087 observantions. This method brings less bias and more efficient estimates for
20089 (license license:gpl2)))
20091 (define-public r-adapenetclass
20093 (name "r-adapenetclass")
20098 (uri (cran-uri "AdapEnetClass" version))
20101 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
20102 (properties `((upstream-name . "AdapEnetClass")))
20103 (build-system r-build-system)
20105 `(("r-glmnet" ,r-glmnet)
20106 ("r-imputeyn" ,r-imputeyn)
20108 ("r-quadprog" ,r-quadprog)))
20109 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
20110 (synopsis "Class of adaptive elastic net methods for censored data")
20112 "This package provides methods for variable selection for AFT models.")
20113 (license license:gpl2)))
20115 (define-public r-flock
20122 (uri (cran-uri "flock" version))
20125 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
20126 (properties `((upstream-name . "flock")))
20127 (build-system r-build-system)
20128 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
20129 (home-page "https://cran.r-project.org/web/packages/flock/")
20130 (synopsis "Process synchronization using file locks")
20132 "This package implements synchronization between R processes (spawned by
20133 using the @code{parallel} package for instance) using file locks. It supports
20134 both exclusive and shared locking.")
20135 (license license:asl2.0)))
20137 (define-public r-archivist
20139 (name "r-archivist")
20144 (uri (cran-uri "archivist" version))
20147 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
20148 (properties `((upstream-name . "archivist")))
20149 (build-system r-build-system)
20152 ("r-digest" ,r-digest)
20153 ("r-flock" ,r-flock)
20155 ("r-lubridate" ,r-lubridate)
20156 ("r-magrittr" ,r-magrittr)
20157 ("r-rcurl" ,r-rcurl)
20158 ("r-rsqlite" ,r-rsqlite)))
20159 (home-page "https://pbiecek.github.io/archivist/")
20160 (synopsis "Tools for storing, restoring and searching for R objects")
20162 "Data exploration and modelling is a process in which a lot of data
20163 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
20164 statistical models, different versions of data sets and different versions of
20165 results. Archivist helps to store and manage artifacts created in R. It
20166 allows you to store selected artifacts as binary files together with their
20167 metadata and relations. Archivist allows sharing artifacts with others. It
20168 can look for already created artifacts by using its class, name, date of the
20169 creation or other properties. It also makes it easy to restore such
20171 (license license:gpl2)))
20173 (define-public r-versions
20175 (name "r-versions")
20180 (uri (cran-uri "versions" version))
20183 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
20184 (properties `((upstream-name . "versions")))
20185 (build-system r-build-system)
20186 (home-page "https://cran.r-project.org/web/packages/versions/")
20187 (synopsis "Query and install specific versions of CRAN packages")
20189 "This package allows you to install specified versions of R packages
20190 hosted on CRAN and provides functions to list available versions and the
20191 versions of currently installed packages.")
20192 (license license:bsd-3)))
20194 (define-public r-adapr
20201 (uri (cran-uri "adapr" version))
20204 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20205 (properties `((upstream-name . "adapr")))
20206 (build-system r-build-system)
20208 `(("r-archivist" ,r-archivist)
20209 ("r-devtools" ,r-devtools)
20210 ("r-digest" ,r-digest)
20211 ("r-doparallel" ,r-doparallel)
20212 ("r-gdata" ,r-gdata)
20213 ("r-ggplot2" ,r-ggplot2)
20214 ("r-git2r" ,r-git2r)
20215 ("r-igraph" ,r-igraph)
20216 ("r-knitr" ,r-knitr)
20217 ("r-plotly" ,r-plotly)
20219 ("r-rmarkdown" ,r-rmarkdown)
20220 ("r-shiny" ,r-shiny)
20221 ("r-shinydashboard" ,r-shinydashboard)
20222 ("r-versions" ,r-versions)))
20223 (home-page "https://cran.r-project.org/web/packages/adapr/")
20224 (synopsis "Implementation of an accountable data analysis process")
20226 "This package tracks reading and writing within R scripts that are
20227 organized into a directed acyclic graph. It contains an interactive Shiny
20228 application @code{adaprApp()}. It uses Git and file hashes to track version
20229 histories of inputs and outputs.")
20230 (license license:lgpl2.0)))
20232 (define-public r-adapsamp
20234 (name "r-adapsamp")
20239 (uri (cran-uri "AdapSamp" version))
20242 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20243 (properties `((upstream-name . "AdapSamp")))
20244 (build-system r-build-system)
20245 (propagated-inputs `(("r-pracma" ,r-pracma)))
20246 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20247 (synopsis "Adaptive sampling algorithms")
20249 "For distributions whose probability density functions are log-concave,
20250 the adaptive rejection sampling algorithm can be used to build envelope
20251 functions for sampling. For others, the modified adaptive rejection sampling
20252 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20253 adaptive slice sampling algorithm can be used. This R package mainly includes
20254 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20255 @code{rASS()}. These functions can realize sampling based on the algorithms
20257 (license license:gpl2)))
20259 (define-public r-adaptalint
20261 (name "r-adaptalint")
20266 (uri (cran-uri "adaptalint" version))
20269 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20270 (properties `((upstream-name . "adaptalint")))
20271 (build-system r-build-system)
20273 `(("r-dplyr" ,r-dplyr)
20274 ("r-lintr" ,r-lintr)
20275 ("r-purrr" ,r-purrr)))
20276 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20277 (synopsis "Check R code style")
20279 "This package provides tools to infer the code style (which style rules
20280 are followed and which ones are not) from one package and use it to check
20281 another. This makes it easier to find and correct the most important problems
20283 (license license:gpl3)))
20285 (define-public r-fracdiff
20287 (name "r-fracdiff")
20292 (uri (cran-uri "fracdiff" version))
20295 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20296 (properties `((upstream-name . "fracdiff")))
20297 (build-system r-build-system)
20298 (home-page "https://github.com/mmaechler/fracdiff")
20300 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20302 "This package provides tools for the maximum likelihood estimation of the
20303 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20304 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20305 (license license:gpl2+)))
20307 (define-public r-forecast
20309 (name "r-forecast")
20314 (uri (cran-uri "forecast" version))
20317 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20318 (properties `((upstream-name . "forecast")))
20319 (build-system r-build-system)
20321 `(("r-colorspace" ,r-colorspace)
20322 ("r-fracdiff" ,r-fracdiff)
20323 ("r-ggplot2" ,r-ggplot2)
20324 ("r-lmtest" ,r-lmtest)
20325 ("r-magrittr" ,r-magrittr)
20328 ("r-rcpparmadillo" ,r-rcpparmadillo)
20329 ("r-timedate" ,r-timedate)
20330 ("r-tseries" ,r-tseries)
20334 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20335 (home-page "https://pkg.robjhyndman.com/forecast/")
20336 (synopsis "Forecasting functions for time series and linear models")
20338 "This package provides methods and tools for displaying and analysing
20339 univariate time series forecasts including exponential smoothing via state
20340 space models and automatic ARIMA modelling.")
20341 (license license:gpl3)))
20343 (define-public r-xmisc
20350 (uri (cran-uri "Xmisc" version))
20353 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20354 (properties `((upstream-name . "Xmisc")))
20355 (build-system r-build-system)
20356 (home-page "https://cran.r-project.org/package=Xmisc")
20358 "Xiaobei's miscellaneous classes and functions")
20360 "This package provides Xiaobei's miscellaneous classes and functions,
20361 which are useful when developing R packages for @dfn{object oriented
20362 programming} (OOP) using R Reference Class.")
20363 (license license:gpl2+)))
20365 (define-public r-proxyc
20372 (uri (cran-uri "proxyC" version))
20375 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20376 (properties `((upstream-name . "proxyC")))
20377 (build-system r-build-system)
20379 `(("r-matrix" ,r-matrix)
20381 ("r-rcpparmadillo" ,r-rcpparmadillo)
20382 ("r-rcppparallel" ,r-rcppparallel)))
20383 (home-page "https://cran.r-project.org/package=proxyC")
20384 (synopsis "Compute proximity in large sparse matrices")
20386 "This package provides efficient tools to compute the proximity between
20387 rows or columns of large matrices. Functions are optimised for large sparse
20388 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20389 similarity/distance measures, computation of correlation, cosine similarity
20390 and Euclidean distance is particularly fast.")
20391 (license license:gpl3)))
20393 (define-public r-isocodes
20395 (name "r-isocodes")
20396 (version "2020.03.16")
20400 (uri (cran-uri "ISOcodes" version))
20403 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20404 (properties `((upstream-name . "ISOcodes")))
20405 (build-system r-build-system)
20406 (home-page "https://cran.r-project.org/package=ISOcodes")
20407 (synopsis "Selected ISO codes")
20409 "This package provides ISO language, territory, currency, script and
20410 character codes. It provides ISO 639 language codes, ISO 3166 territory
20411 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20412 character codes as well as the UN M.49 area codes.")
20413 (license license:gpl2)))
20415 (define-public r-stopwords
20417 (name "r-stopwords")
20422 (uri (cran-uri "stopwords" version))
20425 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20426 (properties `((upstream-name . "stopwords")))
20427 (build-system r-build-system)
20429 `(("r-desc" ,r-desc)
20430 ("r-isocodes" ,r-isocodes)
20431 ("r-usethis" ,r-usethis)))
20432 (home-page "https://github.com/quanteda/stopwords")
20433 (synopsis "Multilingual stopword lists")
20435 "This package provides multiple sources of stopwords, for use in text
20436 analysis and natural language processing.")
20437 (license license:expat)))
20439 (define-public r-spacyr
20446 (uri (cran-uri "spacyr" version))
20449 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20450 (properties `((upstream-name . "spacyr")))
20451 (build-system r-build-system)
20453 `(("r-data-table" ,r-data-table)
20454 ("r-reticulate" ,r-reticulate)))
20455 (home-page "https://spacyr.quanteda.io")
20456 (synopsis "R wrapper for the spaCy NLP library")
20458 "This package provides an R wrapper to the Python @dfn{natural language
20459 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20460 (license license:gpl3)))
20462 (define-public r-snowballc
20464 (name "r-snowballc")
20469 (uri (cran-uri "SnowballC" version))
20472 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20473 (properties `((upstream-name . "SnowballC")))
20474 (build-system r-build-system)
20475 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20476 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20478 "This package provides an R interface to the C @code{libstemmer} library
20479 that implements Porter's word stemming algorithm for collapsing words to a
20480 common root to aid comparison of vocabulary. Currently supported languages
20481 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20482 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20483 (license license:bsd-3)))
20485 (define-public r-quanteda
20487 (name "r-quanteda")
20492 (uri (cran-uri "quanteda" version))
20495 "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8"))))
20496 (properties `((upstream-name . "quanteda")))
20497 (build-system r-build-system)
20499 `(("r-data-table" ,r-data-table)
20500 ("r-digest" ,r-digest)
20501 ("r-extrafont" ,r-extrafont)
20502 ("r-fastmatch" ,r-fastmatch)
20503 ("r-ggplot2" ,r-ggplot2)
20504 ("r-ggrepel" ,r-ggrepel)
20505 ("r-jsonlite" ,r-jsonlite)
20506 ("r-magrittr" ,r-magrittr)
20507 ("r-matrix" ,r-matrix)
20508 ("r-network" ,r-network)
20509 ("r-proxyc" ,r-proxyc)
20511 ("r-rcpparmadillo" ,r-rcpparmadillo)
20512 ("r-rcppparallel" ,r-rcppparallel)
20514 ("r-snowballc" ,r-snowballc)
20515 ("r-stopwords" ,r-stopwords)
20516 ("r-stringi" ,r-stringi)
20518 ("r-yaml" ,r-yaml)))
20520 `(("r-knitr" ,r-knitr)))
20521 (home-page "https://quanteda.io")
20522 (synopsis "Quantitative analysis of textual data")
20524 "This package provides a fast, flexible, and comprehensive framework for
20525 quantitative text analysis in R. It provides functionality for corpus
20526 management, creating and manipulating tokens and ngrams, exploring keywords in
20527 context, forming and manipulating sparse matrices of documents by features and
20528 feature co-occurrences, analyzing keywords, computing feature similarities and
20529 distances, applying content dictionaries, applying supervised and unsupervised
20530 machine learning, visually representing text and text analyses, and more.")
20531 (license license:gpl3)))
20533 (define-public r-topicmodels
20535 (name "r-topicmodels")
20540 (uri (cran-uri "topicmodels" version))
20543 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20544 (properties `((upstream-name . "topicmodels")))
20545 (build-system r-build-system)
20549 `(("r-modeltools" ,r-modeltools)
20552 (home-page "https://cran.r-project.org/package=topicmodels")
20553 (synopsis "Topic models")
20555 "This package provides an interface to the C code for @dfn{Latent
20556 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20557 David M. Blei and co-authors and the C++ code for fitting LDA models using
20558 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20559 (license license:gpl2)))
20561 (define-public r-stm
20568 (uri (cran-uri "stm" version))
20571 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20572 (properties `((upstream-name . "stm")))
20573 (build-system r-build-system)
20575 `(("r-data-table" ,r-data-table)
20576 ("r-glmnet" ,r-glmnet)
20578 ("r-matrix" ,r-matrix)
20579 ("r-matrixstats" ,r-matrixstats)
20580 ("r-quadprog" ,r-quadprog)
20581 ("r-quanteda" ,r-quanteda)
20583 ("r-rcpparmadillo" ,r-rcpparmadillo)
20585 ("r-stringr" ,r-stringr)))
20586 (home-page "http://www.structuraltopicmodel.com/")
20587 (synopsis "Estimation of the Structural Topic Model")
20589 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20590 topic models with document-level covariates. The package also includes tools
20591 for model selection, visualization, and estimation of topic-covariate
20593 (license license:expat)))
20595 (define-public r-polycor
20602 (uri (cran-uri "polycor" version))
20605 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20606 (properties `((upstream-name . "polycor")))
20607 (build-system r-build-system)
20609 `(("r-matrix" ,r-matrix)
20610 ("r-mvtnorm" ,r-mvtnorm)))
20611 (home-page "https://r-forge.r-project.org/projects/polycor/")
20612 (synopsis "Polychoric and polyserial correlations")
20614 "This package provides tools to compute polychoric and polyserial
20615 correlations by quick \"two-step\" methods or ML, optionally with standard
20616 errors; tetrachoric and biserial correlations are special cases.")
20617 (license license:gpl2+)))
20619 (define-public r-msm
20626 (uri (cran-uri "msm" version))
20629 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20630 (properties `((upstream-name . "msm")))
20631 (build-system r-build-system)
20633 `(("r-expm" ,r-expm)
20634 ("r-mvtnorm" ,r-mvtnorm)
20635 ("r-survival" ,r-survival)))
20636 (home-page "https://github.com/chjackson/msm")
20637 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20639 "This package provides functions for fitting continuous-time Markov and
20640 hidden Markov multi-state models to longitudinal data. It was designed for
20641 processes observed at arbitrary times in continuous time (panel data) but some
20642 other observation schemes are supported. Both Markov transition rates and the
20643 hidden Markov output process can be modelled in terms of covariates, which may
20644 be constant or piecewise-constant in time.")
20645 (license license:gpl2+)))
20647 (define-public r-ltm
20654 (uri (cran-uri "ltm" version))
20657 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20658 (properties `((upstream-name . "ltm")))
20659 (build-system r-build-system)
20661 `(("r-mass" ,r-mass)
20663 ("r-polycor" ,r-polycor)))
20664 (home-page "https://github.com/drizopoulos/ltm")
20665 (synopsis "Latent trait models under IRT")
20667 "This is a package supporting the analysis of multivariate dichotomous
20668 and polytomous data using latent trait models under the Item Response Theory
20669 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20670 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20672 (license license:gpl2+)))
20674 (define-public r-mi
20681 (uri (cran-uri "mi" version))
20684 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20685 (properties `((upstream-name . "mi")))
20686 (build-system r-build-system)
20689 ("r-matrix" ,r-matrix)))
20690 (home-page "http://www.stat.columbia.edu/~gelman/")
20691 (synopsis "Missing data imputation and model checking")
20693 "This package provides functions for data manipulation, imputing missing
20694 values in an approximate Bayesian framework, diagnostics of the models used to
20695 generate the imputations, confidence-building mechanisms to validate some of
20696 the assumptions of the imputation algorithm, and functions to analyze multiply
20697 imputed data sets with the appropriate degree of sampling uncertainty.")
20698 (license license:gpl2+)))
20700 (define-public r-matrixcalc
20702 (name "r-matrixcalc")
20707 (uri (cran-uri "matrixcalc" version))
20710 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20711 (properties `((upstream-name . "matrixcalc")))
20712 (build-system r-build-system)
20713 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20714 (synopsis "Collection of functions for matrix calculations")
20716 "This package provides a collection of functions to support matrix
20717 calculations for probability, econometric and numerical analysis. There are
20718 additional functions that are comparable to APL functions which are useful for
20719 actuarial models such as pension mathematics.")
20720 (license license:gpl2+)))
20722 (define-public r-sem
20729 (uri (cran-uri "sem" version))
20732 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20733 (properties `((upstream-name . "sem")))
20734 (build-system r-build-system)
20736 `(("r-boot" ,r-boot)
20738 ("r-matrixcalc" ,r-matrixcalc)
20740 (home-page "https://cran.r-project.org/package=sem")
20741 (synopsis "Structural equation models")
20743 "This package provides functions for fitting general linear structural
20744 equation models (with observed and latent variables) using the RAM approach,
20745 and for fitting structural equations in observed-variable models by two-stage
20747 (license license:gpl2+)))
20749 (define-public r-semtools
20751 (name "r-semtools")
20756 (uri (cran-uri "semTools" version))
20759 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20760 (properties `((upstream-name . "semTools")))
20761 (build-system r-build-system)
20763 `(("r-lavaan" ,r-lavaan)))
20764 (home-page "https://github.com/simsem/semTools/wiki")
20765 (synopsis "Useful tools for structural equation modeling")
20767 "This package provides useful tools for structural equation modeling.")
20768 (license license:gpl2+)))
20770 (define-public r-regsem
20777 (uri (cran-uri "regsem" version))
20780 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20781 (properties `((upstream-name . "regsem")))
20782 (build-system r-build-system)
20784 `(("r-lavaan" ,r-lavaan)
20786 ("r-rcpparmadillo" ,r-rcpparmadillo)
20787 ("r-rsolnp" ,r-rsolnp)))
20788 (home-page "https://cran.r-project.org/package=regsem")
20789 (synopsis "Regularized structural equation modeling")
20791 "This package uses both ridge and lasso penalties (and extensions) to
20792 penalize specific parameters in structural equation models. The package
20793 offers additional cost functions, cross validation, and other extensions
20794 beyond traditional structural equation models. It also contains a function to
20795 perform @dfn{exploratory mediation} (XMed).")
20796 (license license:gpl2+)))
20798 (define-public r-stanheaders
20800 (name "r-stanheaders")
20801 (version "2.21.0-6")
20805 (uri (cran-uri "StanHeaders" version))
20808 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20809 (properties `((upstream-name . "StanHeaders")))
20810 (build-system r-build-system)
20811 (inputs `(("pandoc" ,pandoc)))
20813 `(("r-rcppeigen" ,r-rcppeigen)
20814 ("r-rcppparallel" ,r-rcppparallel)))
20816 `(("gfortran" ,gfortran)
20817 ("r-knitr" ,r-knitr))) ; for vignettes
20818 (home-page "https://mc-stan.org/")
20819 (synopsis "C++ header files for Stan")
20821 "The C++ header files of the Stan project are provided by this package.
20822 There is a shared object containing part of the @code{CVODES} library, but it
20823 is not accessible from R. @code{r-stanheaders} is only useful for developers
20824 who want to utilize the @code{LinkingTo} directive of their package's
20825 DESCRIPTION file to build on the Stan library without incurring unnecessary
20828 The Stan project develops a probabilistic programming language that implements
20829 full or approximate Bayesian statistical inference via Markov Chain Monte
20830 Carlo or variational methods and implements (optionally penalized) maximum
20831 likelihood estimation via optimization. The Stan library includes an advanced
20832 automatic differentiation scheme, templated statistical and linear algebra
20833 functions that can handle the automatically differentiable scalar types (and
20834 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20835 package provides user-facing R functions to parse, compile, test, estimate,
20836 and analyze Stan models.")
20837 (license license:bsd-3)))
20839 (define-public r-rpf
20846 (uri (cran-uri "rpf" version))
20849 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20850 (properties `((upstream-name . "rpf")))
20851 (build-system r-build-system)
20853 `(("r-lifecycle" ,r-lifecycle)
20854 ("r-mvtnorm" ,r-mvtnorm)
20856 ("r-rcppeigen" ,r-rcppeigen)))
20858 `(("r-knitr" ,r-knitr)))
20859 (home-page "https://github.com/jpritikin/rpf")
20860 (synopsis "Response probability functions")
20862 "The purpose of this package is to factor out logic and math common to
20863 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20864 core support code suitable for more specialized IRT packages to build upon.
20865 Complete access to optimized C functions is made available with
20866 @code{R_RegisterCCallable()}.")
20867 (license license:gpl3+)))
20869 (define-public r-openmx
20876 (uri (cran-uri "OpenMx" version))
20879 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
20880 (properties `((upstream-name . "OpenMx")))
20881 (build-system r-build-system)
20884 ("r-digest" ,r-digest)
20885 ("r-lifecycle" ,r-lifecycle)
20887 ("r-matrix" ,r-matrix)
20889 ("r-rcppeigen" ,r-rcppeigen)
20891 ("r-stanheaders" ,r-stanheaders)))
20892 (native-inputs `(("gfortran" ,gfortran)))
20893 (home-page "http://openmx.ssri.psu.edu")
20894 (synopsis "Extended structural equation modelling")
20896 "This package allows for the estimation of a wide variety of advanced
20897 multivariate statistical models. It consists of a library of functions and
20898 optimizers that allow you to quickly and flexibly define an SEM model and
20899 estimate parameters given observed data.")
20900 (license license:asl2.0)))
20902 (define-public r-kutils
20909 (uri (cran-uri "kutils" version))
20912 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20913 (properties `((upstream-name . "kutils")))
20914 (build-system r-build-system)
20916 `(("r-foreign" ,r-foreign)
20917 ("r-openxlsx" ,r-openxlsx)
20919 ("r-runit" ,r-runit)
20920 ("r-xtable" ,r-xtable)))
20921 (home-page "https://cran.r-project.org/package=kutils")
20922 (synopsis "Project management tools")
20924 "This package provides tools for data importation, recoding, and
20925 inspection. There are functions to create new project folders, R code
20926 templates, create uniquely named output directories, and to quickly obtain a
20927 visual summary for each variable in a data frame. The main feature here is
20928 the systematic implementation of the \"variable key\" framework for data
20929 importation and recoding.")
20930 (license license:gpl2)))
20932 (define-public r-rockchalk
20934 (name "r-rockchalk")
20935 (version "1.8.144")
20939 (uri (cran-uri "rockchalk" version))
20942 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20943 (properties `((upstream-name . "rockchalk")))
20944 (build-system r-build-system)
20946 `(("r-cardata" ,r-cardata)
20947 ("r-kutils" ,r-kutils)
20949 ("r-mass" ,r-mass)))
20950 (home-page "https://cran.r-project.org/package=rockchalk")
20951 (synopsis "Regression estimation and presentation")
20953 "This package provides a collection of functions for interpretation and
20954 presentation of regression analysis. These functions are used to produce the
20955 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20956 includes regression diagnostics, regression tables, and plots of interactions
20957 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20958 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20959 fairly comprehensive overview.")
20960 (license license:gpl3+)))
20962 (define-public r-lisreltor
20964 (name "r-lisreltor")
20969 (uri (cran-uri "lisrelToR" version))
20972 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20973 (properties `((upstream-name . "lisrelToR")))
20974 (build-system r-build-system)
20975 (home-page "https://cran.r-project.org/package=lisrelToR")
20976 (synopsis "Import output from LISREL into R")
20978 "This is an unofficial package aimed at automating the import of LISREL
20980 (license license:gpl2)))
20982 (define-public r-bdgraph
20989 (uri (cran-uri "BDgraph" version))
20992 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
20993 (properties `((upstream-name . "BDgraph")))
20994 (build-system r-build-system)
20996 `(("r-igraph" ,r-igraph)))
20997 (home-page "https://www.uva.nl/profile/a.mohammadi")
20998 (synopsis "Bayesian structure learning in graphical models")
21000 "This package provides statistical tools for Bayesian structure learning
21001 in undirected graphical models for continuous, discrete, and mixed data. It
21002 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
21003 on a continuous-time birth-death process.")
21004 (license license:gpl2+)))
21006 (define-public r-d3network
21008 (name "r-d3network")
21009 (version "0.5.2.1")
21013 (uri (cran-uri "d3Network" version))
21016 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
21017 (properties `((upstream-name . "d3Network")))
21018 (build-system r-build-system)
21020 `(("r-plyr" ,r-plyr)
21021 ("r-rjson" ,r-rjson)
21022 ("r-whisker" ,r-whisker)))
21023 (home-page "http://christophergandrud.github.io/d3Network/")
21024 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
21026 "This package is intended to make it easy to create D3 JavaScript
21027 network, tree, dendrogram, and Sankey graphs from R using data frames.")
21028 (license license:gpl3+)))
21030 (define-public r-qgraph
21037 (uri (cran-uri "qgraph" version))
21040 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
21041 (properties `((upstream-name . "qgraph")))
21042 (build-system r-build-system)
21044 `(("r-abind" ,r-abind)
21045 ("r-bdgraph" ,r-bdgraph)
21046 ("r-colorspace" ,r-colorspace)
21047 ("r-corpcor" ,r-corpcor)
21048 ("r-d3network" ,r-d3network)
21049 ("r-dplyr" ,r-dplyr)
21050 ("r-fdrtool" ,r-fdrtool)
21051 ("r-ggplot2" ,r-ggplot2)
21052 ("r-ggraph" ,r-ggraph)
21053 ("r-glasso" ,r-glasso)
21054 ("r-gtools" ,r-gtools)
21055 ("r-hmisc" ,r-hmisc)
21057 ("r-igraph" ,r-igraph)
21059 ("r-lavaan" ,r-lavaan)
21060 ("r-matrix" ,r-matrix)
21061 ("r-pbapply" ,r-pbapply)
21064 ("r-psych" ,r-psych)
21066 ("r-reshape2" ,r-reshape2)
21067 ("r-tidygraph" ,r-tidygraph)))
21068 (home-page "http://sachaepskamp.com/qgraph/")
21069 (synopsis "Weighted network visualization and analysis")
21071 "This package implements tools for weighted network visualization and
21072 analysis, as well as Gaussian graphical model computation. It contains graph
21073 plotting methods, and tools for psychometric data visualization and graphical
21074 model estimation. See Epskamp et al. (2012)
21075 @url{doi:10.18637/jss.v048.i04}.")
21076 (license license:gpl2)))
21078 (define-public r-semplot
21085 (uri (cran-uri "semPlot" version))
21088 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
21089 (properties `((upstream-name . "semPlot")))
21090 (build-system r-build-system)
21092 `(("r-colorspace" ,r-colorspace)
21093 ("r-corpcor" ,r-corpcor)
21094 ("r-igraph" ,r-igraph)
21095 ("r-lavaan" ,r-lavaan)
21096 ("r-lisreltor" ,r-lisreltor)
21097 ("r-openmx" ,r-openmx)
21099 ("r-qgraph" ,r-qgraph)
21100 ("r-regsem" ,r-regsem)
21101 ("r-rockchalk" ,r-rockchalk)
21104 (home-page "https://github.com/SachaEpskamp/semPlot")
21105 (synopsis "Unified visualizations of structural equation models")
21107 "Structural equation modeling (SEM) has a long history of representing
21108 models graphically as path diagrams. The semPlot package for R fills the gap
21109 between advanced, but time-consuming, graphical software and the limited
21110 graphics produced automatically by SEM software. In addition, semPlot offers
21111 more functionality than drawing path diagrams: it can act as a common ground
21112 for importing SEM results into R. Any result usable as input to semPlot can
21113 also be represented in any of the three popular SEM frame-works, as well as
21114 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
21115 (license license:gpl2)))
21117 (define-public r-cdm
21124 (uri (cran-uri "CDM" version))
21127 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
21128 (properties `((upstream-name . "CDM")))
21129 (build-system r-build-system)
21131 `(("r-mvtnorm" ,r-mvtnorm)
21132 ("r-polycor" ,r-polycor)
21134 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21136 "https://github.com/alexanderrobitzsch/CDM")
21137 (synopsis "Cognitive diagnosis modeling")
21139 "This package provides functions for cognitive diagnosis modeling and
21140 multidimensional item response modeling for dichotomous and polytomous item
21141 responses. It enables the estimation of the DINA and DINO model, the multiple
21142 group (polytomous) GDINA model, the multiple choice DINA model, the general
21143 diagnostic model (GDM), the structured latent class model (SLCA), and
21144 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
21145 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
21146 estimation and the package structure. For tutorials on how to use the CDM
21147 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
21148 well as Ravand and Robitzsch (2015).")
21149 (license license:gpl2+)))
21151 (define-public r-tam
21158 (uri (cran-uri "TAM" version))
21161 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
21162 (properties `((upstream-name . "TAM")))
21163 (build-system r-build-system)
21167 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21168 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
21169 (synopsis "Test analysis modules")
21171 "This package includes tools for marginal maximum likelihood estimation
21172 and joint maximum likelihood estimation for unidimensional and
21173 multidimensional item response models. The package functionality covers the
21174 Rasch model, 2PL model, 3PL model, generalized partial credit model,
21175 multi-faceted Rasch model, nominal item response model, structured latent
21176 class model, mixture distribution IRT models, and located latent class models.
21177 Latent regression models and plausible value imputation are also supported.")
21178 (license license:gpl2+)))
21180 (define-public r-erm
21187 (uri (cran-uri "eRm" version))
21190 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
21191 (properties `((upstream-name . "eRm")))
21192 (build-system r-build-system)
21194 `(("r-colorspace" ,r-colorspace)
21195 ("r-lattice" ,r-lattice)
21197 ("r-matrix" ,r-matrix)
21198 ("r-psych" ,r-psych)))
21199 (native-inputs `(("gfortran" ,gfortran)))
21200 (home-page "https://cran.r-project.org/package=eRm")
21201 (synopsis "Extended Rasch modeling")
21203 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21204 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21205 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21206 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21207 data matrix. Additional features are the ML estimation of the person
21208 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21209 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21210 infit and outfit measures, ICC and other plots, automated stepwise item
21211 elimination, and a simulation module for various binary data matrices.")
21212 (license license:gpl3)))
21214 (define-public r-irtoys
21221 (uri (cran-uri "irtoys" version))
21224 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21225 (properties `((upstream-name . "irtoys")))
21226 (build-system r-build-system)
21230 (home-page "https://cran.r-project.org/package=irtoys")
21231 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21233 "This package provides a collection of functions useful in learning and
21234 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21235 programs. It provides basic CTT analysis, a simple common interface to the
21236 estimation of item parameters in IRT models for binary responses with three
21237 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21238 EAP, WLE, plausible values), item and person fit statistics, scaling
21239 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21240 array of parametric and non-parametric (kernel) plots. It estimates and plots
21241 Haberman's interaction model when all items are dichotomously scored.")
21242 (license license:gpl2+)))
21244 (define-public r-iheatmapr
21246 (name "r-iheatmapr")
21251 (uri (cran-uri "iheatmapr" version))
21254 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21255 (properties `((upstream-name . "iheatmapr")))
21256 (build-system r-build-system)
21258 `(("r-fastcluster" ,r-fastcluster)
21259 ("r-ggdendro" ,r-ggdendro)
21260 ("r-htmlwidgets" ,r-htmlwidgets)
21261 ("r-jsonlite" ,r-jsonlite)
21262 ("r-knitr" ,r-knitr)
21263 ("r-magrittr" ,r-magrittr)
21264 ("r-rcolorbrewer" ,r-rcolorbrewer)
21265 ("r-scales" ,r-scales)))
21267 `(("r-knitr" ,r-knitr)))
21268 (home-page "https://docs.ropensci.org/iheatmapr")
21269 (synopsis "Interactive, Complex Heatmaps")
21271 "iheatmapr is an R package for building complex, interactive heatmaps
21272 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21273 subplots along the rows or columns of the main heatmap add more information
21274 about each row or column. For example, a one column additional heatmap may
21275 indicate what group a particular row or column belongs to. Complex heatmaps
21276 may also include multiple side by side heatmaps which show different types of
21277 data for the same conditions. Interactivity can improve complex heatmaps by
21278 providing tooltips with information about each cell and enabling zooming into
21279 interesting features. iheatmapr uses the plotly library for interactivity.")
21280 (license license:expat)))
21282 (define-public r-packrat
21289 (uri (cran-uri "packrat" version))
21292 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21293 (properties `((upstream-name . "packrat")))
21294 (build-system r-build-system)
21295 (home-page "https://github.com/rstudio/packrat/")
21296 (synopsis "Dependency management R projects")
21298 "This package provides a dependency manager for R projects that allows
21299 you to manage the R packages your project depends on in an isolated, portable,
21300 and reproducible way.")
21301 (license license:gpl2)))
21303 (define-public r-rsconnect
21305 (name "r-rsconnect")
21310 (uri (cran-uri "rsconnect" version))
21313 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21314 (properties `((upstream-name . "rsconnect")))
21315 (build-system r-build-system)
21317 `(("r-curl" ,r-curl)
21318 ("r-digest" ,r-digest)
21319 ("r-jsonlite" ,r-jsonlite)
21320 ("r-openssl" ,r-openssl)
21321 ("r-packrat" ,r-packrat)
21322 ("r-rstudioapi" ,r-rstudioapi)
21323 ("r-yaml" ,r-yaml)))
21324 (home-page "https://github.com/rstudio/rsconnect")
21325 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21327 "This package provides a programmatic deployment interface for RPubs,
21328 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21329 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21330 (license license:gpl2)))
21332 ;; This package includes minified JavaScript files. When upgrading please
21333 ;; check that there are no new minified JavaScript files.
21334 (define-public r-dygraphs
21336 (name "r-dygraphs")
21337 (version "1.1.1.6")
21341 (uri (cran-uri "dygraphs" version))
21344 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21345 (properties `((upstream-name . "dygraphs")))
21346 (build-system r-build-system)
21348 `(#:modules ((guix build utils)
21349 (guix build r-build-system)
21353 (modify-phases %standard-phases
21354 (add-after 'unpack 'process-javascript
21355 (lambda* (#:key inputs #:allow-other-keys)
21356 (with-directory-excursion "inst/htmlwidgets/lib/"
21360 `(("dygraphs/dygraph-combined-dev.js"
21361 "dygraph-combined.js")
21362 (,(assoc-ref inputs "js-jquery")
21363 "jquery/jquery.min.js")
21364 (,(assoc-ref inputs "js-fquarter")
21365 "fquarter/moment-fquarter.min.js"))))
21366 (lambda (sources targets)
21367 (for-each (lambda (source target)
21368 (format #t "Processing ~a --> ~a~%"
21370 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21371 (call-with-output-file target
21373 (dump-port minified port)))))
21374 sources targets))))
21377 `(("uglify-js" ,uglify-js)
21378 ;; They actually use version 1.11.1, but this more recent version
21379 ;; should be just fine.
21383 (uri "https://code.jquery.com/jquery-1.12.4.js")
21386 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21390 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21391 "moment-fquarter/1.0.1/moment-fquarter.js"))
21394 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21396 `(("r-htmltools" ,r-htmltools)
21397 ("r-htmlwidgets" ,r-htmlwidgets)
21398 ("r-magrittr" ,r-magrittr)
21401 (home-page "https://github.com/rstudio/dygraphs")
21402 (synopsis "Interface to Dygraphs interactive time series charting library")
21404 "This package provides an R interface to the dygraphs JavaScript charting
21405 library (a copy of which is included in the package). It provides rich
21406 facilities for charting time-series data in R, including highly configurable
21407 series- and axis-display and interactive features like zoom/pan and
21408 series/point highlighting.")
21409 (license license:expat)))
21411 (define-public r-shinystan
21413 (name "r-shinystan")
21418 (uri (cran-uri "shinystan" version))
21421 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21422 (properties `((upstream-name . "shinystan")))
21423 (build-system r-build-system)
21425 `(("r-bayesplot" ,r-bayesplot)
21426 ("r-colourpicker" ,r-colourpicker)
21428 ("r-dygraphs" ,r-dygraphs)
21429 ("r-ggplot2" ,r-ggplot2)
21430 ("r-gridextra" ,r-gridextra)
21431 ("r-gtools" ,r-gtools)
21432 ("r-markdown" ,r-markdown)
21433 ("r-reshape2" ,r-reshape2)
21434 ("r-rsconnect" ,r-rsconnect)
21435 ("r-rstan" ,r-rstan)
21436 ("r-shiny" ,r-shiny)
21437 ("r-shinyjs" ,r-shinyjs)
21438 ("r-shinythemes" ,r-shinythemes)
21439 ("r-threejs" ,r-threejs)
21440 ("r-xtable" ,r-xtable)
21442 (home-page "https://mc-stan.org/")
21443 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21445 "This package provides a graphical user interface for interactive
21446 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21447 for analyzing a posterior sample. The interface is powered by the Shiny web
21448 application framework and works with the output of MCMC programs written in
21449 any programming language (and has extended functionality for Stan models fit
21450 using the @code{rstan} and @code{rstanarm} packages).")
21451 (license license:gpl3+)))
21453 (define-public r-rstantools
21455 (name "r-rstantools")
21460 (uri (cran-uri "rstantools" version))
21463 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21464 (properties `((upstream-name . "rstantools")))
21465 (build-system r-build-system)
21466 (inputs `(("pandoc" ,pandoc)))
21468 `(("r-desc" ,r-desc)
21470 ("r-rcppparallel" ,r-rcppparallel)))
21472 `(("r-knitr" ,r-knitr)))
21473 (home-page "https://mc-stan.org/rstantools/")
21474 (synopsis "Tools for developing R packages interfacing with Stan")
21476 "This package provides various tools for developers of R packages
21477 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21478 up the required package structure, S3 generics and default methods to unify
21479 function naming across Stan-based R packages, and vignettes with
21480 recommendations for developers.")
21481 (license license:gpl3+)))
21483 (define-public r-loo
21490 (uri (cran-uri "loo" version))
21492 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21493 (properties `((upstream-name . "loo")))
21494 (build-system r-build-system)
21496 `(("pandoc" ,pandoc)
21497 ("pandoc-citeproc" ,pandoc-citeproc)))
21499 `(("r-checkmate" ,r-checkmate)
21500 ("r-matrixstats" ,r-matrixstats)))
21502 `(("r-knitr" ,r-knitr)))
21503 (home-page "https://mc-stan.org/loo/")
21504 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21506 "This package provides an implementation of efficient approximate
21507 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21508 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21509 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21510 procedure for regularizing importance weights. As a byproduct of the
21511 calculations, we also obtain approximate standard errors for estimated
21512 predictive errors and for the comparison of predictive errors between models.
21513 The package also provides methods for using stacking and other model weighting
21514 techniques to average Bayesian predictive distributions.")
21515 (license license:gpl3+)))
21517 (define-public r-rstan
21524 (uri (cran-uri "rstan" version))
21527 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21528 (properties `((upstream-name . "rstan")))
21529 (build-system r-build-system)
21532 (modify-phases %standard-phases
21533 (add-before 'install 'set-timezone
21534 ;; This package is picky about timezones.
21535 (lambda* (#:key inputs #:allow-other-keys)
21536 (setenv "TZ" "UTC+1")
21538 (string-append (assoc-ref inputs "tzdata")
21539 "/share/zoneinfo"))
21542 `(("tzdata" ,tzdata-for-tests)
21544 ("r-knitr" ,r-knitr)))
21547 ("r-ggplot2" ,r-ggplot2)
21548 ("r-gridextra" ,r-gridextra)
21549 ("r-inline" ,r-inline)
21551 ("r-pkgbuild" ,r-pkgbuild)
21553 ("r-rcppeigen" ,r-rcppeigen)
21554 ("r-rcppparallel" ,r-rcppparallel)
21555 ("r-stanheaders" ,r-stanheaders)
21557 ("r-withr" ,r-withr)))
21558 (home-page "https://discourse.mc-stan.org/")
21559 (synopsis "R interface to Stan")
21561 "User-facing R functions are provided to parse, compile, test, estimate,
21562 and analyze Stan models by accessing the header-only Stan library provided by
21563 the StanHeaders package. The Stan project develops a probabilistic
21564 programming language that implements full Bayesian statistical inference via
21565 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21566 approximation, and (optionally penalized) maximum likelihood estimation via
21567 optimization. In all three cases, automatic differentiation is used to
21568 quickly and accurately evaluate gradients without burdening the user with the
21569 need to derive the partial derivatives.")
21570 (license license:gpl3+)))
21572 (define-public r-rstanarm
21574 (name "r-rstanarm")
21579 (uri (cran-uri "rstanarm" version))
21582 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21583 (properties `((upstream-name . "rstanarm")))
21584 (build-system r-build-system)
21586 `(("pandoc" ,pandoc)
21587 ("pandoc-citeproc" ,pandoc-citeproc)))
21589 `(("r-bayesplot" ,r-bayesplot)
21591 ("r-ggplot2" ,r-ggplot2)
21594 ("r-matrix" ,r-matrix)
21597 ("r-rcppeigen" ,r-rcppeigen)
21598 ("r-rcppparallel" ,r-rcppparallel)
21599 ("r-rstan" ,r-rstan)
21600 ("r-rstantools" ,r-rstantools)
21601 ("r-shinystan" ,r-shinystan)
21602 ("r-stanheaders" ,r-stanheaders)
21603 ("r-survival" ,r-survival)))
21605 `(("r-knitr" ,r-knitr)))
21606 (home-page "https://mc-stan.org/rstanarm/")
21607 (synopsis "Bayesian applied regression modeling via Stan")
21609 "This package estimates previously compiled regression models using the
21610 @code{rstan} package, which provides the R interface to the Stan C++ library
21611 for Bayesian estimation. Users specify models via the customary R syntax with
21612 a formula and @code{data.frame} plus some additional arguments for priors.")
21613 (license license:gpl3+)))
21615 (define-public r-kendall
21622 (uri (cran-uri "Kendall" version))
21625 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21626 (properties `((upstream-name . "Kendall")))
21627 (build-system r-build-system)
21629 `(("r-boot" ,r-boot)))
21631 `(("gfortran" ,gfortran)))
21632 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21633 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21635 "This package computes the Kendall rank correlation and Mann-Kendall
21637 (license license:gpl2+)))
21639 (define-public r-zyp
21642 (version "0.10-1.1")
21646 (uri (cran-uri "zyp" version))
21649 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21650 (properties `((upstream-name . "zyp")))
21651 (build-system r-build-system)
21653 `(("r-kendall" ,r-kendall)))
21654 (home-page "https://cran.r-project.org/web/packages/zyp/")
21655 (synopsis "Zhang + Yue-Pilon Trends Package")
21657 "This package contains an efficient implementation of Sen's slope
21658 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21659 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21661 (license license:lgpl2.1)))
21663 (define-public r-rlinsolve
21665 (name "r-rlinsolve")
21670 (uri (cran-uri "Rlinsolve" version))
21673 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21674 (properties `((upstream-name . "Rlinsolve")))
21675 (build-system r-build-system)
21677 `(("r-matrix" ,r-matrix)
21679 ("r-rcpparmadillo" ,r-rcpparmadillo)
21680 ("r-rdpack" ,r-rdpack)))
21681 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21682 (synopsis "Iterative solvers for (sparse) linear system of equations")
21684 "Solving a system of linear equations is one of the most fundamental
21685 computational problems for many fields of mathematical studies, such as
21686 regression problems from statistics or numerical partial differential
21687 equations. This package provides basic stationary iterative solvers such as
21688 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21689 Nonstationary, also known as Krylov subspace methods are also provided.
21690 Sparse matrix computation is also supported in that solving large and sparse
21691 linear systems can be manageable using the @code{Matrix} package along with
21692 @code{RcppArmadillo}.")
21693 (license license:gpl3+)))
21695 (define-public r-zvcv
21702 (uri (cran-uri "ZVCV" version))
21705 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21706 (properties `((upstream-name . "ZVCV")))
21707 (build-system r-build-system)
21709 `(("r-abind" ,r-abind)
21711 ("r-dplyr" ,r-dplyr)
21712 ("r-glmnet" ,r-glmnet)
21713 ("r-magrittr" ,r-magrittr)
21714 ("r-mvtnorm" ,r-mvtnorm)
21716 ("r-rcpparmadillo" ,r-rcpparmadillo)
21717 ("r-rlinsolve" ,r-rlinsolve)))
21718 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21719 (synopsis "Zero-Variance Control Variates")
21721 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21722 to reduce the variance of Monte Carlo estimators of expectations using the
21723 derivatives of the log target. Once the derivatives are available, the only
21724 additional computational effort is in solving a linear regression problem.
21725 This method has been extended to higher dimensions using regularisation. This
21726 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21727 samples, derivatives and function evaluations are available. Additional
21728 functions for applying ZV-CV to two estimators for the normalising constant of
21729 the posterior distribution in Bayesian statistics are also supplied.")
21730 (license license:gpl2+)))
21732 (define-public r-ztype
21739 (uri (cran-uri "ztype" version))
21742 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21743 (properties `((upstream-name . "ztype")))
21744 (build-system r-build-system)
21746 `(("r-assertthat" ,r-assertthat)
21747 ("r-dplyr" ,r-dplyr)
21748 ("r-ggplot2" ,r-ggplot2)
21749 ("r-lubridate" ,r-lubridate)
21750 ("r-magrittr" ,r-magrittr)
21751 ("r-rvest" ,r-rvest)
21752 ("r-stringr" ,r-stringr)))
21753 (home-page "https://cran.r-project.org/web/packages/ztype/")
21754 (synopsis "Run a Ztype game loaded with R functions")
21756 "How fast can you type R functions on your keyboard? Find out by running
21757 a @code{zty.pe} game: export R functions as instructions to type to destroy
21758 opponents' vessels.")
21759 (license license:gpl3)))
21761 (define-public r-zseq
21768 (uri (cran-uri "Zseq" version))
21771 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21772 (properties `((upstream-name . "Zseq")))
21773 (build-system r-build-system)
21775 `(("r-gmp" ,r-gmp)))
21776 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21777 (synopsis "Integer sequence generator")
21779 "This package generates well-known integer sequences. The @code{gmp}
21780 package is adopted for computing with arbitrarily large numbers. Every
21781 function has a hyperlink to its corresponding item in the @dfn{On-Line
21782 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21783 (license license:gpl3+)))
21785 (define-public r-isoband
21792 (uri (cran-uri "isoband" version))
21795 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21796 (properties `((upstream-name . "isoband")))
21797 (build-system r-build-system)
21799 `(("r-testthat" ,r-testthat)))
21801 `(("r-knitr" ,r-knitr)))
21802 (home-page "https://github.com/wilkelab/isoband")
21803 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21805 "This package provides a fast C++ implementation to generate contour
21806 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21807 containing elevation data.")
21808 (license license:expat)))
21810 (define-public r-ppcor
21817 (uri (cran-uri "ppcor" version))
21820 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21821 (properties `((upstream-name . "ppcor")))
21822 (build-system r-build-system)
21824 `(("r-mass" ,r-mass)))
21825 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21826 (synopsis "Partial and semi-partial correlation")
21828 "This package provides users not only with a function to readily
21829 calculate the higher-order partial and semi-partial correlations but also with
21830 statistics and p-values of the correlation coefficients.")
21831 (license license:gpl2)))
21833 (define-public r-hrbrthemes
21835 (name "r-hrbrthemes")
21840 (uri (cran-uri "hrbrthemes" version))
21842 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21843 (properties `((upstream-name . "hrbrthemes")))
21844 (build-system r-build-system)
21846 `(("r-extrafont" ,r-extrafont)
21847 ("r-gdtools" ,r-gdtools)
21848 ("r-ggplot2" ,r-ggplot2)
21849 ("r-htmltools" ,r-htmltools)
21850 ("r-knitr" ,r-knitr)
21851 ("r-magrittr" ,r-magrittr)
21852 ("r-rmarkdown" ,r-rmarkdown)
21853 ("r-scales" ,r-scales)))
21855 `(("r-knitr" ,r-knitr)))
21856 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21857 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21859 "This package provides a compilation of extra @code{ggplot2} themes,
21860 scales and utilities, including a spell check function for plot label fields
21861 and an overall emphasis on typography.")
21862 (license license:expat)))
21864 (define-public r-crochet
21871 (uri (cran-uri "crochet" version))
21874 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21875 (build-system r-build-system)
21877 `(("r-knitr" ,r-knitr)))
21878 (home-page "https://github.com/agrueneberg/crochet")
21879 (synopsis "Implementation Helper for Matrix-Like Types")
21881 "Functions to help implement the extraction / subsetting / indexing
21882 function @code{[} and replacement function @code{[<-} of custom matrix-like
21883 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21884 as possible (with tests to prove it).")
21885 (license license:expat)))
21887 (define-public r-boa
21890 (version "1.1.8-2")
21894 (uri (cran-uri "boa" version))
21897 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21898 (properties `((upstream-name . "boa")))
21899 (build-system r-build-system)
21900 (home-page "http://www.jstatsoft.org/v21/i11")
21901 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21903 "This package provides a menu-driven program and library of functions for
21904 carrying out convergence diagnostics and statistical and graphical analysis of
21905 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21906 (license license:gpl2+)))
21908 (define-public r-httpcode
21910 (name "r-httpcode")
21914 (uri (cran-uri "httpcode" version))
21917 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21918 (build-system r-build-system)
21919 (home-page "https://github.com/sckott/httpcode")
21920 (synopsis "HTTP status code helper")
21921 (description "@code{httpcode} provides functionality for finding and
21922 explaining the meaning of @code{HTTP} status codes. Functions are included for
21923 searching for codes by full or partial number, by message, and to get
21924 appropriate dog and cat images for many status codes.")
21925 (license license:expat)))
21927 (define-public r-latex2exp
21929 (name "r-latex2exp")
21933 (uri (cran-uri "latex2exp" version))
21936 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21937 (build-system r-build-system)
21939 `(("r-stringr" ,r-stringr)
21940 ("r-magrittr", r-magrittr)))
21941 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21942 (synopsis "Use LaTeX expressions in plots")
21943 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21944 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21945 rendered as text, axis labels, etc. throughout R's plotting system.")
21946 (license license:expat)))
21948 (define-public r-oai
21954 (uri (cran-uri "oai" version))
21957 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21958 (build-system r-build-system)
21960 `(("r-xml2" ,r-xml2)
21963 ("r-stringr" ,r-stringr)
21964 ("r-tibble" ,r-tibble)))
21965 (home-page "https://github.com/ropensci/oai/")
21966 (synopsis "General purpose OAI-PMH services client")
21967 (description "@code{oai} provides a general purpose client to work with
21968 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21969 service. Functions are provided to work with the OAI-PMH verbs:
21970 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21971 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21972 (license license:expat)))
21974 (define-public r-argon2
21981 (uri (cran-uri "argon2" version))
21984 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21985 (properties `((upstream-name . "argon2")))
21986 (build-system r-build-system)
21987 (home-page "https://github.com/wrathematics/argon2")
21988 (synopsis "Secure password hashing based on the argon2 algorithm")
21990 "This package provides utilities for secure password hashing via the
21991 argon2 algorithm.")
21992 (license license:bsd-2)))
21994 (define-public r-getpass
22001 (uri (cran-uri "getPass" version))
22004 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
22005 (properties `((upstream-name . "getPass")))
22006 (build-system r-build-system)
22008 `(("r-rstudioapi" ,r-rstudioapi)))
22009 (home-page "https://github.com/wrathematics/getPass")
22010 (synopsis "Masked user input")
22012 "This package provides a micro-package for reading \"passwords\", i.e.
22013 reading user input with masking, so that the input is not displayed as it is
22014 typed. Currently, RStudio, the command line (every OS), and any platform
22015 where tcltk is present are supported.")
22016 (license license:bsd-2)))
22018 (define-public r-remoter
22025 (uri (cran-uri "remoter" version))
22028 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
22029 (properties `((upstream-name . "remoter")))
22030 (build-system r-build-system)
22032 `(("r-argon2" ,r-argon2)
22033 ("r-getpass" ,r-getpass)
22034 ("r-pbdzmq" ,r-pbdzmq)
22036 (home-page "https://github.com/RBigData/remoter")
22037 (synopsis "Control a remote R session from a local one")
22039 "This package provides a set of utilities for client/server computing
22040 with R, controlling a remote R session (the server) from a local one (the
22042 (license license:bsd-2)))
22044 (define-public r-asd
22051 (uri (cran-uri "asd" version))
22054 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
22055 (properties `((upstream-name . "asd")))
22056 (build-system r-build-system)
22058 `(("r-mvtnorm" ,r-mvtnorm)))
22059 (home-page "https://cran.r-project.org/web/packages/asd")
22060 (synopsis "Simulations for Adaptive Seamless Designs")
22062 "This package provdes means to run simulations for adaptive seamless
22063 designs with and without early outcomes for treatment selection and
22064 subpopulation type designs.")
22065 (license license:gpl3)))
22067 (define-public r-nbconvertr
22069 (name "r-nbconvertr")
22074 (uri (cran-uri "nbconvertR" version))
22077 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
22078 (properties `((upstream-name . "nbconvertR")))
22079 (build-system r-build-system)
22081 `(("jupyter" ,python-nbconvert)
22082 ("pandoc" ,pandoc)))
22083 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
22084 (synopsis "Vignette engine wrapping Jupyter notebooks")
22086 "This package calls the Jupyter script @code{nbconvert} to create
22087 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
22088 containing rich text, code, and its output. Code cells can be edited and
22089 evaluated interactively.")
22090 (license license:gpl3)))
22092 (define-public r-bridgesampling
22094 (name "r-bridgesampling")
22099 (uri (cran-uri "bridgesampling" version))
22102 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
22104 `((upstream-name . "bridgesampling")))
22105 (build-system r-build-system)
22107 `(("r-brobdingnag" ,r-brobdingnag)
22109 ("r-matrix" ,r-matrix)
22110 ("r-mvtnorm" ,r-mvtnorm)
22111 ("r-scales" ,r-scales)
22112 ("r-stringr" ,r-stringr)))
22114 `(("r-knitr" ,r-knitr)))
22115 (home-page "https://github.com/quentingronau/bridgesampling")
22116 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
22118 "This package provides functions for estimating marginal likelihoods,
22119 Bayes factors, posterior model probabilities, and normalizing constants in
22120 general, via different versions of bridge sampling.")
22121 (license license:gpl2+)))
22123 (define-public r-tea
22130 (uri (cran-uri "tea" version))
22133 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
22135 `((upstream-name . "tea")))
22136 (build-system r-build-system)
22138 `(("r-matrix" ,r-matrix)))
22139 (home-page "https://cran.r-project.org/web/packages/tea/")
22140 (synopsis "Threshold estimation approaches")
22142 "This package provides different approaches for selecting the threshold
22143 in generalized Pareto distributions. Most of them are based on minimizing the
22144 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
22145 Others are heuristically motivated by searching for stable sample paths, i.e.
22146 a nearly constant region of the tail index estimator with respect to k, which
22147 is the number of data in the tail. The third class is motivated by graphical
22148 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
22149 is also implemented here.")
22150 (license license:gpl3)))
22152 (define-public r-awsmethods
22154 (name "r-awsmethods")
22159 (uri (cran-uri "awsMethods" version))
22162 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
22164 `((upstream-name . "awsMethods")))
22165 (build-system r-build-system)
22166 (home-page "http://www.wias-berlin.de/software/imaging/")
22167 (synopsis "Class and methods definitions")
22169 "This package defines the generic method @code{extract} and provides
22170 @code{openMP} support as needed in several packages like
22171 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
22172 (license license:gpl2+)))
22174 (define-public r-aws
22181 (uri (cran-uri "aws" version))
22184 "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5"))))
22186 `((upstream-name . "aws")))
22187 (build-system r-build-system)
22189 `(("r-awsmethods" ,r-awsmethods)
22192 `(("gfortran" ,gfortran)))
22193 (home-page "https://cran.r-project.org/web/packages/aws/")
22194 (synopsis "Adaptive weights smoothing")
22196 "This package provides a collection of R-functions implementing adaptive
22197 smoothing procedures in 1D, 2D and 3D. This includes the
22198 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22199 Confidence Intervals} (ICI), variational approaches, and a non-local means
22201 (license license:gpl2+)))
22203 (define-public r-sgloptim
22205 (name "r-sgloptim")
22210 (uri (cran-uri "sglOptim" version))
22213 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22215 `((upstream-name . "sglOptim")))
22216 (build-system r-build-system)
22219 ("r-doparallel" ,r-doparallel)
22220 ("r-foreach" ,r-foreach)
22221 ("r-matrix" ,r-matrix)
22223 ("r-rcpparmadillo" ,r-rcpparmadillo)
22224 ("r-rcppprogress" ,r-rcppprogress)))
22226 `(("r-knitr" ,r-knitr)))
22227 (home-page "https://github.com/nielsrhansen/sglOptim")
22228 (synopsis "Generic sparse group Lasso solver")
22230 "This package provides a fast generic solver for sparse group lasso
22231 optimization problems. The loss (objective) function must be defined in a C++
22232 module. The optimization problem is solved using a coordinate gradient
22233 descent algorithm. Convergence of the algorithm is established and the
22234 algorithm is applicable to a broad class of loss functions. Use of parallel
22235 computing for cross validation and subsampling is supported through the
22236 @code{foreach} and @code{doParallel} packages.")
22237 (license license:gpl2+)))
22239 (define-public r-grouped
22246 (uri (cran-uri "grouped" version))
22249 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22251 `((upstream-name . "grouped")))
22252 (build-system r-build-system)
22254 `(("r-mass" ,r-mass)))
22255 (home-page "https://cran.r-project.org/web/packages/grouped/")
22256 (synopsis "Regression analysis of grouped and coarse data")
22258 "This package provides regression models for grouped and coarse data,
22259 under the coarsened at random assumption.")
22260 (license license:gpl2+)))
22262 (define-public r-stam
22269 (uri (cran-uri "stam" version))
22272 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22274 `((upstream-name . "stam")))
22275 (build-system r-build-system)
22279 (home-page "https://cran.r-project.org/web/packages/stam")
22280 (synopsis "Spatio-temporal analysis and modelling")
22282 "This package provides various methods to conduct Spatio-Temporal
22283 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22284 Inferred Spatio-Temporal Modelling.")
22285 (license license:gpl2+)))
22287 (define-public r-dcv
22294 (uri (cran-uri "dcv" version))
22297 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22299 `((upstream-name . "dcv")))
22300 (build-system r-build-system)
22302 `(("r-lmtest" ,r-lmtest)))
22303 (home-page "https://cran.r-project.org/web/packages/dcv/")
22304 (synopsis "Conventional cross-validation statistics for climate-growth model")
22306 "This package performs several conventional cross-validation statistical
22307 methods for climate-growth model in the climate reconstruction from tree
22308 rings, including Sign Test statistic, Reduction of Error statistic, Product
22309 Mean Test, Durbin-Watson statistic etc.")
22310 (license license:gpl2)))
22312 (define-public r-rcdd
22319 (uri (cran-uri "rcdd" version))
22322 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22324 `((upstream-name . "rcdd")))
22325 (build-system r-build-system)
22328 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22329 (synopsis "Computational geometry")
22331 "This package converts back and forth between two representations of a
22332 convex polytope: as solution of a set of linear equalities and inequalities
22333 and as convex hull of set of points and rays. Also does linear programming
22334 and redundant generator elimination. All functions can use exact
22335 infinite-precision rational arithmetic.")
22336 (license license:gpl2)))
22338 (define-public r-rxnat
22345 (uri (cran-uri "Rxnat" version))
22348 "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb"))))
22350 `((upstream-name . "Rxnat")))
22351 (build-system r-build-system)
22353 `(("r-dplyr" ,r-dplyr)
22355 ("r-rcurl" ,r-rcurl)))
22357 `(("r-knitr" ,r-knitr)))
22358 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22359 (synopsis "Queries and extracts images from neuroimaging datasets")
22361 "This package allows communication with the Extensible Neuroimaging
22362 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22364 (license license:gpl2)))
22366 (define-public r-rserve
22373 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22374 version ".tar.gz"))
22377 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22378 (build-system r-build-system)
22380 `(("r-checkmate" ,r-checkmate)
22382 ("r-jsonlite" ,r-jsonlite)
22383 ("r-knitr" ,r-knitr)
22386 ("r-uuid" ,r-uuid)))
22388 `(("openssl" ,openssl)
22390 (home-page "https://github.com/s-u/Rserve")
22392 "Server providing access to R from many languages and systems")
22394 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22395 binary requests to be sent to R. Every connection has a separate workspace
22396 and working directory. Client-side implementations are available for popular
22397 languages such as C/C++ and Java, allowing any application to use facilities
22398 of R without the need of linking to R code. Rserve supports remote
22399 connection, user authentication and file transfer. A simple R client is
22400 included in this package as well.")
22401 (license license:gpl2)))
22403 (define-public r-brms
22410 (uri (cran-uri "brms" version))
22413 "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69"))))
22414 (properties `((upstream-name . "brms")))
22415 (build-system r-build-system)
22417 `(("r-abind" ,r-abind)
22418 ("r-backports" ,r-backports)
22419 ("r-bayesplot" ,r-bayesplot)
22420 ("r-bridgesampling" ,r-bridgesampling)
22422 ("r-future" ,r-future)
22423 ("r-ggplot2" ,r-ggplot2)
22426 ("r-matrix" ,r-matrix)
22427 ("r-matrixstats" ,r-matrixstats)
22429 ("r-nleqslv" ,r-nleqslv)
22432 ("r-rstan" ,r-rstan)
22433 ("r-rstantools" ,r-rstantools)
22434 ("r-shinystan" ,r-shinystan)))
22435 (native-inputs `(("r-knitr" ,r-knitr)))
22437 "https://github.com/paul-buerkner/brms")
22439 "Bayesian Regression Models using 'Stan'")
22441 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22442 using 'Stan' for full Bayesian inference. A wide range of distributions and
22443 link functions are supported, allowing users to fit -- among others -- linear,
22444 robust linear, count data, survival, response times, ordinal, zero-inflated,
22445 hurdle, and even self-defined mixture models all in a multilevel context.
22446 Further modeling options include non-linear and smooth terms, auto-correlation
22447 structures, censored data, meta-analytic standard errors, and quite a few
22448 more. In addition, all parameters of the response distribution can be
22449 predicted in order to perform distributional regression. Prior specifications
22450 are flexible and explicitly encourage users to apply prior distributions that
22451 actually reflect their beliefs. Model fit can easily be assessed and compared
22452 with posterior predictive checks and leave-one-out cross-validation.")
22453 (license license:gpl2)))
22455 (define-public r-mstate
22462 (uri (cran-uri "mstate" version))
22465 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22466 (properties `((upstream-name . "mstate")))
22467 (build-system r-build-system)
22469 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22470 ("r-survival" ,r-survival)))
22472 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22474 "Data Preparation, Estimation and Prediction in Multi-State Models")
22476 "Contains functions for data preparation, descriptives, hazard estimation
22477 and prediction with Aalen-Johansen or simulation in competing risks and
22478 multi-state models.")
22479 (license license:gpl2+)))
22481 (define-public r-scatterpie
22483 (name "r-scatterpie")
22488 (uri (cran-uri "scatterpie" version))
22491 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22492 (properties `((upstream-name . "scatterpie")))
22493 (build-system r-build-system)
22495 `(("r-ggforce" ,r-ggforce)
22496 ("r-ggplot2" ,r-ggplot2)
22497 ("r-rlang" ,r-rlang)
22498 ("r-rvcheck" ,r-rvcheck)
22499 ("r-tidyr" ,r-tidyr)))
22501 `(("r-knitr" ,r-knitr)))
22502 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22503 (synopsis "Scatter pie plot")
22505 "This package creates scatterpie plots, especially useful for plotting
22507 (license license:artistic2.0)))
22509 (define-public r-boruta
22516 (uri (cran-uri "Boruta" version))
22519 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22520 (properties `((upstream-name . "Boruta")))
22521 (build-system r-build-system)
22522 (propagated-inputs `(("r-ranger" ,r-ranger)))
22523 (home-page "https://gitlab.com/mbq/Boruta/")
22524 (synopsis "Wrapper algorithm for all relevant feature selection")
22526 "This package provides an all relevant feature selection wrapper
22527 algorithm. It finds relevant features by comparing original attributes'
22528 importance with importance achievable at random, estimated using their
22529 permuted copies (shadows).")
22530 (license license:gpl2+)))
22532 (define-public r-directlabels
22534 (name "r-directlabels")
22535 (version "2020.6.17")
22539 (uri (cran-uri "directlabels" version))
22542 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22543 (build-system r-build-system)
22545 `(("r-quadprog" ,r-quadprog)))
22547 `(("r-knitr" ,r-knitr)))
22548 (home-page "http://directlabels.r-forge.r-project.org/")
22549 (synopsis "Direct labels for multicolor plots")
22551 "This package provides an extensible framework for automatically placing
22552 direct labels onto multicolor plots. Label positions are described using
22553 positioning methods that can be re-used across several different plots. There
22554 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22555 inferring an appropriate positioning method.")
22556 (license license:gpl3)))
22558 (define-public r-lsd
22565 (uri (cran-uri "LSD" version))
22567 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22568 (properties `((upstream-name . "LSD")))
22569 (build-system r-build-system)
22570 (home-page "https://cran.r-project.org/web/packages/LSD/")
22571 (synopsis "Lots of superior depictions tool creates colorful plots")
22573 "This package creates lots of colorful plots in a multitude of variations.
22574 Try a demo of the LSD by running @code{demotour()}.")
22576 (license (list license:gpl2 license:gpl3))))
22578 (define-public r-fourcseq
22580 (name "r-fourcseq")
22585 (uri (bioconductor-uri "FourCSeq" version))
22587 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
22588 (properties `((upstream-name . "FourCSeq")))
22589 (build-system r-build-system)
22591 `(("r-biobase" ,r-biobase)
22592 ("r-biostrings" ,r-biostrings)
22593 ("r-deseq2" ,r-deseq2)
22595 ("r-genomicalignments" ,r-genomicalignments)
22596 ("r-genomicranges" ,r-genomicranges)
22597 ("r-ggbio" ,r-ggbio)
22598 ("r-ggplot2" ,r-ggplot2)
22599 ("r-gtools" ,r-gtools)
22601 ("r-matrix" ,r-matrix)
22602 ("r-reshape2" ,r-reshape2)
22603 ("r-rsamtools" ,r-rsamtools)
22604 ("r-rtracklayer" ,r-rtracklayer)
22605 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22607 `(("r-knitr" ,r-knitr)))
22609 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22610 (synopsis "Analysis of multiplexed 4C sequencing data")
22612 "This package is an R package dedicated to the analysis of (multiplexed)
22613 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22614 interactions between DNA elements and identify differential interactions
22615 between conditions. The statistical analysis in R starts with individual bam
22616 files for each sample as inputs. To obtain these files, the package contains
22617 a Python script to demultiplex libraries and trim off primer sequences. With
22618 a standard alignment software the required bam files can be then be
22620 (license license:gpl3+)))
22622 (define-public r-phylogram
22624 (name "r-phylogram")
22629 (uri (cran-uri "phylogram" version))
22631 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22632 (properties `((upstream-name . "phylogram")))
22633 (build-system r-build-system)
22634 (propagated-inputs `(("r-ape" ,r-ape)))
22635 (home-page "https://github.com/ropensci/phylogram/")
22636 (synopsis "Dendrograms for evolutionary analysis")
22638 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22639 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22640 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22641 as well as several tools for command-line tree manipulation and import/export
22642 via Newick parenthetic text. This improves accessibility to the comprehensive
22643 range of object-specific analytical and tree-visualization functions found
22644 across a wide array of bioinformatic R packages.")
22645 (license license:gpl3)))
22647 (define-public r-kmer
22654 (uri (cran-uri "kmer" version))
22656 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22657 (properties `((upstream-name . "kmer")))
22658 (build-system r-build-system)
22660 `(("r-openssl" ,r-openssl)
22661 ("r-phylogram" ,r-phylogram)
22662 ("r-rcpp" ,r-rcpp)))
22663 (home-page "https://github.com/shaunpwilkinson/kmer/")
22664 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22666 "@code{r-kmer} is an R package for rapidly computing distance matrices
22667 and clustering large sequence datasets using fast alignment-free k-mer
22668 counting and recursive k-means partitioning.")
22669 (license license:gpl3)))
22671 (define-public r-hardhat
22678 (uri (cran-uri "hardhat" version))
22681 "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
22682 (properties `((upstream-name . "hardhat")))
22683 (build-system r-build-system)
22685 `(("r-glue" ,r-glue)
22686 ("r-rlang" ,r-rlang)
22687 ("r-tibble" ,r-tibble)
22688 ("r-vctrs" ,r-vctrs)))
22690 `(("r-knitr" ,r-knitr)))
22691 (home-page "https://github.com/tidymodels/hardhat")
22692 (synopsis "Construct modeling packages")
22694 "Building modeling packages is hard. A large amount of effort generally
22695 goes into providing an implementation for a new method that is efficient,
22696 fast, and correct, but often less emphasis is put on the user interface. A
22697 good interface requires specialized knowledge about S3 methods and formulas,
22698 which the average package developer might not have. The goal of
22699 @code{hardhat} is to reduce the burden around building new modeling packages
22700 by providing functionality for preprocessing, predicting, and validating
22702 (license license:expat)))
22704 (define-public r-shapforxgboost
22706 (name "r-shapforxgboost")
22711 (uri (cran-uri "SHAPforxgboost" version))
22714 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22716 `((upstream-name . "SHAPforxgboost")))
22717 (build-system r-build-system)
22719 `(("r-bbmisc" ,r-bbmisc)
22720 ("r-data-table" ,r-data-table)
22721 ("r-ggextra" ,r-ggextra)
22722 ("r-ggforce" ,r-ggforce)
22723 ("r-ggplot2" ,r-ggplot2)
22724 ("r-ggpubr" ,r-ggpubr)
22725 ("r-rcolorbrewer" ,r-rcolorbrewer)
22726 ("r-xgboost" ,r-xgboost)))
22727 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22728 (synopsis "SHAP Plots for XGBoost")
22730 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22731 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22732 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22733 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22735 (license license:expat)))
22737 (define-public r-rismed
22744 (uri (cran-uri "RISmed" version))
22747 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22748 (properties `((upstream-name . "RISmed")))
22749 (build-system r-build-system)
22750 (home-page "https://cran.r-project.org/web/packages/RISmed")
22751 (synopsis "Download content from NCBI databases")
22753 "This package provides a set of tools to extract bibliographic
22754 content from the National Center for Biotechnology Information (NCBI)
22755 databases, including PubMed. The name RISmed is a portmanteau of
22756 RIS (for Research Information Systems, a common tag format for
22757 bibliographic data) and PubMed.")
22758 (license license:gpl2+)))
22760 (define-public r-semver
22767 (uri (cran-uri "semver" version))
22770 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22771 (properties `((upstream-name . "semver")))
22772 (build-system r-build-system)
22774 `(("r-assertthat" ,r-assertthat)
22775 ("r-rcpp" ,r-rcpp)))
22776 (native-inputs `(("r-knitr" ,r-knitr)))
22777 (home-page "https://github.com/johndharrison/semver")
22778 (synopsis "Parser for Semantic Versioning 2.0.0")
22780 "This package provides tools and functions for parsing, rendering and
22781 operating on semantic version strings. Semantic versioning is a simple set of
22782 rules and requirements that dictate how version numbers are assigned and
22783 incremented as outlined at @url{http://semver.org}.")
22784 (license license:expat)))
22786 (define-public r-binman
22793 (uri (cran-uri "binman" version))
22796 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22797 (properties `((upstream-name . "binman")))
22798 (build-system r-build-system)
22800 `(("r-assertthat" ,r-assertthat)
22802 ("r-jsonlite" ,r-jsonlite)
22803 ("r-rappdirs" ,r-rappdirs)
22804 ("r-semver" ,r-semver)
22806 ("r-yaml" ,r-yaml)))
22807 (native-inputs `(("r-knitr" ,r-knitr)))
22808 (home-page "https://github.com/ropensci/binman")
22809 (synopsis "Binary download manager")
22811 "This package provides tools and functions for managing the download of
22812 binary files. Binary repositories are defined in the YAML format. Defining
22813 new pre-download, download and post-download templates allow additional
22814 repositories to be added.")
22815 (license license:expat)))
22817 (define-public r-wdman
22824 (uri (cran-uri "wdman" version))
22827 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22828 (properties `((upstream-name . "wdman")))
22829 (build-system r-build-system)
22831 `(("r-assertthat" ,r-assertthat)
22832 ("r-binman" ,r-binman)
22833 ("r-processx" ,r-processx)
22834 ("r-semver" ,r-semver)
22835 ("r-yaml" ,r-yaml)))
22836 (native-inputs `(("r-knitr" ,r-knitr)))
22837 (home-page "https://docs.ropensci.org/wdman/")
22838 (synopsis "Webdriver/Selenium binary manager")
22840 "There are a number of binary files associated with the
22841 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22842 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22843 @url{https://github.com/mozilla/geckodriver},
22844 @url{http://phantomjs.org/download.html}, and
22845 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22846 more information). This package provides functions to download these binaries
22847 and to manage processes involving them.")
22848 (license license:expat)))
22850 (define-public r-rselenium
22852 (name "r-rselenium")
22857 (uri (cran-uri "RSelenium" version))
22860 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22861 (properties `((upstream-name . "RSelenium")))
22862 (build-system r-build-system)
22864 `(("r-binman" ,r-binman)
22865 ("r-catools" ,r-catools)
22867 ("r-openssl" ,r-openssl)
22868 ("r-wdman" ,r-wdman)
22870 (native-inputs `(("r-knitr" ,r-knitr)))
22871 (home-page "https://docs.ropensci.org/RSelenium/")
22872 (synopsis "R bindings for Selenium WebDriver")
22874 "This package provides a set of R bindings for the Selenium 2.0
22875 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22876 information) using the @code{JsonWireProtocol} (see
22877 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22878 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22879 a user would either locally or on a remote machine using the Selenium server
22880 it marks a leap forward in terms of web browser automation. Selenium
22881 automates web browsers (commonly referred to as browsers). Using RSelenium
22882 you can automate browsers locally or remotely.")
22883 (license license:agpl3+)))
22885 (define-public r-conquer
22892 (uri (cran-uri "conquer" version))
22895 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
22896 (properties `((upstream-name . "conquer")))
22897 (build-system r-build-system)
22899 `(("r-matrix" ,r-matrix)
22900 ("r-matrixstats" ,r-matrixstats)
22902 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22903 (home-page "https://github.com/XiaoouPan/conquer")
22904 (synopsis "Convolution-type smoothed quantile regression")
22906 "This package provides fast and accurate convolution-type smoothed
22907 quantile regression, implemented using Barzilai-Borwein gradient descent with
22908 a Huber regression warm start. Confidence intervals for regression
22909 coefficients are constructed using multiplier bootstrap.")
22910 (license license:gpl3)))
22912 (define-public r-fastshap
22914 (name "r-fastshap")
22919 (uri (cran-uri "fastshap" version))
22922 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22923 (properties `((upstream-name . "fastshap")))
22924 (build-system r-build-system)
22926 `(("r-abind" ,r-abind)
22927 ("r-ggplot2" ,r-ggplot2)
22928 ("r-gridextra" ,r-gridextra)
22929 ("r-matrixstats" ,r-matrixstats)
22932 ("r-rcpparmadillo" ,r-rcpparmadillo)
22933 ("r-tibble" ,r-tibble)))
22934 (home-page "https://github.com/bgreenwell/fastshap")
22935 (synopsis "Fast approximate Shapley values")
22937 "This package computes fast (relative to other implementations)
22938 approximate Shapley values for any supervised learning model. Shapley values
22939 help to explain the predictions from any black box model using ideas from game
22940 theory; see @url{Strumbel and Kononenko (2014),
22941 doi.org/10.1007/s10115-013-0679-x} for details.")
22942 (license license:gpl2+)))
22944 (define-public r-metrics
22951 (uri (cran-uri "Metrics" version))
22954 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22955 (properties `((upstream-name . "Metrics")))
22956 (build-system r-build-system)
22957 (home-page "https://github.com/mfrasco/Metrics")
22958 (synopsis "Evaluation metrics for machine learning")
22960 "This package provides an implementation of evaluation metrics in R that
22961 are commonly used in supervised machine learning. It implements metrics for
22962 regression, time series, binary classification, classification, and
22963 information retrieval problems. It has zero dependencies and a consistent,
22964 simple interface for all functions.")
22965 (license license:bsd-3)))
22967 (define-public r-iml
22974 (uri (cran-uri "iml" version))
22977 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22978 (properties `((upstream-name . "iml")))
22979 (build-system r-build-system)
22981 `(("r-checkmate" ,r-checkmate)
22982 ("r-data-table" ,r-data-table)
22983 ("r-formula" ,r-formula)
22984 ("r-future" ,r-future)
22985 ("r-future-apply" ,r-future-apply)
22986 ("r-ggplot2" ,r-ggplot2)
22987 ("r-gridextra" ,r-gridextra)
22988 ("r-metrics" ,r-metrics)
22989 ("r-prediction" ,r-prediction)
22991 (native-inputs `(("r-knitr" ,r-knitr)))
22992 (home-page "https://github.com/christophM/iml")
22993 (synopsis "Interpretable machine learning")
22995 "This package provides interpretability methods to analyze the behavior
22996 and predictions of any machine learning model. Implemented methods are:
22999 @item Feature importance described by Fisher et al. (2018),
23000 @item accumulated local effects plots described by Apley (2018),
23001 @item partial dependence plots described by Friedman (2001),
23002 @item individual conditional expectation ('ice') plots described by Goldstein
23003 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
23004 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
23005 @item the Shapley Value described by Strumbelj et. al (2014)
23006 @url{https://doi.org/10.1007/s10115-013-0679-x},
23007 @item feature interactions described by Friedman et. al
23008 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
23011 (license license:expat)))
23013 (define-public r-goftest
23020 (uri (cran-uri "goftest" version))
23023 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
23024 (properties `((upstream-name . "goftest")))
23025 (build-system r-build-system)
23026 (home-page "https://github.com/baddstats/goftest")
23027 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
23029 "This package provides Cramer-Von Mises and Anderson-Darling tests of
23030 goodness-of-fit for continuous univariate distributions, using efficient
23032 (license license:gpl2+)))
23034 (define-public r-tensor
23041 (uri (cran-uri "tensor" version))
23044 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
23045 (properties `((upstream-name . "tensor")))
23046 (build-system r-build-system)
23047 (home-page "https://cran.r-project.org/web/packages/tensor/")
23048 (synopsis "Tensor product of arrays")
23050 "The tensor product of two arrays is notionally an outer product of the
23051 arrays collapsed in specific extents by summing along the appropriate
23052 diagonals. This package allows you to compute the tensor product of arrays.")
23053 (license license:gpl2+)))
23055 (define-public r-spatstat-utils
23057 (name "r-spatstat-utils")
23062 (uri (cran-uri "spatstat.utils" version))
23065 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
23067 `((upstream-name . "spatstat.utils")))
23068 (build-system r-build-system)
23069 (home-page "http://www.spatstat.org")
23070 (synopsis "Utility functions for spatstat")
23072 "This package contains utility functions for the @code{spatstat} package
23073 which may also be useful for other purposes.")
23074 (license license:gpl2+)))
23076 (define-public r-spatstat-data
23078 (name "r-spatstat-data")
23083 (uri (cran-uri "spatstat.data" version))
23086 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
23087 (properties `((upstream-name . "spatstat.data")))
23088 (build-system r-build-system)
23090 `(("r-matrix" ,r-matrix)
23091 ("r-spatstat-utils" ,r-spatstat-utils)))
23092 (home-page "http://www.spatstat.org")
23093 (synopsis "Datasets for spatstat")
23095 "This package contains all the datasets for the @code{spatstat}
23097 (license license:gpl2+)))
23099 (define-public r-spatstat
23101 (name "r-spatstat")
23106 (uri (cran-uri "spatstat" version))
23109 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
23110 (properties `((upstream-name . "spatstat")))
23111 (build-system r-build-system)
23113 `(("r-abind" ,r-abind)
23114 ("r-deldir" ,r-deldir)
23115 ("r-goftest" ,r-goftest)
23116 ("r-matrix" ,r-matrix)
23119 ("r-polyclip" ,r-polyclip)
23120 ("r-rpart" ,r-rpart)
23121 ("r-spatstat-data" ,r-spatstat-data)
23122 ("r-spatstat-utils" ,r-spatstat-utils)
23123 ("r-tensor" ,r-tensor)))
23124 (home-page "http://www.spatstat.org")
23125 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
23127 "This package provides a comprehensive toolbox for analysing Spatial
23128 Point Patterns. It is focused mainly on two-dimensional point patterns,
23129 including multitype/marked points, in any spatial region. It also supports
23130 three-dimensional point patterns, space-time point patterns in any number of
23131 dimensions, point patterns on a linear network, and patterns of other
23132 geometrical objects. It supports spatial covariate data such as pixel images
23133 and contains over 2000 functions for plotting spatial data, exploratory data
23134 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
23135 formal inference.")
23136 (license license:gpl2+)))
23138 (define-public r-gaston
23145 (uri (cran-uri "gaston" version))
23148 "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg"))))
23149 (properties `((upstream-name . "gaston")))
23150 (build-system r-build-system)
23151 (inputs `(("zlib" ,zlib)))
23153 `(("r-rcpp" ,r-rcpp)
23154 ("r-rcppeigen" ,r-rcppeigen)
23155 ("r-rcppparallel" ,r-rcppparallel)))
23156 (native-inputs `(("r-knitr" ,r-knitr)))
23157 (home-page "https://cran.r-project.org/web/packages/gaston/")
23158 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
23160 "This is a package for the manipulation of genetic data (SNPs).
23161 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
23162 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
23163 for linear mixed models (AIREML).")
23164 (license license:gpl3)))
23166 (define-public r-cpp11
23173 (uri (cran-uri "cpp11" version))
23176 "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda"))))
23177 (properties `((upstream-name . "cpp11")))
23178 (build-system r-build-system)
23179 (native-inputs `(("r-knitr" ,r-knitr)))
23180 (home-page "https://github.com/r-lib/cpp11")
23181 (synopsis "C++11 Interface for R's C Interface")
23183 "This package provides a header only, C++11 interface to R's C interface.
23184 Compared to other approaches @code{cpp11} strives to be safe against long
23185 jumps from the C API as well as C++ exceptions, conform to normal R function
23186 semantics and supports interaction with @code{ALTREP} vectors.")
23187 (license license:expat)))
23189 (define-public r-rcppziggurat
23191 (name "r-rcppziggurat")
23196 (uri (cran-uri "RcppZiggurat" version))
23199 "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv"))))
23200 (properties `((upstream-name . "RcppZiggurat")))
23201 (build-system r-build-system)
23203 `(("r-rcpp" ,r-rcpp)
23204 ("r-rcppgsl" ,r-rcppgsl)))
23205 (native-inputs `(("r-knitr" ,r-knitr)))
23206 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
23207 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
23209 "The Ziggurat generator for normally distributed random numbers,
23210 originally proposed by Marsaglia and Tsang (2000,
23211 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
23212 times starting with Leong et al (2005,
23213 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
23214 aggregation for comparing different implementations in order to provide a
23215 'faster but good enough' alternative for use with R and C++ code.")
23216 (license license:gpl2+)))
23218 (define-public r-rfast
23225 (uri (cran-uri "Rfast" version))
23228 "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
23229 (properties `((upstream-name . "Rfast")))
23230 (build-system r-build-system)
23232 `(("r-rcpp" ,r-rcpp)
23233 ("r-rcpparmadillo" ,r-rcpparmadillo)
23234 ("r-rcppziggurat" ,r-rcppziggurat)))
23235 (home-page "https://github.com/RfastOfficial/Rfast")
23236 (synopsis "Collection of efficient and fast R functions")
23238 "This package provides a collection of fast (utility) functions for data
23239 analysis. Column- and row- wise means, medians, variances, minimums,
23240 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23241 Poisson), are some of the many fast functions.")
23242 (license license:gpl2+)))
23244 (define-public r-clusterr
23246 (name "r-clusterr")
23251 (uri (cran-uri "ClusterR" version))
23254 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23255 (properties `((upstream-name . "ClusterR")))
23256 (build-system r-build-system)
23258 `(("r-ggplot2" ,r-ggplot2)
23260 ("r-gtools" ,r-gtools)
23262 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23263 (native-inputs `(("r-knitr" ,r-knitr)))
23264 (home-page "https://github.com/mlampros/ClusterR")
23265 (synopsis "Clustering")
23267 "This package provides Gaussian mixture models, k-means,
23268 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23269 option to plot, validate, predict (new data) and estimate the optimal number
23270 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23271 the computationally intensive parts of the functions. For more information,
23275 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23276 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23277 @url{https://doi.org/10.18637/jss.v001.i04};
23278 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23279 Library, @url{https://doi.org/10.1145/1772690.1772862};
23280 @item \"Armadillo: a template-based C++ library
23281 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23282 Software, @url{https://doi.org/10.21105/joss.00026};
23283 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23284 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23285 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23288 (license license:gpl3)))
23290 (define-public r-spectrum
23292 (name "r-spectrum")
23297 (uri (cran-uri "Spectrum" version))
23300 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23301 (properties `((upstream-name . "Spectrum")))
23302 (build-system r-build-system)
23304 `(("r-clusterr" ,r-clusterr)
23305 ("r-diptest" ,r-diptest)
23306 ("r-ggplot2" ,r-ggplot2)
23307 ("r-rfast" ,r-rfast)))
23308 (native-inputs `(("r-knitr" ,r-knitr)))
23309 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23310 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23312 "This package provides a self-tuning spectral clustering method for
23313 single or multi-view data. Spectrum uses a new type of adaptive density aware
23314 kernel that strengthens connections in the graph based on common nearest
23315 neighbours. It uses a tensor product graph data integration and diffusion
23316 procedure to integrate different data sources and reduce noise. Spectrum uses
23317 either the eigengap or multimodality gap heuristics to determine the number of
23318 clusters. The method is sufficiently flexible so that a wide range of
23319 Gaussian and non-Gaussian structures can be clustered with automatic selection
23321 (license license:agpl3+)))
23323 (define-public r-nabor
23330 (uri (cran-uri "nabor" version))
23333 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23334 (properties `((upstream-name . "nabor")))
23335 (build-system r-build-system)
23339 ("r-rcppeigen" ,r-rcppeigen)))
23340 (home-page "https://cran.r-project.org/web/packages/nabor/")
23341 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23343 "This package provides an R wrapper for libnabo, an exact or approximate
23344 k nearest neighbour library which is optimised for low dimensional
23345 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23346 designed as a drop-in replacement for the RANN function @code{nn2}. In
23347 addition, objects which include the k-d tree search structure can be returned
23348 to speed up repeated queries of the same set of target points.")
23349 (license license:bsd-3)))
23351 (define-public r-muhaz
23354 (version "1.2.6.1")
23358 (uri (cran-uri "muhaz" version))
23361 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
23362 (properties `((upstream-name . "muhaz")))
23363 (build-system r-build-system)
23365 `(("r-survival" ,r-survival)))
23367 `(("gfortran" ,gfortran)))
23368 (home-page "https://cran.r-project.org/web/packages/muhaz/")
23369 (synopsis "Hazard function estimation in survival analysis")
23371 "This package produces a smooth estimate of the hazard function for
23373 ;; Any version of the GPL.
23374 (license license:gpl3+)))
23376 (define-public r-flexsurv
23378 (name "r-flexsurv")
23383 (uri (cran-uri "flexsurv" version))
23386 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
23387 (properties `((upstream-name . "flexsurv")))
23388 (build-system r-build-system)
23390 `(("r-desolve" ,r-desolve)
23391 ("r-mstate" ,r-mstate)
23392 ("r-muhaz" ,r-muhaz)
23393 ("r-mvtnorm" ,r-mvtnorm)
23394 ("r-quadprog" ,r-quadprog)
23396 ("r-survival" ,r-survival)
23397 ("r-tibble" ,r-tibble)
23398 ("r-tidyr" ,r-tidyr)))
23400 `(("r-knitr" ,r-knitr)))
23401 (home-page "https://github.com/chjackson/flexsurv-dev")
23402 (synopsis "Flexible parametric survival and multi-state models")
23404 "This package provides flexible parametric models for time-to-event data,
23405 including the Royston-Parmar spline model, generalized gamma and generalized F
23406 distributions. Any user-defined parametric distribution can be fitted, given
23407 at least an R function defining the probability density or hazard. There are
23408 also tools for fitting and predicting from fully parametric multi-state
23410 (license license:gpl2+)))
23412 (define-public r-transphylo
23414 (name "r-transphylo")
23419 (uri (cran-uri "TransPhylo" version))
23422 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
23423 (properties `((upstream-name . "TransPhylo")))
23424 (build-system r-build-system)
23427 ("r-rcpp" ,r-rcpp)))
23429 `(("r-knitr" ,r-knitr)))
23430 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
23431 (synopsis "Inference of transmission tree from a dated phylogeny")
23433 "This is a package to infer transmission trees from a dated phylogeny.
23434 It includes methods to simulate and analyze outbreaks. The methodology is
23435 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
23436 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
23437 (license license:gpl2+)))
23439 (define-public r-km-ci
23446 (uri (cran-uri "km.ci" version))
23449 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
23450 (properties `((upstream-name . "km.ci")))
23451 (build-system r-build-system)
23453 `(("r-survival" ,r-survival)))
23454 (home-page "https://cran.r-project.org/web/packages/km.ci/")
23455 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
23457 "This package computes various @dfn{confidence intervals} (CI) for the
23458 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
23459 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
23460 Nair and Hall and Wellner.")
23461 (license license:gpl2+)))
23463 (define-public r-kmsurv
23470 (uri (cran-uri "KMsurv" version))
23473 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
23474 (properties `((upstream-name . "KMsurv")))
23475 (build-system r-build-system)
23476 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
23477 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
23479 "This package provides data sets and functions for Klein and Moeschberger
23480 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
23482 (license license:gpl3+)))
23484 (define-public r-survmisc
23486 (name "r-survmisc")
23491 (uri (cran-uri "survMisc" version))
23494 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
23495 (properties `((upstream-name . "survMisc")))
23496 (build-system r-build-system)
23498 `(("r-data-table" ,r-data-table)
23499 ("r-ggplot2" ,r-ggplot2)
23500 ("r-gridextra" ,r-gridextra)
23501 ("r-km-ci" ,r-km-ci)
23502 ("r-kmsurv" ,r-kmsurv)
23503 ("r-knitr" ,r-knitr)
23504 ("r-survival" ,r-survival)
23505 ("r-xtable" ,r-xtable)
23508 `(("r-knitr" ,r-knitr)))
23509 (home-page "https://cran.r-project.org/web/packages/survMisc/")
23510 (synopsis "Miscellaneous functions for survival data")
23512 "This package provides a collection of functions to help in the analysis
23513 of right-censored survival data. These extend the methods available in
23514 the @code{survival} package.")
23515 (license license:gpl2)))
23517 (define-public r-exactranktests
23519 (name "r-exactranktests")
23524 (uri (cran-uri "exactRankTests" version))
23527 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
23529 `((upstream-name . "exactRankTests")))
23530 (build-system r-build-system)
23531 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
23532 (synopsis "Exact distributions for rank and permutation tests")
23534 "This package computes exact conditional p-values and quantiles using an
23535 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
23536 (license license:gpl2+)))
23538 (define-public r-maxstat
23545 (uri (cran-uri "maxstat" version))
23548 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
23549 (properties `((upstream-name . "maxstat")))
23550 (build-system r-build-system)
23552 `(("r-exactranktests" ,r-exactranktests)
23553 ("r-mvtnorm" ,r-mvtnorm)))
23554 (home-page "https://cran.r-project.org/web/packages/maxstat/")
23555 (synopsis "Maximally selected rank statistics")
23557 "This package provides maximally selected rank statistics with several
23558 p-value approximations.")
23559 (license license:gpl2+)))
23561 (define-public r-survminer
23563 (name "r-survminer")
23568 (uri (cran-uri "survminer" version))
23571 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
23572 (properties `((upstream-name . "survminer")))
23573 (build-system r-build-system)
23575 `(("r-broom" ,r-broom)
23576 ("r-dplyr" ,r-dplyr)
23577 ("r-ggplot2" ,r-ggplot2)
23578 ("r-ggpubr" ,r-ggpubr)
23579 ("r-gridextra" ,r-gridextra)
23580 ("r-magrittr" ,r-magrittr)
23581 ("r-maxstat" ,r-maxstat)
23582 ("r-purrr" ,r-purrr)
23583 ("r-rlang" ,r-rlang)
23584 ("r-scales" ,r-scales)
23585 ("r-survival" ,r-survival)
23586 ("r-survmisc" ,r-survmisc)
23587 ("r-tibble" ,r-tibble)
23588 ("r-tidyr" ,r-tidyr)))
23590 `(("r-knitr" ,r-knitr)))
23591 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
23592 (synopsis "Drawing survival curves using ggplot2")
23594 "This package contains the function @code{ggsurvplot()} for easily
23595 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
23596 risk' table and 'censoring count plot'. Other functions are also available to
23597 plot adjusted curves for Cox model and to visually examine Cox model
23599 (license license:gpl2)))
23601 (define-public r-forge
23608 (uri (cran-uri "forge" version))
23611 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
23612 (properties `((upstream-name . "forge")))
23613 (build-system r-build-system)
23615 `(("r-magrittr" ,r-magrittr)
23616 ("r-rlang" ,r-rlang)))
23617 (home-page "https://cran.r-project.org/web/packages/forge/")
23618 (synopsis "Cast values into shape")
23620 "This package provides helper functions with a consistent interface to
23621 coerce and verify the types and shapes of values for input checking.")
23622 (license license:asl2.0)))
23624 (define-public r-config
23631 (uri (cran-uri "config" version))
23634 "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
23635 (properties `((upstream-name . "config")))
23636 (build-system r-build-system)
23638 `(("r-yaml" ,r-yaml)))
23640 `(("r-knitr" ,r-knitr)))
23641 (home-page "https://github.com/rstudio/config")
23642 (synopsis "Manage environment specific configuration values")
23644 "This package lets you manage configuration values across multiple
23645 environments (e.g. development, test, production). It reads values using a
23646 function that determines the current environment and returns the appropriate
23648 (license license:gpl3)))
23650 (define-public r-adaptivesparsity
23652 (name "r-adaptivesparsity")
23656 (uri (cran-uri "AdaptiveSparsity" version))
23659 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
23661 `((upstream-name . "AdaptiveSparsity")))
23662 (build-system r-build-system)
23665 (modify-phases %standard-phases
23666 (add-after 'unpack 'link-against-armadillo
23668 (substitute* "src/Makevars"
23669 (("PKG_LIBS=" prefix)
23670 (string-append prefix "-larmadillo")))
23673 `(("r-mass" ,r-mass)
23674 ("r-matrix" ,r-matrix)
23676 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23678 `(("armadillo" ,armadillo)))
23679 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
23680 (synopsis "Adaptive sparsity models")
23682 "This package implements the Figueiredo machine learning algorithm for
23683 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
23684 geometric models.")
23685 (license license:lgpl3+)))
23687 (define-public r-diffusionmap
23689 (name "r-diffusionmap")
23694 (uri (cran-uri "diffusionMap" version))
23697 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
23698 (properties `((upstream-name . "diffusionMap")))
23699 (build-system r-build-system)
23701 `(("r-igraph" ,r-igraph)
23702 ("r-matrix" ,r-matrix)
23703 ("r-scatterplot3d" ,r-scatterplot3d)))
23704 (home-page "https://www.r-project.org")
23705 (synopsis "Diffusion map")
23706 (description "This package implements the diffusion map method of data
23707 parametrization, including creation and visualization of diffusion maps,
23708 clustering with diffusion K-means and regression using the adaptive regression
23710 (license license:gpl2)))
23712 (define-public r-igraph
23719 (uri (cran-uri "igraph" version))
23722 "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
23723 (build-system r-build-system)
23725 `(("gfortran" ,gfortran)))
23729 ("libxml2" ,libxml2)
23732 `(("r-magrittr" ,r-magrittr)
23733 ("r-matrix" ,r-matrix)
23734 ("r-pkgconfig" ,r-pkgconfig)))
23735 (home-page "https://igraph.org")
23736 (synopsis "Network analysis and visualization")
23738 "This package provides routines for simple graphs and network analysis.
23739 It can handle large graphs very well and provides functions for generating
23740 random and regular graphs, graph visualization, centrality methods and much
23742 (license license:gpl2+)))
23744 (define-public r-workflows
23746 (name "r-workflows")
23751 (uri (cran-uri "workflows" version))
23754 "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m"))))
23755 (properties `((upstream-name . "workflows")))
23756 (build-system r-build-system)
23759 ("r-ellipsis" ,r-ellipsis)
23760 ("r-generics" ,r-generics)
23762 ("r-hardhat" ,r-hardhat)
23763 ("r-parsnip" ,r-parsnip)
23764 ("r-rlang" ,r-rlang)))
23766 `(("r-knitr" ,r-knitr)))
23767 (home-page "https://github.com/tidymodels/workflows")
23768 (synopsis "Modeling workflows")
23770 "A workflow is an object that can bundle together your pre-processing,
23771 modeling, and post-processing requests. For example, if you have a
23772 @code{recipe} and @code{parsnip} model, these can be combined into a
23773 workflow. The advantages are:
23776 @item You don’t have to keep track of separate objects in your workspace.
23777 @item The recipe prepping and model fitting can be executed using a single
23778 call to @code{fit()}.
23779 @item If you have custom tuning parameter settings, these can be defined using
23780 a simpler interface when combined with @code{tune}.
23781 @item In the future, workflows will be able to add post-processing operations,
23782 such as modifying the probability cutoff for two-class models.
23785 (license license:expat)))
23787 (define-public r-gpfit
23794 (uri (cran-uri "GPfit" version))
23797 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
23798 (properties `((upstream-name . "GPfit")))
23799 (build-system r-build-system)
23801 `(("r-lattice" ,r-lattice)
23803 (home-page "https://cran.r-project.org/web/packages/GPfit/")
23804 (synopsis "Gaussian Processes modeling")
23806 "This package provides a computationally stable approach of fitting a
23807 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
23808 (license license:gpl2)))
23810 (define-public r-yardstick
23812 (name "r-yardstick")
23817 (uri (cran-uri "yardstick" version))
23820 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
23821 (properties `((upstream-name . "yardstick")))
23822 (build-system r-build-system)
23824 `(("r-dplyr" ,r-dplyr)
23825 ("r-generics" ,r-generics)
23827 ("r-rlang" ,r-rlang)
23828 ("r-tidyselect" ,r-tidyselect)))
23830 `(("r-knitr" ,r-knitr)))
23831 (home-page "https://github.com/tidymodels/yardstick")
23832 (synopsis "Tidy characterizations of model performance")
23834 "This package provides tidy tools for quantifying how well a model fits
23835 to a data set such as confusion matrices, class probability curve summaries,
23836 and regression metrics (e.g., RMSE).")
23837 (license license:gpl2)))
23839 (define-public r-rsample
23846 (uri (cran-uri "rsample" version))
23849 "0s6hgq0rcv3ianyidq3n9z34y5ww51gaggqkwmwns9yyxmwfjcm8"))))
23850 (properties `((upstream-name . "rsample")))
23851 (build-system r-build-system)
23853 `(("r-dplyr" ,r-dplyr)
23854 ("r-furrr" ,r-furrr)
23855 ("r-generics" ,r-generics)
23856 ("r-purrr" ,r-purrr)
23857 ("r-rlang" ,r-rlang)
23858 ("r-tibble" ,r-tibble)
23859 ("r-tidyr" ,r-tidyr)
23860 ("r-tidyselect" ,r-tidyselect)
23861 ("r-vctrs" ,r-vctrs)))
23863 `(("r-knitr" ,r-knitr)))
23864 (home-page "https://rsample.tidymodels.org")
23865 (synopsis "General resampling infrastructure")
23867 "This package provides classes and functions to create and summarize
23868 different types of resampling objects (e.g. bootstrap, cross-validation).")
23869 (license license:gpl2)))
23871 (define-public r-dicedesign
23873 (name "r-dicedesign")
23878 (uri (cran-uri "DiceDesign" version))
23881 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
23882 (properties `((upstream-name . "DiceDesign")))
23883 (build-system r-build-system)
23884 (home-page "http://dice.emse.fr/")
23885 (synopsis "Designs of computer experiments")
23887 "This package provides tools to create some specific @code{Space-Filling
23888 Design} (SFD) and to test their quality.")
23889 (license license:gpl3)))
23891 (define-public r-dials
23898 (uri (cran-uri "dials" version))
23901 "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p"))))
23902 (properties `((upstream-name . "dials")))
23903 (build-system r-build-system)
23905 `(("r-dicedesign" ,r-dicedesign)
23906 ("r-dplyr" ,r-dplyr)
23908 ("r-purrr" ,r-purrr)
23909 ("r-rlang" ,r-rlang)
23910 ("r-scales" ,r-scales)
23911 ("r-tibble" ,r-tibble)
23912 ("r-vctrs" ,r-vctrs)
23913 ("r-withr" ,r-withr)))
23914 (native-inputs `(("r-knitr" ,r-knitr)))
23915 (home-page "https://dials.tidymodels.org/")
23916 (synopsis "Tools for creating tuning parameter values")
23918 "Many models contain tuning parameters (i.e. parameters that cannot be
23919 directly estimated from the data). These tools can be used to define objects
23920 for creating, simulating, or validating values for such parameters.")
23921 (license license:gpl2)))
23923 (define-public r-tune
23930 (uri (cran-uri "tune" version))
23933 "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
23934 (properties `((upstream-name . "tune")))
23935 (build-system r-build-system)
23938 ("r-crayon" ,r-crayon)
23939 ("r-dials" ,r-dials)
23940 ("r-dplyr" ,r-dplyr)
23941 ("r-foreach" ,r-foreach)
23942 ("r-ggplot2" ,r-ggplot2)
23944 ("r-gpfit" ,r-gpfit)
23945 ("r-hardhat" ,r-hardhat)
23946 ("r-lifecycle" ,r-lifecycle)
23947 ("r-parsnip" ,r-parsnip)
23948 ("r-purrr" ,r-purrr)
23949 ("r-recipes" ,r-recipes)
23950 ("r-rlang" ,r-rlang)
23951 ("r-rsample" ,r-rsample)
23952 ("r-tibble" ,r-tibble)
23953 ("r-tidyr" ,r-tidyr)
23954 ("r-vctrs" ,r-vctrs)
23955 ("r-workflows" ,r-workflows)
23956 ("r-yardstick" ,r-yardstick)))
23957 (home-page "https://github.com/tidymodels/tune")
23958 (synopsis "Tidy tuning tools")
23960 "The ability to tune models is important. @code{tune} contains functions
23961 and classes to be used in conjunction with other @code{tidymodels} packages
23962 for finding reasonable values of hyper-parameters in models, pre-processing
23963 methods, and post-processing steps.")
23964 (license license:expat)))
23966 (define-public r-tidyposterior
23968 (name "r-tidyposterior")
23973 (uri (cran-uri "tidyposterior" version))
23976 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
23977 (properties `((upstream-name . "tidyposterior")))
23978 (build-system r-build-system)
23980 `(("r-dplyr" ,r-dplyr)
23981 ("r-generics" ,r-generics)
23982 ("r-ggplot2" ,r-ggplot2)
23983 ("r-lifecycle" ,r-lifecycle)
23984 ("r-purrr" ,r-purrr)
23985 ("r-rlang" ,r-rlang)
23986 ("r-rsample" ,r-rsample)
23987 ("r-rstanarm" ,r-rstanarm)
23988 ("r-tibble" ,r-tibble)
23989 ("r-tidyr" ,r-tidyr)
23990 ("r-vctrs" ,r-vctrs)))
23992 `(("r-knitr" ,r-knitr)))
23993 (home-page "https://tidyposterior.tidymodels.org")
23994 (synopsis "Bayesian analysis to compare models using resampling statistics")
23996 "This package can be used to conduct post hoc analyses of resampling
23997 results generated by models. For example, if two models are evaluated with
23998 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
23999 are 10 paired statistics. These can be used to make comparisons between
24000 models without involving a test set.")
24001 (license license:gpl2)))
24003 (define-public r-tidypredict
24005 (name "r-tidypredict")
24010 (uri (cran-uri "tidypredict" version))
24013 "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
24014 (properties `((upstream-name . "tidypredict")))
24015 (build-system r-build-system)
24017 `(("r-dplyr" ,r-dplyr)
24018 ("r-generics" ,r-generics)
24019 ("r-knitr" ,r-knitr)
24020 ("r-purrr" ,r-purrr)
24021 ("r-rlang" ,r-rlang)
24022 ("r-tibble" ,r-tibble)))
24024 `(("r-knitr" ,r-knitr)))
24025 (home-page "https://tidypredict.tidymodels.org")
24026 (synopsis "Run predictions inside the database")
24028 "This package parses a fitted R model object, and returns a formula in
24029 Tidy Eval code that calculates the predictions. It works with several
24030 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
24031 final SQL translation of the algorithm. It currently supports @code{lm()},
24032 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
24033 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
24034 (license license:gpl3)))
24036 (define-public r-janeaustenr
24038 (name "r-janeaustenr")
24043 (uri (cran-uri "janeaustenr" version))
24046 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
24047 (properties `((upstream-name . "janeaustenr")))
24048 (build-system r-build-system)
24049 (home-page "https://github.com/juliasilge/janeaustenr")
24050 (synopsis "Jane Austen's complete novels")
24052 "This package provides the full texts for Jane Austen's six completed
24053 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
24054 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
24055 and \"Persuasion\".")
24056 (license license:expat)))
24058 (define-public r-tokenizers
24060 (name "r-tokenizers")
24065 (uri (cran-uri "tokenizers" version))
24068 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
24069 (properties `((upstream-name . "tokenizers")))
24070 (build-system r-build-system)
24072 `(("r-rcpp" ,r-rcpp)
24073 ("r-snowballc" ,r-snowballc)
24074 ("r-stringi" ,r-stringi)))
24076 `(("r-knitr" ,r-knitr)))
24077 (home-page "https://lincolnmullen.com/software/tokenizers/")
24078 (synopsis "Fast, consistent tokenization of natural language text")
24080 "This is a package for converting natural language text into tokens.
24081 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
24082 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
24083 Treebank, regular expressions, as well as functions for counting characters,
24084 words, and sentences, and a function for splitting longer texts into separate
24085 documents, each with the same number of words. The tokenizers have a
24086 consistent interface, and the package is built on the @code{stringi} and
24087 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
24088 (license license:expat)))
24090 (define-public r-hunspell
24092 (name "r-hunspell")
24097 (uri (cran-uri "hunspell" version))
24100 "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
24101 (properties `((upstream-name . "hunspell")))
24102 (build-system r-build-system)
24104 `(("r-digest" ,r-digest)
24105 ("r-rcpp" ,r-rcpp)))
24107 `(("r-knitr" ,r-knitr)))
24108 (home-page "https://github.com/ropensci/hunspell#readme")
24109 (synopsis "High-performance stemmer, tokenizer, and spell checker")
24111 "This package provides a low-level spell checker and morphological
24112 analyzer based on the famous @code{hunspell} library. The package can analyze
24113 or check individual words as well as parse text, LaTeX, HTML or XML documents.
24114 For a more user-friendly interface use the @code{spelling} package which
24115 builds on this package to automate checking of files, documentation and
24116 vignettes in all common formats.")
24117 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
24118 ;; MPL; in addition to these licenses the rest of the R wrapper is also
24119 ;; available under the Expat license.
24120 (license (list license:gpl2
24125 (define-public r-tidytext
24127 (name "r-tidytext")
24132 (uri (cran-uri "tidytext" version))
24135 "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
24136 (properties `((upstream-name . "tidytext")))
24137 (build-system r-build-system)
24139 `(("r-dplyr" ,r-dplyr)
24140 ("r-generics" ,r-generics)
24141 ("r-hunspell" ,r-hunspell)
24142 ("r-janeaustenr" ,r-janeaustenr)
24143 ("r-matrix" ,r-matrix)
24144 ("r-purrr" ,r-purrr)
24145 ("r-rlang" ,r-rlang)
24146 ("r-stringr" ,r-stringr)
24147 ("r-tibble" ,r-tibble)
24148 ("r-tokenizers" ,r-tokenizers)))
24150 `(("r-knitr" ,r-knitr)))
24151 (home-page "https://github.com/juliasilge/tidytext")
24152 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
24154 "This is a package for text mining for word processing and sentiment
24155 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
24156 (license license:expat)))
24158 (define-public r-parsnip
24165 (uri (cran-uri "parsnip" version))
24168 "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
24169 (properties `((upstream-name . "parsnip")))
24170 (build-system r-build-system)
24172 `(("r-dplyr" ,r-dplyr)
24173 ("r-generics" ,r-generics)
24174 ("r-globals" ,r-globals)
24176 ("r-magrittr" ,r-magrittr)
24177 ("r-prettyunits" ,r-prettyunits)
24178 ("r-purrr" ,r-purrr)
24179 ("r-rlang" ,r-rlang)
24180 ("r-tibble" ,r-tibble)
24181 ("r-tidyr" ,r-tidyr)
24182 ("r-vctrs" ,r-vctrs)))
24184 `(("r-knitr" ,r-knitr)))
24185 (home-page "https://parsnip.tidymodels.org")
24186 (synopsis "Common API to modeling and analysis functions")
24188 "This package provides a common interface to allow users to specify a
24189 model without having to remember the different argument names across different
24190 functions or computational engines (e.g. R, Spark, Stan, etc).")
24191 (license license:gpl2)))
24193 (define-public r-infer
24200 (uri (cran-uri "infer" version))
24203 "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
24204 (properties `((upstream-name . "infer")))
24205 (build-system r-build-system)
24207 `(("r-dplyr" ,r-dplyr)
24208 ("r-ggplot2" ,r-ggplot2)
24210 ("r-magrittr" ,r-magrittr)
24211 ("r-purrr" ,r-purrr)
24212 ("r-rlang" ,r-rlang)
24213 ("r-tibble" ,r-tibble)))
24215 `(("r-knitr" ,r-knitr)))
24216 (home-page "https://github.com/tidymodels/infer")
24217 (synopsis "Tidy statistical inference")
24219 "The objective of this package is to perform inference using an
24220 expressive statistical grammar that coheres with the Tidy design framework.")
24221 (license license:cc0)))
24223 (define-public r-modeldata
24225 (name "r-modeldata")
24230 (uri (cran-uri "modeldata" version))
24233 "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
24234 (properties `((upstream-name . "modeldata")))
24235 (build-system r-build-system)
24236 (home-page "https://modeldata.tidymodels.org")
24237 (synopsis "Data sets useful for modeling packages")
24239 "This package provides data sets used for demonstrating or testing
24240 model-related packages.")
24241 (license license:expat)))
24243 (define-public r-tidymodels
24245 (name "r-tidymodels")
24250 (uri (cran-uri "tidymodels" version))
24253 "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
24254 (properties `((upstream-name . "tidymodels")))
24255 (build-system r-build-system)
24257 `(("r-broom" ,r-broom)
24259 ("r-crayon" ,r-crayon)
24260 ("r-dials" ,r-dials)
24261 ("r-dplyr" ,r-dplyr)
24262 ("r-ggplot2" ,r-ggplot2)
24263 ("r-infer" ,r-infer)
24264 ("r-magrittr" ,r-magrittr)
24265 ("r-modeldata" ,r-modeldata)
24266 ("r-parsnip" ,r-parsnip)
24267 ("r-purrr" ,r-purrr)
24268 ("r-recipes" ,r-recipes)
24269 ("r-rlang" ,r-rlang)
24270 ("r-rsample" ,r-rsample)
24271 ("r-rstudioapi" ,r-rstudioapi)
24272 ("r-tibble" ,r-tibble)
24273 ("r-tidyr" ,r-tidyr)
24275 ("r-workflows" ,r-workflows)
24276 ("r-yardstick" ,r-yardstick)))
24278 `(("r-knitr" ,r-knitr)
24279 ("r-rmarkdown" ,r-rmarkdown)
24281 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
24282 (home-page "https://github.com/tidymodels/tidymodels")
24283 (synopsis "Tidy collection for modeling and statistical analysis")
24285 "The tidy modeling \"verse\" is a collection of packages for modeling and
24286 statistical analysis that share the underlying design philosophy, grammar, and
24287 data structures of the tidyverse.")
24288 (license license:gpl3)))
24290 (define-public r-mlecens
24297 (uri (cran-uri "MLEcens" version))
24300 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
24301 (properties `((upstream-name . "MLEcens")))
24302 (build-system r-build-system)
24303 (home-page "http://stat.ethz.ch/~maathuis/")
24304 (synopsis "Computation of the MLE for bivariate (interval) censored data")
24306 "This package contains functions to compute the nonparametric
24307 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
24308 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
24309 To be more precise, we consider the situation where we observe a set of
24310 rectangles that are known to contain the unobservable realizations of (X,Y).
24311 We compute the MLE based on such a set of rectangles. The methods can also be
24312 used for univariate censored data (see data set @code{cosmesis}), and for
24313 censored data with competing risks (see data set @code{menopause}). The
24314 package also provides functions to visualize the observed data and the MLE.")
24315 (license license:gpl2+)))
24317 (define-public r-perm
24320 (version "1.0-0.0")
24324 (uri (cran-uri "perm" version))
24327 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
24328 (properties `((upstream-name . "perm")))
24329 (build-system r-build-system)
24330 (home-page "https://cran.r-project.org/web/packages/perm/")
24331 (synopsis "Exact or asymptotic permutation tests")
24333 "This package provides several methods for performing permutation tests.
24334 It has three main functions, to perform linear permutation tests. These tests
24335 are tests where the test statistic is the sum of the product of a
24336 covariate (usually group indicator) and the scores.")
24337 ;; Any version of the GPL
24338 (license license:gpl2+)))
24340 (define-public r-qtl
24347 (uri (cran-uri "qtl" version))
24350 "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
24351 (build-system r-build-system)
24352 (home-page "https://rqtl.org/")
24353 (synopsis "R package for analyzing QTL experiments in genetics")
24354 (description "R/qtl is an extension library for the R statistics system.
24355 It is used to analyze experimental crosses for identifying genes contributing
24356 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
24358 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
24359 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
24361 (license license:gpl3)))
24363 (define-public r-qtl2
24366 (version "0.22-11")
24369 (uri (cran-uri "qtl2" version))
24371 (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
24372 (build-system r-build-system)
24374 `(("r-data-table" ,r-data-table)
24375 ("r-jsonlite" ,r-jsonlite)
24377 ("r-rcppeigen" ,r-rcppeigen)
24378 ("r-rsqlite" ,r-rsqlite)
24379 ("r-yaml" ,r-yaml)))
24380 (home-page "https://kbroman.org/qtl2/")
24381 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
24383 "This package provides a set of tools to perform @dfn{Quantitative Trait
24384 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
24385 @code{R/qtl} package to better handle high-dimensional data and complex cross
24386 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
24387 (license license:gpl3)))
24389 (define-public r-seqminer
24391 (name "r-seqminer")
24396 (uri (cran-uri "seqminer" version))
24399 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
24400 (build-system r-build-system)
24403 (home-page "http://seqminer.genomic.codes")
24404 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
24406 "This package provides tools to integrate nucleotide sequencing
24407 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
24408 ;; Any version of the GPL is acceptable
24409 (license (list license:gpl2+ license:gpl3+))))
24411 (define-public r-maldiquant
24413 (name "r-maldiquant")
24418 (uri (cran-uri "MALDIquant" version))
24421 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
24422 (properties `((upstream-name . "MALDIquant")))
24423 (build-system r-build-system)
24424 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
24425 (synopsis "Quantitative analysis of mass spectrometry data")
24427 "This package provides a complete analysis pipeline for matrix-assisted
24428 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
24429 two-dimensional mass spectrometry data. In addition to commonly used plotting
24430 and processing methods it includes distinctive features, namely baseline
24431 subtraction methods such as morphological filters (TopHat) or the
24432 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
24433 alignment using warping functions, handling of replicated measurements as well
24434 as allowing spectra with different resolutions.")
24435 (license license:gpl3+)))
24437 (define-public r-seurat
24443 (uri (cran-uri "Seurat" version))
24446 "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
24447 (properties `((upstream-name . "Seurat")))
24448 (build-system r-build-system)
24451 ("r-cluster" ,r-cluster)
24452 ("r-cowplot" ,r-cowplot)
24453 ("r-fitdistrplus" ,r-fitdistrplus)
24454 ("r-future" ,r-future)
24455 ("r-future-apply" ,r-future-apply)
24456 ("r-ggplot2" ,r-ggplot2)
24457 ("r-ggrepel" ,r-ggrepel)
24458 ("r-ggridges" ,r-ggridges)
24461 ("r-igraph" ,r-igraph)
24462 ("r-irlba" ,r-irlba)
24463 ("r-jsonlite" ,r-jsonlite)
24464 ("r-kernsmooth" ,r-kernsmooth)
24465 ("r-leiden" ,r-leiden)
24466 ("r-lmtest" ,r-lmtest)
24468 ("r-matrix" ,r-matrix)
24469 ("r-miniui" ,r-miniui)
24470 ("r-patchwork" ,r-patchwork)
24471 ("r-pbapply" ,r-pbapply)
24472 ("r-plotly" ,r-plotly)
24475 ("r-rcolorbrewer" ,r-rcolorbrewer)
24477 ("r-rcppannoy" ,r-rcppannoy)
24478 ("r-rcppeigen" ,r-rcppeigen)
24479 ("r-rcppprogress" ,r-rcppprogress)
24480 ("r-reticulate" ,r-reticulate)
24481 ("r-rlang" ,r-rlang)
24484 ("r-rtsne" ,r-rtsne)
24485 ("r-scales" ,r-scales)
24486 ("r-sctransform" ,r-sctransform)
24487 ("r-shiny" ,r-shiny)
24488 ("r-spatstat" ,r-spatstat)
24489 ("r-tibble" ,r-tibble)
24490 ("r-uwot" ,r-uwot)))
24491 (home-page "http://www.satijalab.org/seurat")
24492 (synopsis "Seurat is an R toolkit for single cell genomics")
24494 "This package is an R package designed for QC, analysis, and
24495 exploration of single cell RNA-seq data. It easily enables widely-used
24496 analytical techniques, including the identification of highly variable genes,
24497 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
24498 algorithms; density clustering, hierarchical clustering, k-means, and the
24499 discovery of differentially expressed genes and markers.")
24500 (license license:gpl3)))
24502 (define-public r-phangorn
24504 (name "r-phangorn")
24509 (uri (cran-uri "phangorn" version))
24512 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
24513 (build-system r-build-system)
24516 ("r-fastmatch" ,r-fastmatch)
24517 ("r-igraph" ,r-igraph)
24518 ("r-magrittr" ,r-magrittr)
24519 ("r-matrix" ,r-matrix)
24520 ("r-quadprog" ,r-quadprog)
24521 ("r-rcpp" ,r-rcpp)))
24522 (home-page "https://github.com/KlausVigo/phangorn")
24523 (synopsis "Phylogenetic analysis in R")
24525 "Phangorn is a package for phylogenetic analysis in R. It supports
24526 estimation of phylogenetic trees and networks using Maximum Likelihood,
24527 Maximum Parsimony, distance methods and Hadamard conjugation.")
24528 (license license:gpl2+)))
24530 (define-public r-diversitree
24532 (name "r-diversitree")
24537 (uri (cran-uri "diversitree" version))
24540 "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
24541 (build-system r-build-system)
24543 `(("gfortran" ,gfortran)))
24544 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
24547 ("r-desolve" ,r-desolve)
24549 ("r-subplex" ,r-subplex)))
24550 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
24551 (synopsis "Comparative 'phylogenetic' analyses of diversification")
24552 (description "This package contains a number of comparative \"phylogenetic\"
24553 methods, mostly focusing on analysing diversification and character evolution.
24554 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
24555 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
24556 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
24557 include Markov models of discrete and continuous trait evolution and constant
24558 rate speciation and extinction.")
24559 (license license:gpl2+)))
24561 (define-public r-absfiltergsea
24563 (name "r-absfiltergsea")
24568 (uri (cran-uri "AbsFilterGSEA" version))
24570 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
24571 (properties `((upstream-name . "AbsFilterGSEA")))
24572 (build-system r-build-system)
24574 `(("r-biobase" ,r-biobase)
24575 ("r-deseq" ,r-deseq)
24576 ("r-limma" ,r-limma)
24578 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24579 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
24580 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
24582 "This package provides a function that performs gene-permuting of a gene-set
24583 enrichment analysis (GSEA) calculation with or without the absolute filtering.
24584 Without filtering, users can perform (original) two-tailed or one-tailed
24586 (license license:gpl2)))