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 © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
21 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
22 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
23 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
25 ;;; This file is part of GNU Guix.
27 ;;; GNU Guix is free software; you can redistribute it and/or modify it
28 ;;; under the terms of the GNU General Public License as published by
29 ;;; the Free Software Foundation; either version 3 of the License, or (at
30 ;;; your option) any later version.
32 ;;; GNU Guix is distributed in the hope that it will be useful, but
33 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
34 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 ;;; GNU General Public License for more details.
37 ;;; You should have received a copy of the GNU General Public License
38 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
40 (define-module (gnu packages cran)
41 #:use-module ((guix licenses) #:prefix license:)
42 #:use-module (guix packages)
43 #:use-module (guix download)
44 #:use-module (guix git-download)
45 #:use-module (guix utils)
46 #:use-module (guix build-system r)
47 #:use-module (gnu packages algebra)
48 #:use-module (gnu packages autotools)
49 #:use-module (gnu packages base)
50 #:use-module (gnu packages bioinformatics)
51 #:use-module (gnu packages c)
52 #:use-module (gnu packages compression)
53 #:use-module (gnu packages curl)
54 #:use-module (gnu packages databases)
55 #:use-module (gnu packages fontutils)
56 #:use-module (gnu packages gcc)
57 #:use-module (gnu packages geo)
58 #:use-module (gnu packages ghostscript)
59 #:use-module (gnu packages gl)
60 #:use-module (gnu packages gnome)
61 #:use-module (gnu packages graph)
62 #:use-module (gnu packages gtk)
63 #:use-module (gnu packages haskell-xyz)
64 #:use-module (gnu packages icu4c)
65 #:use-module (gnu packages image)
66 #:use-module (gnu packages imagemagick)
67 #:use-module (gnu packages java)
68 #:use-module (gnu packages javascript)
69 #:use-module (gnu packages lisp-xyz)
70 #:use-module (gnu packages machine-learning)
71 #:use-module (gnu packages maths)
72 #:use-module (gnu packages mpi)
73 #:use-module (gnu packages multiprecision)
74 #:use-module (gnu packages networking)
75 #:use-module (gnu packages pcre)
76 #:use-module (gnu packages perl)
77 #:use-module (gnu packages pkg-config)
78 #:use-module (gnu packages python)
79 #:use-module (gnu packages python-xyz)
80 #:use-module (gnu packages statistics)
81 #:use-module (gnu packages tcl)
82 #:use-module (gnu packages tls)
83 #:use-module (gnu packages web)
84 #:use-module (gnu packages xorg))
86 (define-public r-bezier
92 (uri (cran-uri "bezier" version))
95 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
96 (build-system r-build-system)
97 (home-page "https://cran.r-project.org/web/packages/bezier/")
98 (synopsis "Bezier curve and spline toolkit")
100 "This package is a toolkit for working with Bezier curves and splines.
101 The package provides functions for point generation, arc length estimation,
102 degree elevation and curve fitting.")
103 (license license:gpl2+)))
105 (define-public r-clipr
112 (uri (cran-uri "clipr" version))
115 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
116 (build-system r-build-system)
117 (home-page "https://github.com/mdlincoln/clipr")
118 (synopsis "Read and write from the system clipboard")
120 "This package provides simple utility functions to read from and write to
121 the system clipboards.")
122 (license license:gpl3)))
124 (define-public r-ggpmisc
130 (uri (cran-uri "ggpmisc" version))
133 "0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
134 (build-system r-build-system)
136 `(("r-broom" ,r-broom)
138 ("r-ggplot2" ,r-ggplot2)
139 ("r-gridextra" ,r-gridextra)
140 ("r-lubridate" ,r-lubridate)
143 ("r-polynom" ,r-polynom)
144 ("r-splus2r" ,r-splus2r)
145 ("r-tibble" ,r-tibble)
148 (home-page "https://www.r4photobiology.info/")
149 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
150 (description "This package provides extensions to @code{ggplot2},
151 respecting the grammar of its graphics paradigm.")
152 (license license:gpl2+)))
154 (define-public r-oenb
161 (uri (cran-uri "oenb" version))
164 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
165 (properties `((upstream-name . "oenb")))
166 (build-system r-build-system)
168 `(("r-dplyr" ,r-dplyr)
170 (native-inputs `(("r-knitr" ,r-knitr)))
171 (home-page "https://github.com/franzmohr/oenb")
172 (synopsis "Tools for the OeNB Data Web Service")
174 "Tools to access data from the data web service of the
175 @acronym{OeNB, Oesterreichische Nationalbank},
176 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
177 (license license:gpl2+)))
179 (define-public r-scales
186 (uri (cran-uri "scales" version))
188 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
189 (build-system r-build-system)
191 `(("r-farver" ,r-farver)
192 ("r-labeling" ,r-labeling)
193 ("r-lifecycle" ,r-lifecycle)
194 ("r-munsell" ,r-munsell)
195 ("r-rcolorbrewer" ,r-rcolorbrewer)
197 ("r-viridislite" ,r-viridislite)))
198 (home-page "https://github.com/hadley/scales")
199 (synopsis "Scale functions for visualization")
201 "This package provides graphical scales that map data to aesthetics, and
202 provides methods for automatically determining breaks and labels for axes and
204 (license license:expat)))
206 (define-public r-pheatmap
213 (uri (cran-uri "pheatmap" version))
216 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
217 (build-system r-build-system)
219 `(("r-gtable" ,r-gtable)
220 ("r-rcolorbrewer" ,r-rcolorbrewer)
221 ("r-scales" ,r-scales)))
222 (home-page "https://cran.r-project.org/web/packages/pheatmap")
223 (synopsis "Pretty heatmaps")
225 "This package provides an implementation of heatmaps that offers more
226 control over dimensions and appearance.")
227 (license license:gpl2+)))
235 (uri (cran-uri "ecp" version))
238 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
239 (build-system r-build-system)
241 `(("r-rcpp" ,r-rcpp)))
242 (home-page "https://cran.r-project.org/web/packages/ecp/")
243 (synopsis "Multiple change-point analysis of multivariate data")
245 "This package implements various procedures for finding multiple
246 change-points. Two methods make use of dynamic programming and pruning, with
247 no distributional assumptions other than the existence of certain absolute
248 moments in one method. Hierarchical and exact search methods are included.
249 All methods return the set of estimated change-points as well as other summary
251 (license license:gpl2+)))
253 (define-public r-ellipsis
260 (uri (cran-uri "ellipsis" version))
263 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
264 (build-system r-build-system)
266 `(("r-rlang" ,r-rlang)))
267 (home-page "https://github.com/hadley/ellipsis")
268 (synopsis "Tools for working with additional arguments")
270 "In S3 generics, it's useful to take @code{...} so that methods can have
271 additional arguments. But this flexibility comes at a cost: misspelled
272 arguments will be silently ignored. The @code{ellipsis} package is an
273 experiment that allows a generic to warn if any arguments passed in @code{...}
275 (license license:gpl3)))
284 (uri (cran-uri "grr" version))
287 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
288 (build-system r-build-system)
289 (home-page "https://cran.r-project.org/web/packages/grr")
290 (synopsis "Alternative implementations of base R functions")
292 "This package provides alternative implementations of some base R
293 functions, including @code{sort}, @code{order}, and @code{match}. The
294 functions are simplified but can be faster or have other advantages.")
295 (license license:gpl3)))
297 (define-public r-matrix-utils
299 (name "r-matrix-utils")
304 (uri (cran-uri "Matrix.utils" version))
307 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
308 (properties `((upstream-name . "Matrix.utils")))
309 (build-system r-build-system)
312 ("r-matrix" ,r-matrix)))
313 (home-page "https://github.com/cvarrichio/Matrix.utils")
315 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
317 "This package implements data manipulation methods such as @code{cast},
318 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
320 (license license:gpl3)))
329 (uri (cran-uri "sys" version))
332 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
333 (build-system r-build-system)
334 (home-page "https://github.com/jeroen/sys")
335 (synopsis "Powerful and reliable tools for running system commands in R")
337 "This package provides drop-in replacements for the base @code{system2()}
338 function with fine control and consistent behavior across platforms. It
339 supports clean interruption, timeout, background tasks, and streaming STDIN /
340 STDOUT / STDERR over binary or text connections. The package also provides
341 functions for evaluating expressions inside a temporary fork. Such
342 evaluations have no side effects on the main R process, and support reliable
343 interrupts and timeouts. This provides the basis for a sandboxing
345 (license license:expat)))
347 (define-public r-askpass
354 (uri (cran-uri "askpass" version))
357 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
358 (build-system r-build-system)
359 (propagated-inputs `(("r-sys" ,r-sys)))
360 (home-page "https://github.com/jeroen/askpass")
361 (synopsis "Safe password entry for R")
363 "This package provides cross-platform utilities for prompting the user
364 for credentials or a passphrase, for example to authenticate with a server or
365 read a protected key.")
366 (license license:expat)))
368 (define-public r-vegan
375 (uri (cran-uri "vegan" version))
378 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
379 (build-system r-build-system)
381 `(("gfortran" ,gfortran)))
383 `(("r-cluster" ,r-cluster)
384 ("r-knitr" ,r-knitr) ; needed for vignettes
385 ("r-lattice" ,r-lattice)
388 ("r-permute" ,r-permute)))
389 (home-page "https://cran.r-project.org/web/packages/vegan")
390 (synopsis "Functions for community ecology")
392 "The vegan package provides tools for descriptive community ecology. It
393 has most basic functions of diversity analysis, community ordination and
394 dissimilarity analysis. Most of its multivariate tools can be used for other
395 data types as well.")
396 (license license:gpl2+)))
398 (define-public r-tidyverse
405 (uri (cran-uri "tidyverse" version))
408 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
409 (build-system r-build-system)
411 `(("r-broom" ,r-broom)
413 ("r-crayon" ,r-crayon)
414 ("r-dbplyr" ,r-dbplyr)
416 ("r-forcats" ,r-forcats)
417 ("r-ggplot2" ,r-ggplot2)
421 ("r-jsonlite" ,r-jsonlite)
422 ("r-lubridate" ,r-lubridate)
423 ("r-magrittr" ,r-magrittr)
424 ("r-modelr" ,r-modelr)
425 ("r-pillar" ,r-pillar)
428 ("r-readxl" ,r-readxl)
429 ("r-reprex" ,r-reprex)
431 ("r-rstudioapi" ,r-rstudioapi)
433 ("r-stringr" ,r-stringr)
434 ("r-tibble" ,r-tibble)
437 (home-page "https://tidyverse.tidyverse.org")
438 (synopsis "Install and load packages from the \"Tidyverse\"")
440 "The @code{tidyverse} is a set of packages that work in harmony because
441 they share common data representations and API design. This package is
442 designed to make it easy to install and load multiple tidyverse packages in a
444 (license license:gpl3)))
446 (define-public r-rvest
453 (uri (cran-uri "rvest" version))
455 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
456 (build-system r-build-system)
459 ("r-magrittr" ,r-magrittr)
460 ("r-selectr" ,r-selectr)
462 (home-page "https://github.com/hadley/rvest")
463 (synopsis "Simple web scraping for R")
465 "@code{r-rvest} helps you scrape information from web pages. It is
466 designed to work with @code{magrittr} to make it easy to express common web
467 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
468 (license license:gpl3)))
470 (define-public r-selectr
477 (uri (cran-uri "selectr" version))
479 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
480 (build-system r-build-system)
482 `(("r-stringr" ,r-stringr)
484 (home-page "https://sjp.co.nz/projects/selectr/")
485 (synopsis "Translate CSS selectors to XPath expressions")
487 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
488 expression. This allows you to use CSS selectors when working with the XML
489 package as it can only evaluate XPath expressions. Also provided are
490 convenience functions useful for using CSS selectors on XML nodes. This
491 package is a port of the Python package @code{cssselect}.")
492 (license license:bsd-3)))
494 (define-public r-reprex
501 (uri (cran-uri "reprex" version))
504 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
505 (build-system r-build-system)
507 `(("r-callr" ,r-callr)
511 ("r-rmarkdown" ,r-rmarkdown)
512 ("r-whisker" ,r-whisker)
513 ("r-withr" ,r-withr)))
514 (home-page "https://github.com/tidyverse/reprex")
515 (synopsis "Prepare reproducible R code examples for sharing")
517 "This package provides a convenience wrapper that uses the
518 @code{rmarkdown} package to render small snippets of code to target formats
519 that include both code and output. The goal is to encourage the sharing of
520 small, reproducible, and runnable examples on code-oriented websites or email.
521 @code{reprex} also extracts clean, runnable R code from various common formats,
522 such as copy/paste from an R session.")
523 (license license:expat)))
525 (define-public r-reordercluster
527 (name "r-reordercluster")
531 (uri (cran-uri "ReorderCluster" version))
534 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
535 (build-system r-build-system)
537 `(("r-gplots" ,r-gplots)
539 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
540 (synopsis "Reordering the dendrogram according to the class labels")
541 (description "This package provides tools for performing the leaf reordering
542 for the dendrogram that preserves the hierarchical clustering result and at the
543 same time tries to group instances from the same class together.")
544 (license license:gpl3+)))
546 (define-public r-callr
553 (uri (cran-uri "callr" version))
556 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
557 (build-system r-build-system)
560 ("r-processx" ,r-processx)))
561 (home-page "https://github.com/r-lib/callr#readme")
562 (synopsis "Call R from R")
564 "It is sometimes useful to perform a computation in a separate R process,
565 without affecting the current R process at all. This package does exactly
567 (license license:expat)))
569 (define-public r-readxl
576 (uri (cran-uri "readxl" version))
579 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
580 (build-system r-build-system)
582 `(("r-cellranger" ,r-cellranger)
583 ("r-progress" ,r-progress)
585 ("r-tibble" ,r-tibble)))
586 (home-page "https://readxl.tidyverse.org")
587 (synopsis "Read Excel files")
589 "This package lets you import Excel files into R. It supports
590 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
591 the embedded @code{RapidXML} C++ library.")
592 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
593 ;; 'rapidxml' which is Boost.
594 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
596 (define-public r-modelr
603 (uri (cran-uri "modelr" version))
606 "1x2m34m4qirb401krmgc5wg3g7ndbcglfab2l0655rmky3fz7rfp"))))
607 (build-system r-build-system)
609 `(("r-broom" ,r-broom)
611 ("r-magrittr" ,r-magrittr)
614 ("r-tibble" ,r-tibble)
616 ("r-tidyselect" ,r-tidyselect)))
617 (home-page "https://github.com/tidyverse/modelr")
618 (synopsis "Helper functions for modelling in pipelines")
620 "Functions for modelling that help you seamlessly integrate modelling
621 into a pipeline of data manipulation and visualisation.")
622 (license license:gpl3)))
624 (define-public r-httpuv
630 (uri (cran-uri "httpuv" version))
633 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
634 (build-system r-build-system)
638 ("r-promises" ,r-promises)
641 (home-page "https://github.com/rstudio/httpuv")
642 (synopsis "HTTP and WebSocket server library for R")
644 "The httpuv package provides low-level socket and protocol support for
645 handling HTTP and WebSocket requests directly from within R. It is primarily
646 intended as a building block for other packages, rather than making it
647 particularly easy to create complete web applications using httpuv alone.")
648 ;; This package includes third-party code that was originally released
649 ;; under various non-copyleft licenses. Full licensing information can be
650 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
651 (license license:gpl3+)))
653 (define-public r-jsonlite
659 (uri (cran-uri "jsonlite" version))
662 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
663 (build-system r-build-system)
664 (home-page "https://arxiv.org/abs/1403.2805")
665 (synopsis "Robust, high performance JSON parser and generator for R")
667 "The jsonlite package provides a fast JSON parser and generator optimized
668 for statistical data and the web. It offers flexible, robust, high
669 performance tools for working with JSON in R and is particularly powerful for
670 building pipelines and interacting with a web API. In addition to converting
671 JSON data from/to R objects, jsonlite contains functions to stream, validate,
672 and prettify JSON data. The unit tests included with the package verify that
673 all edge cases are encoded and decoded consistently for use with dynamic data
674 in systems and applications.")
675 (license license:expat)))
677 (define-public r-servr
683 (uri (cran-uri "servr" version))
686 "106skz04iq4dkblr17idxsxfcfqic6rcaz8mahydkwjjppnhp5fc"))))
687 (build-system r-build-system)
689 `(("r-httpuv" ,r-httpuv)
690 ("r-jsonlite" ,r-jsonlite)
693 (home-page "https://github.com/yihui/servr")
694 (synopsis "Simple HTTP server to serve static files or dynamic documents")
696 "Servr provides an HTTP server in R to serve static files, or dynamic
697 documents that can be converted to HTML files (e.g., R Markdown) under a given
699 (license license:expat)))
701 (define-public r-htmltools
707 (uri (cran-uri "htmltools" version))
710 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
711 (build-system r-build-system)
713 `(("r-digest" ,r-digest)
715 ("r-rlang" ,r-rlang)))
716 (home-page "https://cran.r-project.org/web/packages/htmltools")
717 (synopsis "R tools for HTML")
719 "This package provides tools for HTML generation and output in R.")
720 (license license:expat)))
722 (define-public r-htmlwidgets
724 (name "r-htmlwidgets")
728 (uri (cran-uri "htmlwidgets" version))
731 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
732 (build-system r-build-system)
734 `(("r-htmltools" ,r-htmltools)
735 ("r-jsonlite" ,r-jsonlite)
737 (home-page "https://github.com/ramnathv/htmlwidgets")
738 (synopsis "HTML Widgets for R")
740 "HTML widgets is a framework for creating HTML widgets that render in
741 various contexts including the R console, R Markdown documents, and Shiny web
743 (license license:expat)))
745 (define-public r-htmltable
752 (uri (cran-uri "htmlTable" version))
755 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
756 (properties `((upstream-name . "htmlTable")))
757 (build-system r-build-system)
759 `(("r-checkmate" ,r-checkmate)
760 ("r-htmltools" ,r-htmltools)
761 ("r-htmlwidgets" ,r-htmlwidgets)
763 ("r-magrittr" ,r-magrittr)
764 ("r-rstudioapi" ,r-rstudioapi)
765 ("r-stringr" ,r-stringr)))
766 (home-page "http://gforge.se/packages/")
767 (synopsis "Advanced tables for Markdown/HTML")
769 "This package provides functions to build tables with advanced layout
770 elements such as row spanners, column spanners, table spanners, zebra
771 striping, and more. While allowing advanced layout, the underlying
772 CSS-structure is simple in order to maximize compatibility with word
773 processors such as LibreOffice. The package also contains a few text
774 formatting functions that help outputting text compatible with HTML or
776 (license license:gpl3+)))
778 (define-public r-curl
784 (uri (cran-uri "curl" version))
787 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
788 (build-system r-build-system)
791 (modify-phases %standard-phases
792 ;; The environment variable CURL_CA_BUNDLE is only respected when
793 ;; running Windows, so we disable the platform checks.
794 ;; This can be removed once the libcurl has been patched.
795 (add-after 'unpack 'allow-CURL_CA_BUNDLE
797 (substitute* "R/onload.R"
798 (("if \\(!grepl\\(\"mingw\".*")
800 (substitute* "src/handle.c"
803 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
804 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
811 `(("pkg-config" ,pkg-config)))
812 (home-page "https://github.com/jeroenooms/curl")
813 (synopsis "HTTP client for R")
815 "The @code{curl()} and @code{curl_download()} functions provide highly
816 configurable drop-in replacements for base @code{url()} and
817 @code{download.file()} with better performance, support for encryption, gzip
818 compression, authentication, and other @code{libcurl} goodies. The core of
819 the package implements a framework for performing fully customized requests
820 where data can be processed either in memory, on disk, or streaming via the
821 callback or connection interfaces.")
822 (license license:expat)))
824 (define-public r-hwriter
831 (uri (cran-uri "hwriter" version))
834 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
835 (build-system r-build-system)
836 (home-page "https://cran.r-project.org/web/packages/hwriter")
837 (synopsis "Output R objects in HTML format")
839 "This package provides easy-to-use and versatile functions to output R
840 objects in HTML format.")
841 (license license:lgpl2.1+)))
843 (define-public r-rjson
850 (uri (cran-uri "rjson" version))
853 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
854 (build-system r-build-system)
855 (home-page "https://cran.r-project.org/web/packages/rjson")
856 (synopsis "JSON library for R")
858 "This package provides functions to convert R objects into JSON objects
860 (license license:gpl2+)))
862 (define-public r-fastmap
869 (uri (cran-uri "fastmap" version))
872 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
873 (properties `((upstream-name . "fastmap")))
874 (build-system r-build-system)
875 (home-page "https://r-lib.github.io/fastmap/")
876 (synopsis "Fast implementation of a key-value store")
878 "This package provides a fast implementation of a key-value store.
879 Environments are commonly used as key-value stores, but every time a new key
880 is used, it is added to R's global symbol table, causing a small amount of
881 memory leakage. This can be problematic in cases where many different keys
882 are used. Fastmap avoids this memory leak issue by implementing the map using
883 data structures in C++.")
884 (license license:expat)))
886 (define-public r-shiny
894 (url "https://github.com/rstudio/shiny.git")
895 (commit (string-append "v" version))))
896 (file-name (git-file-name name version))
899 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
900 (build-system r-build-system)
902 `(#:modules ((guix build r-build-system)
903 (guix build minify-build-system)
906 #:imported-modules (,@%r-build-system-modules
907 (guix build minify-build-system))
909 (modify-phases (@ (guix build r-build-system) %standard-phases)
910 (add-after 'unpack 'replace-bundled-minified-JavaScript
911 (lambda* (#:key inputs #:allow-other-keys)
912 (let ((replace-file (lambda (old new)
913 (format #t "replacing ~a with ~a\n" old new)
916 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
917 ;; contain just data. They are not minified code, so we don't
919 (with-directory-excursion "inst/www/shared"
920 (replace-file "bootstrap/shim/respond.min.js"
921 (string-append (assoc-ref inputs "js-respond")
922 "/share/javascript/respond.min.js"))
923 (replace-file "bootstrap/shim/html5shiv.min.js"
924 (string-append (assoc-ref inputs "js-html5shiv")
925 "/share/javascript/html5shiv.min.js"))
926 (replace-file "json2-min.js"
927 (string-append (assoc-ref inputs "js-json2")
928 "/share/javascript/json2-min.js"))
929 (replace-file "strftime/strftime-min.js"
930 (string-append (assoc-ref inputs "js-strftime")
931 "/share/javascript/strftime.min.js"))
932 (replace-file "highlight/highlight.pack.js"
933 (string-append (assoc-ref inputs "js-highlight")
934 "/share/javascript/highlight.min.js"))
935 (replace-file "datatables/js/jquery.dataTables.min.js"
936 (string-append (assoc-ref inputs "js-datatables")
937 "/share/javascript/jquery.dataTables.min.js"))
938 (replace-file "selectize/js/selectize.min.js"
939 (string-append (assoc-ref inputs "js-selectize")
940 "/share/javascript/selectize.min.js"))
941 (replace-file "selectize/js/es5-shim.min.js"
942 (string-append (assoc-ref inputs "js-es5-shim")
943 "/share/javascript/es5-shim.min.js"))
944 (for-each (match-lambda
947 (minify source #:target target)))
948 '(("jqueryui/jquery-ui.js" .
949 "jqueryui/jquery-ui.min.js")
950 ("datepicker/js/bootstrap-datepicker.js" .
951 "datepicker/js/bootstrap-datepicker.min.js")
952 ("ionrangeslider/js/ion.rangeSlider.js" .
953 "ionrangeslider/js/ion.rangeSlider.min.js")
954 ("bootstrap/js/bootstrap.js" .
955 "bootstrap/js/bootstrap.min.js")
960 ("legacy/jquery.js" .
961 "legacy/jquery.min.js")
962 ("showdown/src/showdown.js" .
963 "showdown/compressed/showdown.js")))))
966 `(("r-crayon" ,r-crayon)
967 ("r-digest" ,r-digest)
968 ("r-fastmap" ,r-fastmap)
969 ("r-htmltools" ,r-htmltools)
970 ("r-httpuv" ,r-httpuv)
971 ("r-jsonlite" ,r-jsonlite)
974 ("r-promises" ,r-promises)
977 ("r-sourcetools" ,r-sourcetools)
979 ("r-xtable" ,r-xtable)))
981 `(("js-datatables" ,js-datatables)
982 ("js-html5shiv" ,js-html5shiv)
983 ("js-json2" ,js-json2)
984 ("js-respond" ,js-respond)
985 ("js-selectize" ,js-selectize)
986 ("js-strftime" ,js-strftime)
987 ("js-highlight" ,js-highlight)
988 ("js-es5-shim" ,js-es5-shim)))
990 `(("uglify-js" ,uglify-js)
991 ("gfortran" ,gfortran)))
992 (home-page "http://shiny.rstudio.com")
993 (synopsis "Easy interactive web applications with R")
995 "Makes it incredibly easy to build interactive web applications
996 with R. Automatic \"reactive\" binding between inputs and outputs and
997 extensive prebuilt widgets make it possible to build beautiful,
998 responsive, and powerful applications with minimal effort.")
999 (license license:artistic2.0)))
1001 ;; This package includes minified JavaScript files. When upgrading please
1002 ;; check that there are no new minified JavaScript files.
1003 (define-public r-shinytree
1005 (name "r-shinytree")
1010 (uri (cran-uri "shinyTree" version))
1013 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1014 (modules '((guix build utils)))
1017 ;; Delete minified JavaScript
1018 (for-each delete-file
1019 '("inst/www/jsTree-3.3.7/libs/require.js"
1020 "inst/www/jsTree-3.3.7/libs/jquery.js"
1021 "inst/www/jsTree-3.3.7/jstree.min.js"))
1023 (properties `((upstream-name . "shinyTree")))
1024 (build-system r-build-system)
1026 `(#:modules ((guix build utils)
1027 (guix build r-build-system)
1031 (modify-phases %standard-phases
1032 (add-after 'unpack 'replace-minified-javascript
1033 (lambda* (#:key inputs #:allow-other-keys)
1034 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1035 (symlink (string-append (assoc-ref inputs "js-requirejs")
1036 "/share/javascript/require.min.js")
1041 `((,(assoc-ref inputs "js-jquery")
1045 (lambda (sources targets)
1046 (for-each (lambda (source target)
1047 (format #t "Processing ~a --> ~a~%"
1049 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1050 (call-with-output-file target
1052 (dump-port minified port)))))
1056 `(("r-htmlwidgets" ,r-htmlwidgets)
1057 ("r-jsonlite" ,r-jsonlite)
1058 ("r-promises" ,r-promises)
1059 ("r-shiny" ,r-shiny)
1060 ("r-stringr" ,r-stringr)))
1062 `(("js-requirejs" ,js-requirejs)))
1064 `(("uglify-js" ,uglify-js)
1068 (uri "https://code.jquery.com/jquery-3.3.1.js")
1071 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1072 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1073 (synopsis "jsTree bindings for Shiny")
1075 "This package exposes R bindings to jsTree, a JavaScript library that
1076 supports interactive trees, to enable rich, editable trees in Shiny.")
1077 (license license:expat)))
1079 (define-public r-shinydashboard
1081 (name "r-shinydashboard")
1085 (uri (cran-uri "shinydashboard" version))
1088 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1089 (build-system r-build-system)
1090 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1091 ;; Regenerate it from the included sources.
1093 `(#:modules ((guix build utils)
1094 (guix build r-build-system)
1097 (modify-phases %standard-phases
1098 (add-after 'unpack 'generate-minified-javascript
1100 (with-directory-excursion "inst/AdminLTE"
1101 (delete-file "app.min.js")
1102 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1103 (call-with-output-file "app.min.js"
1105 (dump-port minified port))))))))))
1107 `(("r-htmltools" ,r-htmltools)
1108 ("r-promises" ,r-promises)
1109 ("r-shiny" ,r-shiny)))
1111 `(("uglify-js" ,uglify-js)))
1112 (home-page "https://rstudio.github.io/shinydashboard/")
1113 (synopsis "Create dashboards with shiny")
1114 (description "This package provides an extension to the Shiny web
1115 application framework for R, making it easy to create attractive dashboards.")
1116 ;; This package includes software that was released under the Expat
1117 ;; license, but the whole package is released under GPL version 2 or
1119 (license license:gpl2+)))
1121 (define-public r-shinyfiles
1123 (name "r-shinyfiles")
1128 (uri (cran-uri "shinyFiles" version))
1130 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1131 (properties `((upstream-name . "shinyFiles")))
1132 (build-system r-build-system)
1135 ("r-htmltools" ,r-htmltools)
1136 ("r-jsonlite" ,r-jsonlite)
1137 ("r-shiny" ,r-shiny)
1138 ("r-tibble" ,r-tibble)))
1139 (home-page "https://github.com/thomasp85/shinyFiles")
1140 (synopsis "Server-side file system viewer for Shiny")
1142 "This package provides functionality for client-side navigation of the
1143 server side file system in shiny apps. In case the app is running locally
1144 this gives the user direct access to the file system without the need to
1145 \"download\" files to a temporary location. Both file and folder selection as
1146 well as file saving is available.")
1147 (license license:gpl2+)))
1149 (define-public r-shinythemes
1151 (name "r-shinythemes")
1156 (uri (cran-uri "shinythemes" version))
1159 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1160 (properties `((upstream-name . "shinythemes")))
1161 (build-system r-build-system)
1162 (propagated-inputs `(("r-shiny" ,r-shiny)))
1163 (home-page "https://rstudio.github.io/shinythemes/")
1164 (synopsis "Themes for Shiny")
1166 "This package provides themes for use with Shiny. It includes several
1167 Bootstrap themes, which are packaged for use with Shiny applications.")
1168 ;; The package is released under version 3 of the GPL, but it includes
1169 ;; source files that are covered by the Expat license. It also includes
1170 ;; fonts under SIL or the ASL.
1171 (license (list license:gpl3 license:expat
1172 license:silofl1.1 license:asl2.0))))
1174 ;; The package sources include minified variants of d3.js and non-minified
1175 ;; source code of d3-jetpack.
1176 (define-public r-d3r
1183 (uri (cran-uri "d3r" version))
1186 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1187 (build-system r-build-system)
1189 `(#:modules ((guix build utils)
1190 (guix build r-build-system)
1194 (modify-phases %standard-phases
1195 (add-after 'unpack 'process-javascript
1196 (lambda* (#:key inputs #:allow-other-keys)
1197 (with-directory-excursion "inst/www/d3/"
1201 `((,(assoc-ref inputs "d3.v3.js")
1202 "v3/dist/d3.min.js")
1203 (,(assoc-ref inputs "d3.v4.js")
1204 "v4/dist/d3.min.js")
1205 (,(assoc-ref inputs "d3.v5.js")
1206 "v5/dist/d3.min.js"))))
1207 (lambda (sources targets)
1208 (for-each (lambda (source target)
1209 (format #t "Processing ~a --> ~a~%"
1211 (delete-file target)
1212 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1213 (call-with-output-file target
1215 (dump-port minified port)))))
1219 `(("r-dplyr" ,r-dplyr)
1220 ("r-htmltools" ,r-htmltools)
1221 ("r-tidyr" ,r-tidyr)))
1223 `(("uglify-js" ,uglify-js)
1227 (uri "https://d3js.org/d3.v3.js")
1230 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1234 (uri "https://d3js.org/d3.v4.js")
1237 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1241 (uri "https://d3js.org/d3.v5.js")
1244 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1245 (home-page "https://github.com/timelyportfolio/d3r")
1246 (synopsis "d3.js utilities for R")
1248 "This package provides a suite of functions to help ease the use of the
1249 d3.js visualization library in R. These helpers include
1250 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1251 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1252 R objects into the JSON format that the d3.js library expects.")
1253 (license license:bsd-3)))
1255 ;; We use the latest commit here because the last release was in 2016 while
1256 ;; the latest commit was in 2018.
1257 (define-public r-sankeyd3
1258 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1262 (version (git-version "0.3.2" revision commit))
1267 (url "https://github.com/fbreitwieser/sankeyD3.git")
1269 (file-name (git-file-name name version))
1272 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1273 (build-system r-build-system)
1276 ("r-htmlwidgets" ,r-htmlwidgets)
1277 ("r-shiny" ,r-shiny)
1278 ("r-magrittr" ,r-magrittr)))
1279 (home-page "https://github.com/fbreitwieser/sankeyD3")
1280 (synopsis "Sankey network graphs from R")
1282 "This package provides an R library to generate Sankey network graphs
1283 in R and Shiny via the D3 visualization library.")
1284 ;; The R code is licensed under GPLv3+. It includes the non-minified
1285 ;; JavaScript source code of d3-sankey, which is released under the
1286 ;; 3-clause BSD license.
1287 (license (list license:gpl3+ license:bsd-3)))))
1289 (define-public r-crosstalk
1291 (name "r-crosstalk")
1296 (uri (cran-uri "crosstalk" version))
1299 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1300 (build-system r-build-system)
1302 `(("r-htmltools" ,r-htmltools)
1303 ("r-jsonlite" ,r-jsonlite)
1304 ("r-lazyeval" ,r-lazyeval)
1306 (home-page "https://rstudio.github.io/crosstalk/")
1307 (synopsis "Inter-widget interactivity for HTML widgets")
1309 "This package provides building blocks for allowing HTML widgets to
1310 communicate with each other, with Shiny or without (i.e. static @code{.html}
1311 files). It currently supports linked brushing and filtering.")
1312 (license license:expat)))
1314 (define-public r-rook
1321 (uri (cran-uri "Rook" version))
1324 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1325 (properties `((upstream-name . "Rook")))
1326 (build-system r-build-system)
1327 (propagated-inputs `(("r-brew" ,r-brew)))
1328 (home-page "https://cran.r-project.org/web/packages/Rook")
1329 (synopsis "Web server interface for R")
1331 "This package contains the Rook specification and convenience software
1332 for building and running Rook applications. A Rook application is an R
1333 reference class object that implements a @code{call} method or an R closure
1334 that takes exactly one argument, an environment, and returns a list with three
1335 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1336 (license license:gpl2)))
1338 (define-public r-miniui
1345 (uri (cran-uri "miniUI" version))
1348 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1349 (properties `((upstream-name . "miniUI")))
1350 (build-system r-build-system)
1352 `(("r-htmltools" ,r-htmltools)
1353 ("r-shiny" ,r-shiny)))
1354 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1355 (synopsis "Shiny UI widgets for small screens")
1357 "This package provides UI widget and layout functions for writing Shiny apps that
1358 work well on small screens.")
1359 (license license:gpl3)))
1361 (define-public r-feather
1368 (uri (cran-uri "feather" version))
1371 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1372 (build-system r-build-system)
1376 ("r-tibble" ,r-tibble)))
1377 (home-page "https://github.com/wesm/feather")
1378 (synopsis "R Bindings to the Feather API")
1379 (description "Read and write feather files, a lightweight binary columnar
1380 data store designed for maximum speed.")
1381 (license license:asl2.0)))
1383 (define-public r-maps
1390 (uri (cran-uri "maps" version))
1393 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1394 (build-system r-build-system)
1395 (home-page "https://cran.r-project.org/web/packages/maps")
1396 (synopsis "Draw geographical maps")
1397 (description "This package provides an R module for display of maps.
1398 Projection code and larger maps are in separate packages (@code{mapproj} and
1400 (license license:gpl2)))
1402 (define-public r-mapproj
1409 (uri (cran-uri "mapproj" version))
1412 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1413 (build-system r-build-system)
1414 (propagated-inputs `(("r-maps" ,r-maps)))
1415 (home-page "https://cran.r-project.org/web/packages/mapproj")
1416 (synopsis "Map projection in R")
1417 (description "This package converts latitude/longitude into projected
1419 (license (list license:gpl2 ; The R interface
1420 (license:non-copyleft ; The C code
1421 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1422 "Lucent Public License Version 1.02")))))
1424 (define-public r-rgooglemaps
1426 (name "r-rgooglemaps")
1431 (uri (cran-uri "RgoogleMaps" version))
1434 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1435 (properties `((upstream-name . "RgoogleMaps")))
1436 (build-system r-build-system)
1440 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1441 (synopsis "Use Google Maps in R")
1442 (description "This package serves two purposes:
1444 @item Provide a comfortable R interface to query the Google server for static
1446 @item Use the map as a background image to overlay plots within R. This
1447 requires proper coordinate scaling.
1449 (license license:gpl2+)))
1451 (define-public r-geosphere
1453 (name "r-geosphere")
1458 (uri (cran-uri "geosphere" version))
1461 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1462 (build-system r-build-system)
1463 (propagated-inputs `(("r-sp" ,r-sp)))
1464 (home-page "https://cran.r-project.org/web/packages/geosphere")
1465 (synopsis "Spherical trigonometry")
1466 (description "This package computes spherical trigonometry for geographic
1467 applications. That is, compute distances and related measures for angular
1468 (longitude/latitude) locations.")
1469 (license license:gpl3+)))
1471 (define-public r-jpeg
1478 (uri (cran-uri "jpeg" version))
1481 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1482 (build-system r-build-system)
1483 (inputs `(("libjpeg" ,libjpeg-turbo)))
1484 (home-page "https://www.rforge.net/jpeg/")
1485 (synopsis "Read and write JPEG images with R")
1486 (description "This package provides a way to read, write and display
1487 bitmap images stored in the JPEG format with R. It can read and write both
1488 files and in-memory raw vectors.")
1489 (license license:gpl2+)))
1491 (define-public r-ggmap
1498 (uri (cran-uri "ggmap" version))
1501 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1502 (build-system r-build-system)
1504 `(("r-bitops" ,r-bitops)
1505 ("r-digest" ,r-digest)
1506 ("r-dplyr" ,r-dplyr)
1507 ("r-ggplot2" ,r-ggplot2)
1511 ("r-magrittr" ,r-magrittr)
1514 ("r-purrr" ,r-purrr)
1515 ("r-rgooglemaps" ,r-rgooglemaps)
1516 ("r-rjson" ,r-rjson)
1517 ("r-scales" ,r-scales)
1518 ("r-stringr" ,r-stringr)
1519 ("r-tibble" ,r-tibble)
1520 ("r-tidyr" ,r-tidyr)))
1521 (home-page "https://github.com/dkahle/ggmap")
1522 (synopsis "Spatial visualization with ggplot2")
1523 (description "This package provides a collection of functions to visualize
1524 spatial data and models on top of static maps from various online sources (e.g
1525 Google Maps and Stamen Maps). It includes tools common to those tasks,
1526 including functions for geolocation and routing.")
1527 (license license:gpl2)))
1529 (define-public r-haven
1536 (uri (cran-uri "haven" version))
1539 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1540 (build-system r-build-system)
1544 `(("r-forcats" ,r-forcats)
1547 ("r-rlang" ,r-rlang)
1548 ("r-readr" ,r-readr)
1549 ("r-tibble" ,r-tibble)
1550 ("r-tidyselect" ,r-tidyselect)))
1551 (home-page "https://haven.tidyverse.org")
1552 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1554 "This package lets you mport foreign statistical formats into R via the
1555 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1556 (license license:expat)))
1558 (define-public r-amap
1564 (uri (cran-uri "amap" version))
1567 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1568 (build-system r-build-system)
1570 `(("gfortran" ,gfortran)))
1571 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1572 (synopsis "Another multidimensional analysis package")
1573 (description "This package provides tools for clustering and principal
1574 component analysis (with robust methods, and parallelized functions).")
1575 (license license:gpl2+)))
1577 (define-public r-ape
1584 (uri (cran-uri "ape" version))
1587 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1588 (build-system r-build-system)
1590 `(("r-lattice" ,r-lattice)
1592 ("r-rcpp" ,r-rcpp)))
1593 (home-page "http://ape-package.ird.fr/")
1594 (synopsis "Analyses of phylogenetics and evolution")
1596 "This package provides functions for reading, writing, plotting, and
1597 manipulating phylogenetic trees, analyses of comparative data in a
1598 phylogenetic framework, ancestral character analyses, analyses of
1599 diversification and macroevolution, computing distances from DNA sequences,
1600 and several other tools.")
1601 (license license:gpl2+)))
1603 (define-public r-abbyyr
1610 (uri (cran-uri "abbyyR" version))
1613 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1614 (properties `((upstream-name . "abbyyR")))
1615 (build-system r-build-system)
1617 `(("r-curl" ,r-curl)
1620 ("r-progress" ,r-progress)
1621 ("r-readr" ,r-readr)
1623 (home-page "https://github.com/soodoku/abbyyR")
1624 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1626 "This package provides tools to get text from images of text using Abbyy
1627 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1628 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1629 passports and get the results in a variety of formats including plain text and
1630 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1631 (license license:expat)))
1633 (define-public r-colorspace
1635 (name "r-colorspace")
1640 (uri (cran-uri "colorspace" version))
1642 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1643 (build-system r-build-system)
1644 (home-page "https://cran.r-project.org/web/packages/colorspace")
1645 (synopsis "Color space manipulation")
1647 "This package carries out a mapping between assorted color spaces
1648 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1649 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1650 colors are provided.")
1651 (license license:bsd-3)))
1653 (define-public r-glue
1660 (uri (cran-uri "glue" version))
1663 "1hb9j2519jv9zgkgjb25hnqi22i7zxnaksqd16m4nxa1f6gl0v7a"))))
1664 (build-system r-build-system)
1665 ;; knitr depends on glue, so we can't add knitr here to build the
1669 `(("r-knitr" ,r-knitr)))
1670 (home-page "https://github.com/tidyverse/glue")
1671 (synopsis "Interpreted string literals")
1673 "This package provides an implementation of interpreted string literals,
1674 inspired by Python's Literal String Interpolation (PEP-0498) and
1675 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1676 (license license:expat)))
1678 (define-public r-pastecs
1684 (uri (cran-uri "pastecs" version))
1687 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1688 (build-system r-build-system)
1690 `(("r-boot" ,r-boot)))
1691 (home-page "http://www.sciviews.org/pastecs")
1692 (synopsis "Analysis of space-time ecological series")
1694 "This package provides functions for regulation, decomposition and analysis
1695 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1696 initiative to bring PASSTEC 2000 functionalities to R.")
1697 (license license:gpl2+)))
1699 (define-public r-plogr
1706 (uri (cran-uri "plogr" version))
1709 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1710 (build-system r-build-system)
1711 (home-page "https://github.com/krlmlr/plogr")
1712 (synopsis "R bindings for the plog C++ logging library")
1714 "This package provides the header files for a stripped-down version of
1715 the plog header-only C++ logging library, and a method to log to R's standard
1717 (license license:expat)))
1719 (define-public r-pls
1726 (uri (cran-uri "pls" version))
1728 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1729 (build-system r-build-system)
1730 (home-page "https://mevik.net/work/software/pls.html")
1731 (synopsis "Partial Least Squares and Principal Component Regression")
1733 "The pls package implements multivariate regression methods: Partial Least
1734 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1735 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1738 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1739 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1740 @item multi-response models (or @dfn{PLS2})
1741 @item flexible cross-validation
1742 @item Jackknife variance estimates of regression coefficients
1743 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1744 (R)MSEP, R², and correlation loadings
1745 @item formula interface, modelled after @code{lm()}, with methods for predict,
1746 print, summary, plot, update, etc.
1747 @item extraction functions for coefficients, scores, and loadings
1748 @item MSEP, RMSEP, and R² estimates
1749 @item multiplicative scatter correction (@dfn{MSC})
1751 (license license:gpl2)))
1760 (uri (cran-uri "ps" version))
1762 (base32 "0127q6pw9iw8hhcfp231gmdh29nahh2n5jzc38avrzy7yrm4bwl9"))))
1763 (build-system r-build-system)
1764 (home-page "https://ps.r-lib.org")
1765 (synopsis "List, query, and manipulate system processes")
1767 "The ps package implements an API to list, query, and manipulate system
1768 processes. Most of its code is based on the @code{psutil} Python package.")
1769 (license license:bsd-3)))
1771 (define-public r-pkgbuild
1778 (uri (cran-uri "pkgbuild" version))
1780 (base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
1781 (build-system r-build-system)
1783 `(("r-callr" ,r-callr)
1785 ("r-crayon" ,r-crayon)
1787 ("r-prettyunits" ,r-prettyunits)
1789 ("r-rprojroot" ,r-rprojroot)
1790 ("r-withr" ,r-withr)))
1791 (home-page "https://github.com/r-pkgs/pkgbuild")
1792 (synopsis "Find tools needed to build R packages")
1794 "This package provides functions used to build R packages. It locates
1795 compilers needed to build R packages on various platforms and ensures the PATH
1796 is configured appropriately so R can use them.")
1797 (license license:gpl3)))
1799 (define-public r-pkgload
1806 (uri (cran-uri "pkgload" version))
1809 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1810 (build-system r-build-system)
1812 `(("r-desc" ,r-desc)
1813 ("r-pkgbuild" ,r-pkgbuild)
1814 ("r-rlang" ,r-rlang)
1815 ("r-rprojroot" ,r-rprojroot)
1816 ("r-rstudioapi" ,r-rstudioapi)
1817 ("r-withr" ,r-withr)))
1818 (home-page "https://github.com/r-lib/pkgload")
1819 (synopsis "Simulate package installation and attach")
1821 "This package simulates the process of installing a package and then
1822 attaching it. This is a key part of the @code{devtools} package as it allows
1823 you to rapidly iterate while developing a package.")
1824 (license license:gpl3)))
1826 (define-public r-rcpp
1833 (uri (cran-uri "Rcpp" version))
1835 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
1836 (build-system r-build-system)
1837 (home-page "http://www.rcpp.org")
1838 (synopsis "Seamless R and C++ integration")
1840 "The Rcpp package provides R functions as well as C++ classes which offer
1841 a seamless integration of R and C++. Many R data types and objects can be
1842 mapped back and forth to C++ equivalents which facilitates both writing of new
1843 code as well as easier integration of third-party libraries. Documentation
1844 about Rcpp is provided by several vignettes included in this package, via the
1845 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1846 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1847 @code{citation(\"Rcpp\")} for details on these last two.")
1848 (license license:gpl2+)))
1850 (define-public r-bindr
1857 (uri (cran-uri "bindr" version))
1860 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1861 (build-system r-build-system)
1862 (home-page "https://github.com/krlmlr/bindr")
1863 (synopsis "Parametrized active bindings")
1865 "This package provides a simple interface for creating active bindings
1866 where the bound function accepts additional arguments.")
1867 (license license:expat)))
1869 (define-public r-bindrcpp
1876 (uri (cran-uri "bindrcpp" version))
1879 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1880 (build-system r-build-system)
1882 `(("r-bindr" ,r-bindr)
1883 ("r-plogr" ,r-plogr)
1884 ("r-rcpp" ,r-rcpp)))
1885 (home-page "https://github.com/krlmlr/bindrcpp")
1886 (synopsis "Rcpp interface to active bindings")
1888 "This package provides an easy way to fill an environment with active
1889 bindings that call a C++ function.")
1890 (license license:expat)))
1892 (define-public r-auc
1899 (uri (cran-uri "AUC" version))
1902 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1903 (properties `((upstream-name . "AUC")))
1904 (build-system r-build-system)
1905 (home-page "https://cran.r-project.org/web/packages/AUC")
1906 (synopsis "Compute the area under the curve of selected measures")
1908 "This package includes functions to compute the area under the curve of
1909 selected measures: the area under the sensitivity curve (AUSEC), the area
1910 under the specificity curve (AUSPC), the area under the accuracy
1911 curve (AUACC), and the area under the receiver operating characteristic
1912 curve (AUROC). The curves can also be visualized. Support for partial areas
1914 (license license:gpl2+)))
1916 (define-public r-calibrate
1918 (name "r-calibrate")
1923 (uri (cran-uri "calibrate" version))
1925 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1926 (build-system r-build-system)
1928 `(("r-mass" ,r-mass)))
1929 (home-page "https://cran.r-project.org/web/packages/calibrate")
1930 (synopsis "Calibration of scatterplot and biplot axes")
1932 "This is a package for drawing calibrated scales with tick marks
1933 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1934 (license license:gpl2)))
1936 (define-public r-shape
1943 (uri (cran-uri "shape" version))
1946 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1947 (build-system r-build-system)
1948 (home-page "https://cran.r-project.org/web/packages/shape")
1949 (synopsis "Functions for plotting graphical shapes")
1951 "This package provides functions for plotting graphical shapes such as
1952 ellipses, circles, cylinders, arrows, ...")
1953 (license license:gpl3+)))
1955 (define-public r-globaloptions
1957 (name "r-globaloptions")
1962 (uri (cran-uri "GlobalOptions" version))
1964 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1965 (properties `((upstream-name . "GlobalOptions")))
1966 (build-system r-build-system)
1967 (home-page "https://github.com/jokergoo/GlobalOptions")
1968 (synopsis "Generate functions to get or set global options")
1970 "This package provides more controls on the option values such as
1971 validation and filtering on the values, making options invisible or private.")
1972 (license license:gpl2+)))
1974 (define-public r-circlize
1981 (uri (cran-uri "circlize" version))
1984 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1985 (build-system r-build-system)
1987 `(("r-colorspace" ,r-colorspace)
1988 ("r-globaloptions" ,r-globaloptions)
1989 ("r-shape" ,r-shape)))
1990 (home-page "https://github.com/jokergoo/circlize")
1991 (synopsis "Circular visualization")
1993 "Circular layout is an efficient way to visualise huge amounts of
1994 information. This package provides an implementation of circular layout
1995 generation in R as well as an enhancement of available software. Its
1996 flexibility is based on the usage of low-level graphics functions such that
1997 self-defined high-level graphics can be easily implemented by users for
1998 specific purposes. Together with the seamless connection between the powerful
1999 computational and visual environment in R, it gives users more convenience and
2000 freedom to design figures for better understanding complex patterns behind
2001 multi-dimensional data.")
2002 (license license:gpl2+)))
2004 (define-public r-powerlaw
2011 (uri (cran-uri "poweRlaw" version))
2013 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2014 (properties `((upstream-name . "poweRlaw")))
2015 (build-system r-build-system)
2017 `(("r-pracma" ,r-pracma)))
2019 `(("r-knitr" ,r-knitr)))
2020 (home-page "https://github.com/csgillespie/poweRlaw")
2021 (synopsis "Tools for the analysis of heavy tailed distributions")
2023 "This package provides an implementation of maximum likelihood estimators
2024 for a variety of heavy tailed distributions, including both the discrete and
2025 continuous power law distributions. Additionally, a goodness-of-fit based
2026 approach is used to estimate the lower cut-off for the scaling region.")
2027 ;; Any of these GPL versions.
2028 (license (list license:gpl2 license:gpl3))))
2030 (define-public r-compare
2037 (uri (cran-uri "compare" version))
2040 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2041 (build-system r-build-system)
2042 (home-page "https://cran.r-project.org/web/packages/compare")
2043 (synopsis "Comparing objects for differences")
2045 "This package provides functions to compare a model object to a
2046 comparison object. If the objects are not identical, the functions can be
2047 instructed to explore various modifications of the objects (e.g., sorting
2048 rows, dropping names) to see if the modified versions are identical.")
2049 (license license:gpl2+)))
2051 (define-public r-dendextend
2053 (name "r-dendextend")
2058 (uri (cran-uri "dendextend" version))
2061 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2062 (build-system r-build-system)
2064 `(("r-ggplot2" ,r-ggplot2)
2065 ("r-magrittr" ,r-magrittr)
2066 ("r-viridis" ,r-viridis)))
2067 (home-page "https://cran.r-project.org/web/packages/dendextend")
2068 (synopsis "Extending 'dendrogram' functionality in R")
2070 "This package offers a set of functions for extending @code{dendrogram}
2071 objects in R, letting you visualize and compare trees of hierarchical
2072 clusterings. You can adjust a tree's graphical parameters (the color, size,
2073 type, etc of its branches, nodes and labels) and visually and statistically
2074 compare different dendrograms to one another.")
2075 ;; Any of these versions
2076 (license (list license:gpl2 license:gpl3))))
2078 (define-public r-getoptlong
2080 (name "r-getoptlong")
2085 (uri (cran-uri "GetoptLong" version))
2088 "1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
2089 (properties `((upstream-name . "GetoptLong")))
2090 (build-system r-build-system)
2094 `(("r-globaloptions" ,r-globaloptions)
2095 ("r-rjson" ,r-rjson)))
2096 (home-page "https://github.com/jokergoo/GetoptLong")
2097 (synopsis "Parsing command-line arguments and variable interpolation")
2099 "This is yet another command-line argument parser which wraps the
2100 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2101 use in R. It also provides a simple way for variable interpolation in R.")
2102 (license license:gpl2+)))
2104 (define-public r-fastmatch
2106 (name "r-fastmatch")
2111 (uri (cran-uri "fastmatch" version))
2114 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2115 (build-system r-build-system)
2116 (home-page "https://www.rforge.net/fastmatch")
2117 (synopsis "Fast match function")
2119 "This package provides a fast @code{match} replacement for cases that
2120 require repeated look-ups. It is slightly faster that R's built-in
2121 @code{match} function on first match against a table, but extremely fast on
2122 any subsequent lookup as it keeps the hash table in memory.")
2123 (license license:gpl2)))
2128 (version "2.2-14.2")
2132 (uri (cran-uri "ff" version))
2135 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2136 (build-system r-build-system)
2137 (propagated-inputs `(("r-bit" ,r-bit)))
2138 (home-page "http://ff.r-forge.r-project.org/")
2139 (synopsis "Memory-efficient storage of large data on disk and access functions")
2141 "This package provides data structures that are stored on disk but
2142 behave (almost) as if they were in RAM by transparently mapping only a section
2144 ;; error Architecture not supported.
2145 (supported-systems (delete "aarch64-linux" %supported-systems))
2146 (license license:gpl2)))
2148 (define-public r-ffbase
2155 (uri (cran-uri "ffbase" version))
2158 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2159 (build-system r-build-system)
2162 ("r-fastmatch" ,r-fastmatch)
2164 (home-page "http://github.com/edwindj/ffbase")
2165 (synopsis "Basic statistical functions for package 'ff'")
2167 "This package extends the out of memory vectors of @code{ff} with
2168 statistical functions and other utilities to ease their usage.")
2169 (license license:gpl3)))
2171 (define-public r-prettyunits
2173 (name "r-prettyunits")
2178 (uri (cran-uri "prettyunits" version))
2181 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2182 (build-system r-build-system)
2183 (home-page "https://github.com/gaborcsardi/prettyunits")
2184 (synopsis "Pretty, human readable formatting of quantities")
2186 "This package provides tools for pretty, human readable formatting of
2188 (license license:expat)))
2190 (define-public r-reshape
2197 (uri (cran-uri "reshape" version))
2200 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2201 (build-system r-build-system)
2203 `(("r-plyr" ,r-plyr)
2204 ("r-rcpp" ,r-rcpp)))
2205 (home-page "http://had.co.nz/reshape")
2206 (synopsis "Flexibly reshape data")
2208 "Flexibly restructure and aggregate data using just two functions:
2209 @code{melt} and @code{cast}. This package provides them.")
2210 (license license:expat)))
2212 (define-public r-progress
2219 (uri (cran-uri "progress" version))
2222 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2223 (build-system r-build-system)
2225 `(("r-crayon" ,r-crayon)
2227 ("r-prettyunits" ,r-prettyunits)
2229 (home-page "https://github.com/gaborcsardi/progress")
2230 (synopsis "Terminal progress bars")
2232 "This package provides configurable progress bars. They may include
2233 percentage, elapsed time, and/or the estimated completion time. They work in
2234 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2235 package also provides a C++ API, that works with or without Rcpp.")
2236 (license license:expat)))
2238 (define-public r-ggally
2245 (uri (cran-uri "GGally" version))
2248 "082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
2249 (properties `((upstream-name . "GGally")))
2250 (build-system r-build-system)
2252 `(("libressl" ,libressl)))
2254 `(("r-ggplot2" ,r-ggplot2)
2255 ("r-gtable" ,r-gtable)
2257 ("r-progress" ,r-progress)
2258 ("r-rcolorbrewer" ,r-rcolorbrewer)
2259 ("r-reshape" ,r-reshape)
2260 ("r-rlang" ,r-rlang)))
2261 (home-page "https://ggobi.github.io/ggally")
2262 (synopsis "Extension to ggplot2")
2264 "The R package ggplot2 is a plotting system based on the grammar of
2265 graphics. GGally extends ggplot2 by adding several functions to reduce the
2266 complexity of combining geometric objects with transformed data. Some of
2267 these functions include a pairwise plot matrix, a two group pairwise plot
2268 matrix, a parallel coordinates plot, a survival plot, and several functions to
2270 (license license:gpl2+)))
2272 (define-public r-proxy
2279 (uri (cran-uri "proxy" version))
2282 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2283 (build-system r-build-system)
2284 (home-page "https://cran.r-project.org/web/packages/proxy")
2285 (synopsis "Distance and similarity measures")
2287 "This package provides an extensible framework for the efficient
2288 calculation of auto- and cross-proximities, along with implementations of the
2289 most popular ones.")
2290 (license license:gpl2)))
2299 (uri (cran-uri "sp" version))
2301 (base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg"))))
2302 (build-system r-build-system)
2304 `(("r-lattice" ,r-lattice)))
2305 (home-page "https://cran.r-project.org/web/packages/sp")
2306 (synopsis "Classes and methods for spatial data")
2308 "This package provides classes and methods for spatial data; the classes
2309 document where the spatial location information resides, for 2D or 3D data.
2310 Utility functions are provided, e.g. for plotting data as maps, spatial
2311 selection, as well as methods for retrieving coordinates, for subsetting,
2312 print, summary, etc.")
2313 (license license:gpl2+)))
2315 (define-public r-rmtstat
2322 (uri (cran-uri "RMTstat" version))
2325 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2326 (properties `((upstream-name . "RMTstat")))
2327 (build-system r-build-system)
2328 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2329 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2331 "This package provides functions for working with the Tracy-Widom laws
2332 and other distributions related to the eigenvalues of large Wishart
2334 (license license:bsd-3)))
2336 (define-public r-rmpi
2342 (uri (cran-uri "Rmpi" version))
2345 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2346 (properties `((upstream-name . "Rmpi")))
2347 (build-system r-build-system)
2349 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2350 #:phases (modify-phases %standard-phases
2351 (add-before 'install 'mpi-setup
2354 `(("openmpi" ,openmpi)))
2356 `(("pkg-config" ,pkg-config)))
2357 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2358 (synopsis "R interface to message-passing interface (MPI)")
2360 "This package provides an interface (wrapper) to MPI APIs. It also
2361 provides an interactive R manager and worker environment.")
2362 (license license:gpl2+)))
2364 (define-public r-lmoments
2371 (uri (cran-uri "Lmoments" version))
2374 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2375 (properties `((upstream-name . "Lmoments")))
2376 (build-system r-build-system)
2378 `(("r-rcpp" ,r-rcpp)
2379 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2380 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2381 (synopsis "L-moments and quantile mixtures")
2383 "This package contains functions to estimate L-moments and trimmed
2384 L-moments from the data. It also contains functions to estimate the
2385 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2386 quantile mixture from L-moments and trimmed L-moments.")
2387 (license license:gpl2)))
2389 (define-public r-distillery
2391 (name "r-distillery")
2396 (uri (cran-uri "distillery" version))
2399 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2400 (build-system r-build-system)
2401 (home-page "https://ral.ucar.edu/staff/ericg/")
2402 (synopsis "Functions for confidence intervals and object information")
2404 "This package provides some very simple method functions for confidence
2405 interval calculation and to distill pertinent information from a potentially
2406 complex object; primarily used in common with the packages extRemes and
2408 (license license:gpl2+)))
2410 (define-public r-extremes
2417 (uri (cran-uri "extRemes" version))
2420 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2421 (properties `((upstream-name . "extRemes")))
2422 (build-system r-build-system)
2424 `(("r-distillery" ,r-distillery)
2425 ("r-lmoments" ,r-lmoments)))
2426 (home-page "https://www.assessment.ucar.edu/toolkit/")
2427 (synopsis "Extreme value analysis")
2429 "ExtRemes is a suite of functions for carrying out analyses on the
2430 extreme values of a process of interest; be they block maxima over long blocks
2431 or excesses over a high threshold.")
2432 (license license:gpl2+)))
2434 (define-public r-lmtest
2441 (uri (cran-uri "lmtest" version))
2444 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2445 (build-system r-build-system)
2447 `(("r-zoo" ,r-zoo)))
2449 `(("gfortran" ,gfortran)))
2450 (home-page "https://cran.r-project.org/web/packages/lmtest")
2451 (synopsis "Testing linear regression models")
2453 "This package provides a collection of tests, data sets, and examples for
2454 diagnostic checking in linear regression models. Furthermore, some generic
2455 tools for inference in parametric models are provided.")
2456 ;; Either version is okay
2457 (license (list license:gpl2 license:gpl3))))
2459 (define-public r-idr
2465 (uri (cran-uri "idr" version))
2468 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2469 (build-system r-build-system)
2470 (home-page "https://cran.r-project.org/web/packages/idr/")
2471 (synopsis "Irreproducible discovery rate")
2473 "This is a package for estimating the copula mixture model and plotting
2474 correspondence curves in \"Measuring reproducibility of high-throughput
2475 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2476 by Li, Brown, Huang, and Bickel")
2477 (license license:gpl2+)))
2479 (define-public r-inline
2485 (uri (cran-uri "inline" version))
2488 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2489 (build-system r-build-system)
2490 (home-page "https://cran.r-project.org/web/packages/inline")
2491 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2493 "This package provides functionality to dynamically define R functions
2494 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2495 @code{.Call} calling conventions.")
2496 ;; Any version of the LGPL.
2497 (license license:lgpl3+)))
2499 (define-public r-inum
2505 (uri (cran-uri "inum" version))
2508 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2509 (build-system r-build-system)
2511 `(("r-libcoin" ,r-libcoin)))
2512 (home-page "https://cran.r-project.org/web/packages/inum/")
2513 (synopsis "Interval and enum-type representation of vectors")
2515 "This package provides an enum-type representation of vectors and
2516 representation of intervals, including a method of coercing variables
2518 (license license:gpl2)))
2520 (define-public r-bdsmatrix
2522 (name "r-bdsmatrix")
2527 (uri (cran-uri "bdsmatrix" version))
2530 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2531 (properties `((upstream-name . "bdsmatrix")))
2532 (build-system r-build-system)
2533 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2534 (synopsis "Routines for block diagonal symmetric matrices")
2536 "This package provides procedures to work with block diagonal symmetric
2537 matrices, a special case of sparse matrices.")
2538 (license license:lgpl2.0)))
2540 (define-public r-bbmle
2543 (version "1.0.23.1")
2547 (uri (cran-uri "bbmle" version))
2550 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2551 (build-system r-build-system)
2553 `(("r-bdsmatrix" ,r-bdsmatrix)
2554 ("r-lattice" ,r-lattice)
2556 ("r-matrix" ,r-matrix)
2557 ("r-mvtnorm" ,r-mvtnorm)
2558 ("r-numderiv" ,r-numderiv)))
2559 (home-page "https://cran.r-project.org/web/packages/bbmle")
2560 (synopsis "Tools for General Maximum Likelihood Estimation")
2562 "This package provides methods and functions for fitting maximum
2563 likelihood models in R. This package modifies and extends the @code{mle}
2564 classes in the @code{stats4} package.")
2565 ;; Any version of the GPL
2566 (license license:gpl2+)))
2568 (define-public r-emdbook
2575 (uri (cran-uri "emdbook" version))
2578 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2579 (build-system r-build-system)
2581 `(("r-bbmle" ,r-bbmle)
2583 ("r-lattice" ,r-lattice)
2585 ("r-plyr" ,r-plyr)))
2586 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2587 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2589 "This package provides auxiliary functions and data sets for \"Ecological
2590 Models and Data\", a book presenting maximum likelihood estimation and related
2591 topics for ecologists (ISBN 978-0-691-12522-0).")
2593 (license (list license:gpl2 license:gpl3))))
2595 (define-public r-lpsolve
2602 (uri (cran-uri "lpSolve" version))
2605 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2606 (properties `((upstream-name . "lpSolve")))
2607 (build-system r-build-system)
2608 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2609 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2611 "Lp_solve is software for solving linear, integer and mixed integer
2612 programs. This implementation supplies a \"wrapper\" function in C and some R
2613 functions that solve general linear/integer problems, assignment problems, and
2614 transportation problems.")
2615 (license license:lgpl2.0)))
2617 (define-public r-limsolve
2624 (uri (cran-uri "limSolve" version))
2627 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2628 (properties `((upstream-name . "limSolve")))
2629 (build-system r-build-system)
2631 `(("r-lpsolve" ,r-lpsolve)
2633 ("r-quadprog" ,r-quadprog)))
2634 (native-inputs `(("gfortran" ,gfortran)))
2635 (home-page "https://cran.r-project.org/web/packages/limSolve")
2636 (synopsis "Solving linear inverse models")
2638 "This package provides functions that:
2641 @item find the minimum/maximum of a linear or quadratic function,
2642 @item sample an underdetermined or overdetermined system,
2643 @item solve a linear system Ax=B for the unknown x.
2646 It includes banded and tridiagonal linear systems. The package calls Fortran
2647 functions from LINPACK.")
2649 (license (list license:gpl2+ license:gpl3+))))
2651 (define-public r-fitdistrplus
2653 (name "r-fitdistrplus")
2658 (uri (cran-uri "fitdistrplus" version))
2661 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2662 (build-system r-build-system)
2664 `(("r-mass" ,r-mass)
2665 ("r-npsurv" ,r-npsurv)
2666 ("r-survival" ,r-survival)))
2667 (home-page "http://riskassessment.r-forge.r-project.org")
2668 (synopsis "Fitting a parametric distribution from data")
2670 "This package extends the @code{fitdistr} function of the MASS package
2671 with several functions to help the fit of a parametric distribution to
2672 non-censored or censored data. Censored data may contain left-censored,
2673 right-censored and interval-censored values, with several lower and upper
2674 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2675 provides moment matching (MME), quantile matching (QME) and maximum
2676 goodness-of-fit estimation (MGE) methods (available only for non-censored
2677 data). Weighted versions of MLE, MME and QME are available.")
2678 (license license:gpl2+)))
2680 (define-public r-energy
2687 (uri (cran-uri "energy" version))
2690 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2691 (build-system r-build-system)
2693 `(("r-boot" ,r-boot)
2694 ("r-rcpp" ,r-rcpp)))
2695 (home-page "https://cran.r-project.org/web/packages/energy")
2696 (synopsis "Multivariate inference via the energy of data")
2698 "This package provides e-statistics (energy) tests and statistics for
2699 multivariate and univariate inference, including distance correlation,
2700 one-sample, two-sample, and multi-sample tests for comparing multivariate
2701 distributions, are implemented. Measuring and testing multivariate
2702 independence based on distance correlation, partial distance correlation,
2703 multivariate goodness-of-fit tests, clustering based on energy distance,
2704 testing for multivariate normality, distance components (disco) for
2705 non-parametric analysis of structured data, and other energy
2706 statistics/methods are implemented.")
2707 (license license:gpl2+)))
2709 (define-public r-suppdists
2711 (name "r-suppdists")
2716 (uri (cran-uri "SuppDists" version))
2719 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2720 (properties `((upstream-name . "SuppDists")))
2721 (build-system r-build-system)
2722 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2723 (synopsis "Supplementary distributions")
2725 "This package provides ten distributions supplementing those built into
2726 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2727 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2728 coefficient, Johnson distributions, normal scores and generalized
2729 hypergeometric distributions. In addition two random number generators of
2730 George Marsaglia are included.")
2731 (license license:gpl2+)))
2733 (define-public r-ksamples
2740 (uri (cran-uri "kSamples" version))
2743 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2744 (properties `((upstream-name . "kSamples")))
2745 (build-system r-build-system)
2747 `(("r-suppdists" ,r-suppdists)))
2748 (home-page "https://cran.r-project.org/web/packages/kSamples")
2749 (synopsis "K-Sample rank tests and their combinations")
2751 "This package provides tools to compares k samples using the
2752 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2753 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2754 test. It computes asymptotic, simulated or (limited) exact P-values, all
2755 valid under randomization, with or without ties, or conditionally under random
2756 sampling from populations, given the observed tie pattern. Except for Steel's
2757 test and the JT test it also combines these tests across several blocks of
2759 (license license:gpl2+)))
2761 (define-public r-cvst
2768 (uri (cran-uri "CVST" version))
2771 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2772 (properties `((upstream-name . "CVST")))
2773 (build-system r-build-system)
2775 `(("r-kernlab" ,r-kernlab)
2776 ("r-matrix" ,r-matrix)))
2777 (home-page "https://cran.r-project.org/web/packages/CVST")
2778 (synopsis "Fast cross-validation via sequential testing")
2780 "This package implements the fast cross-validation via sequential
2781 testing (CVST) procedure. CVST is an improved cross-validation procedure
2782 which uses non-parametric testing coupled with sequential analysis to
2783 determine the best parameter set on linearly increasing subsets of the data.
2784 Additionally to the CVST the package contains an implementation of the
2785 ordinary k-fold cross-validation with a flexible and powerful set of helper
2786 objects and methods to handle the overall model selection process. The
2787 implementations of the Cochran's Q test with permutations and the sequential
2788 testing framework of Wald are generic and can therefore also be used in other
2790 (license license:gpl2+)))
2792 (define-public r-squarem
2799 (uri (cran-uri "SQUAREM" version))
2802 "1j6sa93xjvynnzx9jx79a3fysbykmbqyknknsqif5bcha6xp6cvf"))))
2803 (properties `((upstream-name . "SQUAREM")))
2804 (build-system r-build-system)
2805 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2806 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2808 "This package provides algorithms for accelerating the convergence of
2809 slow, monotone sequences from smooth, contraction mapping such as the EM
2810 algorithm. It can be used to accelerate any smooth, linearly convergent
2811 acceleration scheme. A tutorial style introduction to this package is
2812 available in a vignette.")
2813 (license license:gpl2+)))
2815 (define-public r-lava
2822 (uri (cran-uri "lava" version))
2825 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2826 (build-system r-build-system)
2828 `(("r-numderiv" ,r-numderiv)
2829 ("r-squarem" ,r-squarem)
2830 ("r-survival" ,r-survival)))
2831 (home-page "https://github.com/kkholst/lava")
2832 (synopsis "Latent variable models")
2834 "This package provides tools for the estimation and simulation of latent
2836 (license license:gpl3)))
2838 (define-public r-drr
2845 (uri (cran-uri "DRR" version))
2848 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
2849 (properties `((upstream-name . "DRR")))
2850 (build-system r-build-system)
2852 `(("r-cvst" ,r-cvst)
2853 ("r-kernlab" ,r-kernlab)
2854 ("r-matrix" ,r-matrix)))
2855 (home-page "https://cran.r-project.org/web/packages/DRR")
2856 (synopsis "Dimensionality reduction via regression")
2858 "This package provides an implementation of dimensionality reduction via
2859 regression using Kernel Ridge Regression.")
2860 (license license:gpl3)))
2862 (define-public r-prodlim
2865 (version "2019.11.13")
2869 (uri (cran-uri "prodlim" version))
2872 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2873 (build-system r-build-system)
2875 `(("r-kernsmooth" ,r-kernsmooth)
2878 ("r-survival" ,r-survival)))
2879 (home-page "https://cran.r-project.org/web/packages/prodlim")
2880 (synopsis "Product-limit estimation for censored event history analysis")
2882 "This package provides a fast and user-friendly implementation of
2883 nonparametric estimators for censored event history (survival) analysis with
2884 the Kaplan-Meier and Aalen-Johansen methods.")
2885 (license license:gpl2+)))
2887 (define-public r-dimred
2894 (uri (cran-uri "dimRed" version))
2897 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2898 (properties `((upstream-name . "dimRed")))
2899 (build-system r-build-system)
2902 ("r-magrittr" ,r-magrittr)))
2903 (home-page "https://github.com/gdkrmr/dimRed")
2904 (synopsis "Framework for dimensionality reduction")
2906 "This package provides a collection of dimensionality reduction
2907 techniques from R packages and provides a common interface for calling the
2909 (license license:gpl3)))
2911 (define-public r-timedate
2914 (version "3043.102")
2918 (uri (cran-uri "timeDate" version))
2921 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2922 (properties `((upstream-name . "timeDate")))
2923 (build-system r-build-system)
2924 (home-page "https://www.rmetrics.org")
2925 (synopsis "Chronological and calendar objects")
2927 "This package provides an environment for teaching \"Financial
2928 Engineering and Computational Finance\" and for managing chronological and
2930 (license license:gpl2+)))
2932 (define-public r-magic
2939 (uri (cran-uri "magic" version))
2942 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2943 (build-system r-build-system)
2945 `(("r-abind" ,r-abind)))
2946 (home-page "https://github.com/RobinHankin/magic.git")
2947 (synopsis "Create and investigate magic squares")
2949 "This package provides a collection of efficient, vectorized algorithms
2950 for the creation and investigation of magic squares and hypercubes, including
2951 a variety of functions for the manipulation and analysis of arbitrarily
2952 dimensioned arrays.")
2953 (license license:gpl2)))
2955 (define-public r-rmysql
2962 (uri (cran-uri "RMySQL" version))
2965 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
2966 (properties `((upstream-name . "RMySQL")))
2967 (build-system r-build-system)
2969 `(("mariadb" ,mariadb "lib")
2970 ("mariadb-dev" ,mariadb "dev")
2973 `(("r-dbi" ,r-dbi)))
2974 (home-page "https://github.com/r-dbi/RMySQL")
2975 (synopsis "Database interface and MySQL driver for R")
2977 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2978 package contains an old implementation based on legacy code from S-PLUS which
2979 is being phased out. A modern MySQL client based on Rcpp is available from
2980 the RMariaDB package.")
2981 (license license:gpl2)))
2983 (define-public r-rpostgresql
2985 (name "r-rpostgresql")
2990 (uri (cran-uri "RPostgreSQL" version))
2993 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2994 (properties `((upstream-name . "RPostgreSQL")))
2995 (build-system r-build-system)
2997 `(("postgresql" ,postgresql)))
2999 `(("r-dbi" ,r-dbi)))
3000 (home-page "https://github.com/tomoakin/RPostgreSQL")
3001 (synopsis "R interface to the PostgreSQL database system")
3003 "This package provides a Database Interface (DBI) compliant driver for R
3004 to access PostgreSQL database systems.")
3005 ;; The whole package is released under GPL version 2. It includes code
3006 ;; under the PostgreSQL license.
3007 (license license:gpl2)))
3009 (define-public r-linprog
3016 (uri (cran-uri "linprog" version))
3019 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3020 (build-system r-build-system)
3021 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3022 (home-page "http://linprog.r-forge.r-project.org/")
3023 (synopsis "Linear programming and optimization")
3025 "This package can be used to solve Linear Programming / Linear
3026 Optimization problems by using the simplex algorithm.")
3027 (license license:gpl2+)))
3029 (define-public r-geometry
3036 (uri (cran-uri "geometry" version))
3039 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3040 (build-system r-build-system)
3042 `(("r-magic" ,r-magic)
3043 ("r-linprog" ,r-linprog)
3044 ("r-lpsolve" ,r-lpsolve)
3046 ("r-rcppprogress" ,r-rcppprogress)))
3047 (home-page "http://geometry.r-forge.r-project.org/")
3048 (synopsis "Mesh generation and surface tesselation")
3050 "This package makes the qhull library available in R, in a similar manner
3051 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3052 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3053 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3054 and higher dimensions. It implements the Quickhull algorithm for computing
3055 the convex hull. Qhull does not support constrained Delaunay triangulations,
3056 or mesh generation of non-convex objects, but the package does include some R
3057 functions that allow for this. Currently the package only gives access to
3058 Delaunay triangulation and convex hull computation.")
3059 ;; The Qhull sources are included and are distributed under a custom
3060 ;; non-copyleft license. The R sources are released under GPL version 2.
3061 (license (list license:gpl2
3062 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3064 (define-public r-ddalpha
3071 (uri (cran-uri "ddalpha" version))
3074 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3075 (build-system r-build-system)
3078 ("r-class" ,r-class)
3079 ("r-geometry" ,r-geometry)
3082 ("r-robustbase" ,r-robustbase)
3083 ("r-sfsmisc" ,r-sfsmisc)))
3085 `(("gfortran" ,gfortran)))
3086 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3087 (synopsis "Depth-Based classification and calculation of data depth")
3089 "This package contains procedures for depth-based supervised learning,
3090 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3091 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3092 statistical depth function to a compact low-dimensional space, where the final
3093 classification is done. It also offers an extension to functional data and
3094 routines for calculating certain notions of statistical depth functions. 50
3095 multivariate and 5 functional classification problems are included.")
3096 (license license:gpl2)))
3098 (define-public r-gower
3105 (uri (cran-uri "gower" version))
3108 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
3109 (build-system r-build-system)
3110 (home-page "https://github.com/markvanderloo/gower")
3111 (synopsis "Gower's distance")
3113 "This package provides tools to compute Gower's distance (or similarity)
3114 coefficient between records, and to compute the top-n matches between records.
3115 Core algorithms are executed in parallel on systems supporting OpenMP.")
3116 (license license:gpl3)))
3118 (define-public r-rcpproll
3125 (uri (cran-uri "RcppRoll" version))
3128 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3129 (properties `((upstream-name . "RcppRoll")))
3130 (build-system r-build-system)
3132 `(("r-rcpp" ,r-rcpp)))
3133 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3134 (synopsis "Efficient rolling and windowed operations")
3136 "This package provides fast and efficient routines for common rolling /
3137 windowed operations. Routines for the efficient computation of windowed mean,
3138 median, sum, product, minimum, maximum, standard deviation and variance are
3140 (license license:gpl2+)))
3142 (define-public r-ipred
3149 (uri (cran-uri "ipred" version))
3152 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3153 (build-system r-build-system)
3155 `(("r-class" ,r-class)
3158 ("r-prodlim" ,r-prodlim)
3159 ("r-rpart" ,r-rpart)
3160 ("r-survival" ,r-survival)))
3161 (home-page "https://cran.r-project.org/web/packages/ipred")
3162 (synopsis "Improved predictors")
3164 "This package provides improved predictive models by indirect
3165 classification and bagging for classification, regression and survival
3166 problems as well as resampling based estimators of prediction error.")
3167 (license license:gpl2+)))
3169 (define-public r-psych
3172 (version "1.9.12.31")
3176 (uri (cran-uri "psych" version))
3179 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3180 (build-system r-build-system)
3182 `(("r-lattice" ,r-lattice)
3183 ("r-mnormt" ,r-mnormt)
3184 ("r-nlme" ,r-nlme)))
3185 (home-page "https://cran.r-project.org/web/packages/psych/")
3186 (synopsis "Procedures for psychological, psychometric, and personality research")
3188 "This package provides a general purpose toolbox for personality,
3189 psychometric theory and experimental psychology. Functions are primarily for
3190 multivariate analysis and scale construction using factor analysis, principal
3191 component analysis, cluster analysis and reliability analysis, although others
3192 provide basic descriptive statistics. Item Response Theory is done using
3193 factor analysis of tetrachoric and polychoric correlations. Functions for
3194 analyzing data at multiple levels include within and between group statistics,
3195 including correlations and factor analysis. Functions for simulating and
3196 testing particular item and test structures are included. Several functions
3197 serve as a useful front end for structural equation modeling. Graphical
3198 displays of path diagrams, factor analysis and structural equation models are
3199 created using basic graphics.")
3200 (license license:gpl2+)))
3202 (define-public r-generics
3209 (uri (cran-uri "generics" version))
3212 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3213 (build-system r-build-system)
3214 (home-page "https://github.com/r-lib/generics")
3215 (synopsis "Common S3 generics not provided by base R methods")
3217 "In order to reduce potential package dependencies and conflicts,
3218 generics provides a number of commonly used S3 generics that are not provided
3219 by base R methods related to model fitting.")
3220 (license license:gpl2)))
3222 (define-public r-broom
3229 (uri (cran-uri "broom" version))
3232 "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
3233 (build-system r-build-system)
3235 `(("r-backports" ,r-backports)
3236 ("r-dplyr" ,r-dplyr)
3237 ("r-generics" ,r-generics)
3239 ("r-purrr" ,r-purrr)
3240 ("r-reshape2" ,r-reshape2)
3241 ("r-stringr" ,r-stringr)
3242 ("r-tibble" ,r-tibble)
3243 ("r-tidyr" ,r-tidyr)))
3245 `(("r-knitr" ,r-knitr)))
3246 (home-page "https://github.com/tidyverse/broom")
3247 (synopsis "Convert statistical analysis objects into tidy data frames")
3249 "This package provides tools to convert statistical analysis objects from
3250 R into tidy data frames, so that they can more easily be combined, reshaped
3251 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3252 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3253 summarizes a model's statistical findings such as coefficients of a
3254 regression; @code{augment}, which adds columns to the original data such as
3255 predictions, residuals and cluster assignments; and @code{glance}, which
3256 provides a one-row summary of model-level statistics.")
3257 (license license:expat)))
3259 (define-public r-recipes
3266 (uri (cran-uri "recipes" version))
3269 "11f96aanrzi2v6cn49fhvf9y4cmhra63wcy6nvpv6hcfaqqmwd2g"))))
3270 (build-system r-build-system)
3272 `(("r-dplyr" ,r-dplyr)
3273 ("r-generics" ,r-generics)
3275 ("r-gower" ,r-gower)
3276 ("r-ipred" ,r-ipred)
3277 ("r-lubridate" ,r-lubridate)
3278 ("r-magrittr" ,r-magrittr)
3279 ("r-matrix" ,r-matrix)
3280 ("r-purrr" ,r-purrr)
3281 ("r-rlang" ,r-rlang)
3282 ("r-tibble" ,r-tibble)
3283 ("r-tidyr" ,r-tidyr)
3284 ("r-tidyselect" ,r-tidyselect)
3285 ("r-timedate" ,r-timedate)
3286 ("r-withr" ,r-withr)))
3288 `(("r-knitr" ,r-knitr)))
3289 (home-page "https://github.com/topepo/recipes")
3290 (synopsis "Preprocessing tools to create design matrices")
3292 "Recipes is an extensible framework to create and preprocess design
3293 matrices. Recipes consist of one or more data manipulation and analysis
3294 \"steps\". Statistical parameters for the steps can be estimated from an
3295 initial data set and then applied to other data sets. The resulting design
3296 matrices can then be used as inputs into statistical or machine learning
3298 (license license:gpl2)))
3300 (define-public r-pdist
3307 (uri (cran-uri "pdist" version))
3310 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3311 (build-system r-build-system)
3312 (home-page "https://github.com/jeffwong/pdist")
3313 (synopsis "Partitioned distance function")
3315 "Pdist computes the euclidean distance between rows of a matrix X and
3316 rows of another matrix Y. Previously, this could be done by binding the two
3317 matrices together and calling @code{dist}, but this creates unnecessary
3318 computation by computing the distances between a row of X and another row of
3319 X, and likewise for Y. Pdist strictly computes distances across the two
3320 matrices, not within the same matrix, making computations significantly faster
3321 for certain use cases.")
3322 (license license:gpl3+)))
3324 (define-public r-ggrepel
3331 (uri (cran-uri "ggrepel" version))
3334 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3335 (build-system r-build-system)
3337 `(("r-ggplot2" ,r-ggplot2)
3339 ("r-scales" ,r-scales)))
3341 `(("r-knitr" ,r-knitr))) ; for vignettes
3342 (home-page "http://github.com/slowkow/ggrepel")
3343 (synopsis "Repulsive text and label geometries for ggplot2")
3345 "This package provides text and label geometries for ggplot2 that help to
3346 avoid overlapping text labels. Labels repel away from each other and away
3347 from the data points.")
3348 (license license:gpl3)))
3350 (define-public r-corrplot
3357 (uri (cran-uri "corrplot" version))
3360 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3361 (build-system r-build-system)
3362 (home-page "https://github.com/taiyun/corrplot")
3363 (synopsis "Visualization of a correlation matrix")
3365 "This package provides a graphical display of a correlation matrix or
3366 general matrix. It also contains some algorithms to do matrix reordering. In
3367 addition, corrplot is good at details, including choosing color, text labels,
3368 color labels, layout, etc.")
3369 ;; Any version of the GPL
3370 (license license:gpl2+)))
3372 (define-public r-stringdist
3374 (name "r-stringdist")
3379 (uri (cran-uri "stringdist" version))
3381 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3382 (build-system r-build-system)
3383 (home-page "https://github.com/markvanderloo/stringdist")
3384 (synopsis "Approximate string matching and string distance functions")
3386 "This package implements an approximate string matching version of R's
3387 native @code{match} function. It can calculate various string distances based
3388 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3389 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3390 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3391 can be computed between character vectors while taking proper care of encoding
3392 or between integer vectors representing generic sequences.")
3393 (license license:gpl3+)))
3395 (define-public r-ucminf
3402 (uri (cran-uri "ucminf" version))
3405 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3406 (build-system r-build-system)
3407 (native-inputs `(("gfortran" ,gfortran)))
3408 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3409 (synopsis "General-purpose unconstrained non-linear optimization")
3411 "This package provides an implementation of an algorithm for
3412 general-purpose unconstrained non-linear optimization. The algorithm is of
3413 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3414 search with a trust region type monitoring of the input to the line search
3415 algorithm. The interface of @code{ucminf} is designed for easy interchange
3416 with the package @code{optim}.")
3417 (license license:gpl2+)))
3419 (define-public r-ordinal
3422 (version "2019.12-10")
3426 (uri (cran-uri "ordinal" version))
3429 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3430 (build-system r-build-system)
3432 `(("r-mass" ,r-mass)
3433 ("r-matrix" ,r-matrix)
3434 ("r-numderiv" ,r-numderiv)
3435 ("r-ucminf" ,r-ucminf)))
3436 (home-page "https://github.com/runehaubo/ordinal")
3437 (synopsis "Regression models for ordinal data")
3439 "This package provides an implementation of cumulative link (mixed)
3440 models also known as ordered regression models, proportional odds models,
3441 proportional hazards models for grouped survival times and ordered models.
3442 Estimation is via maximum likelihood and mixed models are fitted with the
3443 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3444 (license license:gpl2+)))
3446 (define-public r-jomo
3453 (uri (cran-uri "jomo" version))
3456 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3457 (build-system r-build-system)
3459 `(("r-lme4" ,r-lme4)
3461 ("r-ordinal" ,r-ordinal)
3462 ("r-survival" ,r-survival)))
3463 (home-page "https://cran.r-project.org/web/packages/jomo/")
3464 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3466 "Similarly to Schafer's package pan, jomo is a package for multilevel
3467 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3468 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3469 possibility of handling binary and categorical data through latent normal
3470 variables, the option to use cluster-specific covariance matrices and to
3471 impute compatibly with the substantive model.")
3472 (license license:gpl2)))
3474 (define-public r-pan
3481 (uri (cran-uri "pan" version))
3484 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3485 (build-system r-build-system)
3486 (native-inputs `(("gfortran" ,gfortran)))
3487 (home-page "https://cran.r-project.org/web/packages/pan/")
3488 (synopsis "Multiple imputation for multivariate panel or clustered data")
3490 "This package implements multiple imputation for multivariate panel or
3492 (license license:gpl3)))
3494 (define-public r-mitml
3501 (uri (cran-uri "mitml" version))
3504 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3505 (build-system r-build-system)
3507 `(("r-haven" ,r-haven)
3510 (home-page "https://cran.r-project.org/web/packages/mitml/")
3511 (synopsis "Tools for multiple imputation in multilevel modeling")
3513 "This package provides tools for multiple imputation of missing data in
3514 multilevel modeling. It includes a user-friendly interface to the packages
3515 pan and jomo, and several functions for visualization, data management and the
3516 analysis of multiply imputed data sets.")
3517 (license license:gpl2+)))
3519 (define-public r-mice
3526 (uri (cran-uri "mice" version))
3529 "1ibybvigqkkla4xwhqs2w4m6c68alfcdsljx99nn4p92rzb1ig04"))))
3530 (build-system r-build-system)
3532 `(("r-broom" ,r-broom)
3533 ("r-dplyr" ,r-dplyr)
3534 ("r-lattice" ,r-lattice)
3536 ("r-tidyr" ,r-tidyr)))
3537 (home-page "https://cran.r-project.org/web/packages/mice/")
3538 (synopsis "Multivariate imputation by chained equations")
3540 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3541 implemented by the MICE algorithm as described in @url{Van Buuren and
3542 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3543 variable has its own imputation model. Built-in imputation models are
3544 provided for continuous data (predictive mean matching, normal), binary
3545 data (logistic regression), unordered categorical data (polytomous logistic
3546 regression) and ordered categorical data (proportional odds). MICE can also
3547 impute continuous two-level data (normal model, pan, second-level variables).
3548 Passive imputation can be used to maintain consistency between variables.
3549 Various diagnostic plots are available to inspect the quality of the
3551 ;; Any of these two versions.
3552 (license (list license:gpl2 license:gpl3))))
3554 (define-public r-truncnorm
3556 (name "r-truncnorm")
3561 (uri (cran-uri "truncnorm" version))
3564 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3565 (build-system r-build-system)
3566 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3567 (synopsis "Truncated normal distribution")
3568 (description "This package provides functions for the truncated normal
3569 distribution with mean equal to @code{mean} and standard deviation equal to
3570 @code{sd}. It includes density, distribution, quantile, and expected value
3571 functions, as well as a random generation function.")
3572 (license license:gpl2)))
3574 (define-public r-rsolnp
3581 (uri (cran-uri "Rsolnp" version))
3584 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3585 (properties `((upstream-name . "Rsolnp")))
3586 (build-system r-build-system)
3588 `(("r-truncnorm" ,r-truncnorm)))
3589 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3590 (synopsis "General non-linear optimization")
3591 (description "The Rsolnp package implements a general non-linear augmented
3592 Lagrange multiplier method solver, a @dfn{sequential quadratic
3593 programming} (SQP) based solver).")
3594 ;; Any version of the GPL.
3595 (license license:gpl2+)))
3597 (define-public r-hardyweinberg
3599 (name "r-hardyweinberg")
3604 (uri (cran-uri "HardyWeinberg" version))
3607 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3608 (properties `((upstream-name . "HardyWeinberg")))
3609 (build-system r-build-system)
3611 `(("r-mice" ,r-mice)
3613 ("r-rsolnp" ,r-rsolnp)))
3614 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3615 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3617 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3618 diallelic genetic marker data. All classical tests (chi-square, exact,
3619 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3620 included in the package, as well as functions for power computation and for
3621 the simulation of marker data under equilibrium and disequilibrium. Routines
3622 for dealing with markers on the X-chromosome are included. Functions for
3623 testing equilibrium in the presence of missing data by using multiple
3624 imputation are also provided. Implements several graphics for exploring the
3625 equilibrium status of a large set of diallelic markers: ternary plots with
3626 acceptance regions, log-ratio plots and Q-Q plots.")
3627 (license license:gpl2+)))
3636 (uri (cran-uri "sm" version))
3639 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3640 (build-system r-build-system)
3641 (native-inputs `(("gfortran" ,gfortran)))
3642 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3643 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3645 "This is software accompanying the book 'Applied Smoothing Techniques for
3646 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3647 University Press. It provides smoothing methods for nonparametric regression
3648 and density estimation")
3649 (license license:gpl2+)))
3651 (define-public r-venndiagram
3653 (name "r-venndiagram")
3657 (uri (cran-uri "VennDiagram" version))
3660 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3661 (properties `((upstream-name . "VennDiagram")))
3662 (build-system r-build-system)
3664 `(("r-futile-logger" ,r-futile-logger)))
3665 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3666 (synopsis "Generate High-Resolution Venn and Euler Plots")
3668 "This package provides a set of functions to generate high-resolution
3669 Venn and Euler plots. It includes handling for several special cases,
3670 including two-case scaling, and extensive customization of plot shape and
3672 (license license:gpl2+)))
3674 (define-public r-vioplot
3681 (uri (cran-uri "vioplot" version))
3684 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3685 (build-system r-build-system)
3689 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3690 (synopsis "Violin plot")
3692 "This package provides a violin plot, which is a combination of a box
3693 plot and a kernel density plot.")
3694 (license license:bsd-3)))
3696 (define-public r-rsofia
3702 ;; This package has been removed from CRAN, so we can
3703 ;; only fetch it from the archives.
3704 (uri (string-append "https://cran.r-project.org/src/"
3705 "contrib/Archive/RSofia/RSofia_"
3709 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3710 (properties `((upstream-name . "RSofia")))
3711 (build-system r-build-system)
3713 `(("r-rcpp" ,r-rcpp)))
3714 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3715 (synopsis "Port of sofia-ml to R")
3716 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3717 suite of fast incremental algorithms for machine learning that can be used for
3718 training models for classification or ranking.")
3719 (license license:asl2.0)))
3721 (define-public r-xts
3728 (uri (cran-uri "xts" version))
3731 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3732 (build-system r-build-system)
3733 (propagated-inputs `(("r-zoo" ,r-zoo)))
3734 (home-page "https://github.com/joshuaulrich/xts")
3735 (synopsis "Extensible time series")
3737 "This package provides for uniform handling of R's different time-based
3738 data classes by extending @code{zoo}, maximizing native format information
3739 preservation and allowing for user-level customization and extension, while
3740 simplifying cross-class interoperability.")
3741 (license license:gpl2+)))
3743 (define-public r-performanceanalytics
3745 (name "r-performanceanalytics")
3750 (uri (cran-uri "PerformanceAnalytics" version))
3753 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3755 `((upstream-name . "PerformanceAnalytics")))
3756 (build-system r-build-system)
3758 `(("r-quadprog" ,r-quadprog)
3761 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3762 (synopsis "Econometric tools for performance and risk analysis")
3763 (description "This is a collection of econometric functions for
3764 performance and risk analysis. This package aims to aid practitioners and
3765 researchers in utilizing the latest research in analysis of non-normal return
3766 streams. In general, it is most tested on return (rather than price) data on
3767 a regular scale, but most functions will work with irregular return data as
3768 well, and increasing numbers of functions will work with P&L or price data
3770 ;; Either version may be picked.
3771 (license (list license:gpl2 license:gpl3))))
3773 (define-public r-laeken
3780 (uri (cran-uri "laeken" version))
3783 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3784 (build-system r-build-system)
3786 `(("r-boot" ,r-boot)
3787 ("r-mass" ,r-mass)))
3788 (home-page "https://cran.r-project.org/web/packages/laeken/")
3789 (synopsis "Estimation of indicators on social exclusion and poverty")
3790 (description "This package provides tools for the estimation of indicators
3791 on social exclusion and poverty, as well as an implementation of Pareto tail
3792 modeling for empirical income distributions.")
3793 (license license:gpl2+)))
3795 (define-public r-vcd
3802 (uri (cran-uri "vcd" version))
3805 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3806 (build-system r-build-system)
3808 `(("r-colorspace" ,r-colorspace)
3809 ("r-lmtest" ,r-lmtest)
3810 ("r-mass" ,r-mass)))
3811 (home-page "https://cran.r-project.org/web/packages/vcd/")
3812 (synopsis "Visualizing categorical data")
3813 (description "This package provides visualization techniques, data sets,
3814 summary and inference procedures aimed particularly at categorical data.
3815 Special emphasis is given to highly extensible grid graphics. The package was
3816 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3817 Friendly and is now the main support package for a new book, \"Discrete Data
3818 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3819 (license license:gpl2)))
3821 (define-public r-ica
3828 (uri (cran-uri "ica" version))
3831 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3832 (build-system r-build-system)
3833 (home-page "https://cran.r-project.org/web/packages/ica/")
3834 (synopsis "Independent component analysis")
3835 (description "This package provides tools for @dfn{Independent Component
3836 Analysis} (ICA) using various algorithms: FastICA,
3837 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3838 of Eigenmatrices} (JADE).")
3839 (license license:gpl2+)))
3841 (define-public r-dtw
3848 (uri (cran-uri "dtw" version))
3851 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3852 (build-system r-build-system)
3853 (propagated-inputs `(("r-proxy" ,r-proxy)))
3854 (home-page "http://dtw.r-forge.r-project.org/")
3855 (synopsis "Dynamic Time Warping Algorithms")
3856 (description "This package provides a comprehensive implementation of
3857 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3858 optimal (least cumulative distance) alignment between points of two time
3859 series. Common DTW variants covered include local (slope) and global (window)
3860 constraints, subsequence matches, arbitrary distance definitions,
3861 normalizations, minimum variance matching, and so on.")
3862 (license license:gpl2+)))
3864 (define-public r-sdmtools
3867 (version "1.1-221.2")
3871 (uri (cran-uri "SDMTools" version))
3874 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3875 (properties `((upstream-name . "SDMTools")))
3876 (build-system r-build-system)
3877 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3878 (home-page "https://www.rforge.net/SDMTools/")
3879 (synopsis "Species distribution modelling tools")
3880 (description "This package provides a set of tools for post processing
3881 the outcomes of species distribution modeling exercises. It includes novel
3882 methods for comparing models and tracking changes in distributions through
3883 time. It further includes methods for visualizing outcomes, selecting
3884 thresholds, calculating measures of accuracy and landscape fragmentation
3886 (license license:gpl3+)))
3888 (define-public r-scatterplot3d
3890 (name "r-scatterplot3d")
3895 (uri (cran-uri "scatterplot3d" version))
3898 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3899 (build-system r-build-system)
3900 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3901 (synopsis "3D scatter plot")
3902 (description "This package provides an implementation of scatter plots for
3903 plotting. a three dimensional point cloud.")
3904 (license license:gpl2)))
3906 (define-public r-ggridges
3913 (uri (cran-uri "ggridges" version))
3916 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
3917 (build-system r-build-system)
3919 `(("r-ggplot2" ,r-ggplot2)
3921 ("r-scales" ,r-scales)
3922 ("r-withr" ,r-withr)))
3923 (home-page "https://github.com/clauswilke/ggridges")
3924 (synopsis "Ridgeline plots in ggplot2")
3926 "Ridgeline plots provide a convenient way of visualizing changes in
3927 distributions over time or space. This package enables the creation of such
3928 plots in @code{ggplot2}.")
3929 (license license:gpl2)))
3931 (define-public r-ggjoy
3938 (uri (cran-uri "ggjoy" version))
3941 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3942 (build-system r-build-system)
3944 `(("r-ggplot2" ,r-ggplot2)
3945 ("r-ggridges" ,r-ggridges)))
3946 (home-page "https://github.com/clauswilke/ggjoy")
3947 (synopsis "Joyplots in ggplot2")
3948 (description "Joyplots provide a convenient way of visualizing changes in
3949 distributions over time or space. This package enables the creation of such
3950 plots in @code{ggplot2}.")
3951 (license license:gpl2)))
3953 (define-public r-cli
3960 (uri (cran-uri "cli" version))
3963 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
3964 (build-system r-build-system)
3966 `(("r-assertthat" ,r-assertthat)
3967 ("r-crayon" ,r-crayon)
3968 ("r-fansi" ,r-fansi)
3969 ("r-glue" ,r-glue)))
3970 (home-page "https://github.com/r-lib/cli#readme")
3971 (synopsis "Helpers for developing command line interfaces")
3972 (description "This package provides a suite of tools designed to build
3973 attractive command line interfaces (CLIs). It includes tools for drawing
3974 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3975 (license license:expat)))
3977 (define-public r-argparser
3979 (name "r-argparser")
3984 (uri (cran-uri "argparser" version))
3987 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3988 (build-system r-build-system)
3989 (home-page "https://bitbucket.org/djhshih/argparser")
3990 (synopsis "Command-line argument parser")
3992 "This package provides a cross-platform command-line argument parser
3993 written purely in R with no external dependencies. It is useful with the
3994 Rscript front-end and facilitates turning an R script into an executable
3996 (license license:gpl3+)))
3998 (define-public r-debugme
4005 (uri (cran-uri "debugme" version))
4008 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4009 (build-system r-build-system)
4010 (propagated-inputs `(("r-crayon" ,r-crayon)))
4011 (home-page "https://github.com/r-lib/debugme#readme")
4012 (synopsis "Debug R packages")
4014 "This package allows the user to specify debug messages as special string
4015 constants, and control debugging of packages via environment variables.")
4016 (license license:expat)))
4018 (define-public r-processx
4025 (uri (cran-uri "processx" version))
4028 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
4029 (build-system r-build-system)
4033 (home-page "https://github.com/r-lib/processx3")
4034 (synopsis "Execute and control system processes")
4036 "This package provides portable tools to run system processes in the
4037 background. It can check if a background process is running; wait on a
4038 background process to finish; get the exit status of finished processes; kill
4039 background processes and their children; restart processes. It can read the
4040 standard output and error of the processes, using non-blocking connections.
4041 @code{processx} can poll a process for standard output or error, with a
4042 timeout. It can also poll several processes at once.")
4043 (license license:expat)))
4045 (define-public r-tsp
4052 (uri (cran-uri "TSP" version))
4055 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4056 (properties `((upstream-name . "TSP")))
4057 (build-system r-build-system)
4058 (propagated-inputs `(("r-foreach" ,r-foreach)))
4059 (home-page "https://cran.r-project.org/web/packages/TSP/")
4060 (synopsis "Traveling salesperson problem (TSP)")
4061 (description "This package provides basic infrastructure and some
4062 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4063 traveling salesman problem).")
4064 (license license:gpl3)))
4066 (define-public r-qap
4073 (uri (cran-uri "qap" version))
4076 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4077 (build-system r-build-system)
4078 (native-inputs `(("gfortran" ,gfortran)))
4079 (home-page "https://cran.r-project.org/web/packages/qap/")
4080 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4081 (description "This package implements heuristics for the @dfn{quadratic
4082 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4084 (license license:gpl3)))
4086 (define-public r-gclus
4093 (uri (cran-uri "gclus" version))
4096 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4097 (build-system r-build-system)
4098 (propagated-inputs `(("r-cluster" ,r-cluster)))
4099 (home-page "https://cran.r-project.org/web/packages/gclus/")
4100 (synopsis "Clustering graphics")
4101 (description "This package orders panels in scatterplot matrices and
4102 parallel coordinate displays by some merit index. It contains various indices
4103 of merit, ordering functions, and enhanced versions of @code{pairs} and
4104 @code{parcoord} which color panels according to their merit level.")
4105 (license license:gpl2+)))
4107 (define-public r-webshot
4114 (uri (cran-uri "webshot" version))
4117 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4118 (build-system r-build-system)
4120 `(("r-callr" ,r-callr)
4121 ("r-jsonlite" ,r-jsonlite)
4122 ("r-magrittr" ,r-magrittr)))
4123 (home-page "https://github.com/wch/webshot/")
4124 (synopsis "Take screenshots of web pages")
4126 "Webshot makes it easy to take screenshots of web pages from within R.
4127 It can also run Shiny applications locally and take screenshots of the
4128 application; and it can render and screenshot static as well as interactive R
4129 Markdown documents.")
4130 (license license:gpl2)))
4132 (define-public r-seriation
4134 (name "r-seriation")
4139 (uri (cran-uri "seriation" version))
4142 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4143 (build-system r-build-system)
4145 `(("r-cluster" ,r-cluster)
4146 ("r-colorspace" ,r-colorspace)
4147 ("r-dendextend" ,r-dendextend)
4148 ("r-gclus" ,r-gclus)
4149 ("r-gplots" ,r-gplots)
4152 ("r-registry" ,r-registry)
4154 (native-inputs `(("gfortran" ,gfortran)))
4155 (home-page "https://s2.smu.edu/IDA/seriation/")
4156 (synopsis "Infrastructure for ordering objects using seriation")
4158 "This package provides infrastructure for seriation with an
4159 implementation of several seriation/sequencing techniques to reorder matrices,
4160 dissimilarity matrices, and dendrograms. It also provides (optimally)
4161 reordered heatmaps, color images and clustering visualizations like
4162 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4164 (license license:gpl3)))
4166 (define-public r-xfun
4173 (uri (cran-uri "xfun" version))
4175 (base32 "03iyqgx9mmdbd3qih70qzijjqcdg7k7ps5r1y6q8praanx9qvnm3"))))
4176 (build-system r-build-system)
4177 ;; knitr itself depends on xfun
4180 `(("r-knitr" ,r-knitr)))
4181 (home-page "https://github.com/yihui/xfun")
4182 (synopsis "Miscellaneous functions")
4184 "This package provides miscellaneous functions commonly used in other
4185 packages maintained by Yihui Xie.")
4186 (license license:expat)))
4188 (define-public r-utf8
4195 (uri (cran-uri "utf8" version))
4198 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4199 (build-system r-build-system)
4200 (home-page "https://github.com/patperry/r-utf8")
4201 (synopsis "Unicode text processing")
4203 "This package provides tools to process and print UTF-8 encoded
4204 international text (Unicode). Input, validate, normalize, encode, format, and
4206 (license license:asl2.0)))
4208 (define-public r-zeallot
4215 (uri (cran-uri "zeallot" version))
4218 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4219 (build-system r-build-system)
4220 (home-page "https://github.com/nteetor/zeallot")
4221 (synopsis "Multiple, unpacking, and destructuring assignment")
4223 "This package provides a @code{%<-%} operator to perform multiple,
4224 unpacking, and destructuring assignment in R. The operator unpacks the
4225 right-hand side of an assignment into multiple values and assigns these values
4226 to variables on the left-hand side of the assignment.")
4227 (license license:expat)))
4229 (define-public r-vctrs
4236 (uri (cran-uri "vctrs" version))
4239 "15sgzs6afvmhssk6jcg41rn3bvmzmbm4sgca6f6x8lfrsazvdj6w"))))
4240 (build-system r-build-system)
4242 `(("r-digest" ,r-digest)
4243 ("r-ellipsis" ,r-ellipsis)
4245 ("r-rlang" ,r-rlang)))
4247 `(("r-knitr" ,r-knitr)))
4248 (home-page "https://github.com/r-lib/vctrs")
4249 (synopsis "Vector helpers")
4251 "There are three main goals to the @code{vctrs} package:
4254 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4255 @code{length()} and @code{class()}. These definitions are paired with a
4256 framework for type-coercion and size-recycling.
4257 @item To define type- and size-stability as desirable function properties, use
4258 them to analyse existing base function, and to propose better alternatives.
4259 This work has been particularly motivated by thinking about the ideal
4260 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4261 @item To provide a new @code{vctr} base class that makes it easy to create new
4262 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4263 a few new @code{vctrs} generics, making implementation considerably simpler
4266 (license license:gpl3)))
4268 (define-public r-pillar
4275 (uri (cran-uri "pillar" version))
4278 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4279 (build-system r-build-system)
4282 ("r-crayon" ,r-crayon)
4283 ("r-fansi" ,r-fansi)
4284 ("r-rlang" ,r-rlang)
4286 ("r-vctrs" ,r-vctrs)))
4287 (home-page "https://github.com/r-lib/pillar")
4288 (synopsis "Coloured formatting for columns")
4290 "This package provides a @code{pillar} generic designed for formatting
4291 columns of data using the full range of colours provided by modern
4293 (license license:gpl3)))
4295 (define-public r-uuid
4302 (uri (cran-uri "uuid" version))
4305 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4306 (build-system r-build-system)
4307 (home-page "https://www.rforge.net/uuid")
4308 (synopsis "Tools for generating and handling of UUIDs")
4310 "This package provides tools for generating and handling of
4311 @dfn{Universally Unique Identifiers} (UUIDs).")
4312 (license license:expat)))
4314 (define-public r-tinytex
4321 (uri (cran-uri "tinytex" version))
4324 "0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b"))))
4325 (build-system r-build-system)
4327 `(("r-xfun" ,r-xfun)))
4328 (home-page "https://github.com/yihui/tinytex")
4329 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4331 "This package provides helper functions to install and maintain the LaTeX
4332 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4333 easy-to-maintain version of TeX Live. This package also contains helper
4334 functions to compile LaTeX documents, and install missing LaTeX packages
4336 (license license:expat)))
4338 (define-public r-network
4345 (uri (cran-uri "network" version))
4348 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4349 (build-system r-build-system)
4351 `(("r-magrittr" ,r-magrittr)
4352 ("r-tibble" ,r-tibble)))
4353 (home-page "https://statnet.org/")
4354 (synopsis "Classes for relational data")
4356 "This package provides tools to create and modify network objects. The
4357 @code{network} class can represent a range of relational data types, and
4358 supports arbitrary vertex/edge/graph attributes.")
4359 (license license:gpl2+)))
4361 (define-public r-statnet-common
4363 (name "r-statnet-common")
4368 (uri (cran-uri "statnet.common" version))
4371 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4373 `((upstream-name . "statnet.common")))
4374 (build-system r-build-system)
4376 `(("r-coda" ,r-coda)))
4377 (home-page "https://statnet.org")
4378 (synopsis "R scripts and utilities used by the Statnet software")
4379 (description "This package provides non-statistical utilities used by the
4380 software developed by the Statnet Project.")
4381 (license license:gpl3)))
4383 (define-public r-statcheck
4385 (name "r-statcheck")
4390 (uri (cran-uri "statcheck" version))
4393 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4394 (build-system r-build-system)
4396 `(("r-ggplot2" ,r-ggplot2)
4398 ("r-rmarkdown" ,r-rmarkdown)))
4399 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4400 (synopsis "Extract statistics from articles and recompute p-values")
4401 (description "This package can automatically extract statistical
4402 null-hypothesis significant testing (NHST) results from articles and recompute
4403 the p-values based on the reported test statistic and degrees of freedom to
4404 detect possible inconsistencies.")
4405 (license license:gpl2)))
4407 (define-public r-sna
4414 (uri (cran-uri "sna" version))
4417 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4418 (build-system r-build-system)
4420 `(("r-network" ,r-network)
4421 ("r-statnet-common" ,r-statnet-common)))
4422 (home-page "https://statnet.org")
4423 (synopsis "Tools for social network analysis")
4425 "This package provides a range of tools for social network analysis,
4426 including node and graph-level indices, structural distance and covariance
4427 methods, structural equivalence detection, network regression, random graph
4428 generation, and 2D/3D network visualization.")
4429 (license license:gpl2+)))
4431 (define-public r-tfisher
4438 (uri (cran-uri "TFisher" version))
4441 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4442 (properties `((upstream-name . "TFisher")))
4443 (build-system r-build-system)
4445 `(("r-matrix" ,r-matrix)
4446 ("r-mvtnorm" ,r-mvtnorm)
4448 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4449 (synopsis "Optimal thresholding Fisher's p-value combination method")
4451 "This package provides the @dfn{cumulative distribution function} (CDF),
4452 quantile, and statistical power calculator for a collection of thresholding
4453 Fisher's p-value combination methods, including Fisher's p-value combination
4454 method, truncated product method and, in particular, soft-thresholding
4455 Fisher's p-value combination method which is proven to be optimal in some
4456 context of signal detection. The p-value calculator for the omnibus version
4457 of these tests are also included.")
4458 (license license:gpl2)))
4460 (define-public r-ttr
4467 (uri (cran-uri "TTR" version))
4470 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4471 (properties `((upstream-name . "TTR")))
4472 (build-system r-build-system)
4474 `(("r-curl" ,r-curl)
4477 (home-page "https://github.com/joshuaulrich/TTR")
4478 (synopsis "Technical trading rules")
4480 "This package provides functions and data to construct technical trading
4482 (license license:gpl2)))
4484 (define-public r-leaps
4491 (uri (cran-uri "leaps" version))
4494 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4495 (build-system r-build-system)
4496 (native-inputs `(("gfortran" ,gfortran)))
4497 (home-page "https://cran.r-project.org/web/packages/leaps/")
4498 (synopsis "Regression subset selection")
4500 "This package provides tools for regression subset selection, including
4501 exhaustive search.")
4502 (license license:gpl2+)))
4504 (define-public r-splus2r
4511 (uri (cran-uri "splus2R" version))
4514 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4515 (properties `((upstream-name . "splus2R")))
4516 (build-system r-build-system)
4517 (native-inputs `(("gfortran" ,gfortran)))
4518 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4519 (synopsis "Supplemental S-PLUS functionality in R")
4521 "Currently there are many functions in S-PLUS that are missing in R. To
4522 facilitate the conversion of S-PLUS packages to R packages, this package
4523 provides some missing S-PLUS functionality in R.")
4524 (license license:gpl2)))
4526 (define-public r-ifultools
4528 (name "r-ifultools")
4533 (uri (cran-uri "ifultools" version))
4536 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4537 (build-system r-build-system)
4539 `(("r-mass" ,r-mass)
4540 ("r-splus2r" ,r-splus2r)))
4541 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4542 (synopsis "Insightful research tools")
4543 (description "This package provides C code used by the wmtsa, fractal, and
4545 (license license:gpl2)))
4547 (define-public r-sapa
4554 (uri (cran-uri "sapa" version))
4557 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4558 (build-system r-build-system)
4560 `(("r-ifultools" ,r-ifultools)
4561 ("r-splus2r" ,r-splus2r)))
4562 (home-page "https://cran.r-project.org/web/packages/sapa/")
4563 (synopsis "Spectral analysis for physical applications")
4564 (description "This package provides software for the book Spectral
4565 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4566 Cambridge University Press, 1993.")
4567 (license license:gpl2)))
4569 (define-public r-aggregation
4571 (name "r-aggregation")
4576 (uri (cran-uri "aggregation" version))
4579 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4580 (build-system r-build-system)
4581 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4582 (synopsis "Methods for p-value aggregation")
4584 "This package contains functionality for performing the following methods
4585 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4586 Fisher's method), and Sidak correction.")
4587 (license license:gpl3)))
4589 (define-public r-quantmod
4596 (uri (cran-uri "quantmod" version))
4599 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4600 (build-system r-build-system)
4602 `(("r-curl" ,r-curl)
4606 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4607 (synopsis "Quantitative financial modelling framework")
4608 (description "This package provides a quantitative financial modelling
4609 framework to allow users to specify, build, trade, and analyse quantitative
4610 financial trading strategies.")
4611 (license license:gpl3)))
4613 (define-public r-tseries
4620 (uri (cran-uri "tseries" version))
4623 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4624 (build-system r-build-system)
4626 `(("r-quadprog" ,r-quadprog)
4627 ("r-quantmod" ,r-quantmod)
4630 `(("gfortran" ,gfortran)))
4631 (home-page "https://cran.r-project.org/web/packages/tseries/")
4632 (synopsis "Time series analysis and computational finance")
4634 "This package provides functions relating to time series analysis and
4635 computational finance.")
4636 (license license:gpl2)))
4638 (define-public r-wmtsa
4645 (uri (cran-uri "wmtsa" version))
4648 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4649 (build-system r-build-system)
4651 `(("r-ifultools" ,r-ifultools)
4653 ("r-splus2r" ,r-splus2r)))
4654 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4655 (synopsis "Wavelet methods for time series analysis")
4657 "This package provides software to accompany the book \"Wavelet Methods
4658 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4659 University Press, 2000.")
4660 (license license:gpl2)))
4662 (define-public r-tsa
4669 (uri (cran-uri "TSA" version))
4672 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4673 (properties `((upstream-name . "TSA")))
4674 (build-system r-build-system)
4676 `(("r-leaps" ,r-leaps)
4677 ("r-locfit" ,r-locfit)
4678 ("r-mgcv" ,r-mgcv)))
4679 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4680 (synopsis "Time series analysis")
4682 "This package contains R functions and datasets detailed in the book
4683 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4684 Cryer and Kung-Sik Chan.")
4685 (license license:gpl2+)))
4687 (define-public r-extradistr
4689 (name "r-extradistr")
4694 (uri (cran-uri "extraDistr" version))
4697 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4698 (properties `((upstream-name . "extraDistr")))
4699 (build-system r-build-system)
4701 `(("r-rcpp" ,r-rcpp)))
4702 (home-page "https://github.com/twolodzko/extraDistr")
4703 (synopsis "Additional univariate and multivariate distributions")
4705 "This package implements density, distribution functions, quantile
4706 functions and random generation functions for a large number of univariate and
4707 multivariate distributions.")
4708 (license license:gpl2)))
4710 (define-public r-fractal
4717 (uri (cran-uri "fractal" version))
4720 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4721 (build-system r-build-system)
4723 `(("r-ifultools" ,r-ifultools)
4726 ("r-scatterplot3d" ,r-scatterplot3d)
4727 ("r-splus2r" ,r-splus2r)
4728 ("r-wmtsa" ,r-wmtsa)))
4729 (home-page "https://cran.r-project.org/web/packages/fractal/")
4730 (synopsis "Fractal time series modeling and analysis")
4732 "This package provides tools for stochastic fractal and deterministic
4733 chaotic time series analysis.")
4734 (license license:gpl2)))
4736 (define-public r-urca
4743 (uri (cran-uri "urca" version))
4746 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4747 (build-system r-build-system)
4748 (propagated-inputs `(("r-nlme" ,r-nlme)))
4749 (native-inputs `(("gfortran" ,gfortran)))
4750 (home-page "https://cran.r-project.org/web/packages/urca/")
4751 (synopsis "Unit root and cointegration tests for time series data")
4753 "This package provides unit root and cointegration tests encountered in
4754 applied econometric analysis.")
4755 (license license:gpl2+)))
4757 (define-public r-cubature
4764 (uri (cran-uri "cubature" version))
4767 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4768 (build-system r-build-system)
4770 `(("r-rcpp" ,r-rcpp)))
4771 (home-page "https://github.com/bnaras/cubature")
4772 (synopsis "Adaptive multivariate integration over hypercubes")
4774 "This package is an R wrapper around the cubature C library for adaptive
4775 multivariate integration over hypercubes. This version provides both
4776 @code{hcubature} and @code{pcubature} routines in addition to a vector
4778 ;; The included cubature C library is released under GPLv2+, but the
4779 ;; wrapper declares the license to be GPLv3+.
4780 (license (list license:gpl2+ license:gpl3+))))
4782 (define-public r-trend
4789 (uri (cran-uri "trend" version))
4792 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4793 (build-system r-build-system)
4795 `(("r-extradistr" ,r-extradistr)))
4797 `(("gfortran" ,gfortran)))
4798 (home-page "https://cran.r-project.org/web/packages/trend/")
4799 (synopsis "Non-parametric trend tests and change-point detection")
4801 "The analysis of environmental data often requires the detection of
4802 trends and change-points. This package includes tests for trend
4803 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4804 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4805 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4806 correlation trend test), change-point detection (Lanzante's test procedures,
4807 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4808 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4809 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4810 sample Robust Rank-Order Distributional Test.")
4811 (license license:gpl3)))
4813 (define-public r-expm
4820 (uri (cran-uri "expm" version))
4823 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4824 (build-system r-build-system)
4825 (propagated-inputs `(("r-matrix" ,r-matrix)))
4826 (native-inputs `(("gfortran" ,gfortran)))
4827 (home-page "https://r-forge.r-project.org/projects/expm/")
4828 (synopsis "Tools for matrix exponentials and related quantities")
4830 "This package provides tools for the computation of the matrix
4831 exponential, logarithm, square root, and related quantities.")
4832 (license license:gpl2+)))
4834 (define-public r-complexplus
4836 (name "r-complexplus")
4841 (uri (cran-uri "complexplus" version))
4844 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4845 (build-system r-build-system)
4847 `(("r-expm" ,r-expm)
4848 ("r-matrix" ,r-matrix)))
4849 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4850 (synopsis "Functions of complex or real variables")
4852 "This package extends several functions to the complex domain, including
4853 the matrix exponential and logarithm, and the determinant.")
4854 (license license:gpl2)))
4856 (define-public r-phontools
4858 (name "r-phontools")
4863 (uri (cran-uri "phonTools" version))
4866 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4867 (properties `((upstream-name . "phonTools")))
4868 (build-system r-build-system)
4869 (home-page "http://www.santiagobarreda.com/rscripts.html")
4870 (synopsis "Tools for phonetic and acoustic analyses")
4872 "This package contains tools for the organization, display, and analysis
4873 of the sorts of data frequently encountered in phonetics research and
4874 experimentation, including the easy creation of IPA vowel plots, and the
4875 creation and manipulation of WAVE audio files.")
4876 (license license:bsd-2)))
4885 (uri (cran-uri "np" version))
4888 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
4889 (build-system r-build-system)
4891 `(("r-boot" ,r-boot)
4892 ("r-cubature" ,r-cubature)
4893 ("r-quadprog" ,r-quadprog)
4894 ("r-quantreg" ,r-quantreg)))
4895 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4896 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4897 (description "This package provides non-parametric (and semi-parametric)
4898 kernel methods that seamlessly handle a mix of continuous, unordered, and
4899 ordered factor data types.")
4900 ;; Any version of the GPL.
4901 (license license:gpl3+)))
4903 (define-public r-powerplus
4905 (name "r-powerplus")
4910 (uri (cran-uri "powerplus" version))
4913 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4914 (build-system r-build-system)
4916 `(("r-complexplus" ,r-complexplus)
4919 ("r-matrix" ,r-matrix)
4920 ("r-phontools" ,r-phontools)))
4921 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4922 (synopsis "Exponentiation operations")
4924 "This package provides tools for the computation of matrix and scalar
4926 (license license:gpl2)))
4928 (define-public r-egg
4935 (uri (cran-uri "egg" version))
4938 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4939 (properties `((upstream-name . "egg")))
4940 (build-system r-build-system)
4942 `(("r-ggplot2" ,r-ggplot2)
4943 ("r-gridextra" ,r-gridextra)
4944 ("r-gtable" ,r-gtable)))
4945 (home-page "https://cran.r-project.org/web/packages/egg")
4946 (synopsis "Extensions for ggplot2")
4948 "This package provides miscellaneous functions to help customize ggplot2
4949 objects. High-level functions are provided to post-process ggplot2 layouts
4950 and allow alignment between plot panels, as well as setting panel sizes to
4951 fixed values. Other functions include a custom @code{geom}, and helper
4952 functions to enforce symmetric scales or add tags to facetted plots.")
4953 (license license:gpl3)))
4955 (define-public r-heatmaply
4957 (name "r-heatmaply")
4962 (uri (cran-uri "heatmaply" version))
4965 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
4966 (build-system r-build-system)
4968 `(("r-assertthat" ,r-assertthat)
4969 ("r-colorspace" ,r-colorspace)
4970 ("r-dendextend" ,r-dendextend)
4972 ("r-ggplot2" ,r-ggplot2)
4973 ("r-htmlwidgets" ,r-htmlwidgets)
4974 ("r-magrittr" ,r-magrittr)
4975 ("r-plotly" ,r-plotly)
4976 ("r-rcolorbrewer" ,r-rcolorbrewer)
4977 ("r-reshape2" ,r-reshape2)
4978 ("r-scales" ,r-scales)
4979 ("r-seriation" ,r-seriation)
4980 ("r-viridis" ,r-viridis)
4981 ("r-webshot" ,r-webshot)))
4983 `(("r-knitr" ,r-knitr)))
4984 (home-page "https://cran.r-project.org/package=heatmaply")
4985 (synopsis "Interactive cluster heat maps using plotly")
4987 "This package enables you to create interactive cluster heatmaps that can
4988 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4989 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4990 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4991 a popular graphical method for visualizing high-dimensional data, in which a
4992 table of numbers is encoded as a grid of colored cells. The rows and columns
4993 of the matrix are ordered to highlight patterns and are often accompanied by
4995 ;; Either version of the license.
4996 (license (list license:gpl2 license:gpl3))))
5005 (uri (cran-uri "h5" version))
5008 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5009 (build-system r-build-system)
5014 `(("which" ,which)))
5016 `(("r-rcpp" ,r-rcpp)))
5017 (home-page "https://github.com/mannau/h5")
5018 (synopsis "Interface to the HDF5 Library")
5020 "This package provides an S4 interface to the HDF5 library supporting
5021 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5022 binary files in a language independent format. The HDF5 format can therefore
5023 be used as an alternative to R's save/load mechanism. Since h5 is able to
5024 access only subsets of stored data it can also handle data sets which do not
5026 (license license:bsd-2)))
5028 (define-public r-cgdsr
5035 (uri (cran-uri "cgdsr" version))
5038 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5039 (build-system r-build-system)
5041 `(("r-httr" ,r-httr)
5042 ("r-r-methodss3" ,r-r-methodss3)
5043 ("r-r-oo" ,r-r-oo)))
5044 (home-page "https://github.com/cBioPortal/cgdsr")
5045 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5047 "This package provides a basic set of R functions for querying the Cancer
5048 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5049 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5050 (license license:lgpl3)))
5052 (define-public r-import
5059 (uri (cran-uri "import" version))
5062 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5063 (build-system r-build-system)
5064 (home-page "https://github.com/smbache/import")
5065 (synopsis "Import mechanism for R")
5067 "This is an alternative mechanism for importing objects from packages.
5068 The syntax allows for importing multiple objects from a package with a single
5069 command in an expressive way. The import package bridges some of the gap
5070 between using @code{library} (or @code{require}) and direct (single-object)
5071 imports. Furthermore the imported objects are not placed in the current
5072 environment. It is also possible to import objects from stand-alone @code{.R}
5074 (license license:expat)))
5076 (define-public r-shinyace
5083 (uri (cran-uri "shinyAce" version))
5086 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5087 (properties `((upstream-name . "shinyAce")))
5088 (build-system r-build-system)
5090 `(("r-shiny" ,r-shiny)
5091 ("r-jsonlite" ,r-jsonlite)))
5092 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5093 (synopsis "Ace editor bindings for Shiny")
5095 "This package provides Ace editor bindings to enable a rich text editing
5096 environment within Shiny.")
5097 (license license:expat)))
5099 (define-public r-randomizr
5101 (name "r-randomizr")
5106 (uri (cran-uri "randomizr" version))
5109 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5110 (properties `((upstream-name . "randomizr")))
5111 (build-system r-build-system)
5113 `(("r-knitr" ,r-knitr)))
5114 (home-page "https://declaredesign.org/r/randomizr/")
5115 (synopsis "Tools for common forms of random assignment and sampling")
5117 "This package provides tools for generating random assignments for common
5118 experimental designs and random samples for common sampling designs.")
5119 (license license:expat)))
5121 (define-public r-base64url
5123 (name "r-base64url")
5128 (uri (cran-uri "base64url" version))
5131 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5132 (build-system r-build-system)
5134 `(("r-backports" ,r-backports)))
5135 (home-page "https://github.com/mllg/base64url")
5136 (synopsis "Fast and URL-safe base64 encoder and decoder")
5138 "This package provides a URL-safe base64 encoder and decoder. In
5139 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5140 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5141 encoder does not fill the string with trailing @code{=}. The resulting
5142 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5143 and thus are safe to use in URLs or for file names. The package also comes
5144 with a simple base32 encoder/decoder suited for case insensitive file
5146 (license license:gpl3)))
5148 (define-public r-radiant-data
5150 (name "r-radiant-data")
5155 (uri (cran-uri "radiant.data" version))
5158 "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs"))
5159 (modules '((guix build utils)))
5162 ;; Delete files that are under CC-NC-SA.
5163 (delete-file-recursively "inst/app/tools/help")
5165 (properties `((upstream-name . "radiant.data")))
5166 (build-system r-build-system)
5168 `(("r-base64enc" ,r-base64enc)
5169 ("r-broom" ,r-broom)
5172 ("r-dplyr" ,r-dplyr)
5175 ("r-ggplot2" ,r-ggplot2)
5176 ("r-import" ,r-import)
5177 ("r-jsonlite" ,r-jsonlite)
5178 ("r-knitr" ,r-knitr)
5179 ("r-lubridate" ,r-lubridate)
5180 ("r-magrittr" ,r-magrittr)
5181 ("r-markdown" ,r-markdown)
5183 ("r-patchwork" ,r-patchwork)
5184 ("r-plotly" ,r-plotly)
5185 ("r-psych" ,r-psych)
5186 ("r-randomizr" ,r-randomizr)
5187 ("r-readr" ,r-readr)
5188 ("r-readxl" ,r-readxl)
5189 ("r-rlang" ,r-rlang)
5190 ("r-rmarkdown" ,r-rmarkdown)
5191 ("r-rstudioapi" ,r-rstudioapi)
5192 ("r-scales" ,r-scales)
5193 ("r-shiny" ,r-shiny)
5194 ("r-shinyfiles" ,r-shinyfiles)
5195 ("r-shinyace" ,r-shinyace)
5196 ("r-stringi" ,r-stringi)
5197 ("r-tibble" ,r-tibble)
5198 ("r-tidyr" ,r-tidyr)
5199 ("r-writexl" ,r-writexl)))
5200 (home-page "https://github.com/radiant-rstats/radiant.data")
5201 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5203 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5204 visualizing, summarizing, transforming, and combining data. It also contains
5205 functionality to generate reproducible reports of the analyses conducted in
5207 (license license:agpl3)))
5209 (define-public r-algdesign
5211 (name "r-algdesign")
5216 (uri (cran-uri "AlgDesign" version))
5218 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5219 (properties `((upstream-name . "AlgDesign")))
5220 (build-system r-build-system)
5221 (home-page "https://github.com/jvbraun/AlgDesign")
5222 (synopsis "Algorithmic experimental design")
5224 "This package provides tools to calculate exact and approximate theory
5225 experimental designs for D, A, and I criteria. Very large designs may be
5226 created. Experimental designs may be blocked or blocked designs created from
5227 a candidate list, using several criteria. The blocking can be done when whole
5228 and within plot factors interact.")
5229 (license license:gpl2+)))
5231 (define-public r-signal
5238 (uri (cran-uri "signal" version))
5241 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5242 (build-system r-build-system)
5243 (propagated-inputs `(("r-mass" ,r-mass)))
5244 (native-inputs `(("gfortran" ,gfortran)))
5245 (home-page "https://cran.r-project.org/web/packages/signal/")
5246 (synopsis "Signal processing")
5248 "This package provides a set of signal processing functions originally
5249 written for Matlab and GNU Octave. It includes filter generation utilities,
5250 filtering functions, resampling routines, and visualization of filter models.
5251 It also includes interpolation functions.")
5252 (license license:gpl2)))
5254 (define-public r-gsubfn
5261 (uri (cran-uri "gsubfn" version))
5264 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5265 (build-system r-build-system)
5266 (propagated-inputs `(("r-proto" ,r-proto)))
5267 (home-page "https://code.google.com/archive/p/gsubfn/")
5268 (synopsis "Utilities for strings and function arguments.")
5270 "This package provides @code{gsubfn} which is like @code{gsub} but can
5271 take a replacement function or certain other objects instead of the
5272 replacement string. Matches and back references are input to the replacement
5273 function and replaced by the function output. @code{gsubfn} can be used to
5274 split strings based on content rather than delimiters and for quasi-perl-style
5275 string interpolation. The package also has facilities for translating
5276 formulas to functions and allowing such formulas in function calls instead of
5278 (license license:gpl2+)))
5280 (define-public r-sqldf
5287 (uri (cran-uri "sqldf" version))
5290 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5291 (build-system r-build-system)
5293 `(("r-chron" ,r-chron)
5295 ("r-gsubfn" ,r-gsubfn)
5296 ("r-proto" ,r-proto)
5297 ("r-rsqlite" ,r-rsqlite)))
5298 (home-page "https://github.com/ggrothendieck/sqldf")
5299 (synopsis "Manipulate R data frames using SQL")
5301 "The @code{sqldf} function is typically passed a single argument which is
5302 an SQL select statement where the table names are ordinary R data frame names.
5303 @code{sqldf} transparently sets up a database, imports the data frames into
5304 that database, performs the SQL statement and returns the result using a
5305 heuristic to determine which class to assign to each column of the returned
5306 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5307 used to read filtered files into R even if the original files are larger than
5308 R itself can handle.")
5309 (license license:gpl2)))
5311 (define-public r-abind
5318 (uri (cran-uri "abind" version))
5321 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5322 (build-system r-build-system)
5323 (home-page "https://cran.r-project.org/web/packages/abind/")
5324 (synopsis "Combine multidimensional arrays")
5326 "This package provides tools to combine multidimensional arrays into a
5327 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5328 works with vectors, matrices, and higher-dimensional arrays. It also provides
5329 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5330 extracting and replacing data in arrays.")
5331 (license license:lgpl2.0+)))
5333 (define-public r-prroc
5340 (uri (cran-uri "PRROC" version))
5343 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5344 (properties `((upstream-name . "PRROC")))
5345 (build-system r-build-system)
5346 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5347 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5349 "This package computes the areas under the @dfn{precision-recall} (PR)
5350 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5351 contrast to other implementations, the interpolation between points of the PR
5352 curve is done by a non-linear piecewise function. In addition to the areas
5353 under the curves, the curves themselves can also be computed and plotted by a
5354 specific S3-method.")
5355 (license license:gpl3)))
5357 (define-public r-vim
5364 (uri (cran-uri "VIM" version))
5367 "0w22ir0gvym7gqd6nw2j7w5ivlb3az1dkfxv33imimkb7c83056a"))))
5368 (properties `((upstream-name . "VIM")))
5369 (build-system r-build-system)
5372 ("r-colorspace" ,r-colorspace)
5373 ("r-data-table" ,r-data-table)
5374 ("r-e1071" ,r-e1071)
5375 ("r-laeken" ,r-laeken)
5376 ("r-magrittr" ,r-magrittr)
5379 ("r-ranger" ,r-ranger)
5381 ("r-robustbase" ,r-robustbase)
5384 (home-page "https://github.com/alexkowa/VIM")
5385 (synopsis "Visualization and imputation of missing values")
5387 "This package provides tools for the visualization of missing and/or
5388 imputed values are introduced, which can be used for exploring the data and
5389 the structure of the missing and/or imputed values. Depending on this
5390 structure of the missing values, the corresponding methods may help to
5391 identify the mechanism generating the missing values and allows to explore the
5392 data including missing values. In addition, the quality of imputation can be
5393 visually explored using various univariate, bivariate, multiple and
5394 multivariate plot methods.")
5395 (license license:gpl2+)))
5397 (define-public r-fnn
5404 (uri (cran-uri "FNN" version))
5407 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5408 (properties `((upstream-name . "FNN")))
5409 (build-system r-build-system)
5410 (home-page "https://cran.r-project.org/web/packages/FNN")
5411 (synopsis "Fast nearest neighbor search algorithms and applications")
5413 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5414 search algorithms. Related applications including KNN classification,
5415 regression and information measures are implemented.")
5416 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5417 ;; later can be used.
5418 (license license:gpl2+)))
5420 (define-public r-smoother
5427 (uri (cran-uri "smoother" version))
5430 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5431 (build-system r-build-system)
5433 `(("r-ttr" ,r-ttr)))
5434 (home-page "https://cran.r-project.org/web/packages/smoother")
5435 (synopsis "Functions relating to the smoothing of numerical data")
5437 "This package provides a collection of methods for smoothing numerical
5438 data, commencing with a port of the Matlab gaussian window smoothing function.
5439 In addition, several functions typically used in smoothing of financial data
5441 (license license:gpl2)))
5443 (define-public r-riverplot
5445 (name "r-riverplot")
5450 (uri (cran-uri "riverplot" version))
5453 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5454 (build-system r-build-system)
5455 (home-page "https://logfc.wordpress.com")
5456 (synopsis "Sankey or ribbon plots")
5458 "Sankey plots are a type of diagram that is convenient to illustrate how
5459 flow of information, resources etc. separates and joins, much like observing
5460 how rivers split and merge. For example, they can be used to compare
5461 different clusterings. This package provides an implementation of Sankey
5463 (license license:gpl2+)))
5465 (define-public r-dyn
5472 (uri (cran-uri "dyn" version))
5475 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5476 (build-system r-build-system)
5478 `(("r-zoo" ,r-zoo)))
5479 (home-page "https://cran.r-project.org/web/packages/dyn")
5480 (synopsis "Time series regression")
5482 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5483 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5484 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5485 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5486 @code{randomForest::randomForest()} and other regression functions, allowing
5487 those functions to be used with time series including specifications that may
5488 contain lags, diffs and missing values.")
5490 (license license:gpl2+)))
5492 (define-public r-catdap
5499 (uri (cran-uri "catdap" version))
5502 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5503 (build-system r-build-system)
5505 `(("gfortran" ,gfortran)))
5506 (home-page "https://cran.r-project.org/web/packages/catdap/")
5507 (synopsis "Tools for categorical data analysis")
5509 "This package provides functions for analyzing multivariate data.
5510 Dependencies of the distribution of the specified variable (response
5511 variable) to other variables (explanatory variables) are derived and
5512 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5513 (license license:gpl2+)))
5515 (define-public r-arules
5522 (uri (cran-uri "arules" version))
5525 "0bcvfn8lvcv74vv9z3kgg7yq5hm7wjqhmzadi55cbm8zxd76g84v"))))
5526 (build-system r-build-system)
5528 `(("r-matrix" ,r-matrix)))
5529 (home-page "https://github.com/mhahsler/arules")
5530 (synopsis "Mining association rules and frequent itemsets")
5532 "This package provides an infrastructure for representing, manipulating
5533 and analyzing transaction data and patterns (frequent itemsets and association rules).
5534 It also provides C implementations of the association mining algorithms Apriori
5536 (license license:gpl3)))
5538 (define-public r-parsedate
5540 (name "r-parsedate")
5545 (uri (cran-uri "parsedate" version))
5548 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5549 (build-system r-build-system)
5551 `(("r-rematch2" ,r-rematch2)))
5552 (home-page "https://github.com/gaborcsardi/parsedate")
5554 "Recognize and parse dates in various formats")
5556 "This package provides three functions for dealing with dates:
5557 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5558 time formats, @code{parse_date} parses dates in unspecified formats,
5559 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5560 (license license:gpl2)))
5562 (define-public r-abc-data
5569 (uri (cran-uri "abc.data" version))
5572 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5573 (properties `((upstream-name . "abc.data")))
5574 (build-system r-build-system)
5575 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5576 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5578 "This package contains data which are used by functions of the abc
5579 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5580 algorithms for performing parameter estimation, model selection, and
5582 (license license:gpl3+)))
5584 (define-public r-abc
5591 (uri (cran-uri "abc" version))
5594 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5595 (build-system r-build-system)
5597 `(("r-abc-data" ,r-abc-data)
5598 ("r-locfit" ,r-locfit)
5601 ("r-quantreg" ,r-quantreg)))
5602 (home-page "https://cran.r-project.org/web/packages/abc/")
5603 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5605 "This package implements several @dfn{Approximate Bayesian
5606 Computation} (ABC) algorithms for performing parameter estimation, model
5607 selection, and goodness-of-fit. Cross-validation tools are also available for
5608 measuring the accuracy of ABC estimates, and to calculate the
5609 misclassification probabilities of different models.")
5610 (license license:gpl3+)))
5612 (define-public r-zip
5619 (uri (cran-uri "zip" version))
5622 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5623 (build-system r-build-system)
5624 (home-page "https://github.com/gaborcsardi/zip")
5625 (synopsis "Cross-platform Zip compression")
5627 "This package provides a cross-platform Zip compression library for R.
5628 It is a replacement for the @code{zip} function, that does not require any
5629 additional external tools on any platform.")
5630 (license license:cc0)))
5632 (define-public r-openxlsx
5639 (uri (cran-uri "openxlsx" version))
5642 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5643 (build-system r-build-system)
5645 `(("r-rcpp" ,r-rcpp)
5646 ("r-stringi" ,r-stringi)
5648 (home-page "https://github.com/awalker89/openxlsx")
5649 (synopsis "Read, write and edit XLSX files")
5651 "This package simplifies the creation of Excel @code{.xlsx} files by
5652 providing a high level interface to writing, styling and editing worksheets.
5653 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5654 and @code{XLConnect} packages with the added benefit of removing the
5655 dependency on Java.")
5656 (license license:gpl3)))
5658 (define-public r-rio
5665 (uri (cran-uri "rio" version))
5668 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5669 (build-system r-build-system)
5671 `(("r-curl" ,r-curl)
5672 ("r-data-table" ,r-data-table)
5673 ("r-foreign" ,r-foreign)
5674 ("r-haven" ,r-haven)
5675 ("r-openxlsx" ,r-openxlsx)
5676 ("r-readxl" ,r-readxl)
5677 ("r-tibble" ,r-tibble)))
5678 (home-page "https://github.com/leeper/rio")
5679 (synopsis "Swiss-army knife for data I/O")
5681 "This package provides streamlined data import and export infrastructure
5682 by making assumptions that the user is probably willing to make: @code{import}
5683 and @code{export} determine the data structure from the file extension,
5684 reasonable defaults are used for data import and export (e.g.,
5685 @code{stringsAsFactors=FALSE}), web-based import is natively
5686 supported (including from SSL/HTTPS), compressed files can be read directly
5687 without explicit decompression, and fast import packages are used where
5688 appropriate. An additional convenience function, @code{convert}, provides a
5689 simple method for converting between file types.")
5690 (license license:gpl2)))
5692 (define-public r-maptools
5699 (uri (cran-uri "maptools" version))
5702 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5703 (build-system r-build-system)
5705 `(("r-foreign" ,r-foreign)
5706 ("r-lattice" ,r-lattice)
5708 (home-page "https://r-forge.r-project.org/projects/maptools/")
5709 (synopsis "Tools for reading and handling spatial objects")
5711 "This package provides a set of tools for manipulating and reading
5712 geographic data, in particular ESRI Shapefiles. It includes binary access to
5713 GSHHG shoreline files. The package also provides interface wrappers for
5714 exchanging spatial objects with other R packages.")
5715 ;; The C source files from shapelib are released under the Expat license.
5716 ;; The R code is released under GPL version 2 or later.
5717 (license (list license:gpl2+
5720 (define-public r-later
5727 (uri (cran-uri "later" version))
5730 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5731 (build-system r-build-system)
5735 ("r-rlang" ,r-rlang)))
5736 (home-page "https://github.com/r-lib/later")
5737 (synopsis "Utilities for delaying function execution")
5739 "This package provides tools to execute arbitrary R or C functions some
5740 time after the current time, after the R execution stack has emptied.")
5741 (license license:gpl2+)))
5743 (define-public r-promises
5750 (uri (cran-uri "promises" version))
5753 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5754 (build-system r-build-system)
5756 `(("r-later" ,r-later)
5757 ("r-magrittr" ,r-magrittr)
5760 ("r-rlang" ,r-rlang)))
5761 (home-page "https://rstudio.github.io/promises")
5762 (synopsis "Abstractions for promise-based asynchronous programming")
5764 "This package provides fundamental abstractions for doing asynchronous
5765 programming in R using promises. Asynchronous programming is useful for
5766 allowing a single R process to orchestrate multiple tasks in the background
5767 while also attending to something else. Semantics are similar to JavaScript
5768 promises, but with a syntax that is idiomatic R.")
5769 (license license:expat)))
5771 (define-public r-dosnow
5778 (uri (cran-uri "doSNOW" version))
5781 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5782 (properties `((upstream-name . "doSNOW")))
5783 (build-system r-build-system)
5785 `(("r-foreach" ,r-foreach)
5786 ("r-iterators" ,r-iterators)
5787 ("r-snow" ,r-snow)))
5788 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5789 (synopsis "Foreach parallel adaptor for the snow package")
5791 "This package provides a parallel backend for the @code{%dopar%} function
5792 using the @code{snow} package.")
5793 (license license:gpl2)))
5795 (define-public r-snowfall
5798 (version "1.84-6.1")
5801 (uri (cran-uri "snowfall" version))
5803 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5804 (build-system r-build-system)
5806 `(("r-snow" ,r-snow)))
5807 (home-page "https://cran.r-project.org/web/packages/snowfall/")
5808 (synopsis "Easier cluster computing")
5809 (description "This package is a usability wrapper around snow for easier
5810 development of parallel R programs. This package offers e.g. extended error
5811 checks, and additional functions. All functions work in sequential mode, too,
5812 if no cluster is present or wished. The package is also designed as connector
5813 to the cluster management tool @code{sfCluster}, but can also used without
5815 (license license:gpl2+)))
5817 (define-public r-rappdirs
5824 (uri (cran-uri "rappdirs" version))
5827 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5828 (build-system r-build-system)
5829 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5830 (synopsis "Determine where to save data, caches, and logs")
5832 "This package provides an easy way to determine which directories on the
5833 user's computer should be used to save data, caches and logs. It is a port of
5834 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5835 (license license:expat)))
5837 (define-public r-renv
5844 (uri (cran-uri "renv" version))
5847 "02ayfgbpw4b58148dcxz31anaxncwczmxs1zzkskwj0rzhb2x60r"))))
5848 (properties `((upstream-name . "renv")))
5849 (build-system r-build-system)
5850 (home-page "https://rstudio.github.io/renv")
5851 (synopsis "Project environments")
5853 "This package provides a dependency management toolkit for R. Using
5854 renv, you can create and manage project-local R libraries, save the state of
5855 these libraries to a lockfile, and later restore your library as required.
5856 Together, these tools can help make your projects more isolated, portable, and
5858 (license license:expat)))
5860 (define-public r-learnr
5867 (uri (cran-uri "learnr" version))
5870 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
5871 (build-system r-build-system)
5873 `(("r-checkmate" ,r-checkmate)
5874 ("r-ellipsis" ,r-ellipsis)
5875 ("r-evaluate" ,r-evaluate)
5876 ("r-htmltools" ,r-htmltools)
5877 ("r-htmlwidgets" ,r-htmlwidgets)
5878 ("r-jsonlite" ,r-jsonlite)
5879 ("r-knitr" ,r-knitr)
5880 ("r-markdown" ,r-markdown)
5881 ("r-rappdirs" ,r-rappdirs)
5883 ("r-rmarkdown" ,r-rmarkdown)
5884 ("r-rprojroot" ,r-rprojroot)
5885 ("r-shiny" ,r-shiny)
5886 ("r-withr" ,r-withr)))
5887 (home-page "https://rstudio.github.io/learnr/")
5888 (synopsis "Interactive tutorials for R")
5890 "This package provides tools to create interactive tutorials using R
5891 Markdown. Use a combination of narrative, figures, videos, exercises, and
5892 quizzes to create self-paced tutorials for learning about R and R packages.")
5893 (license license:asl2.0)))
5895 (define-public r-analytics
5897 (name "r-analytics")
5902 (uri (cran-uri "analytics" version))
5905 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5906 (build-system r-build-system)
5909 ("r-cluster" ,r-cluster)
5910 ("r-fractal" ,r-fractal)
5911 ("r-lmtest" ,r-lmtest)
5914 ("r-powerplus" ,r-powerplus)
5915 ("r-robust" ,r-robust)
5916 ("r-trend" ,r-trend)
5920 (home-page "https://cran.r-project.org/web/packages/analytics/")
5921 (synopsis "Collection of data analysis tools")
5923 "This package is a collection of data analysis tools. It includes tools
5924 for regression outlier detection in a fitted linear model, stationary
5925 bootstrap using a truncated geometric distribution, a comprehensive test for
5926 weak stationarity, column means by group, weighted biplots, and a heuristic to
5927 obtain a better initial configuration in non-metric MDS.")
5928 (license license:gpl2)))
5930 (define-public r-reticulate
5932 (name "r-reticulate")
5937 (uri (cran-uri "reticulate" version))
5940 "03dmnx9jhxx6vfbv2i5n6sln38kb9zkshz982pg3l9i4jjf3xns7"))))
5941 (build-system r-build-system)
5942 (inputs `(("python" ,python)))
5944 `(("r-rappdirs" ,r-rappdirs)
5945 ("r-jsonlite" ,r-jsonlite)
5946 ("r-matrix" ,r-matrix)
5947 ("r-rcpp" ,r-rcpp)))
5949 `(("r-knitr" ,r-knitr)))
5950 (home-page "https://github.com/rstudio/reticulate")
5951 (synopsis "R interface to Python")
5953 "This package provides an interface from R to Python modules, classes,
5954 and functions. When calling into Python, R data types are automatically
5955 converted to their equivalent Python types. When values are returned from
5956 Python to R they are converted back to R types.")
5957 (license license:asl2.0)))
5959 (define-public r-bibtex
5966 (uri (cran-uri "bibtex" version))
5969 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
5970 (build-system r-build-system)
5971 (propagated-inputs `(("r-stringr" ,r-stringr)))
5972 (home-page "https://github.com/romainfrancois/bibtex")
5973 (synopsis "Bibtex parser")
5974 (description "This package provides a utility for R to parse a bibtex
5976 (license license:gpl2+)))
5978 (define-public r-ggseqlogo
5980 (name "r-ggseqlogo")
5985 (uri (cran-uri "ggseqlogo" version))
5988 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5989 (build-system r-build-system)
5990 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5991 (home-page "https://github.com/omarwagih/ggseqlogo")
5992 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5994 "The range of functions provided by this package makes it possible to
5995 draw highly versatile genomic sequence logos. Features include, but are not
5996 limited to, modifying colour schemes and fonts used to draw the logo,
5997 generating multiple logo plots, and aiding the visualisation with annotations.
5998 Sequence logos can easily be combined with other ggplot2 plots.")
5999 ;; Unspecified version of the LGPL.
6000 (license license:lgpl3+)))
6002 (define-public r-ggsci
6009 (uri (cran-uri "ggsci" version))
6012 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6013 (build-system r-build-system)
6015 `(("r-ggplot2" ,r-ggplot2)
6016 ("r-scales" ,r-scales)))
6017 (home-page "https://nanx.me/ggsci/")
6018 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6020 "This package provides a collection of ggplot2 color palettes inspired by
6021 plots in scientific journals, data visualization libraries, science fiction
6022 movies, and TV shows.")
6023 (license license:gpl3)))
6025 (define-public r-ggsignif
6032 (uri (cran-uri "ggsignif" version))
6035 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6036 (build-system r-build-system)
6038 `(("r-knitr" ,r-knitr)))
6040 `(("r-ggplot2" ,r-ggplot2)))
6041 (home-page "https://github.com/const-ae/ggsignif")
6042 (synopsis "Significance brackets for ggplot2")
6044 "Enrich your ggplots with group-wise comparisons. This package provides
6045 an easy way to indicate if two groups are significantly different. Commonly
6046 this is shown by a bracket on top connecting the groups of interest which
6047 itself is annotated with the level of significance. The package provides a
6048 single layer that takes the groups for comparison and the test as arguments
6049 and adds the annotation to the plot.")
6050 (license license:gpl3)))
6052 (define-public r-ggpubr
6059 (uri (cran-uri "ggpubr" version))
6062 "0kb3hpmnhj4mkbx1kx0kv5y22himr8dijqx7ra0h8hi0pf2l2ha7"))))
6063 (build-system r-build-system)
6065 `(("r-cowplot" ,r-cowplot)
6066 ("r-dplyr" ,r-dplyr)
6067 ("r-ggplot2" ,r-ggplot2)
6068 ("r-ggrepel" ,r-ggrepel)
6069 ("r-ggsci" ,r-ggsci)
6070 ("r-ggsignif" ,r-ggsignif)
6072 ("r-gridextra" ,r-gridextra)
6073 ("r-magrittr" ,r-magrittr)
6074 ("r-polynom" ,r-polynom)
6075 ("r-purrr" ,r-purrr)
6076 ("r-rlang" ,r-rlang)
6077 ("r-scales" ,r-scales)
6078 ("r-tidyr" ,r-tidyr)))
6079 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6080 (synopsis "ggplot2-based publication-ready plots")
6082 "The ggplot2 package is an excellent and flexible package for elegant
6083 data visualization in R. However the default generated plots require some
6084 formatting before we can send them for publication. The ggpubr package
6085 provides some easy-to-use functions for creating and customizing ggplot2-based
6086 publication-ready plots.")
6087 (license license:gpl2)))
6089 (define-public r-ellipse
6096 (uri (cran-uri "ellipse" version))
6099 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
6100 (build-system r-build-system)
6101 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6102 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6104 "This package contains various routines for drawing ellipses and
6105 ellipse-like confidence regions, implementing the plots described in Murdoch
6106 and Chow (1996), A graphical display of large correlation matrices, The
6107 American Statistician 50, 178-180. There are also routines implementing the
6108 profile plots described in Bates and Watts (1988), Nonlinear Regression
6109 Analysis and its Applications.")
6110 (license license:gpl2+)))
6112 (define-public r-flashclust
6114 (name "r-flashclust")
6119 (uri (cran-uri "flashClust" version))
6122 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6123 (properties `((upstream-name . "flashClust")))
6124 (build-system r-build-system)
6125 (native-inputs `(("gfortran" ,gfortran)))
6126 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6127 (synopsis "Implementation of optimal hierarchical clustering")
6129 "This package provides a fast implementation of hierarchical
6131 (license license:gpl2+)))
6133 (define-public r-factominer
6135 (name "r-factominer")
6140 (uri (cran-uri "FactoMineR" version))
6143 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6144 (properties `((upstream-name . "FactoMineR")))
6145 (build-system r-build-system)
6148 ("r-cluster" ,r-cluster)
6149 ("r-ellipse" ,r-ellipse)
6150 ("r-flashclust" ,r-flashclust)
6151 ("r-ggplot2" ,r-ggplot2)
6152 ("r-ggrepel" ,r-ggrepel)
6153 ("r-lattice" ,r-lattice)
6154 ("r-leaps" ,r-leaps)
6156 ("r-scatterplot3d" ,r-scatterplot3d)))
6157 (home-page "http://factominer.free.fr")
6158 (synopsis "Multivariate exploratory data analysis and data mining")
6160 "This package provides exploratory data analysis methods to summarize,
6161 visualize and describe datasets. The main principal component methods are
6162 available, those with the largest potential in terms of applications:
6163 principal component analysis (PCA) when variables are quantitative,
6164 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6165 variables are categorical, Multiple Factor Analysis when variables are
6166 structured in groups, etc. and hierarchical cluster analysis.")
6167 (license license:gpl2+)))
6169 (define-public r-factoextra
6171 (name "r-factoextra")
6176 (uri (cran-uri "factoextra" version))
6179 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6180 (build-system r-build-system)
6182 `(("r-abind" ,r-abind)
6183 ("r-cluster" ,r-cluster)
6184 ("r-dendextend" ,r-dendextend)
6185 ("r-factominer" ,r-factominer)
6186 ("r-ggplot2" ,r-ggplot2)
6187 ("r-ggpubr" ,r-ggpubr)
6188 ("r-ggrepel" ,r-ggrepel)
6189 ("r-reshape2" ,r-reshape2)
6190 ("r-tidyr" ,r-tidyr)))
6191 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6192 (synopsis "Extract and visualize the results of multivariate data analyses")
6194 "This package provides some easy-to-use functions to extract and
6195 visualize the output of multivariate data analyses, including
6196 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6197 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6198 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6199 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6200 packages. It contains also functions for simplifying some clustering analysis
6201 steps and provides ggplot2-based elegant data visualization.")
6202 (license license:gpl2)))
6204 (define-public r-fansi
6211 (uri (cran-uri "fansi" version))
6214 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6215 (build-system r-build-system)
6217 `(("r-knitr" ,r-knitr))) ; for vignettes
6218 (home-page "https://github.com/brodieG/fansi")
6219 (synopsis "ANSI control sequence aware string functions")
6221 "This package provides counterparts to R string manipulation functions
6222 that account for the effects of ANSI text formatting control sequences.")
6223 (license license:gpl2+)))
6225 (define-public r-nbclust
6232 (uri (cran-uri "NbClust" version))
6235 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6236 (properties `((upstream-name . "NbClust")))
6237 (build-system r-build-system)
6238 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6239 (synopsis "Determine the best number of clusters in a data set")
6241 "NbClust provides 30 indexes for determining the optimal number of
6242 clusters in a data set and offers the best clustering scheme from different
6243 results to the user.")
6244 (license license:gpl2)))
6246 (define-public r-hdf5r
6253 (uri (cran-uri "hdf5r" version))
6256 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6257 (build-system r-build-system)
6262 `(("r-bit64" ,r-bit64)
6265 `(("r-knitr" ,r-knitr)))
6266 (home-page "https://hhoeflin.github.io/hdf5r")
6267 (synopsis "Interface to the HDF5 binary data format")
6269 "HDF5 is a data model, library and file format for storing and managing
6270 large amounts of data. This package provides a nearly feature complete,
6271 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6272 functionality is added so that HDF5 objects behave very similar to their
6273 corresponding R counterparts.")
6274 (license license:asl2.0)))
6276 (define-public r-itertools
6278 (name "r-itertools")
6283 (uri (cran-uri "itertools" version))
6286 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6287 (build-system r-build-system)
6289 `(("r-iterators" ,r-iterators)))
6290 (home-page "https://cran.r-project.org/web/packages/itertools/")
6291 (synopsis "Iterator tools")
6293 "This package provides various tools for creating iterators, many
6294 patterned after functions in the Python @code{itertools} module, and others
6295 patterned after functions in the snow package.")
6296 (license license:gpl2)))
6298 (define-public r-polynom
6305 (uri (cran-uri "polynom" version))
6308 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6309 (build-system r-build-system)
6310 (home-page "https://cran.r-project.org/web/packages/polynom/")
6311 (synopsis "Functions for univariate polynomial manipulations")
6313 "This package provides a collection of functions to implement a class for
6314 univariate polynomial manipulations.")
6315 (license license:gpl2)))
6317 (define-public r-gbrd
6324 (uri (cran-uri "gbRd" version))
6327 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6328 (properties `((upstream-name . "gbRd")))
6329 (build-system r-build-system)
6330 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6331 (synopsis "Utilities for processing Rd objects and files")
6333 "This package provides utilities for processing Rd objects and files.
6334 Extract argument descriptions and other parts of the help pages of
6336 (license license:gpl2+)))
6338 (define-public r-rjags
6345 (uri (cran-uri "rjags" version))
6348 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6349 (build-system r-build-system)
6351 `(("r-coda" ,r-coda)))
6355 `(("pkg-config" ,pkg-config)))
6356 (home-page "http://mcmc-jags.sourceforge.net")
6357 (synopsis "Bayesian graphical models using MCMC")
6359 "This package provides an R interface to the JAGS MCMC library. JAGS is
6360 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6361 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6362 (license license:gpl2)))
6364 (define-public r-rdpack
6371 (uri (cran-uri "Rdpack" version))
6374 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6375 (properties `((upstream-name . "Rdpack")))
6376 (build-system r-build-system)
6378 `(("r-bibtex" ,r-bibtex)
6379 ("r-gbrd" ,r-gbrd)))
6380 (home-page "https://github.com/GeoBosh/Rdpack")
6381 (synopsis "Update and manipulate Rd documentation objects")
6383 "This package provides functions for manipulation of R documentation
6384 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6385 updating Rd documentation for functions, methods and classes; it also includes
6386 Rd macros for citations and import of references from bibtex files for use in
6387 Rd files and roxygen2 comments, as well as many functions for manipulation of
6388 references and Rd files.")
6389 (license license:gpl2+)))
6391 (define-public r-officer
6398 (uri (cran-uri "officer" version))
6401 "0xhx5n6qksyh2s9hvwhnc8y0hn362asc5y94ld06snad786hz0rw"))))
6402 (build-system r-build-system)
6404 `(("r-magrittr" ,r-magrittr)
6410 `(("r-knitr" ,r-knitr)))
6411 (home-page "https://davidgohel.github.io/officer")
6412 (synopsis "Manipulation of Word and PowerPoint documents")
6414 "This package provides tools to access and manipulate Word and PowerPoint
6415 documents from R. The package focuses on tabular and graphical reporting from
6416 R; it also provides two functions that let users get document content into
6417 data objects. A set of functions lets add and remove images, tables and
6418 paragraphs of text in new or existing documents. When working with PowerPoint
6419 presentations, slides can be added or removed; shapes inside slides can also
6420 be added or removed. When working with Word documents, a cursor can be used
6421 to help insert or delete content at a specific location in the document.")
6422 (license license:gpl3)))
6424 (define-public r-abn
6431 (uri (cran-uri "abn" version))
6434 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6435 (build-system r-build-system)
6439 `(("r-lme4" ,r-lme4)
6443 ("r-rcpparmadillo" ,r-rcpparmadillo)
6444 ("r-rjags" ,r-rjags)))
6445 (home-page "https://r-bayesian-networks.org/")
6446 (synopsis "Modelling multivariate data with additive bayesian networks")
6448 "Bayesian network analysis is a form of probabilistic graphical models
6449 which derives from empirical data a directed acyclic graph, DAG, describing
6450 the dependency structure between random variables. An additive Bayesian
6451 network model consists of a form of a DAG where each node comprises a
6452 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6453 equivalent to Bayesian multivariate regression using graphical modelling, they
6454 generalises the usual multivariable regression, GLM, to multiple dependent
6455 variables. This package provides routines to help determine optimal Bayesian
6456 network models for a given data set, where these models are used to identify
6457 statistical dependencies in messy, complex data.")
6458 (license license:gpl2+)))
6460 (define-public r-acd
6467 (uri (cran-uri "ACD" version))
6470 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6471 (properties `((upstream-name . "ACD")))
6472 (build-system r-build-system)
6473 (home-page "https://cran.r-project.org/web/packages/ACD/")
6474 (synopsis "Categorical data analysis with complete or missing responses")
6476 "This package provides tools for categorical data analysis with complete
6477 or missing responses.")
6478 (license license:gpl2+)))
6480 (define-public r-acdm
6487 (uri (cran-uri "ACDm" version))
6490 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6491 (properties `((upstream-name . "ACDm")))
6492 (build-system r-build-system)
6494 `(("r-dplyr" ,r-dplyr)
6495 ("r-ggplot2" ,r-ggplot2)
6497 ("r-rsolnp" ,r-rsolnp)
6499 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6500 (synopsis "Tools for Autoregressive Conditional Duration Models")
6502 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6503 and Russell, 1998) models. It creates trade, price or volume durations from
6504 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6506 (license license:gpl2+)))
6508 (define-public r-overlap
6515 (uri (cran-uri "overlap" version))
6518 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6519 (build-system r-build-system)
6520 (home-page "https://cran.r-project.org/web/packages/overlap/")
6521 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6523 "This package provides functions to fit kernel density functions to data
6524 on temporal activity patterns of animals; estimate coefficients of overlapping
6525 of densities for two species; and calculate bootstrap estimates of confidence
6527 (license license:gpl3+)))
6529 (define-public r-snakecase
6531 (name "r-snakecase")
6536 (uri (cran-uri "snakecase" version))
6539 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6540 (build-system r-build-system)
6542 `(("r-stringi" ,r-stringi)
6543 ("r-stringr" ,r-stringr)))
6544 (home-page "https://github.com/Tazinho/snakecase")
6545 (synopsis "Convert strings into any case")
6547 "This package provides a consistent, flexible and easy to use tool to
6548 parse and convert strings into cases like snake or camel among others.")
6549 (license license:gpl3)))
6551 (define-public r-prediction
6553 (name "r-prediction")
6558 (uri (cran-uri "prediction" version))
6561 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6562 (build-system r-build-system)
6564 `(("r-data-table" ,r-data-table)))
6565 (home-page "https://github.com/leeper/prediction")
6566 (synopsis "Tidy, type-safe prediction methods")
6568 "This package provides the @code{prediction()} function, a type-safe
6569 alternative to @code{predict()} that always returns a data frame. The package
6570 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6571 from the @code{stats} package, as well as numerous other model classes from
6572 other add-on packages.")
6573 (license license:expat)))
6575 (define-public r-insight
6582 (uri (cran-uri "insight" version))
6585 "0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj"))))
6586 (build-system r-build-system)
6588 `(("r-knitr" ,r-knitr)))
6589 (home-page "https://easystats.github.io/insight/")
6590 (synopsis "Easy access to model information for various model objects")
6592 "This package provides a tool to provide an easy, intuitive and
6593 consistent access to information contained in various R models, like model
6594 formulas, model terms, information about random effects, data that was used to
6595 fit the model or data from response variables. The package mainly revolves
6596 around two types of functions: Functions that find (the names of) information,
6597 starting with @code{find_}, and functions that get the underlying data,
6598 starting with @code{get_}. The package has a consistent syntax and works with
6599 many different model objects, where otherwise functions to access these
6600 information are missing.")
6601 (license license:gpl3)))
6603 (define-public r-sjlabelled
6605 (name "r-sjlabelled")
6610 (uri (cran-uri "sjlabelled" version))
6613 "1amq7i9sxf0pkxhskqc53xq5wvc9rdxm7cxyb4b6xh6qsskjnlsj"))))
6614 (build-system r-build-system)
6616 `(("r-haven" ,r-haven)
6617 ("r-insight" ,r-insight)))
6618 (home-page "https://github.com/strengejacke/sjlabelled")
6619 (synopsis "Labelled data utility functions")
6621 "This package provides a collection of functions dealing with labelled
6622 data, like reading and writing data between R and other statistical software
6623 packages. This includes easy ways to get, set or change value and variable
6624 label attributes, to convert labelled vectors into factors or numeric (and
6625 vice versa), or to deal with multiple declared missing values.")
6626 (license license:gpl3)))
6628 (define-public r-sjmisc
6635 (uri (cran-uri "sjmisc" version))
6638 "1ad7ca71w0v9ja4wb47aygczc987zz1lnjljhh2n497nzrpzzv64"))))
6639 (build-system r-build-system)
6641 `(("r-dplyr" ,r-dplyr)
6642 ("r-insight" ,r-insight)
6643 ("r-magrittr" ,r-magrittr)
6644 ("r-purrr" ,r-purrr)
6645 ("r-rlang" ,r-rlang)
6646 ("r-sjlabelled" ,r-sjlabelled)
6647 ("r-tidyselect" ,r-tidyselect)))
6649 `(("r-knitr" ,r-knitr)))
6650 (home-page "https://github.com/strengejacke/sjmisc")
6651 (synopsis "Data and variable transformation functions")
6653 "This package is a collection of miscellaneous utility functions,
6654 supporting data transformation tasks like recoding, dichotomizing or grouping
6655 variables, setting and replacing missing values. The data transformation
6656 functions also support labelled data, and all integrate seamlessly into a
6657 tidyverse workflow.")
6658 (license license:gpl3)))
6660 (define-public r-nortest
6667 (uri (cran-uri "nortest" version))
6670 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6671 (build-system r-build-system)
6672 (home-page "https://cran.r-project.org/web/packages/nortest/")
6673 (synopsis "Tests for normality")
6675 "This package provides five omnibus tests for testing the composite
6676 hypothesis of normality.")
6677 (license license:gpl2+)))
6679 (define-public r-moonbook
6686 (uri (cran-uri "moonBook" version))
6689 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6690 (properties `((upstream-name . "moonBook")))
6691 (build-system r-build-system)
6693 `(("r-magrittr" ,r-magrittr)
6694 ("r-nortest" ,r-nortest)
6695 ("r-purrr" ,r-purrr)
6696 ("r-sjmisc" ,r-sjmisc)
6697 ("r-stringr" ,r-stringr)
6698 ("r-survival" ,r-survival)))
6699 (home-page "https://github.com/cardiomoon/moonBook")
6700 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6702 "This package provides several analysis-related functions for the book
6703 entitled \"R statistics and graph for medical articles\" (written in Korean),
6704 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6706 (license license:gpl2)))
6708 (define-public r-flextable
6710 (name "r-flextable")
6715 (uri (cran-uri "flextable" version))
6718 "1rkz0nhwjy1l8sb0kmna5v492n2ydnk7gydswnmf88r8vfyjczhw"))))
6719 (build-system r-build-system)
6721 `(("r-base64enc" ,r-base64enc)
6722 ("r-data-table" ,r-data-table)
6723 ("r-gdtools" ,r-gdtools)
6724 ("r-htmltools" ,r-htmltools)
6725 ("r-knitr" ,r-knitr)
6726 ("r-officer" ,r-officer)
6727 ("r-rlang" ,r-rlang)
6728 ("r-rmarkdown" ,r-rmarkdown)
6729 ("r-xml2" ,r-xml2)))
6730 (home-page "https://davidgohel.github.io/flextable")
6731 (synopsis "Functions for tabular reporting")
6733 "This package provides tools to create pretty tables for HTML documents
6734 and other formats. Functions are provided to let users create tables, modify
6735 and format their content. It extends the @code{officer} package and can be
6736 used within R markdown documents when rendering to HTML and to Word
6738 (license license:gpl3)))
6740 (define-public r-writexl
6747 (uri (cran-uri "writexl" version))
6750 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6751 (build-system r-build-system)
6752 (inputs `(("zlib" ,zlib)))
6753 (home-page "https://github.com/ropensci/writexl")
6754 (synopsis "Export data frames to xlsx format")
6756 "This package provides a data frame to xlsx exporter based on
6758 (license license:bsd-2)))
6760 (define-public r-biasedurn
6762 (name "r-biasedurn")
6767 (uri (cran-uri "BiasedUrn" version))
6770 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6771 (properties `((upstream-name . "BiasedUrn")))
6772 (build-system r-build-system)
6773 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6774 (synopsis "Biased Urn model distributions")
6776 "This package provides statistical models of biased sampling in the form
6777 of univariate and multivariate noncentral hypergeometric distributions,
6778 including Wallenius' noncentral hypergeometric distribution and Fisher's
6779 noncentral hypergeometric distribution (also called extended hypergeometric
6781 (license license:gpl3)))
6783 (define-public r-goplot
6790 (uri (cran-uri "GOplot" version))
6793 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6794 (properties `((upstream-name . "GOplot")))
6795 (build-system r-build-system)
6797 `(("r-ggdendro" ,r-ggdendro)
6798 ("r-ggplot2" ,r-ggplot2)
6799 ("r-gridextra" ,r-gridextra)
6800 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6801 (home-page "https://github.com/wencke/wencke.github.io")
6802 (synopsis "Visualization of functional analysis data")
6804 "This package provides an implementation of multilayered visualizations
6805 for enhanced graphical representation of functional analysis data. It
6806 combines and integrates omics data derived from expression and functional
6807 annotation enrichment analyses. Its plotting functions have been developed
6808 with an hierarchical structure in mind: starting from a general overview to
6809 identify the most enriched categories (modified bar plot, bubble plot) to a
6810 more detailed one displaying different types of relevant information for the
6811 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6812 Venn diagram, heatmap).")
6813 (license license:gpl2)))
6815 (define-public r-getopt
6822 (uri (cran-uri "getopt" version))
6825 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6826 (build-system r-build-system)
6827 (home-page "https://github.com/trevorld/getopt")
6828 (synopsis "Command-line option processor for R")
6830 "This package is designed to be used with Rscript to write shebang
6831 scripts that accept short and long options. Many users will prefer to
6832 use the packages @code{optparse} or @code{argparse} which add extra
6833 features like automatically generated help options and usage texts,
6834 support for default values, positional argument support, etc.")
6835 (license license:gpl2+)))
6837 (define-public r-findpython
6839 (name "r-findpython")
6844 (uri (cran-uri "findpython" version))
6847 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6848 (build-system r-build-system)
6849 (home-page "https://github.com/trevorld/findpython")
6850 (synopsis "Functions to find an acceptable Python binary")
6852 "This package was designed to find an acceptable Python binary that
6853 matches version and feature constraints.")
6854 (license license:expat)))
6856 ;; This in not the same as "r-argparser"
6857 (define-public r-argparse
6864 (uri (cran-uri "argparse" version))
6867 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6868 (build-system r-build-system)
6869 (inputs `(("python" ,python)))
6871 `(("r-findpython" ,r-findpython)
6872 ("r-jsonlite" ,r-jsonlite)
6874 (home-page "https://github.com/trevorld/argparse")
6875 (synopsis "Command line optional and positional argument parser")
6877 "This package provides a command line parser to be used with Rscript to
6878 write shebang scripts that gracefully accept positional and optional arguments
6879 and automatically generate usage notices.")
6880 (license license:gpl2+)))
6882 (define-public r-hash
6889 (uri (cran-uri "hash" version))
6892 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6893 (build-system r-build-system)
6894 (home-page "https://cran.r-project.org/web/packages/hash/")
6895 (synopsis "Implementation of hash/associated arrays/dictionaries")
6897 "This package implements a data structure similar to hashes in Perl and
6898 dictionaries in Python but with a purposefully R flavor. For objects of
6899 appreciable size, access using hashes outperforms native named lists and
6901 (license license:gpl2+)))
6903 (define-public r-orddom
6910 (uri (cran-uri "orddom" version))
6913 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6914 (build-system r-build-system)
6915 (propagated-inputs `(("r-psych" ,r-psych)))
6916 (home-page "https://cran.r-project.org/web/packages/orddom/")
6917 (synopsis "Ordinal dominance statistics")
6919 "This package provides tools to compute ordinal, statistics and effect
6920 sizes as an alternative to mean comparison: Cliff's delta or success rate
6921 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6922 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6923 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6924 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6925 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6926 Group (Non-)Overlap considerations.")
6927 (license license:gpl2)))
6929 (define-public r-deriv
6936 (uri (cran-uri "Deriv" version))
6939 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6940 (properties `((upstream-name . "Deriv")))
6941 (build-system r-build-system)
6942 (home-page "https://cran.r-project.org/web/packages/Deriv")
6943 (synopsis "Symbolic differentiation")
6945 "This package provides an R-based solution for symbolic differentiation.
6946 It admits user-defined functions as well as function substitution in arguments
6947 of functions to be differentiated. Some symbolic simplification is part of
6949 (license license:gpl3+)))
6951 (define-public r-doby
6958 (uri (cran-uri "doBy" version))
6961 "1ckazh701b4ilg8bj17ji903538jmb49d997gm49ah5j5jc1x0g7"))))
6962 (properties `((upstream-name . "doBy")))
6963 (build-system r-build-system)
6965 `(("r-broom" ,r-broom)
6966 ("r-deriv" ,r-deriv)
6967 ("r-dplyr" ,r-dplyr)
6968 ("r-magrittr" ,r-magrittr)
6970 ("r-matrix" ,r-matrix)
6972 ("r-pbkrtest" ,r-pbkrtest)
6973 ("r-tibble" ,r-tibble)))
6974 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6975 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6977 "This package contains:
6980 @item facilities for working with grouped data: @code{do}
6981 something to data stratified @code{by} some variables.
6982 @item implementations of least-squares means, general linear contrasts, and
6983 @item miscellaneous other utilities.
6985 (license license:gpl2+)))
6987 (define-public r-refgenome
6989 (name "r-refgenome")
6994 (uri (cran-uri "refGenome" version))
6997 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6998 (properties `((upstream-name . "refGenome")))
6999 (build-system r-build-system)
7003 ("r-rsqlite" ,r-rsqlite)))
7004 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7006 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7008 "This package contains functionality for importing and managing of
7009 downloaded genome annotation data from the Ensembl genome browser (European
7010 Bioinformatics Institute) and from the UCSC genome browser (University of
7011 California, Santa Cruz) and annotation routines for genomic positions and
7012 splice site positions.")
7013 (license license:gpl2)))
7015 (define-public r-basix
7022 (uri (cran-uri "BASIX" version))
7025 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7026 (properties `((upstream-name . "BASIX")))
7027 (build-system r-build-system)
7028 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7029 (synopsis "Efficient C/C++ toolset for R")
7031 "BASIX provides some efficient C/C++ implementations of native R
7032 procedures to speed up calculations in R.")
7033 (license license:gpl2)))
7035 (define-public r-blockfest
7037 (name "r-blockfest")
7042 (uri (cran-uri "BlockFeST" version))
7045 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7046 (properties `((upstream-name . "BlockFeST")))
7047 (build-system r-build-system)
7048 (propagated-inputs `(("r-basix" ,r-basix)))
7049 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7050 (synopsis "Bayesian calculation of region-specific fixation index")
7052 "This package provides an R implementation of an extension of the
7053 BayeScan software for codominant markers, adding the option to group
7054 individual SNPs into pre-defined blocks. A typical application of this new
7055 approach is the identification of genomic regions, genes, or gene sets
7056 containing one or more SNPs that evolved under directional selection.")
7057 (license license:gpl2)))
7059 (define-public r-proc
7066 (uri (cran-uri "pROC" version))
7069 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7070 (properties `((upstream-name . "pROC")))
7071 (build-system r-build-system)
7073 `(("r-plyr" ,r-plyr)
7074 ("r-rcpp" ,r-rcpp)))
7075 (home-page "https://web.expasy.org/pROC/")
7076 (synopsis "Display and analyze ROC curves")
7078 "This package provides tools for visualizing, smoothing and comparing
7079 receiver operating characteristic (ROC curves). The area under the
7080 curve (AUC) can be compared with statistical tests based on U-statistics or
7081 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7082 (license license:gpl3+)))
7084 (define-public r-rootsolve
7086 (name "r-rootsolve")
7091 (uri (cran-uri "rootSolve" version))
7094 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7095 (properties `((upstream-name . "rootSolve")))
7096 (build-system r-build-system)
7097 (native-inputs `(("gfortran" ,gfortran)))
7098 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7099 (synopsis "Tools for the analysis of ordinary differential equations")
7101 "This package provides routines to find the root of nonlinear functions,
7102 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7103 differential equations} (ODE). It includes routines that:
7106 @item generate gradient and jacobian matrices (full and banded),
7107 @item find roots of non-linear equations by the Newton-Raphson method,
7108 @item estimate steady-state conditions of a system of (differential) equations
7109 in full, banded or sparse form, using the Newton-Raphson method, or by
7110 dynamically running,
7111 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7112 and 3-D partial differential equations, that have been converted to ordinary
7113 differential equations by numerical differencing (using the method-of-lines
7116 (license license:gpl2+)))
7118 (define-public r-abcanalysis
7120 (name "r-abcanalysis")
7125 (uri (cran-uri "ABCanalysis" version))
7127 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7128 (properties `((upstream-name . "ABCanalysis")))
7129 (build-system r-build-system)
7130 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7131 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7132 (synopsis "Computed ABC Analysis")
7134 "Multivariate data sets often differ in several factors or derived statistical
7135 parameters, which have to be selected for a valid interpretation. Basing this
7136 selection on traditional statistical limits leads occasionally to the perception
7137 of losing information from a data set. This package provides tools to calculate
7138 these limits on the basis of the mathematical properties of the distribution of
7139 the analyzed items.")
7140 (license license:gpl3)))
7142 (define-public r-slam
7149 (uri (cran-uri "slam" version))
7151 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7152 (build-system r-build-system)
7153 (home-page "https://cran.r-project.org/web/packages/slam/")
7154 (synopsis "Sparse lightweight arrays and matrices")
7156 "This package contains data structures and algorithms for sparse arrays and matrices,
7157 based on index arrays and simple triplet representations, respectively.")
7158 (license license:gpl2)))
7160 (define-public r-manipulatewidget
7162 (name "r-manipulatewidget")
7167 (uri (cran-uri "manipulateWidget" version))
7169 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7171 `((upstream-name . "manipulateWidget")))
7172 (build-system r-build-system)
7174 `(("r-base64enc" ,r-base64enc)
7175 ("r-codetools" ,r-codetools)
7176 ("r-htmltools" ,r-htmltools)
7177 ("r-htmlwidgets" ,r-htmlwidgets)
7178 ("r-knitr" ,r-knitr)
7179 ("r-miniui" ,r-miniui)
7180 ("r-shiny" ,r-shiny)
7181 ("r-webshot" ,r-webshot)))
7182 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7183 (synopsis "Add even more interactivity to interactive charts")
7185 "This package lets you create in just a few lines of R code a nice user interface to
7186 modify the data or the graphical parameters of one or multiple interactive
7187 charts. It is useful to quickly explore visually some data or for package
7188 developers to generate user interfaces easy to maintain.")
7189 (license license:gpl2+)))
7198 (uri (cran-uri "A3" version))
7200 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7201 (properties `((upstream-name . "A3")))
7202 (build-system r-build-system)
7204 `(("r-pbapply" ,r-pbapply)
7205 ("r-xtable" ,r-xtable)))
7206 (home-page "https://cran.r-project.org/web/packages/A3/")
7207 (synopsis "Error metrics for predictive models")
7209 "This package supplies tools for tabulating and analyzing the results of predictive
7210 models. The methods employed are applicable to virtually any predictive model
7211 and make comparisons between different methodologies straightforward.")
7212 (license license:gpl2+)))
7214 (define-public r-infotheo
7221 (uri (cran-uri "infotheo" version))
7224 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7225 (build-system r-build-system)
7226 (home-page "http://homepage.meyerp.com/software")
7227 (synopsis "Information-theoretic measures")
7229 "This package implements various measures of information theory based on
7230 several entropy estimators.")
7231 (license license:gpl3+)))
7233 (define-public r-abcoptim
7240 (uri (cran-uri "ABCoptim" version))
7242 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7243 (properties `((upstream-name . "ABCoptim")))
7244 (build-system r-build-system)
7245 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7246 (home-page "https://github.com/gvegayon/ABCoptim/")
7247 (synopsis "Optimization of Artificial Bee Colony algorithm")
7249 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7250 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7251 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7252 algorithms, and uses only common control parameters such as colony size and
7253 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7254 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7255 This version is a work-in-progress and is written in R code.")
7256 (license license:expat)))
7258 (define-public r-abcp2
7265 (uri (cran-uri "ABCp2" version))
7267 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7268 (properties `((upstream-name . "ABCp2")))
7269 (build-system r-build-system)
7270 (propagated-inputs `(("r-mass" ,r-mass)))
7271 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7272 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7274 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7275 Poisson, and Gamma distribution and estimates the proportional paternity of the
7276 second male (P2) based on the best fit distribution.")
7277 (license license:gpl2)))
7279 (define-public r-abcrf
7286 (uri (cran-uri "abcrf" version))
7288 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7289 (build-system r-build-system)
7291 `(("r-doparallel" ,r-doparallel)
7292 ("r-foreach" ,r-foreach)
7294 ("r-matrixstats" ,r-matrixstats)
7295 ("r-ranger" ,r-ranger)
7297 ("r-rcpparmadillo" ,r-rcpparmadillo)
7298 ("r-readr" ,r-readr)
7299 ("r-stringr" ,r-stringr)))
7300 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7301 (synopsis "Approximate bayesian computation via random forests")
7303 "This package performs approximate bayesian computation (ABC) model choice and
7304 parameter inference via random forests. This machine learning tool named random
7305 forests (RF) can conduct selection among the highly complex models covered by
7307 (license license:gpl2+)))
7309 (define-public r-abctools
7316 (uri (cran-uri "abctools" version))
7318 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7319 (build-system r-build-system)
7322 ("r-abind" ,r-abind)
7323 ("r-hmisc" ,r-hmisc)
7324 ("r-plyr" ,r-plyr)))
7325 (home-page "https://github.com/dennisprangle/abctools/")
7326 (synopsis "Tools for ABC analyses")
7328 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7329 including summary statistic selection and assessing coverage. This includes
7330 recent dimension reduction algorithms to tune the choice of summary statistics,
7331 and coverage methods to tune the choice of threshold.")
7332 (license license:gpl2+)))
7334 (define-public r-ggstance
7341 (uri (cran-uri "ggstance" version))
7343 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7344 (build-system r-build-system)
7346 `(("r-ggplot2" ,r-ggplot2)
7348 ("r-rlang" ,r-rlang)
7349 ("r-withr" ,r-withr)))
7350 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7351 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7353 "This package is a @code{r-ggplot2} extension that provides flipped components:
7355 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7356 @item vertical versions of @code{r-ggplot2} positions.
7358 (license license:gpl3)))
7360 (define-public r-mosaiccore
7362 (name "r-mosaiccore")
7367 (uri (cran-uri "mosaicCore" version))
7369 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7370 (properties `((upstream-name . "mosaicCore")))
7371 (build-system r-build-system)
7373 `(("r-dplyr" ,r-dplyr)
7374 ("r-lazyeval" ,r-lazyeval)
7376 ("r-rlang" ,r-rlang)
7377 ("r-tidyr" ,r-tidyr)))
7378 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7379 (synopsis "Common utilities for mosaic family packages")
7381 "Common utilities used in other Mosaic family packages are collected here.")
7382 (license license:gpl2+)))
7384 (define-public r-ggformula
7386 (name "r-ggformula")
7391 (uri (cran-uri "ggformula" version))
7393 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7394 (build-system r-build-system)
7396 `(("r-ggforce" ,r-ggforce)
7397 ("r-ggplot2" ,r-ggplot2)
7398 ("r-ggstance" ,r-ggstance)
7399 ("r-magrittr" ,r-magrittr)
7400 ("r-mosaiccore" ,r-mosaiccore)
7401 ("r-rlang" ,r-rlang)
7402 ("r-stringr" ,r-stringr)
7403 ("r-tibble" ,r-tibble)))
7404 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7405 (synopsis "Formula interface for the @code{r-ggplot2}")
7407 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7408 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7409 and extends the excellent simplicity of the lattice-graphics formula interface,
7410 while providing the intuitive capabilities of @code{r-ggplot2}.")
7411 (license license:expat)))
7413 (define-public r-mosaicdata
7415 (name "r-mosaicdata")
7420 (uri (cran-uri "mosaicData" version))
7422 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7423 (properties `((upstream-name . "mosaicData")))
7424 (build-system r-build-system)
7425 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7426 (synopsis "Data sets for project Mosaic")
7428 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7429 used to teach mathematics, statistics, computation and modeling.")
7430 (license license:gpl2+)))
7432 (define-public r-raster
7439 (uri (cran-uri "raster" version))
7442 "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
7443 (build-system r-build-system)
7445 `(("r-rcpp" ,r-rcpp)
7447 (home-page "https://www.rspatial.org/")
7448 (synopsis "Geographic data analysis and modeling")
7450 "The package implements basic and high-level functions for reading,
7451 writing, manipulating, analyzing and modeling of gridded spatial data.
7452 Processing of very large files is supported.")
7453 (license license:gpl3+)))
7455 (define-public r-mosaic
7462 (uri (cran-uri "mosaic" version))
7464 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7465 (build-system r-build-system)
7467 `(("r-broom" ,r-broom)
7468 ("r-dplyr" ,r-dplyr)
7469 ("r-ggdendro" ,r-ggdendro)
7470 ("r-ggformula" ,r-ggformula)
7471 ("r-ggplot2" ,r-ggplot2)
7472 ("r-ggrepel" ,r-ggrepel)
7474 ("r-gridextra" ,r-gridextra)
7475 ("r-lattice" ,r-lattice)
7476 ("r-latticeextra" ,r-latticeextra)
7477 ("r-lazyeval" ,r-lazyeval)
7479 ("r-matrix" ,r-matrix)
7480 ("r-mosaiccore" ,r-mosaiccore)
7481 ("r-mosaicdata" ,r-mosaicdata)
7482 ("r-readr" ,r-readr)
7483 ("r-tidyr" ,r-tidyr)))
7485 `(("r-knitr" ,r-knitr)))
7486 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7487 (synopsis "Mathematics, statistics, and computation teaching utilities")
7489 "This package contain data sets and utilities from
7490 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7491 statistics, computation and modeling. Project MOSAIC is a community of
7492 educators working to tie together aspects of quantitative work that students
7493 in science, technology, engineering and mathematics will need in their
7494 professional lives, but which are usually taught in isolation, if at all.")
7495 (license license:gpl2+)))
7497 (define-public r-abd
7504 (uri (cran-uri "abd" version))
7506 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7507 (build-system r-build-system)
7509 `(("r-lattice" ,r-lattice)
7510 ("r-mosaic" ,r-mosaic)
7511 ("r-nlme" ,r-nlme)))
7512 (home-page "https://cran.r-project.org/web/packages/abd/")
7513 (synopsis "Analysis of biological data")
7515 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7516 biological data by Michael Whitlock and Dolph Schluter.")
7517 (license license:gpl2)))
7519 (define-public r-svgui
7526 (uri (cran-uri "svGUI" version))
7528 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7529 (properties `((upstream-name . "svGUI")))
7530 (build-system r-build-system)
7531 (home-page "https://github.com/SciViews/svGUI/")
7532 (synopsis "Functions for managing GUI clients in R")
7534 "The SciViews @code{svGUI} package eases the management of Graphical User
7535 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7536 centralizes info about GUI elements currently used, and it dispatches GUI
7537 calls to the particular toolkits in use in function of the context.")
7538 (license license:gpl2)))
7540 (define-public r-svdialogs
7542 (name "r-svdialogs")
7547 (uri (cran-uri "svDialogs" version))
7549 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7550 (properties `((upstream-name . "svDialogs")))
7551 (build-system r-build-system)
7554 ("zenity" ,zenity)))
7556 `(("r-rstudioapi" ,r-rstudioapi)
7557 ("r-svgui" ,r-svgui)))
7558 (home-page "https://github.com/SciViews/svDialogs/")
7559 (synopsis "Portable dialog boxes")
7561 "This package helps to construct standard dialog boxes for your GUI, including
7562 message boxes, input boxes, list, file or directory selection, and others. In
7563 case R cannot display GUI dialog boxes, a simpler command line version of these
7564 interactive elements is also provided as a fallback solution.")
7565 (license license:gpl2)))
7567 (define-public r-abe
7574 (uri (cran-uri "abe" version))
7577 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7578 (build-system r-build-system)
7579 (home-page "https://cran.r-project.org/web/packages/abe/")
7580 (synopsis "Augmented backward elimination")
7582 "This package performs augmented backward elimination and checks the
7583 stability of the obtained model. Augmented backward elimination combines
7584 significance or information based criteria with the change in estimate to
7585 either select the optimal model for prediction purposes or to serve as a tool
7586 to obtain a practically sound, highly interpretable model.")
7587 (license license:gpl2+)))
7589 (define-public r-abf2
7596 (uri (cran-uri "abf2" version))
7598 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7599 (build-system r-build-system)
7600 (home-page "https://cran.r-project.org/web/packages/abf2/")
7601 (synopsis "Load gap-free axon @code{r-abf2} files")
7603 "This package loads electrophysiology data from ABF2 files, as created by
7604 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7605 mode are currently supported.")
7606 (license license:artistic2.0)))
7608 (define-public r-abhgenotyper
7610 (name "r-abhgenotyper")
7615 (uri (cran-uri "ABHgenotypeR" version))
7617 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7618 (properties `((upstream-name . "ABHgenotypeR")))
7619 (build-system r-build-system)
7621 `(("r-ggplot2" ,r-ggplot2)
7622 ("r-reshape2" ,r-reshape2)))
7623 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7624 (synopsis "Visualize and manipulate ABH genotypes")
7626 "The @code{r-abhgenotyper} package provides simple imputation,
7627 error-correction and plotting capacities for genotype data. The package is
7628 supposed to serve as an intermediate but independent analysis tool between the
7629 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7630 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7631 genotypes as \"graphical genotypes\".")
7632 (license license:gpl3)))
7634 (define-public r-furrr
7641 (uri (cran-uri "furrr" version))
7644 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7645 (build-system r-build-system)
7647 `(("r-future" ,r-future)
7648 ("r-globals" ,r-globals)
7649 ("r-purrr" ,r-purrr)
7650 ("r-rlang" ,r-rlang)))
7651 (home-page "https://github.com/DavisVaughan/furrr")
7652 (synopsis "Apply mapping functions in parallel using futures")
7654 "This package provides implementations of the family of @code{map()}
7655 functions from the @code{purrr} package that can be resolved using any
7656 @code{future}-supported backend, e.g. parallel on the local machine or
7657 distributed on a compute cluster.")
7658 (license license:lgpl2.1+)))
7660 (define-public r-abjutils
7667 (uri (cran-uri "abjutils" version))
7669 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7670 (build-system r-build-system)
7672 `(("r-devtools" ,r-devtools)
7673 ("r-dplyr" ,r-dplyr)
7674 ("r-furrr" ,r-furrr)
7675 ("r-future" ,r-future)
7678 ("r-magrittr" ,r-magrittr)
7679 ("r-progress" ,r-progress)
7680 ("r-purrr" ,r-purrr)
7681 ("r-readr" ,r-readr)
7682 ("r-rlang" ,r-rlang)
7683 ("r-rstudioapi" ,r-rstudioapi)
7684 ("r-scales" ,r-scales)
7685 ("r-stringi" ,r-stringi)
7686 ("r-stringr" ,r-stringr)
7687 ("r-tibble" ,r-tibble)
7688 ("r-tidyr" ,r-tidyr)))
7689 (home-page "https://github.com/abjur/abjutils/")
7690 (synopsis "Collection of tools for jurimetrical analysis")
7692 "This package implements general purpose tools, such as functions for
7693 sampling and basic manipulation of Brazilian lawsuits identification number.
7694 It also implements functions for text cleaning, such as accentuation
7696 (license license:expat)))
7698 (define-public r-abnormality
7700 (name "r-abnormality")
7705 (uri (cran-uri "abnormality" version))
7707 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7708 (build-system r-build-system)
7710 `(("r-mass" ,r-mass)
7711 ("r-matrix" ,r-matrix)))
7712 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7713 (synopsis "Measure a subject's abnormality with respect to a reference population")
7715 "This package contains functions to implement the methodology and
7716 considerations laid out by Marks et al. in the article \"Measuring abnormality
7717 in high dimensional spaces: applications in biomechanical gait analysis\".
7718 Using high-dimensional datasets to measure a subject's overall level of
7719 abnormality as compared to a reference population is often needed in outcomes
7721 (license license:expat)))
7723 (define-public r-abodoutlier
7725 (name "r-abodoutlier")
7730 (uri (cran-uri "abodOutlier" version))
7732 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7733 (properties `((upstream-name . "abodOutlier")))
7734 (build-system r-build-system)
7736 `(("r-cluster" ,r-cluster)))
7737 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7738 (synopsis "Angle-based outlier detection")
7740 "This package performs angle-based outlier detection on a given data
7741 frame. It offers three methods to process data:
7743 @item full but slow implementation using all the data that has cubic
7745 @item a fully randomized method;
7746 @item a method using k-nearest neighbours.
7748 These algorithms are well suited for high dimensional data outlier
7750 (license license:expat)))
7752 (define-public r-abps
7759 (uri (cran-uri "ABPS" version))
7761 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7762 (properties `((upstream-name . "ABPS")))
7763 (build-system r-build-system)
7764 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7765 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7766 (synopsis "Abnormal blood profile score to detect blood doping")
7768 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7769 The ABPS is a part of the Athlete biological passport program of the World
7770 anti-doping agency, which combines several blood parameters into a single
7771 score in order to detect blood doping. The package also contains functions to
7772 calculate other scores used in anti-doping programs, such as the ratio of
7773 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7774 (license license:gpl2+)))
7776 (define-public r-parmigene
7778 (name "r-parmigene")
7783 (uri (cran-uri "parmigene" version))
7786 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7787 (build-system r-build-system)
7788 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7789 (synopsis "Mutual information estimation for gene network reconstruction")
7791 "This package provides a parallel estimation of the mutual information
7792 based on entropy estimates from k-nearest neighbors distances and algorithms
7793 for the reconstruction of gene regulatory networks.")
7794 (license license:agpl3+)))
7796 (define-public r-pscl
7803 (uri (cran-uri "pscl" version))
7805 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
7806 (build-system r-build-system)
7808 `(("r-mass" ,r-mass)))
7809 (home-page "https://github.com/atahk/pscl/")
7810 (synopsis "Political science computational laboratory")
7812 "The @code{pscl} is an R package providing classes and methods for:
7814 @item Bayesian analysis of roll call data (item-response models);
7815 @item elementary Bayesian statistics;
7816 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7818 @item utility functions.
7820 (license license:gpl2)))
7822 (define-public r-accelmissing
7824 (name "r-accelmissing")
7829 (uri (cran-uri "accelmissing" version))
7831 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7832 (build-system r-build-system)
7834 `(("r-mice" ,r-mice)
7835 ("r-pscl" ,r-pscl)))
7836 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7837 (synopsis "Missing value imputation for accelerometer data")
7839 "This package provides a statistical method to impute the missing values in
7840 accelerometer data. The methodology includes both parametric and
7841 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7842 model. It also provides multiple functions to preprocess the accelerometer data
7843 previous to the missing data imputation. These include detecting the wearing
7844 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7845 (license license:gpl2+)))
7847 (define-public r-mhsmm
7854 (uri (cran-uri "mhsmm" version))
7856 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7857 (build-system r-build-system)
7858 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7859 (home-page "https://github.com/jaredo/mhsmm/")
7860 (synopsis "Inference for hidden Markov and semi-Markov models")
7862 "The @code{r-mhsmm} package implements estimation and prediction methods for
7863 hidden Markov and semi-Markov models for multiple observation sequences. Such
7864 techniques are of interest when observed data is thought to be dependent on some
7865 unobserved (or hidden) state. Also, this package is suitable for equidistant
7866 time series data, with multivariate and/or missing data. Allows user defined
7867 emission distributions.")
7868 (license license:gpl2+)))
7870 (define-public r-nleqslv
7877 (uri (cran-uri "nleqslv" version))
7879 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7880 (build-system r-build-system)
7881 (native-inputs `(("gfortran" ,gfortran)))
7882 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7883 (synopsis "Solve systems of nonlinear equations")
7885 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7886 Broyden or a Newton method with a choice of global strategies such as line
7887 search and trust region. There are options for using a numerical or user
7888 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7889 singular or ill-conditioned Jacobian.")
7890 (license license:gpl2+)))
7892 (define-public r-physicalactivity
7894 (name "r-physicalactivity")
7899 (uri (cran-uri "PhysicalActivity" version))
7901 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7903 `((upstream-name . "PhysicalActivity")))
7904 (build-system r-build-system)
7905 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7906 (synopsis "Procesing accelerometer data for physical activity measurement")
7908 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7909 for classification of monitor wear and nonwear time intervals in accelerometer
7910 data collected to assess physical activity. The package also contains functions
7911 for making plots of accelerometer data and obtaining the summary of various
7912 information including daily monitor wear time and the mean monitor wear time
7913 during valid days. The revised package version 0.2-1 improved the functions
7914 regarding speed, robustness and add better support for time zones and daylight
7915 saving. In addition, several functions were added:
7917 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7918 @item the @code{markPAI} can categorize physical activity intensity level based
7919 on user-defined cut-points of accelerometer counts.
7921 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7922 @code{queryActigraph} functions.")
7923 (license license:gpl3+)))
7925 (define-public r-acc
7932 (uri (cran-uri "acc" version))
7934 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7935 (build-system r-build-system)
7937 `(("r-circlize" ,r-circlize)
7939 ("r-ggplot2" ,r-ggplot2)
7940 ("r-iterators" ,r-iterators)
7941 ("r-mhsmm" ,r-mhsmm)
7942 ("r-nleqslv" ,r-nleqslv)
7943 ("r-physicalactivity" ,r-physicalactivity)
7945 ("r-r-utils" ,r-r-utils)
7947 ("r-rcpparmadillo" ,r-rcpparmadillo)
7948 ("r-rsqlite" ,r-rsqlite)
7950 (home-page "https://cran.r-project.org/web/packages/acc/")
7951 (synopsis "Exploring accelerometer data")
7953 "This package processes accelerometer data from uni-axial and tri-axial devices
7954 and generates data summaries. Also, includes functions to plot, analyze, and
7955 simulate accelerometer data.")
7956 (license license:gpl2+)))
7958 (define-public r-rbenchmark
7960 (name "r-rbenchmark")
7965 (uri (cran-uri "rbenchmark" version))
7967 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7968 (build-system r-build-system)
7969 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7970 (synopsis "Benchmarking routine for R")
7972 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7973 and is intended to facilitate benchmarking of arbitrary R code. The library
7974 consists of just one function, benchmark, which is a simple wrapper around
7975 system.time. Given a specification of the benchmarking process (counts of
7976 replications, evaluation environment) and an arbitrary number of expressions,
7977 benchmark evaluates each of the expressions in the specified environment,
7978 replicating the evaluation as many times as specified, and returning the results
7979 conveniently wrapped into a data frame.")
7980 (license license:gpl2+)))
7982 (define-public r-mitools
7989 (uri (cran-uri "mitools" version))
7992 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7993 (build-system r-build-system)
7994 (propagated-inputs `(("r-dbi" ,r-dbi)))
7995 (home-page "https://cran.r-project.org/web/packages/mitools/")
7996 (synopsis "Tools for multiple imputation of missing data")
7998 "This package provides tools to perform analyses and combine results from
7999 multiple-imputation datasets.")
8000 (license license:gpl2)))
8002 (define-public r-magick
8009 (uri (cran-uri "magick" version))
8012 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
8013 (build-system r-build-system)
8015 `(("imagemagick" ,imagemagick)
8018 `(("r-curl" ,r-curl)
8019 ("r-magrittr" ,r-magrittr)
8020 ("r-rcpp" ,r-rcpp)))
8022 `(("pkg-config" ,pkg-config)))
8023 (home-page "https://github.com/ropensci/magick")
8024 (synopsis "Advanced graphics and image-processing in R")
8026 "This package provides bindings to ImageMagick, a comprehensive image
8027 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8028 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8029 operations are vectorized via the Magick++ STL meaning they operate either on
8030 a single frame or a series of frames for working with layers, collages, or
8031 animation. In RStudio, images are automatically previewed when printed to the
8032 console, resulting in an interactive editing environment.")
8033 (license license:expat)))
8035 (define-public r-survey
8042 (uri (cran-uri "survey" version))
8045 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8046 (build-system r-build-system)
8048 `(("r-lattice" ,r-lattice)
8049 ("r-matrix" ,r-matrix)
8050 ("r-minqa" ,r-minqa)
8051 ("r-mitools" ,r-mitools)
8052 ("r-numderiv" ,r-numderiv)
8053 ("r-survival" ,r-survival)))
8054 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8055 (synopsis "Analysis of complex survey samples")
8057 "This package provides tools for the analysis of complex survey samples.
8058 The provided features include: summary statistics, two-sample tests, rank
8059 tests, generalised linear models, cumulative link models, Cox models,
8060 loglinear models, and general maximum pseudolikelihood estimation for
8061 multistage stratified, cluster-sampled, unequally weighted survey samples;
8062 variances by Taylor series linearisation or replicate weights;
8063 post-stratification, calibration, and raking; two-phase subsampling designs;
8064 graphics; PPS sampling without replacement; principal components, and factor
8066 ;; Either version of the GPL.
8067 (license (list license:gpl2 license:gpl3))))
8069 (define-public r-gee
8076 (uri (cran-uri "gee" version))
8079 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8080 (properties `((upstream-name . "gee")))
8081 (build-system r-build-system)
8083 `(("gfortran" ,gfortran)))
8084 (home-page "https://cran.r-project.org/web/packages/gee/")
8085 (synopsis "Generalized estimation equation solver")
8087 "This package provides a solver for generalized estimation equations.")
8088 (license license:gpl2)))
8090 (define-public r-tab
8097 (uri (cran-uri "tab" version))
8100 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8101 (properties `((upstream-name . "tab")))
8102 (build-system r-build-system)
8104 `(("r-dplyr" ,r-dplyr)
8106 ("r-knitr" ,r-knitr)
8108 ("r-survey" ,r-survey)
8109 ("r-survival" ,r-survival)
8110 ("r-xtable" ,r-xtable)))
8111 (home-page "https://cran.r-project.org/web/packages/tab/")
8112 (synopsis "Create summary tables for statistical reports")
8114 "This package contains functions for creating various types of summary
8115 tables, e.g. comparing characteristics across levels of a categorical variable
8116 and summarizing fitted generalized linear models, generalized estimating
8117 equations, and Cox proportional hazards models. Functions are available to
8118 handle data from simple random samples as well as complex surveys.")
8119 (license license:gpl3+)))
8121 (define-public r-dvmisc
8128 (uri (cran-uri "dvmisc" version))
8130 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8131 (build-system r-build-system)
8133 `(("r-cubature" ,r-cubature)
8134 ("r-data-table" ,r-data-table)
8135 ("r-dplyr" ,r-dplyr)
8136 ("r-ggplot2" ,r-ggplot2)
8138 ("r-mvtnorm" ,r-mvtnorm)
8139 ("r-pracma" ,r-pracma)
8140 ("r-rbenchmark" ,r-rbenchmark)
8142 ("r-survey" ,r-survey)
8144 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8145 (synopsis "Faster computation of common statistics and miscellaneous functions")
8147 "This package implements faster versions of base R functions (e.g. mean, standard
8148 deviation, covariance, weighted mean), mostly written in C++, along with
8149 miscellaneous functions for various purposes (e.g. create the histogram with
8150 fitted probability density function or probability mass function curve, create
8151 the body mass index groups, assess the linearity assumption in logistic
8153 (license license:gpl2)))
8155 (define-public r-accelerometry
8157 (name "r-accelerometry")
8162 (uri (cran-uri "accelerometry" version))
8164 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8165 (build-system r-build-system)
8167 `(("r-dvmisc" ,r-dvmisc)
8168 ("r-rcpp" ,r-rcpp)))
8169 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8170 (synopsis "Functions for processing accelerometer data")
8172 "This package provides a collection of functions that perform operations on
8173 time-series accelerometer data, such as identify the non-wear time, flag minutes
8174 that are part of an activity bout, and find the maximum 10-minute average count
8175 value. The functions are generally very flexible, allowing for a variety of
8176 algorithms to be implemented.")
8177 (license license:gpl3)))
8179 (define-public r-absim
8186 (uri (cran-uri "AbSim" version))
8188 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8189 (properties `((upstream-name . "AbSim")))
8190 (build-system r-build-system)
8193 ("r-powerlaw" ,r-powerlaw)))
8194 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8195 (synopsis "Time resolved simulations of antibody repertoires")
8197 "This package provides simulation methods for the evolution of antibody repertoires.
8198 The heavy and light chain variable region of both human and C57BL/6 mice can
8199 be simulated in a time-dependent fashion. Both single lineages using one set of
8200 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8201 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8202 Upon completion, the main loop of the algorithm begins, with each iteration
8203 representing one simulated time step. Various mutation events are possible at
8204 each time step, contributing to a diverse final repertoire.")
8205 (license license:gpl2)))
8207 (define-public r-quic
8214 (uri (cran-uri "QUIC" version))
8216 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8217 (properties `((upstream-name . "QUIC")))
8218 (build-system r-build-system)
8219 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8220 (synopsis "Regularized sparse inverse covariance matrix estimation")
8222 "This package implements the regularized Gaussian maximum likelihood
8223 estimation of the inverse of a covariance matrix. It uses Newton's method and
8224 coordinate descent to solve the regularized inverse covariance matrix
8225 estimation problem.")
8226 ;; The project home page states that the release is under GPLv3 or later.
8227 ;; The CRAN page only says GPL-3.
8228 (license license:gpl3+)))
8230 (define-public r-abundant
8237 (uri (cran-uri "abundant" version))
8239 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8240 (build-system r-build-system)
8242 `(("r-quic" ,r-quic)))
8243 (home-page "https://cran.r-project.org/web/packages/abundant/")
8244 (synopsis "Abundant regression and high-dimensional principal fitted components")
8246 "This package provides tools to fit and predict with the high-dimensional
8247 principal fitted components model. This model is described by Cook, Forzani,
8248 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8249 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8250 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8251 (license license:gpl2+)))
8253 (define-public r-ac3net
8260 (uri (cran-uri "Ac3net" version))
8262 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8263 (properties `((upstream-name . "Ac3net")))
8264 (build-system r-build-system)
8266 `(("r-data-table" ,r-data-table)))
8267 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8268 (synopsis "Inferring directional conservative causal core gene networks")
8269 (description "This package infers directional Conservative causal core
8270 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8271 directional network.")
8272 (license license:gpl3+)))
8274 (define-public r-aca
8281 (uri (cran-uri "ACA" version))
8283 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8284 (properties `((upstream-name . "ACA")))
8285 (build-system r-build-system)
8286 (home-page "https://cran.r-project.org/web/packages/ACA/")
8287 (synopsis "Abrupt change-point or aberration detection in point series")
8289 "This package offers an interactive function for the detection of breakpoints in
8291 ;; Any version of the GPL
8292 (license (list license:gpl2+ license:gpl3+))))
8294 (define-public r-acceptancesampling
8296 (name "r-acceptancesampling")
8301 (uri (cran-uri "AcceptanceSampling" version))
8303 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8305 `((upstream-name . "AcceptanceSampling")))
8306 (build-system r-build-system)
8307 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8308 (synopsis "Creation and evaluation of acceptance sampling plans")
8310 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8311 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8312 in quality control and improvement. International standards of acceptance
8313 sampling provide sampling plans for specific circumstances. The aim of this
8314 package is to provide an easy-to-use interface to visualize single, double or
8315 multiple sampling plans. In addition, methods have been provided to enable the
8316 user to assess sampling plans against pre-specified levels of performance, as
8317 measured by the probability of acceptance for a given level of quality in the
8319 (license license:gpl3+)))
8321 (define-public r-acclma
8328 (uri (cran-uri "ACCLMA" version))
8330 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8331 (properties `((upstream-name . "ACCLMA")))
8332 (build-system r-build-system)
8333 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8334 (synopsis "ACC & LMA graph plotting")
8336 "This package contains a function that imports data from a @acronym{CSV,
8337 Comma-Separated Values} file, or uses manually entered data from the format (x,
8338 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8339 Curve} vs @acronym{LOI, Line of Independence} graph and
8340 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8341 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8342 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8343 string) was passed, a manual data entry window is opened. The header parameter
8344 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8345 a header row or not. The dataset should contain only one independent variable
8346 (x) and one dependent variable (y) and can contain a weight for each
8348 (license license:gpl2)))
8350 (define-public r-aspi
8357 (uri (cran-uri "aspi" version))
8359 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8360 (build-system r-build-system)
8362 "https://cran.r-project.org/web/packages/aspi/")
8364 "Analysis of symmetry of parasitic infections")
8366 "This package provides tools for the analysis and visualization of bilateral
8367 asymmetry in parasitic infections.")
8368 (license license:gpl3+)))
8370 (define-public r-sandwich
8377 (uri (cran-uri "sandwich" version))
8380 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8381 (build-system r-build-system)
8383 `(("r-zoo" ,r-zoo)))
8384 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8385 (synopsis "Robust Covariance Matrix Estimators")
8387 "This package provides model-robust standard error estimators for
8388 cross-sectional, time series, clustered, panel, and longitudinal data.")
8389 ;; Either version of the license.
8390 (license (list license:gpl2 license:gpl3))))
8392 (define-public r-th-data
8399 (uri (cran-uri "TH.data" version))
8402 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8403 (properties `((upstream-name . "TH.data")))
8404 (build-system r-build-system)
8406 `(("r-mass" ,r-mass)
8407 ("r-survival" ,r-survival)))
8408 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8409 (synopsis "Shared data sets")
8411 "This package contains supporting data sets that are used in other
8412 packages maintained by Torsten Hothorn.")
8413 (license license:gpl3)))
8415 (define-public r-multcomp
8422 (uri (cran-uri "multcomp" version))
8425 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8426 (build-system r-build-system)
8428 `(("r-codetools" ,r-codetools)
8429 ("r-mvtnorm" ,r-mvtnorm)
8430 ("r-sandwich" ,r-sandwich)
8431 ("r-survival" ,r-survival)
8432 ("r-th-data" ,r-th-data)))
8433 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8434 (synopsis "Simultaneous inference in general parametric models")
8436 "Simultaneous tests and confidence intervals for general linear
8437 hypotheses in parametric models, including linear, generalized linear, linear
8438 mixed effects, and survival models. The package includes demos reproducing
8439 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8440 Hothorn, Westfall, 2010, CRC Press).")
8441 (license license:gpl2)))
8443 (define-public r-emmeans
8450 (uri (cran-uri "emmeans" version))
8453 "0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa"))))
8454 (build-system r-build-system)
8456 `(("r-estimability" ,r-estimability)
8457 ("r-mvtnorm" ,r-mvtnorm)
8458 ("r-numderiv" ,r-numderiv)
8460 ("r-xtable" ,r-xtable)))
8462 `(("r-knitr" ,r-knitr)))
8463 (home-page "https://github.com/rvlenth/emmeans")
8464 (synopsis "Estimated marginal means, aka least-squares means")
8466 "This package provides tools to obtain @dfn{estimated marginal
8467 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8468 be used to compute contrasts or linear functions of EMMs, trends, and
8469 comparisons of slopes.")
8470 ;; Either version of the license.
8471 (license (list license:gpl2 license:gpl3))))
8473 (define-public r-pwr
8480 (uri (cran-uri "pwr" version))
8483 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8484 (build-system r-build-system)
8486 `(("r-knitr" ,r-knitr)))
8487 (home-page "https://github.com/heliosdrm/pwr")
8488 (synopsis "Basic functions for power analysis")
8490 "This package provides power analysis functions along the lines of
8492 (license license:gpl3+)))
8494 (define-public r-libcoin
8501 (uri (cran-uri "libcoin" version))
8504 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8505 (build-system r-build-system)
8506 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8507 (home-page "https://cran.r-project.org/web/packages/libcoin")
8508 (synopsis "Linear test statistics for permutation inference")
8510 "This package provides basic infrastructure for linear test statistics
8511 and permutation inference in the framework of Strasser and Weber (1999).")
8512 (license license:gpl2)))
8514 (define-public r-coin
8521 (uri (cran-uri "coin" version))
8524 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8525 (build-system r-build-system)
8527 `(("r-libcoin" ,r-libcoin)
8528 ("r-matrixstats" ,r-matrixstats)
8529 ("r-modeltools" ,r-modeltools)
8530 ("r-multcomp" ,r-multcomp)
8531 ("r-mvtnorm" ,r-mvtnorm)
8532 ("r-survival" ,r-survival)))
8533 (home-page "http://coin.r-forge.r-project.org")
8534 (synopsis "Conditional inference procedures in a permutation test framework")
8536 "This package provides conditional inference procedures for the general
8537 independence problem including two-sample, K-sample (non-parametric ANOVA),
8538 correlation, censored, ordered and multivariate problems.")
8539 (license license:gpl2)))
8541 (define-public r-bayesplot
8543 (name "r-bayesplot")
8548 (uri (cran-uri "bayesplot" version))
8551 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8552 (build-system r-build-system)
8554 `(("pandoc" ,ghc-pandoc)
8555 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8557 `(("r-dplyr" ,r-dplyr)
8558 ("r-ggplot2" ,r-ggplot2)
8559 ("r-ggridges" ,r-ggridges)
8561 ("r-reshape2" ,r-reshape2)
8562 ("r-rlang" ,r-rlang)
8563 ("r-tibble" ,r-tibble)
8564 ("r-tidyselect" ,r-tidyselect)))
8565 (home-page "https://mc-stan.org/bayesplot")
8566 (synopsis "Plotting for Bayesian models")
8568 "This package provides plotting functions for posterior analysis, model
8569 checking, and MCMC diagnostics. The package is designed not only to provide
8570 convenient functionality for users, but also a common set of functions that
8571 can be easily used by developers working on a variety of R packages for
8572 Bayesian modeling.")
8573 (license license:gpl3+)))
8575 (define-public r-tmb
8582 (uri (cran-uri "TMB" version))
8585 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8586 (properties `((upstream-name . "TMB")))
8587 (build-system r-build-system)
8589 `(("r-matrix" ,r-matrix)
8590 ("r-rcppeigen" ,r-rcppeigen)))
8591 (home-page "http://tmb-project.org")
8592 (synopsis "Template model builder: a general random effect tool")
8594 "With this tool, a user should be able to quickly implement complex
8595 random effect models through simple C++ templates. The package combines
8596 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8597 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8598 from R) to obtain an efficient implementation of the applied Laplace
8599 approximation with exact derivatives. Key features are: Automatic sparseness
8600 detection, parallelism through BLAS and parallel user templates.")
8601 (license license:gpl2)))
8603 (define-public r-sjstats
8610 (uri (cran-uri "sjstats" version))
8612 (base32 "0938ac6ixvkif07azd2msa8g3qnn9rabj6jg17almbysl83kg4nm"))))
8613 (build-system r-build-system)
8615 `(("r-bayestestr" ,r-bayestestr)
8616 ("r-broom" ,r-broom)
8617 ("r-dplyr" ,r-dplyr)
8618 ("r-effectsize" ,r-effectsize)
8619 ("r-emmeans" ,r-emmeans)
8620 ("r-insight" ,r-insight)
8622 ("r-magrittr" ,r-magrittr)
8624 ("r-modelr" ,r-modelr)
8625 ("r-parameters" ,r-parameters)
8626 ("r-performance" ,r-performance)
8627 ("r-purrr" ,r-purrr)
8628 ("r-rlang" ,r-rlang)
8629 ("r-sjlabelled" ,r-sjlabelled)
8630 ("r-sjmisc" ,r-sjmisc)
8631 ("r-tidyr" ,r-tidyr)))
8632 (home-page "https://github.com/strengejacke/sjstats")
8633 (synopsis "Functions for common statistical computations")
8635 "This package provides a collection of convenient functions for common
8636 statistical computations, which are not directly provided by R's @code{base}
8637 or @code{stats} packages. This package aims at providing, first, shortcuts
8638 for statistical measures, which otherwise could only be calculated with
8639 additional effort. Second, these shortcut functions are generic, and can be
8640 applied not only to vectors, but also to other objects as well. The focus of
8641 most functions lies on summary statistics or fit measures for regression
8642 models, including generalized linear models, mixed effects models and Bayesian
8644 (license license:gpl3)))
8646 (define-public r-glmmtmb
8653 (uri (cran-uri "glmmTMB" version))
8656 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8657 (properties `((upstream-name . "glmmTMB")))
8658 (build-system r-build-system)
8660 `(("r-lme4" ,r-lme4)
8661 ("r-matrix" ,r-matrix)
8663 ("r-rcppeigen" ,r-rcppeigen)
8666 `(("r-knitr" ,r-knitr))) ; for vignettes
8667 (home-page "https://github.com/glmmTMB")
8668 (synopsis "Generalized linear mixed models")
8670 "Fit linear and generalized linear mixed models with various extensions,
8671 including zero-inflation. The models are fitted using maximum likelihood
8672 estimation via the Template Model Builder. Random effects are assumed to be
8673 Gaussian on the scale of the linear predictor and are integrated out using the
8674 Laplace approximation. Gradients are calculated using automatic
8676 (license license:agpl3+)))
8678 (define-public r-bayestestr
8680 (name "r-bayestestr")
8685 (uri (cran-uri "bayestestR" version))
8688 "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
8689 (properties `((upstream-name . "bayestestR")))
8690 (build-system r-build-system)
8692 `(("r-insight" ,r-insight)))
8694 `(("r-knitr" ,r-knitr)))
8695 (home-page "https://github.com/easystats/bayestestR")
8696 (synopsis "Describe Bayesian models and posterior distributions")
8698 "This package provides utilities to understand and describe posterior
8699 distributions and Bayesian models. It includes point-estimates such as
8700 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8701 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8702 ROPE percentage and pd).")
8703 (license license:gpl3)))
8705 (define-public r-performance
8707 (name "r-performance")
8712 (uri (cran-uri "performance" version))
8715 "0j6wmnwhfdd3v1a17qmg491q50579knjzscmyr4yk3xr0jbsbg8x"))))
8716 (build-system r-build-system)
8718 `(("r-bayestestr" ,r-bayestestr)
8719 ("r-insight" ,r-insight)))
8720 (home-page "https://easystats.github.io/performance/")
8721 (synopsis "Assessment of regression models performance")
8723 "This package provides utilities for computing measures to assess model
8724 quality, which are not directly provided by R's @code{base} or @code{stats}
8725 packages. These include e.g. measures like r-squared, intraclass correlation
8726 coefficient, root mean squared error or functions to check models for
8727 overdispersion, singularity or zero-inflation and more. Functions apply to a
8728 large variety of regression models, including generalized linear models, mixed
8729 effects models and Bayesian models.")
8730 (license license:gpl3)))
8732 (define-public r-ggeffects
8734 (name "r-ggeffects")
8739 (uri (cran-uri "ggeffects" version))
8742 "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
8743 (build-system r-build-system)
8745 `(("r-insight" ,r-insight)
8747 ("r-sjlabelled" ,r-sjlabelled)))
8749 `(("r-knitr" ,r-knitr)))
8750 (home-page "https://github.com/strengejacke/ggeffects")
8751 (synopsis "Create tidy data frames of marginal effects for ggplot")
8753 "This package provides tools to compute marginal effects from statistical
8754 models and return the result as tidy data frames. These data frames are ready
8755 to use with the @code{ggplot2} package. Marginal effects can be calculated
8756 for many different models. Interaction terms, splines and polynomial terms
8757 are also supported. The two main functions are @code{ggpredict()} and
8758 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8759 results using @code{ggplot2}.")
8760 (license license:gpl3)))
8762 (define-public r-effectsize
8764 (name "r-effectsize")
8769 (uri (cran-uri "effectsize" version))
8772 "0kijp4wamkidaxysc11dd4vhvnm4wnbi87871wcbwn27k5b6i5dg"))))
8773 (properties `((upstream-name . "effectsize")))
8774 (build-system r-build-system)
8776 `(("r-bayestestr" ,r-bayestestr)
8777 ("r-insight" ,r-insight)
8778 ("r-parameters" ,r-parameters)))
8780 `(("r-knitr" ,r-knitr)))
8781 (home-page "https://github.com/easystats/effectsize")
8782 (synopsis "Indices of effect size and standardized parameters")
8784 "This package provides utilities to work with indices of effect size and
8785 standardized parameters for a wide variety of models, allowing computation and
8786 conversion of indices such as Cohen's d, r, odds, etc.")
8787 (license license:gpl3)))
8789 (define-public r-sjplot
8796 (uri (cran-uri "sjPlot" version))
8798 (base32 "0ip1rkjlhyf3axlc8qqss1qq1f0xrda890c1jmcbhm98wwjw264f"))))
8799 (properties `((upstream-name . "sjPlot")))
8800 (build-system r-build-system)
8802 `(("r-bayestestr" ,r-bayestestr)
8803 ("r-dplyr" ,r-dplyr)
8804 ("r-effectsize" ,r-effectsize)
8805 ("r-ggeffects" ,r-ggeffects)
8806 ("r-ggplot2" ,r-ggplot2)
8807 ("r-insight" ,r-insight)
8808 ("r-knitr" ,r-knitr)
8810 ("r-parameters" ,r-parameters)
8811 ("r-performance" ,r-performance)
8812 ("r-purrr" ,r-purrr)
8813 ("r-rlang" ,r-rlang)
8814 ("r-scales" ,r-scales)
8815 ("r-sjlabelled" ,r-sjlabelled)
8816 ("r-sjmisc" ,r-sjmisc)
8817 ("r-sjstats" ,r-sjstats)
8818 ("r-tidyr" ,r-tidyr)))
8820 `(("r-knitr" ,r-knitr)))
8821 (home-page "https://strengejacke.github.io/sjPlot/")
8822 (synopsis "Data visualization for statistics in social science")
8824 "This package represents a collection of plotting and table output
8825 functions for data visualization. Results of various statistical
8826 analyses (that are commonly used in social sciences) can be visualized using
8827 this package, including simple and cross tabulated frequencies, histograms,
8828 box plots, (generalized) linear models, mixed effects models, principal
8829 component analysis and correlation matrices, cluster analyses, scatter plots,
8830 stacked scales, effects plots of regression models (including interaction
8831 terms) and much more. This package supports labelled data.")
8832 (license license:gpl3)))
8834 (define-public r-ini
8841 (uri (cran-uri "ini" version))
8844 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8845 (build-system r-build-system)
8846 (home-page "https://github.com/dvdscripter/ini")
8847 (synopsis "Read and write configuration files")
8849 "This package provides tools to parse simple @code{.ini} configuration
8850 files to an structured list. Users can manipulate this resulting list with
8851 @code{lapply()} functions. This same structured list can be used to write
8852 back to file after modifications.")
8853 (license license:gpl3)))
8862 (uri (cran-uri "gh" version))
8865 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
8866 (build-system r-build-system)
8871 ("r-jsonlite" ,r-jsonlite)))
8872 (home-page "https://github.com/r-lib/gh#readme")
8873 (synopsis "Access the GitHub API via R")
8875 "This package provides a minimal R client to access the GitHub API.")
8876 (license license:expat)))
8885 (uri (cran-uri "fs" version))
8888 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
8889 (build-system r-build-system)
8891 `(("pkg-config" ,pkg-config)
8892 ("r-knitr" ,r-knitr)))
8893 (home-page "https://fs.r-lib.org")
8894 (synopsis "Cross-platform file system operations based on libuv")
8896 "This package provides a cross-platform interface to file system
8897 operations, built on top of the libuv C library.")
8898 (license license:gpl3)))
8900 (define-public r-clisymbols
8902 (name "r-clisymbols")
8907 (uri (cran-uri "clisymbols" version))
8910 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8911 (build-system r-build-system)
8912 (home-page "https://github.com/gaborcsardi/clisymbols")
8913 (synopsis "Unicode symbols at the R prompt")
8915 "This package provides a small subset of Unicode symbols, that are useful
8916 when building command line applications. They fall back to alternatives on
8917 terminals that do not support Unicode.")
8918 (license license:expat)))
8920 (define-public r-usethis
8927 (uri (cran-uri "usethis" version))
8930 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
8931 (build-system r-build-system)
8934 ("r-clipr" ,r-clipr)
8935 ("r-crayon" ,r-crayon)
8940 ("r-git2r" ,r-git2r)
8942 ("r-purrr" ,r-purrr)
8943 ("r-rematch2" ,r-rematch2)
8944 ("r-rlang" ,r-rlang)
8945 ("r-rprojroot" ,r-rprojroot)
8946 ("r-rstudioapi" ,r-rstudioapi)
8947 ("r-whisker" ,r-whisker)
8948 ("r-withr" ,r-withr)
8949 ("r-yaml" ,r-yaml)))
8950 (home-page "https://github.com/r-lib/usethis")
8951 (synopsis "Automate R package and project setup")
8953 "This package helps you to automate R package and project setup tasks
8954 that are otherwise performed manually. This includes setting up unit testing,
8955 test coverage, continuous integration, Git, GitHub integration, licenses,
8956 Rcpp, RStudio projects, and more.")
8957 (license license:gpl3)))
8959 (define-public r-sessioninfo
8961 (name "r-sessioninfo")
8966 (uri (cran-uri "sessioninfo" version))
8969 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8970 (build-system r-build-system)
8973 ("r-withr" ,r-withr)))
8974 (home-page "https://github.com/r-lib/sessioninfo#readme")
8975 (synopsis "R session information")
8977 "This package provides tools to query and print information about the
8978 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8979 more information about packages, and where they were installed from.")
8980 (license license:gpl2)))
8982 (define-public r-remotes
8989 (uri (cran-uri "remotes" version))
8992 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
8993 (build-system r-build-system)
8994 (home-page "https://github.com/r-lib/remotes#readme")
8995 (synopsis "R package installation from remote repositories")
8997 "Download and install R packages stored in GitHub, BitBucket, or plain
8998 subversion or git repositories. This package is a lightweight replacement of
8999 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9000 the code was copied over from @code{devtools}.")
9001 (license license:gpl2+)))
9003 (define-public r-xopen
9010 (uri (cran-uri "xopen" version))
9013 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9014 (build-system r-build-system)
9016 `(("r-processx" ,r-processx)))
9017 (home-page "https://github.com/r-lib/xopen#readme")
9018 (synopsis "Open system files, URLs, anything")
9020 "This package provides a cross-platform solution to open files,
9021 directories or URLs with their associated programs.")
9022 (license license:expat)))
9024 (define-public r-rcmdcheck
9026 (name "r-rcmdcheck")
9031 (uri (cran-uri "rcmdcheck" version))
9034 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9035 (build-system r-build-system)
9037 `(("r-callr" ,r-callr)
9039 ("r-crayon" ,r-crayon)
9041 ("r-digest" ,r-digest)
9042 ("r-pkgbuild" ,r-pkgbuild)
9043 ("r-prettyunits" ,r-prettyunits)
9045 ("r-rprojroot" ,r-rprojroot)
9046 ("r-sessioninfo" ,r-sessioninfo)
9047 ("r-withr" ,r-withr)
9048 ("r-xopen" ,r-xopen)))
9049 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9050 (synopsis "Run R CMD check from R and capture results")
9052 "Run @code{R CMD check} from R programmatically, and capture the results
9053 of the individual checks.")
9054 (license license:expat)))
9056 (define-public r-rapportools
9058 (name "r-rapportools")
9063 (uri (cran-uri "rapportools" version))
9066 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9067 (build-system r-build-system)
9069 `(("r-pander" ,r-pander)
9071 ("r-reshape" ,r-reshape)))
9072 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9073 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9075 "This package provides helper functions that act as wrappers to more
9076 advanced statistical methods with the advantage of having sane defaults for
9078 (license license:agpl3+)))
9080 (define-public r-pander
9087 (uri (cran-uri "pander" version))
9090 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9091 (build-system r-build-system)
9093 `(("r-digest" ,r-digest)
9094 ("r-rcpp" ,r-rcpp)))
9095 (home-page "https://rapporter.github.io/pander")
9096 (synopsis "Render R objects into Pandoc's markdown")
9098 "The main aim of the pander R package is to provide a minimal and easy
9099 tool for rendering R objects into Pandoc's markdown. The package is also
9100 capable of exporting/converting complex Pandoc documents (reports) in various
9102 ;; This package is licensed under either the AGPLv3+ or the very rarely
9104 (license license:agpl3+)))
9106 (define-public r-summarytools
9108 (name "r-summarytools")
9113 (uri (cran-uri "summarytools" version))
9116 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9117 (build-system r-build-system)
9119 `(("r-base64enc" ,r-base64enc)
9120 ("r-checkmate" ,r-checkmate)
9121 ("r-dplyr" ,r-dplyr)
9122 ("r-htmltools" ,r-htmltools)
9123 ("r-lubridate" ,r-lubridate)
9124 ("r-magick" ,r-magick)
9125 ("r-matrixstats" ,r-matrixstats)
9126 ("r-pander" ,r-pander)
9128 ("r-rapportools" ,r-rapportools)
9129 ("r-tibble" ,r-tibble)
9130 ("r-tidyr" ,r-tidyr)))
9131 (home-page "https://github.com/dcomtois/summarytools")
9132 (synopsis "Tools to quickly and neatly summarize data")
9134 "This package provides tools for data frame summaries, cross-tabulations,
9135 weight-enabled frequency tables and common univariate statistics in concise
9136 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9137 good point-of-entry for exploring data, both for experienced and new R
9139 (license license:gpl2)))
9141 (define-public r-lsei
9148 (uri (cran-uri "lsei" version))
9151 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
9152 (build-system r-build-system)
9154 `(("gfortran" ,gfortran)))
9155 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9156 (synopsis "Solve regression problems under equality/inequality constraints")
9158 "It contains functions that solve least squares linear regression
9159 problems under linear equality/inequality constraints. Functions for solving
9160 quadratic programming problems are also available, which transform such
9161 problems into least squares ones first.")
9162 (license license:gpl2+)))
9164 (define-public r-npsurv
9171 (uri (cran-uri "npsurv" version))
9174 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
9175 (build-system r-build-system)
9177 `(("r-lsei" ,r-lsei)))
9178 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9179 (synopsis "Nonparametric survival analysis")
9181 "This package contains functions for non-parametric survival analysis of
9182 exact and interval-censored observations.")
9183 (license license:gpl2+)))
9185 (define-public r-clusteval
9187 (name "r-clusteval")
9192 (uri (cran-uri "clusteval" version))
9195 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9196 (build-system r-build-system)
9198 `(("r-mvtnorm" ,r-mvtnorm)
9199 ("r-rcpp" ,r-rcpp)))
9200 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9201 (synopsis "Evaluation of clustering algorithms")
9203 "This R package provides a suite of tools to evaluate clustering
9204 algorithms, clusterings, and individual clusters.")
9205 (license license:expat)))
9207 (define-public r-tweedie
9214 (uri (cran-uri "tweedie" version))
9217 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9218 (build-system r-build-system)
9219 (native-inputs `(("gfortran" ,gfortran)))
9220 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9221 (synopsis "Evaluation of Tweedie exponential family models")
9223 "Maximum likelihood computations for Tweedie families, including the
9224 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9225 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9226 and related methods.")
9227 (license license:gpl2+)))
9229 (define-public r-rcppgsl
9236 (uri (cran-uri "RcppGSL" version))
9238 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9239 (properties `((upstream-name . "RcppGSL")))
9240 (build-system r-build-system)
9242 `(("r-rcpp" ,r-rcpp)
9245 `(("r-knitr" ,r-knitr))) ; for vignettes
9246 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9247 (synopsis "Rcpp integration for GSL vectors and matrices")
9249 "The GNU Scientific Library (or GSL) is a collection of numerical
9250 routines for scientific computing. It is particularly useful for C and C++
9251 programs as it provides a standard C interface to a wide range of mathematical
9252 routines. There are over 1000 functions in total with an extensive test
9253 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9254 structures and R using concepts from Rcpp which is itself a package that eases
9255 the interfaces between R and C++.")
9256 (license license:gpl2+)))
9258 (define-public r-mvabund
9265 (uri (cran-uri "mvabund" version))
9268 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9269 (build-system r-build-system)
9271 `(("r-mass" ,r-mass)
9273 ("r-rcppgsl" ,r-rcppgsl)
9274 ("r-statmod" ,r-statmod)
9275 ("r-tweedie" ,r-tweedie)))
9276 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9277 (synopsis "Statistical methods for analysing multivariate abundance data")
9279 "This package provides a set of tools for displaying, modeling and
9280 analysing multivariate abundance data in community ecology.")
9281 (license license:lgpl2.1+)))
9283 (define-public r-afex
9290 (uri (cran-uri "afex" version))
9293 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9294 (build-system r-build-system)
9298 ("r-lmertest" ,r-lmertest)
9299 ("r-pbkrtest" ,r-pbkrtest)
9300 ("r-reshape2" ,r-reshape2)))
9302 `(("r-knitr" ,r-knitr)))
9303 (home-page "https://afex.singmann.science/")
9304 (synopsis "Analysis of factorial experiments")
9306 "This package provides convenience functions for analyzing factorial
9307 experiments using ANOVA or mixed models.")
9308 (license license:gpl2+)))
9310 (define-public r-lmertest
9317 (uri (cran-uri "lmerTest" version))
9320 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9321 (properties `((upstream-name . "lmerTest")))
9322 (build-system r-build-system)
9324 `(("r-ggplot2" ,r-ggplot2)
9327 ("r-numderiv" ,r-numderiv)))
9328 (home-page "https://github.com/runehaubo/lmerTestR")
9329 (synopsis "Tests in linear mixed effects models")
9331 "This package provides p-values in type I, II or III anova and summary
9332 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9333 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9334 package. Model selection methods include step, drop1 and anova-like tables
9335 for random effects (ranova). Methods for Least-Square means (LS-means) and
9336 tests of linear contrasts of fixed effects are also available.")
9337 (license license:gpl2+)))
9339 (define-public r-r2glmm
9346 (uri (cran-uri "r2glmm" version))
9349 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9350 (build-system r-build-system)
9352 `(("r-afex" ,r-afex)
9353 ("r-data-table" ,r-data-table)
9354 ("r-dplyr" ,r-dplyr)
9355 ("r-ggplot2" ,r-ggplot2)
9356 ("r-gridextra" ,r-gridextra)
9357 ("r-lmertest" ,r-lmertest)
9359 ("r-matrix" ,r-matrix)
9361 ("r-pbkrtest" ,r-pbkrtest)))
9362 (home-page "https://github.com/bcjaeger/r2glmm")
9363 (synopsis "Compute R squared for mixed (multilevel) models")
9365 "This package computes model and semi partial R squared with confidence
9366 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9367 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9368 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9370 (license license:gpl2)))
9372 (define-public r-weights
9379 (uri (cran-uri "weights" version))
9382 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9383 (build-system r-build-system)
9385 `(("r-gdata" ,r-gdata)
9386 ("r-hmisc" ,r-hmisc)
9387 ("r-mice" ,r-mice)))
9389 "https://cran.r-project.org/web/packages/weights/")
9390 (synopsis "Weighting and weighted statistics")
9391 (description "This package Provides a variety of functions for producing
9392 simple weighted statistics, such as weighted Pearson's correlations, partial
9393 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9394 includes some software for quickly recoding survey data and plotting point
9395 estimates from interaction terms in regressions (and multiply imputed
9396 regressions). NOTE: Weighted partial correlation calculations pulled to
9398 (license license:gpl2+)))
9400 (define-public r-rcppannoy
9402 (name "r-rcppannoy")
9407 (uri (cran-uri "RcppAnnoy" version))
9410 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9411 (properties `((upstream-name . "RcppAnnoy")))
9412 (build-system r-build-system)
9414 `(("r-rcpp" ,r-rcpp)))
9415 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9416 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9418 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9419 for efficient memory usage as well an ability to load from and save to disk.
9420 This package provides an R interface.")
9421 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9423 (license (list license:gpl2+ license:asl2.0))))
9425 (define-public r-rcpphnsw
9432 (uri (cran-uri "RcppHNSW" version))
9435 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9436 (properties `((upstream-name . "RcppHNSW")))
9437 (build-system r-build-system)
9438 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9439 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9440 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9442 "Hnswlib is a C++ library for approximate nearest neighbors. This
9443 package provides a minimal R interface by relying on the Rcpp package.")
9444 ;; hnswlib is released under Version 2.0 of the Apache License.
9445 (license (list license:gpl3 license:asl2.0))))
9447 (define-public r-rcppparallel
9449 (name "r-rcppparallel")
9454 (uri (cran-uri "RcppParallel" version))
9457 "1mhd6vp47xmfw533h0pkvydv96m57fspvd85g8m7iqb5rcxvhhdb"))))
9458 (properties `((upstream-name . "RcppParallel")))
9459 (build-system r-build-system)
9460 (home-page "https://rcppcore.github.io/RcppParallel/")
9461 (synopsis "Parallel programming tools for Rcpp")
9463 "This package provides high level functions for parallel programming with
9464 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9465 the work of a standard serial @code{for} loop into a parallel one and the
9466 @code{parallelReduce()} function can be used for accumulating aggregates or
9468 (license license:gpl2)))
9470 (define-public r-ncdf4
9477 (uri (cran-uri "ncdf4" version))
9480 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9481 (build-system r-build-system)
9483 `(("netcdf" ,netcdf)
9485 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9486 (synopsis "R interface to Unidata netCDF format data files")
9488 "This package provides a high-level R interface to data files written
9489 using Unidata's netCDF library (version 4 or earlier), which are binary data
9490 files that are portable across platforms and include metadata information in
9491 addition to the data sets. Using this package, netCDF files can be opened and
9492 data sets read in easily. It is also easy to create new netCDF dimensions,
9493 variables, and files, in either version 3 or 4 format, and manipulate existing
9495 (license license:gpl3+)))
9497 (define-public r-biocmanager
9499 (name "r-biocmanager")
9504 (uri (cran-uri "BiocManager" version))
9506 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9507 (properties `((upstream-name . "BiocManager")))
9508 (build-system r-build-system)
9509 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9510 (synopsis "Access the Bioconductor project package repository")
9512 "This package provides a convenient tool to install and update
9513 Bioconductor packages.")
9514 (license license:artistic2.0)))
9516 (define-public r-rgl
9519 (version "0.100.54")
9523 (uri (cran-uri "rgl" version))
9526 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9527 (build-system r-build-system)
9529 `(("pkg-config" ,pkg-config)))
9531 `(("freetype" ,freetype)
9535 ("ghc-pandoc" ,ghc-pandoc)
9538 `(("r-crosstalk" ,r-crosstalk)
9539 ("r-htmltools" ,r-htmltools)
9540 ("r-htmlwidgets" ,r-htmlwidgets)
9541 ("r-jsonlite" ,r-jsonlite)
9542 ("r-knitr" ,r-knitr)
9543 ("r-magrittr" ,r-magrittr)
9544 ("r-manipulatewidget" ,r-manipulatewidget)
9545 ("r-shiny" ,r-shiny)))
9546 (home-page "https://r-forge.r-project.org/projects/rgl/")
9547 (synopsis "3D visualization using OpenGL")
9549 "This package provides medium to high level functions for 3D interactive graphics,
9550 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9551 as functions for constructing representations of geometric
9552 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9553 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9554 image formats, including PNG, Postscript, SVG, PGF.")
9555 ;; Any version of the GPL.
9556 (license (list license:gpl2+ license:gpl3+))))
9558 (define-public r-multicool
9560 (name "r-multicool")
9565 (uri (cran-uri "multicool" version))
9568 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9569 (build-system r-build-system)
9570 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9571 (home-page "https://cran.r-project.org/web/packages/multicool/")
9572 (synopsis "Permutations of multisets in cool-lex order")
9574 "This package provides a set of tools to permute multisets without loops
9575 or hash tables and to generate integer partitions. Cool-lex order is similar
9576 to colexicographical order.")
9577 (license license:gpl2)))
9579 (define-public r-misc3d
9586 (uri (cran-uri "misc3d" version))
9589 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9590 (build-system r-build-system)
9591 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9592 (synopsis "Miscellaneous 3D Plots")
9594 "This package provides a collection of miscellaneous 3d plots, including
9596 ;; Any version of the GPL.
9597 (license (list license:gpl2+ license:gpl3+))))
9606 (uri (cran-uri "ks" version))
9608 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9609 (build-system r-build-system)
9612 ("r-kernlab" ,r-kernlab)
9613 ("r-kernsmooth" ,r-kernsmooth)
9614 ("r-matrix" ,r-matrix)
9615 ("r-mclust" ,r-mclust)
9617 ("r-multicool" ,r-multicool)
9618 ("r-mvtnorm" ,r-mvtnorm)))
9619 (home-page "http://www.mvstat.net/tduong/")
9620 (synopsis "Kernel smoothing")
9622 "This package provides kernel smoothers for univariate and multivariate
9623 data, including density functions, density derivatives, cumulative
9624 distributions, modal clustering, discriminant analysis, and two-sample
9625 hypothesis testing.")
9626 ;; Either version of the GPL.
9627 (license (list license:gpl2 license:gpl3))))
9629 (define-public r-feature
9636 (uri (cran-uri "feature" version))
9639 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9640 (build-system r-build-system)
9643 ("r-misc3d" ,r-misc3d)
9645 (home-page "http://www.mvstat.net/tduong/")
9646 (synopsis "Inferential feature significance for kernel density estimation")
9648 "The feature package contains functions to display and compute kernel
9649 density estimates, significant gradient and significant curvature regions.
9650 Significant gradient and/or curvature regions often correspond to significant
9651 features (e.g. local modes).")
9652 ;; Either version of the GPL.
9653 (license (list license:gpl2 license:gpl3))))
9655 (define-public r-arm
9662 (uri (cran-uri "arm" version))
9665 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
9666 (build-system r-build-system)
9668 `(("r-abind" ,r-abind)
9672 ("r-matrix" ,r-matrix)
9673 ("r-nlme" ,r-nlme)))
9674 (home-page "https://cran.r-project.org/web/packages/arm/")
9675 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9677 "This package provides functions to accompany A. Gelman and J. Hill,
9678 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9679 University Press, 2007.")
9680 (license license:gpl3+)))
9682 (define-public r-circular
9689 (uri (cran-uri "circular" version))
9692 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9693 (build-system r-build-system)
9695 `(("r-boot" ,r-boot)
9696 ("r-mvtnorm" ,r-mvtnorm)))
9698 `(("gfortran" ,gfortran)))
9699 (home-page "https://cran.r-project.org/web/packages/circular/")
9700 (synopsis "Circular statistics")
9702 "This package provides tools for circular statistics, from \"Topics in
9703 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9705 (license license:gpl2+)))
9707 (define-public r-activity
9714 (uri (cran-uri "activity" version))
9717 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9718 (build-system r-build-system)
9720 `(("r-circular" ,r-circular)
9721 ("r-insol" ,r-insol)
9722 ("r-pbapply" ,r-pbapply)))
9723 (home-page "https://cran.r-project.org/web/packages/activity/")
9724 (synopsis "Animal activity statistics")
9726 "This package provides functions to fit kernel density functions to
9727 animal activity time data; plot activity distributions; quantify overall
9728 levels of activity; statistically compare activity metrics through
9729 bootstrapping; and evaluate variation in linear variables with time (or other
9730 circular variables).")
9731 (license license:gpl3)))
9733 (define-public r-ouch
9740 (uri (cran-uri "ouch" version))
9743 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9744 (build-system r-build-system)
9745 (propagated-inputs `(("r-subplex" ,r-subplex)))
9746 (home-page "https://kingaa.github.io/ouch/")
9747 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9749 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9750 for evolution along a phylogenetic tree.")
9751 (license license:gpl2+)))
9753 (define-public r-fmsb
9760 (uri (cran-uri "fmsb" version))
9763 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9764 (build-system r-build-system)
9765 (home-page "http://minato.sip21c.org/msb/")
9766 (synopsis "Functions for medical statistics book with demographic data")
9768 "This package provides several utility functions for the book entitled
9769 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9770 Japan, 2007) with Japanese demographic data and some demographic analysis
9771 related functions.")
9772 (license license:gpl2+)))
9774 (define-public r-stabledist
9776 (name "r-stabledist")
9781 (uri (cran-uri "stabledist" version))
9784 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9785 (build-system r-build-system)
9786 (home-page "https://www.rmetrics.org")
9787 (synopsis "Stable distribution functions")
9789 "This package provides density, probability and quantile functions, and
9790 random number generation for (skew) stable distributions, using the
9791 parametrizations of Nolan.")
9792 (license license:gpl2+)))
9794 (define-public r-gsl
9801 (uri (cran-uri "gsl" version))
9804 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9805 (build-system r-build-system)
9808 (home-page "https://cran.r-project.org/web/packages/gsl")
9809 (synopsis "Wrapper for the GNU Scientific Library")
9811 "This package provides an R wrapper for the special functions and quasi
9812 random number generators of the GNU Scientific Library.")
9813 (license license:gpl2+)))
9815 (define-public r-adgoftest
9817 (name "r-adgoftest")
9822 (uri (cran-uri "ADGofTest" version))
9825 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9826 (properties `((upstream-name . "ADGofTest")))
9827 (build-system r-build-system)
9828 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9829 (synopsis "Anderson-Darling GoF test")
9831 "This package provides an implementation of the Anderson-Darling GoF test
9832 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9833 Anderson-Darling Distribution\".")
9834 ;; Any version of the GPL.
9835 (license license:gpl3+)))
9837 (define-public r-softimpute
9839 (name "r-softimpute")
9844 (uri (cran-uri "softImpute" version))
9847 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9848 (properties `((upstream-name . "softImpute")))
9849 (build-system r-build-system)
9851 `(("r-matrix" ,r-matrix)))
9853 `(("gfortran" ,gfortran)))
9854 (home-page "https://cran.r-project.org/web/packages/softImpute")
9855 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9857 "This package provides iterative methods for matrix completion that use
9858 nuclear-norm regularization. The package includes procedures for centering
9859 and scaling rows, columns or both, and for computing low-rank @dfn{single
9860 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9862 (license license:gpl2)))
9864 (define-public r-fftwtools
9866 (name "r-fftwtools")
9871 (uri (cran-uri "fftwtools" version))
9874 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9875 (build-system r-build-system)
9876 (inputs `(("fftw" ,fftw)))
9877 (home-page "https://github.com/krahim/fftwtools")
9878 (synopsis "Wrapper for FFTW3")
9880 "This package provides a wrapper for several FFTW functions. It provides
9881 access to the two-dimensional FFT, the multivariate FFT, and the
9882 one-dimensional real to complex FFT using the FFTW3 library. The package
9883 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9884 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9885 The FFT functions have a parameter that allows them to not return the
9886 redundant complex conjugate when the input is real data.")
9887 (license license:gpl2+)))
9889 (define-public r-tiff
9896 (uri (cran-uri "tiff" version))
9899 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9900 (build-system r-build-system)
9902 `(("libtiff" ,libtiff)
9903 ("libjpeg" ,libjpeg-turbo)
9905 (home-page "https://www.rforge.net/tiff/")
9906 (synopsis "Read and write TIFF images")
9908 "This package provides an easy and simple way to read, write and display
9909 bitmap images stored in the TIFF format. It can read and write both files and
9910 in-memory raw vectors.")
9911 ;; Either of these two license versions.
9912 (license (list license:gpl2 license:gpl3))))
9914 (define-public r-nlp
9921 (uri (cran-uri "NLP" version))
9924 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9925 (properties `((upstream-name . "NLP")))
9926 (build-system r-build-system)
9927 (home-page "https://cran.r-project.org/web/packages/NLP/")
9928 (synopsis "Natural language processing infrastructure")
9930 "This package provides basic classes and methods for Natural Language
9932 (license license:gpl3)))
9941 (uri (cran-uri "tm" version))
9944 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9945 (properties `((upstream-name . "tm")))
9946 (build-system r-build-system)
9952 ("r-xml2" ,r-xml2)))
9953 (home-page "http://tm.r-forge.r-project.org/")
9954 (synopsis "Text mining package")
9956 "This package provides a framework for text mining applications within R.")
9957 (license license:gpl3)))
9959 (define-public r-waveslim
9966 (uri (cran-uri "waveslim" version))
9969 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
9970 (build-system r-build-system)
9972 `(("gfortran" ,gfortran)))
9973 (home-page "http://waveslim.blogspot.com")
9974 (synopsis "Basic wavelet routines for signal processing")
9976 "This package provides basic wavelet routines for time series (1D),
9977 image (2D) and array (3D) analysis. The code provided here is based on
9978 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9979 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9980 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9981 pairs (Selesnick 2001, 2002).")
9982 (license license:bsd-3)))
9984 (define-public r-wordcloud
9986 (name "r-wordcloud")
9991 (uri (cran-uri "wordcloud" version))
9994 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9995 (build-system r-build-system)
9997 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9999 ;; The "tm" package is only "suggested" according to CRAN, but the
10000 ;; wordcloud package cannot be loaded without it.
10002 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10003 (synopsis "Word clouds")
10005 "This package provides functionality to create pretty word clouds,
10006 visualize differences and similarity between documents, and avoid
10007 over-plotting in scatter plots with text.")
10008 (license license:lgpl2.1)))
10010 (define-public r-colorramps
10012 (name "r-colorramps")
10017 (uri (cran-uri "colorRamps" version))
10020 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10021 (properties `((upstream-name . "colorRamps")))
10022 (build-system r-build-system)
10023 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10024 (synopsis "Build color tables")
10025 (description "This package provides features to build gradient color
10027 ;; Any version of the GPL
10028 (license license:gpl3+)))
10030 (define-public r-tidytree
10032 (name "r-tidytree")
10037 (uri (cran-uri "tidytree" version))
10039 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10040 (build-system r-build-system)
10043 ("r-dplyr" ,r-dplyr)
10044 ("r-lazyeval" ,r-lazyeval)
10045 ("r-magrittr" ,r-magrittr)
10046 ("r-rlang" ,r-rlang)
10047 ("r-tibble" ,r-tibble)))
10049 `(("r-knitr" ,r-knitr)))
10050 (home-page "https://github.com/GuangchuangYu/tidytree")
10051 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10053 "Phylogenetic trees generally contain multiple components including nodes,
10054 edges, branches and associated data. This package provides an approach to
10055 convert tree objects to tidy data frames. It also provides tidy interfaces to
10056 manipulate tree data.")
10057 (license license:artistic2.0)))
10059 (define-public r-rvcheck
10066 (uri (cran-uri "rvcheck" version))
10068 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10069 (build-system r-build-system)
10071 `(("r-biocmanager" ,r-biocmanager)
10072 ("r-rlang" ,r-rlang)))
10073 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10074 (synopsis "R package version check")
10076 "This package provides tools to check the latest release version of R and
10077 R packages (on CRAN, Bioconductor or Github).")
10078 (license license:artistic2.0)))
10080 (define-public r-docopt
10087 (uri (cran-uri "docopt" version))
10090 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
10091 (build-system r-build-system)
10092 (home-page "https://github.com/docopt/docopt.R")
10093 (synopsis "Command-line interface specification language")
10095 "This package enables you to define a command-line interface by just
10096 giving it a description in the specific format.")
10097 (license license:expat)))
10099 (define-public r-sparsesvd
10101 (name "r-sparsesvd")
10106 (uri (cran-uri "sparsesvd" version))
10109 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10110 (build-system r-build-system)
10111 (propagated-inputs `(("r-matrix" ,r-matrix)))
10112 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10113 (synopsis "Sparse truncated singular value decomposition")
10115 "This package provides a Wrapper around the SVDLIBC library
10116 for (truncated) singular value decomposition of a sparse matrix. Currently,
10117 only sparse real matrices in Matrix package format are supported.")
10118 ;; SVDLIBC is released under BSD-2. The R interface is released under
10120 (license (list license:bsd-3 license:bsd-2))))
10122 (define-public r-speedglm
10124 (name "r-speedglm")
10129 (uri (cran-uri "speedglm" version))
10132 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10133 (build-system r-build-system)
10135 `(("r-mass" ,r-mass)
10136 ("r-matrix" ,r-matrix)))
10137 (home-page "https://cran.r-project.org/web/packages/speedglm")
10138 (synopsis "Fit linear and generalized linear models to large data sets")
10140 "This package provides tools for fitting linear models and generalized
10141 linear models to large data sets by updating algorithms.")
10142 ;; Any version of the GPL
10143 (license license:gpl2+)))
10145 (define-public r-densityclust
10147 (name "r-densityclust")
10152 (uri (cran-uri "densityClust" version))
10155 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10156 (properties `((upstream-name . "densityClust")))
10157 (build-system r-build-system)
10160 ("r-ggplot2" ,r-ggplot2)
10161 ("r-ggrepel" ,r-ggrepel)
10162 ("r-gridextra" ,r-gridextra)
10163 ("r-rcolorbrewer" ,r-rcolorbrewer)
10165 ("r-rtsne" ,r-rtsne)))
10166 (home-page "https://cran.r-project.org/web/packages/densityClust")
10167 (synopsis "Clustering by fast search and find of density peaks")
10169 "This package provides an improved implementation (based on k-nearest
10170 neighbors) of the density peak clustering algorithm, originally described by
10171 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10172 large datasets (> 100,000 samples) very efficiently.")
10173 (license license:gpl2+)))
10175 (define-public r-combinat
10177 (name "r-combinat")
10182 (uri (cran-uri "combinat" version))
10185 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10186 (build-system r-build-system)
10187 (home-page "https://cran.r-project.org/web/packages/combinat")
10188 (synopsis "Combinatorics utilities")
10189 (description "This package provides assorted routines for combinatorics.")
10190 (license license:gpl2)))
10192 (define-public r-qlcmatrix
10194 (name "r-qlcmatrix")
10199 (uri (cran-uri "qlcMatrix" version))
10202 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10203 (properties `((upstream-name . "qlcMatrix")))
10204 (build-system r-build-system)
10206 `(("r-docopt" ,r-docopt)
10207 ("r-matrix" ,r-matrix)
10209 ("r-sparsesvd" ,r-sparsesvd)))
10210 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10211 (synopsis "Sparse matrix functions for quantitative language comparison")
10213 "This package provides an extension of the functionality of the Matrix
10214 package for using sparse matrices. Some of the functions are very general,
10215 while other are highly specific for the special data format used for
10216 @dfn{quantitative language comparison} (QLC).")
10217 (license license:gpl3)))
10219 (define-public r-ddrtree
10226 (uri (cran-uri "DDRTree" version))
10229 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10230 (properties `((upstream-name . "DDRTree")))
10231 (build-system r-build-system)
10234 ("r-irlba" ,r-irlba)
10236 ("r-rcppeigen" ,r-rcppeigen)))
10237 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10238 (synopsis "Learning principal graphs with DDRTree")
10240 "This package provides an implementation of the framework of
10241 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10242 dimensional space while constructs a principal tree which passes through the
10243 middle of the data simultaneously. DDRTree shows superiority to
10244 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10245 intrinsic structure of single cell genomics data. In general, it could be
10246 used to reconstruct the temporal progression as well as the bifurcation
10247 structure of any data type.")
10248 (license license:asl2.0)))
10250 (define-public r-corpcor
10257 (uri (cran-uri "corpcor" version))
10260 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10261 (build-system r-build-system)
10262 (home-page "http://strimmerlab.org/software/corpcor/")
10263 (synopsis "Efficient estimation of covariance and (partial) correlation")
10265 "This package implements a James-Stein-type shrinkage estimator for the
10266 covariance matrix, with separate shrinkage for variances and correlations.
10267 Furthermore, functions are available for fast singular value decomposition,
10268 for computing the pseudoinverse, and for checking the rank and positive
10269 definiteness of a matrix.")
10270 (license license:gpl3+)))
10272 (define-public r-rspectra
10274 (name "r-rspectra")
10279 (uri (cran-uri "RSpectra" version))
10282 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10283 (properties `((upstream-name . "RSpectra")))
10284 (build-system r-build-system)
10286 `(("r-matrix" ,r-matrix)
10288 ("r-rcppeigen" ,r-rcppeigen)))
10289 (home-page "https://github.com/yixuan/RSpectra")
10290 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10292 "This package provides an R interface to the Spectra library for
10293 large-scale eigenvalue and SVD problems. It is typically used to compute a
10294 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10295 which is usually more efficient than @code{eigen()} if k << n.")
10297 (license license:mpl2.0)))
10299 (define-public r-vbsr
10306 (uri (cran-uri "vbsr" version))
10309 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10310 (build-system r-build-system)
10311 (home-page "https://cran.r-project.org/web/packages/vbsr")
10312 (synopsis "Variational Bayes spike regression regularized linear models")
10314 "This package provides an efficient algorithm for solving ultra-sparse
10315 regularized regression models using a variational Bayes algorithm with a spike
10316 prior. The algorithm is solved on a path, with coordinate updates, and is
10317 capable of generating very sparse models. Very general model
10318 diagnostics for controlling type-1 errors are also provided.")
10319 (license license:gpl2)))
10321 (define-public r-flare
10324 (version "1.6.0.2")
10328 (uri (cran-uri "flare" version))
10331 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10332 (build-system r-build-system)
10334 `(("r-igraph" ,r-igraph)
10335 ("r-lattice" ,r-lattice)
10337 ("r-matrix" ,r-matrix)))
10338 (home-page "https://cran.r-project.org/web/packages/flare")
10339 (synopsis "Family of Lasso regression implementations")
10341 "This package provides implementations of a family of Lasso variants
10342 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10343 high dimensional sparse linear models.")
10344 (license license:gpl2)))
10346 (define-public r-lassopv
10353 (uri (cran-uri "lassopv" version))
10356 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10357 (build-system r-build-system)
10358 (propagated-inputs `(("r-lars" ,r-lars)))
10359 (home-page "https://github.com/lingfeiwang/lassopv")
10360 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10362 "This package enables you to estimate the p-values for predictors x
10363 against target variable y in Lasso regression, using the regularization
10364 strength when each predictor enters the active set of regularization path for
10365 the first time as the statistic.")
10366 (license license:gpl3)))
10368 (define-public r-splitstackshape
10370 (name "r-splitstackshape")
10375 (uri (cran-uri "splitstackshape" version))
10378 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10379 (build-system r-build-system)
10381 `(("r-data-table" ,r-data-table)))
10382 (home-page "https://github.com/mrdwab/splitstackshape")
10383 (synopsis "Stack and reshape datasets after splitting concatenated values")
10385 "Online data collection tools like Google Forms often export
10386 multiple-response questions with data concatenated in cells. The
10387 @code{concat.split} (cSplit) family of functions provided by this package
10388 splits such data into separate cells. This package also includes functions to
10389 stack groups of columns and to reshape wide data, even when the data are
10390 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10391 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10393 (license license:gpl3)))
10395 (define-public r-tfmpvalue
10397 (name "r-tfmpvalue")
10402 (uri (cran-uri "TFMPvalue" version))
10405 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10406 (properties `((upstream-name . "TFMPvalue")))
10407 (build-system r-build-system)
10408 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10409 (home-page "https://github.com/ge11232002/TFMPvalue")
10410 (synopsis "P-value computation for position weight matrices")
10412 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10413 identification from sequence/alignments, we are interested in the significance
10414 of certain match scores. TFMPvalue provides the accurate calculation of a
10415 p-value with a score threshold for position weight matrices, or the score with
10416 a given p-value. It is an interface to code originally made available by
10417 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10418 Touzet and Varre (2007).")
10419 (license license:gpl2)))
10421 (define-public r-rnifti
10428 (uri (cran-uri "RNifti" version))
10431 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10432 (properties `((upstream-name . "RNifti")))
10433 (build-system r-build-system)
10434 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10435 (home-page "https://github.com/jonclayden/RNifti")
10436 (synopsis "Fast R and C++ access to NIfTI images")
10438 "This package provides very fast read and write access to images stored
10439 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10440 compiled C and interpreted R code. It also provides a C/C++ API that can be
10441 used by other packages.")
10442 (license license:gpl2)))
10444 (define-public r-shades
10451 (uri (cran-uri "shades" version))
10454 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10455 (build-system r-build-system)
10456 (home-page "https://github.com/jonclayden/shades")
10457 (synopsis "Simple color manipulation")
10459 "This package provides functions for easily manipulating colors,
10460 creating color scales and calculating color distances.")
10461 (license license:bsd-3)))
10463 (define-public r-ore
10470 (uri (cran-uri "ore" version))
10472 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10473 (build-system r-build-system)
10474 (home-page "https://github.com/jonclayden/ore")
10475 (synopsis "R interface to the Onigmo regular expression library")
10477 "This package provides an alternative to R's built-in functionality for
10478 handling regular expressions, based on the Onigmo library. It offers
10479 first-class compiled regex objects, partial matching and function-based
10480 substitutions, amongst other features.")
10481 (license license:bsd-3)))
10483 (define-public r-reportr
10490 (uri (cran-uri "reportr" version))
10493 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10494 (build-system r-build-system)
10495 (propagated-inputs `(("r-ore" ,r-ore)))
10496 (home-page "https://github.com/jonclayden/reportr")
10497 (synopsis "General message and error reporting system")
10499 "This package provides a system for reporting messages, which offers
10500 certain useful features over the standard R system, such as the incorporation
10501 of output consolidation, message filtering, assertions, expression
10502 substitution, automatic generation of stack traces for debugging, and
10503 conditional reporting based on the current \"output level\".")
10504 (license license:gpl2)))
10506 (define-public r-tractor-base
10508 (name "r-tractor-base")
10513 (uri (cran-uri "tractor.base" version))
10516 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10517 (properties `((upstream-name . "tractor.base")))
10518 (build-system r-build-system)
10521 ("r-reportr" ,r-reportr)
10522 ("r-rnifti" ,r-rnifti)
10523 ("r-shades" ,r-shades)))
10524 (home-page "https://www.tractor-mri.org.uk")
10525 (synopsis "Read, manipulate and visualize magnetic resonance images")
10527 "This package provides functions for working with magnetic resonance
10528 images. It supports reading and writing of popular file formats (DICOM,
10529 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10530 visualization; flexible image manipulation; metadata and sparse image
10532 (license license:gpl2)))
10534 (define-public r-grimport
10536 (name "r-grimport")
10541 (uri (cran-uri "grImport" version))
10544 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10545 (properties `((upstream-name . "grImport")))
10546 (build-system r-build-system)
10548 `(("ghostscript" ,ghostscript)))
10550 `(("r-xml" ,r-xml)))
10551 (home-page "https://cran.r-project.org/web/packages/grImport")
10552 (synopsis "Convert, import, and draw PostScript pictures")
10554 "This package provides functions for converting, importing, and drawing
10555 PostScript pictures in R plots.")
10556 (license license:gpl2+)))
10558 (define-public r-grimport2
10560 (name "r-grimport2")
10565 (uri (cran-uri "grImport2" version))
10568 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10569 (properties `((upstream-name . "grImport2")))
10570 (build-system r-build-system)
10572 `(("r-base64enc" ,r-base64enc)
10576 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10577 (synopsis "Import SVG graphics")
10579 "This package provides functions for importing external vector images and
10580 drawing them as part of R plots. This package is different from the
10581 @code{grImport} package because, where that package imports PostScript format
10582 images, this package imports SVG format images. Furthermore, this package
10583 imports a specific subset of SVG, so external images must be preprocessed
10584 using a package like @code{rsvg} to produce SVG that this package can import.
10585 SVG features that are not supported by R graphics, such as gradient fills, can
10586 be imported and then exported via the @code{gridSVG} package.")
10587 (license license:gpl2+)))
10589 (define-public r-kohonen
10596 (uri (cran-uri "kohonen" version))
10599 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10600 (build-system r-build-system)
10602 `(("r-rcpp" ,r-rcpp)))
10603 (home-page "https://cran.r-project.org/web/packages/kohonen")
10604 (synopsis "Supervised and unsupervised self-organising maps")
10606 "This package provides functions to train @dfn{self-organising
10607 maps} (SOMs). Also interrogation of the maps and prediction using trained
10608 maps are supported. The name of the package refers to Teuvo Kohonen, the
10609 inventor of the SOM.")
10610 (license license:gpl2+)))
10612 (define-public r-nnls
10619 (uri (cran-uri "nnls" version))
10622 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10623 (build-system r-build-system)
10624 (native-inputs `(("gfortran" ,gfortran)))
10625 (home-page "https://cran.r-project.org/web/packages/nnls")
10626 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10628 "This package provides an R interface to the Lawson-Hanson implementation
10629 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10630 the combination of non-negative and non-positive constraints.")
10631 (license license:gpl2+)))
10633 (define-public r-iso
10640 (uri (cran-uri "Iso" version))
10643 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10644 (properties `((upstream-name . "Iso")))
10645 (build-system r-build-system)
10646 (native-inputs `(("gfortran" ,gfortran)))
10647 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10648 (synopsis "Functions to perform isotonic regression")
10650 "This package provides support for linear order and unimodal
10651 order (univariate) isotonic regression and bivariate isotonic regression with
10652 linear order on both variables.")
10653 (license license:gpl2+)))
10655 (define-public r-chemometricswithr
10657 (name "r-chemometricswithr")
10662 (uri (cran-uri "ChemometricsWithR" version))
10665 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10667 `((upstream-name . "ChemometricsWithR")))
10668 (build-system r-build-system)
10670 `(("r-devtools" ,r-devtools)
10671 ("r-kohonen" ,r-kohonen)
10674 (home-page "https://github.com/rwehrens/CWR")
10675 (synopsis "Chemometrics with R")
10677 "This package provides functions and scripts used in the book
10678 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10679 Life Sciences\" by Ron Wehrens, Springer (2011).")
10680 (license license:gpl2+)))
10682 (define-public r-als
10689 (uri (cran-uri "ALS" version))
10692 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10693 (properties `((upstream-name . "ALS")))
10694 (build-system r-build-system)
10697 ("r-nnls" ,r-nnls)))
10698 (home-page "https://cran.r-project.org/web/packages/ALS")
10699 (synopsis "Multivariate curve resolution alternating least squares")
10701 "Alternating least squares is often used to resolve components
10702 contributing to data with a bilinear structure; the basic technique may be
10703 extended to alternating constrained least squares. This package provides an
10704 implementation of @dfn{multivariate curve resolution alternating least
10705 squares} (MCR-ALS).
10707 Commonly applied constraints include unimodality, non-negativity, and
10708 normalization of components. Several data matrices may be decomposed
10709 simultaneously by assuming that one of the two matrices in the bilinear
10710 decomposition is shared between datasets.")
10711 (license license:gpl2+)))
10713 (define-public r-strucchange
10715 (name "r-strucchange")
10720 (uri (cran-uri "strucchange" version))
10723 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10724 (build-system r-build-system)
10726 `(("r-sandwich" ,r-sandwich)
10728 (home-page "https://cran.r-project.org/web/packages/strucchange")
10729 (synopsis "Testing, monitoring, and dating structural changes")
10731 "This package provides tools for testing, monitoring and dating
10732 structural changes in (linear) regression models. It features tests/methods
10733 from the generalized fluctuation test framework as well as from the F
10734 test (Chow test) framework. This includes methods to fit, plot and test
10735 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10736 statistics, respectively. It is possible to monitor incoming data online
10737 using fluctuation processes. Finally, the breakpoints in regression models
10738 with structural changes can be estimated together with confidence intervals.
10739 Emphasis is always given to methods for visualizing the data.")
10740 ;; Either of these two GPL versions
10741 (license (list license:gpl2 license:gpl3))))
10743 (define-public r-pixmap
10750 (uri (cran-uri "pixmap" version))
10753 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10754 (build-system r-build-system)
10755 (home-page "https://cran.r-project.org/web/packages/pixmap")
10756 (synopsis "Tools for bitmap images")
10758 "This package provides functions for importing, exporting, plotting and
10759 other manipulations of bitmapped images.")
10760 (license license:gpl2)))
10762 (define-public r-rapidjsonr
10764 (name "r-rapidjsonr")
10769 (uri (cran-uri "rapidjsonr" version))
10772 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
10773 (build-system r-build-system)
10774 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10775 (synopsis "JSON parser")
10777 "This package provides JSON parsing capability through the Rapidjson
10779 (license license:expat)))
10781 (define-public r-ontologyindex
10783 (name "r-ontologyindex")
10788 (uri (cran-uri "ontologyIndex" version))
10791 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10792 (properties `((upstream-name . "ontologyIndex")))
10793 (build-system r-build-system)
10794 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10795 (synopsis "Functions for processing ontologies in R")
10797 "This package provides functions for reading ontologies into R as lists
10798 and manipulating sets of ontological terms.")
10799 (license license:gpl2+)))
10801 (define-public r-gargle
10808 (uri (cran-uri "gargle" version))
10811 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10812 (build-system r-build-system)
10817 ("r-jsonlite" ,r-jsonlite)
10818 ("r-rlang" ,r-rlang)
10819 ("r-withr" ,r-withr)))
10820 (home-page "https://gargle.r-lib.org")
10821 (synopsis "Utilities for working with Google APIs")
10823 "This package provides utilities for working with Google APIs. This
10824 includes functions and classes for handling common credential types and for
10825 preparing, executing, and processing HTTP requests.")
10826 (license license:expat)))
10828 (define-public r-bigrquery
10830 (name "r-bigrquery")
10835 (uri (cran-uri "bigrquery" version))
10838 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10839 (build-system r-build-system)
10841 `(("r-assertthat" ,r-assertthat)
10842 ("r-bit64" ,r-bit64)
10845 ("r-gargle" ,r-gargle)
10848 ("r-jsonlite" ,r-jsonlite)
10849 ("r-prettyunits" ,r-prettyunits)
10850 ("r-progress" ,r-progress)
10851 ("r-rapidjsonr" ,r-rapidjsonr)
10853 ("r-rlang" ,r-rlang)
10854 ("r-tibble" ,r-tibble)))
10855 (home-page "https://github.com/rstats-db/bigrquery")
10856 (synopsis "R interface to Google's BigQuery API")
10858 "This package provides an R interface to Google's BigQuery database.")
10859 (license license:gpl3)))
10861 (define-public r-gmp
10864 (version "0.5-13.6")
10868 (uri (cran-uri "gmp" version))
10871 "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
10872 (build-system r-build-system)
10875 (modify-phases %standard-phases
10876 (add-after 'unpack 'set-CC
10877 (lambda _ (setenv "CC" "gcc") #t)))))
10878 (inputs `(("gmp" ,gmp)))
10879 (home-page "https://cran.r-project.org/web/packages/gmp")
10880 (synopsis "Multiple precision arithmetic")
10882 "This package supports multiple precision arithmetic (big integers and
10883 rationals, prime number tests, matrix computation), \"arithmetic without
10884 limitations\" using the GNU Multiple Precision library.")
10885 ;; Any version of the GPL.
10886 (license license:gpl3+)))
10888 (define-public r-rmpfr
10895 (uri (cran-uri "Rmpfr" version))
10898 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
10899 (properties `((upstream-name . "Rmpfr")))
10900 (build-system r-build-system)
10905 `(("r-gmp" ,r-gmp)))
10907 `(("pkg-config" ,pkg-config)))
10908 (home-page "http://rmpfr.r-forge.r-project.org/")
10909 (synopsis "R bindings to the MPFR library")
10911 "This package supports arithmetic (via S4 classes and methods) for
10912 arbitrary precision floating point numbers, including transcendental
10913 functions. To this end, the package interfaces with the @dfn{Multiple
10914 Precision Floating-Point Reliable} (MPFR) library.")
10915 (license license:gpl2+)))
10917 (define-public r-assertive-base
10919 (name "r-assertive-base")
10924 (uri (cran-uri "assertive.base" version))
10927 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10929 `((upstream-name . "assertive.base")))
10930 (build-system r-build-system)
10931 (home-page "https://bitbucket.org/richierocks/assertive.base")
10932 (synopsis "Core of the assertive package")
10934 "This package provides a minimal set of predicates and assertions used by
10935 the assertive package. This is mainly for use by other package developers who
10936 want to include run-time testing features in their own packages.")
10937 (license license:gpl3+)))
10939 (define-public r-assertive-properties
10941 (name "r-assertive-properties")
10946 (uri (cran-uri "assertive.properties" version))
10949 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10951 `((upstream-name . "assertive.properties")))
10952 (build-system r-build-system)
10954 `(("r-assertive-base" ,r-assertive-base)))
10955 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10956 (synopsis "Assertions to check properties of variables")
10958 "This package provides a set of predicates and assertions for checking
10959 the properties of variables, such as length, names and attributes. This is
10960 mainly for use by other package developers who want to include run-time
10961 testing features in their own packages.")
10962 (license license:gpl3+)))
10964 (define-public r-assertive-numbers
10966 (name "r-assertive-numbers")
10971 (uri (cran-uri "assertive.numbers" version))
10974 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10976 `((upstream-name . "assertive.numbers")))
10977 (build-system r-build-system)
10979 `(("r-assertive-base" ,r-assertive-base)))
10980 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10981 (synopsis "Assertions to check properties of numbers")
10983 "This package provides a set of predicates and assertions for checking
10984 the properties of numbers. This is mainly for use by other package developers
10985 who want to include run-time testing features in their own packages.")
10986 (license license:gpl3+)))
10988 (define-public r-assertive-sets
10990 (name "r-assertive-sets")
10995 (uri (cran-uri "assertive.sets" version))
10998 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11000 `((upstream-name . "assertive.sets")))
11001 (build-system r-build-system)
11003 `(("r-assertive-base" ,r-assertive-base)))
11004 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11005 (synopsis "Assertions to check properties of sets")
11007 "This package provides a set of predicates and assertions for checking
11008 the properties of sets. This is mainly for use by other package developers
11009 who want to include run-time testing features in their own packages.")
11010 (license license:gpl3+)))
11012 (define-public r-assertive-matrices
11014 (name "r-assertive-matrices")
11019 (uri (cran-uri "assertive.matrices" version))
11022 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11024 `((upstream-name . "assertive.matrices")))
11025 (build-system r-build-system)
11027 `(("r-assertive-base" ,r-assertive-base)))
11028 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11029 (synopsis "Assertions to check properties of matrices")
11031 "This package provides a set of predicates and assertions for checking
11032 the properties of matrices. This is mainly for use by other package
11033 developers who want to include run-time testing features in their own
11035 (license license:gpl3+)))
11037 (define-public r-assertive-models
11039 (name "r-assertive-models")
11044 (uri (cran-uri "assertive.models" version))
11047 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11049 `((upstream-name . "assertive.models")))
11050 (build-system r-build-system)
11052 `(("r-assertive-base" ,r-assertive-base)))
11053 (home-page "https://bitbucket.org/richierocks/assertive.models")
11054 (synopsis "Assertions to check properties of models")
11056 "This package provides a set of predicates and assertions for checking
11057 the properties of models. This is mainly for use by other package developers
11058 who want to include run-time testing features in their own packages.")
11059 (license license:gpl3+)))
11061 (define-public r-assertive-reflection
11063 (name "r-assertive-reflection")
11068 (uri (cran-uri "assertive.reflection" version))
11071 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11073 `((upstream-name . "assertive.reflection")))
11074 (build-system r-build-system)
11076 `(("r-assertive-base" ,r-assertive-base)))
11077 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11078 (synopsis "Assertions for checking the state of R")
11080 "This package provides a set of predicates and assertions for checking
11081 the state and capabilities of R, the operating system it is running on, and
11082 the IDE being used. This is mainly for use by other package developers who
11083 want to include run-time testing features in their own packages.")
11084 (license license:gpl3+)))
11086 (define-public r-assertive-types
11088 (name "r-assertive-types")
11093 (uri (cran-uri "assertive.types" version))
11096 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11098 `((upstream-name . "assertive.types")))
11099 (build-system r-build-system)
11101 `(("r-assertive-base" ,r-assertive-base)
11102 ("r-assertive-properties" ,r-assertive-properties)
11103 ("r-codetools" ,r-codetools)))
11104 (home-page "https://bitbucket.org/richierocks/assertive.types")
11105 (synopsis "Assertions to check types of variables")
11107 "This package provides a set of predicates and assertions for checking
11108 the types of variables. This is mainly for use by other package developers
11109 who want to include run-time testing features in their own packages.")
11110 (license license:gpl3+)))
11112 (define-public r-assertive-files
11114 (name "r-assertive-files")
11119 (uri (cran-uri "assertive.files" version))
11122 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11124 `((upstream-name . "assertive.files")))
11125 (build-system r-build-system)
11127 `(("r-assertive-base" ,r-assertive-base)
11128 ("r-assertive-numbers" ,r-assertive-numbers)))
11129 (home-page "https://bitbucket.org/richierocks/assertive.files")
11130 (synopsis "Assertions to check properties of files")
11132 "This package provides a set of predicates and assertions for checking
11133 the properties of files and connections. This is mainly for use by other
11134 package developers who want to include run-time testing features in their own
11136 (license license:gpl3+)))
11138 (define-public r-assertive-code
11140 (name "r-assertive-code")
11145 (uri (cran-uri "assertive.code" version))
11148 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11150 `((upstream-name . "assertive.code")))
11151 (build-system r-build-system)
11153 `(("r-assertive-base" ,r-assertive-base)
11154 ("r-assertive-properties" ,r-assertive-properties)
11155 ("r-assertive-types" ,r-assertive-types)))
11156 (home-page "https://bitbucket.org/richierocks/assertive.code")
11157 (synopsis "Assertions to check properties of code")
11159 "This package provides a set of predicates and assertions for checking
11160 the properties of code. This is mainly for use by other package developers
11161 who want to include run-time testing features in their own packages.")
11162 (license license:gpl3+)))
11164 (define-public r-assertive-datetimes
11166 (name "r-assertive-datetimes")
11171 (uri (cran-uri "assertive.datetimes" version))
11174 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11176 `((upstream-name . "assertive.datetimes")))
11177 (build-system r-build-system)
11179 `(("r-assertive-base" ,r-assertive-base)
11180 ("r-assertive-types" ,r-assertive-types)))
11181 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11182 (synopsis "Assertions to check properties of dates and times")
11184 "This package provides a set of predicates and assertions for checking
11185 the properties of dates and times. This is mainly for use by other package
11186 developers who want to include run-time testing features in their own
11188 (license license:gpl3+)))
11190 (define-public r-assertive-strings
11192 (name "r-assertive-strings")
11197 (uri (cran-uri "assertive.strings" version))
11200 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11202 `((upstream-name . "assertive.strings")))
11203 (build-system r-build-system)
11205 `(("r-assertive-base" ,r-assertive-base)
11206 ("r-assertive-types" ,r-assertive-types)
11207 ("r-stringi" ,r-stringi)))
11208 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11209 (synopsis "Assertions to check properties of strings")
11211 "This package provides a set of predicates and assertions for checking
11212 the properties of strings. This is mainly for use by other package developers
11213 who want to include run-time testing features in their own packages.")
11214 (license license:gpl3+)))
11216 (define-public r-assertive-data-us
11218 (name "r-assertive-data-us")
11223 (uri (cran-uri "assertive.data.us" version))
11226 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11228 `((upstream-name . "assertive.data.us")))
11229 (build-system r-build-system)
11231 `(("r-assertive-base" ,r-assertive-base)
11232 ("r-assertive-strings" ,r-assertive-strings)))
11233 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11234 (synopsis "Assertions to check properties of strings")
11236 "This package provides a set of predicates and assertions for checking
11237 the properties of US-specific complex data types. This is mainly for use by
11238 other package developers who want to include run-time testing features in
11239 their own packages.")
11240 (license license:gpl3+)))
11242 (define-public r-assertive-data-uk
11244 (name "r-assertive-data-uk")
11249 (uri (cran-uri "assertive.data.uk" version))
11252 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11254 `((upstream-name . "assertive.data.uk")))
11255 (build-system r-build-system)
11257 `(("r-assertive-base" ,r-assertive-base)
11258 ("r-assertive-strings" ,r-assertive-strings)))
11259 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11260 (synopsis "Assertions to check properties of strings")
11262 "This package provides a set of predicates and assertions for checking
11263 the properties of UK-specific complex data types. This is mainly for use by
11264 other package developers who want to include run-time testing features in
11265 their own packages.")
11266 (license license:gpl3+)))
11268 (define-public r-assertive-data
11270 (name "r-assertive-data")
11275 (uri (cran-uri "assertive.data" version))
11278 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11280 `((upstream-name . "assertive.data")))
11281 (build-system r-build-system)
11283 `(("r-assertive-base" ,r-assertive-base)
11284 ("r-assertive-strings" ,r-assertive-strings)))
11285 (home-page "https://bitbucket.org/richierocks/assertive.data")
11286 (synopsis "Assertions to check properties of data")
11288 "This package provides a set of predicates and assertions for checking
11289 the properties of (country independent) complex data types. This is mainly
11290 for use by other package developers who want to include run-time testing
11291 features in their own packages.")
11292 (license license:gpl3+)))
11294 (define-public r-assertive
11296 (name "r-assertive")
11301 (uri (cran-uri "assertive" version))
11304 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11305 (build-system r-build-system)
11307 `(("r-assertive-base" ,r-assertive-base)
11308 ("r-assertive-code" ,r-assertive-code)
11309 ("r-assertive-data" ,r-assertive-data)
11310 ("r-assertive-data-uk" ,r-assertive-data-uk)
11311 ("r-assertive-data-us" ,r-assertive-data-us)
11312 ("r-assertive-datetimes" ,r-assertive-datetimes)
11313 ("r-assertive-files" ,r-assertive-files)
11314 ("r-assertive-matrices" ,r-assertive-matrices)
11315 ("r-assertive-models" ,r-assertive-models)
11316 ("r-assertive-numbers" ,r-assertive-numbers)
11317 ("r-assertive-properties" ,r-assertive-properties)
11318 ("r-assertive-reflection" ,r-assertive-reflection)
11319 ("r-assertive-sets" ,r-assertive-sets)
11320 ("r-assertive-strings" ,r-assertive-strings)
11321 ("r-assertive-types" ,r-assertive-types)
11322 ("r-knitr" ,r-knitr)))
11323 (home-page "https://bitbucket.org/richierocks/assertive")
11324 (synopsis "Readable check functions to ensure code integrity")
11326 "This package provides lots of predicates (@code{is_*} functions) to
11327 check the state of your variables, and assertions (@code{assert_*} functions)
11328 to throw errors if they aren't in the right form.")
11329 (license license:gpl3+)))
11331 (define-public r-dotcall64
11333 (name "r-dotcall64")
11338 (uri (cran-uri "dotCall64" version))
11341 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11342 (properties `((upstream-name . "dotCall64")))
11343 (build-system r-build-system)
11344 (native-inputs `(("gfortran" ,gfortran)))
11345 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11346 (synopsis "Enhanced foreign function interface supporting long vectors")
11348 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11349 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11350 supports long vectors, arguments of type 64-bit integer, and provides a
11351 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11352 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11353 (license license:gpl2+)))
11355 (define-public r-spam
11362 (uri (cran-uri "spam" version))
11364 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11365 (build-system r-build-system)
11367 `(("r-dotcall64" ,r-dotcall64)))
11368 (native-inputs `(("gfortran" ,gfortran)))
11369 (home-page "https://www.math.uzh.ch/pages/spam/")
11370 (synopsis "Sparse matrix algebra")
11372 "This package provides a set of functions for sparse matrix algebra.
11373 Differences with other sparse matrix packages are:
11376 @item it only supports (essentially) one sparse matrix format;
11377 @item it is based on transparent and simple structure(s);
11378 @item it is tailored for MCMC calculations within G(M)RF;
11379 @item and it is fast and scalable (with the extension package @code{spam64}).
11381 ;; Either of these licenses
11382 (license (list license:bsd-3 license:lgpl2.0))))
11384 (define-public r-fields
11391 (uri (cran-uri "fields" version))
11393 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11394 (build-system r-build-system)
11396 `(("r-maps" ,r-maps)
11397 ("r-spam" ,r-spam)))
11399 `(("gfortran" ,gfortran)))
11400 (home-page "https://www.image.ucar.edu/fields")
11401 (synopsis "Tools for spatial data")
11403 "This is a package for curve, surface and function fitting with an
11404 emphasis on splines, spatial data and spatial statistics. The major methods
11405 include cubic, and thin plate splines, Kriging, and compactly supported
11406 covariance functions for large data sets.")
11407 (license license:gpl2+)))
11409 (define-public r-spatialextremes
11411 (name "r-spatialextremes")
11416 (uri (cran-uri "SpatialExtremes" version))
11419 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11421 `((upstream-name . "SpatialExtremes")))
11422 (build-system r-build-system)
11424 `(("r-fields" ,r-fields)
11425 ("r-maps" ,r-maps)))
11426 (home-page "http://spatialextremes.r-forge.r-project.org/")
11427 (synopsis "Modelling spatial extremes")
11429 "This package provides tools for the statistical modelling of spatial
11430 extremes using max-stable processes, copula or Bayesian hierarchical models.
11431 More precisely, this package allows (conditional) simulations from various
11432 parametric max-stable models, analysis of the extremal spatial dependence, the
11433 fitting of such processes using composite likelihoods or least square (simple
11434 max-stable processes only), model checking and selection and prediction.")
11435 (license license:gpl2+)))
11437 (define-public r-drc
11444 (uri (cran-uri "drc" version))
11447 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11448 (build-system r-build-system)
11451 ("r-gtools" ,r-gtools)
11453 ("r-multcomp" ,r-multcomp)
11454 ("r-plotrix" ,r-plotrix)
11455 ("r-scales" ,r-scales)))
11456 (home-page "https://cran.r-project.org/web/packages/drc")
11457 (synopsis "Analysis of dose-response curves")
11459 "This package provides a suite of flexible and versatile model fitting
11460 and after-fitting functions for the analysis of dose-response data.")
11461 (license license:gpl2+)))
11463 (define-public r-rmeta
11470 (uri (cran-uri "rmeta" version))
11473 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11474 (build-system r-build-system)
11475 (home-page "https://cran.r-project.org/web/packages/rmeta")
11476 (synopsis "Tools for meta-analysis")
11478 "This package provides functions for simple fixed and random effects
11479 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11480 draws standard summary plots, funnel plots, and computes summaries and tests
11481 for association and heterogeneity.")
11482 (license license:gpl2)))
11484 (define-public r-bootstrap
11486 (name "r-bootstrap")
11491 (uri (cran-uri "bootstrap" version))
11494 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11495 (build-system r-build-system)
11496 (native-inputs `(("gfortran" ,gfortran)))
11497 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11498 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11500 "This package provides software and data for the book \"An Introduction
11501 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11502 This package is primarily provided for projects already based on it, and for
11503 support of the book. New projects should preferentially use the recommended
11504 package \"boot\".")
11505 (license license:bsd-3)))
11507 (define-public r-survivalroc
11509 (name "r-survivalroc")
11514 (uri (cran-uri "survivalROC" version))
11517 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11518 (properties `((upstream-name . "survivalROC")))
11519 (build-system r-build-system)
11520 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11521 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11523 "Compute time-dependent ROC curve from censored survival data using
11524 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11525 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11526 (license license:gpl2+)))
11528 (define-public r-longitudinal
11530 (name "r-longitudinal")
11535 (uri (cran-uri "longitudinal" version))
11538 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11539 (build-system r-build-system)
11540 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11541 (home-page "http://strimmerlab.org/software/longitudinal/")
11542 (synopsis "Analysis of multiple time course data")
11544 "This package contains general data structures and functions for
11545 longitudinal data with multiple variables, repeated measurements, and
11546 irregularly spaced time points. It also implements a shrinkage estimator of
11547 dynamical correlation and dynamical covariance.")
11548 (license license:gpl3+)))
11550 (define-public r-genenet
11557 (uri (cran-uri "GeneNet" version))
11560 "0cdhrj15rz0w0pyw3r8mikrzsdh95y5i1c0pa3cn0c2bjnjx3x3n"))))
11561 (properties `((upstream-name . "GeneNet")))
11562 (build-system r-build-system)
11564 `(("r-corpcor" ,r-corpcor)
11565 ("r-fdrtool" ,r-fdrtool)
11566 ("r-longitudinal" ,r-longitudinal)))
11567 (home-page "http://strimmerlab.org/software/genenet/")
11568 (synopsis "Modeling and inferring gene networks")
11570 "This package analyzes gene expression (time series) data with focus on
11571 the inference of gene networks. In particular, GeneNet implements the methods
11572 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11573 for learning large-scale gene association networks (including assignment of
11574 putative directions).")
11575 (license license:gpl3+)))
11577 (define-public r-rbamtools
11579 (name "r-rbamtools")
11580 (version "2.16.17")
11584 (uri (cran-uri "rbamtools" version))
11587 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11588 (build-system r-build-system)
11589 (inputs `(("zlib" ,zlib)))
11591 `(("r-refgenome" ,r-refgenome)))
11592 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11593 (synopsis "Read and write BAM (binary alignment) files")
11595 "This package provides an R interface to functions of the SAMtools
11597 (license license:artistic2.0)))
11599 (define-public r-protviz
11606 (uri (cran-uri "protViz" version))
11609 "1qq9bf4485x8cviry9fmhnv4hw9aw657w134003myzcv42c4pml6"))))
11610 (properties `((upstream-name . "protViz")))
11611 (build-system r-build-system)
11612 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11613 (home-page "https://github.com/protViz/protViz/")
11614 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11616 "This package helps with quality checks, visualizations and analysis of
11617 mass spectrometry data, coming from proteomics experiments. The package is
11618 developed, tested and used at the Functional Genomics Center Zurich, where it
11619 is used mainly for prototyping, teaching, and having fun with proteomics data.
11620 But it can also be used to do data analysis for small scale data sets.")
11621 (license license:gpl3)))
11623 (define-public r-cmprsk
11630 (uri (cran-uri "cmprsk" version))
11632 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11633 (build-system r-build-system)
11635 `(("r-survival" ,r-survival)))
11637 `(("gfortran" ,gfortran)))
11638 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11639 (synopsis "Subdistribution analysis of competing risks")
11641 "This package provides tool for estimation, testing and regression
11642 modeling of subdistribution functions in competing risks, as described in
11643 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11644 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11645 A proportional hazards model for the subdistribution of a competing risk,
11646 JASA, 94:496-509.")
11647 (license license:gpl2+)))
11649 (define-public r-etm
11656 (uri (cran-uri "etm" version))
11659 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
11660 (build-system r-build-system)
11662 `(("r-data-table" ,r-data-table)
11663 ("r-lattice" ,r-lattice)
11665 ("r-rcpparmadillo" ,r-rcpparmadillo)
11666 ("r-survival" ,r-survival)))
11667 (home-page "https://cran.r-project.org/web/packages/etm")
11668 (synopsis "Empirical transition matrix")
11670 "The @dfn{empirical transition matrix} (etm) package estimates
11671 the matrix of transition probabilities for any time-inhomogeneous multistate
11672 model with finite state space using the Aalen-Johansen estimator.")
11673 (license license:expat)))
11675 (define-public r-epi
11682 (uri (cran-uri "Epi" version))
11685 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11686 (properties `((upstream-name . "Epi")))
11687 (build-system r-build-system)
11689 `(("r-cmprsk" ,r-cmprsk)
11690 ("r-data-table" ,r-data-table)
11693 ("r-matrix" ,r-matrix)
11695 ("r-numderiv" ,r-numderiv)
11697 ("r-survival" ,r-survival)
11699 (home-page "https://BendixCarstensen.com/Epi/")
11700 (synopsis "Statistical analysis in epidemiology")
11702 "This package provides functions for demographic and epidemiological
11703 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11704 particular representation, manipulation and simulation of multistate data -
11705 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11706 @code{etm} and @code{cmprsk} packages. It also contains functions for
11707 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11708 data and some useful functions for tabulation and plotting, as well as a
11709 number of epidemiological data sets.")
11710 (license license:gpl2)))
11712 (define-public r-ppls
11715 (version "1.6-1.1")
11719 (uri (cran-uri "ppls" version))
11722 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11723 (build-system r-build-system)
11724 (propagated-inputs `(("r-mass" ,r-mass)))
11725 (home-page "https://cran.r-project.org/web/packages/ppls")
11726 (synopsis "Penalized partial least squares")
11728 "This package contains linear and nonlinear regression methods based on
11729 partial least squares and penalization techniques. Model parameters are
11730 selected via cross-validation, and confidence intervals ans tests for the
11731 regression coefficients can be conducted via jackknifing.")
11732 (license license:gpl2+)))
11734 (define-public r-huge
11737 (version "1.3.4.1")
11741 (uri (cran-uri "huge" version))
11743 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
11744 (build-system r-build-system)
11746 `(("r-igraph" ,r-igraph)
11748 ("r-matrix" ,r-matrix)
11750 ("r-rcppeigen" ,r-rcppeigen)))
11751 (home-page "https://cran.r-project.org/web/packages/huge")
11752 (synopsis "High-dimensional undirected graph estimation")
11754 "This package provides a general framework for high-dimensional
11755 undirected graph estimation. It integrates data preprocessing, neighborhood
11756 screening, graph estimation, and model selection techniques into a pipeline.")
11757 (license license:gpl2)))
11759 (define-public r-parcor
11766 (uri (cran-uri "parcor" version))
11769 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11770 (build-system r-build-system)
11773 ("r-genenet" ,r-genenet)
11774 ("r-glmnet" ,r-glmnet)
11776 ("r-ppls" ,r-ppls)))
11777 (home-page "https://cran.r-project.org/web/packages/parcor")
11778 (synopsis "Regularized estimation of partial correlation matrices")
11780 "This package estimates the matrix of partial correlations based on
11781 different regularized regression methods: lasso, adaptive lasso, PLS, and
11782 Ridge Regression. In addition, the package provides model selection for
11783 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11784 (license license:gpl2+)))
11786 (define-public r-mcmc
11793 (uri (cran-uri "mcmc" version))
11796 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
11797 (build-system r-build-system)
11798 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
11799 (synopsis "Markov chain Monte Carlo")
11801 "This package simulates continuous distributions of random vectors using
11802 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11803 function that evaluates the log unnormalized density. Algorithms are random
11804 walk Metropolis algorithm (function @code{metrop}), simulated
11805 tempering (function @code{temper}), and morphometric random walk
11806 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11807 by change of variable.")
11808 (license license:expat)))
11810 (define-public r-listenv
11817 (uri (cran-uri "listenv" version))
11820 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11821 (build-system r-build-system)
11823 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11824 (home-page "https://github.com/HenrikBengtsson/listenv")
11825 (synopsis "Environments behaving (almost) as lists")
11827 "This package implements list environments. List environments are
11828 environments that have list-like properties. For instance, the elements of a
11829 list environment are ordered and can be accessed and iterated over using index
11831 (license license:lgpl2.1+)))
11833 (define-public r-globals
11840 (uri (cran-uri "globals" version))
11843 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11844 (build-system r-build-system)
11846 `(("r-codetools" ,r-codetools)))
11847 (home-page "https://github.com/HenrikBengtsson/globals")
11848 (synopsis "Identify global objects in R expressions")
11850 "This package provides tools to identify global (\"unknown\" or \"free\")
11851 objects in R expressions by code inspection using various strategies, e.g.
11852 conservative or liberal. The objective of this package is to make it as
11853 simple as possible to identify global objects for the purpose of exporting
11854 them in distributed compute environments.")
11855 (license license:lgpl2.1+)))
11857 (define-public r-future
11864 (uri (cran-uri "future" version))
11867 "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
11868 (build-system r-build-system)
11870 `(("r-digest" ,r-digest)
11871 ("r-globals" ,r-globals)
11872 ("r-listenv" ,r-listenv)))
11874 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11875 (home-page "https://github.com/HenrikBengtsson/future")
11876 (synopsis "Unified parallel and distributed processing in R")
11878 "The purpose of this package is to provide a lightweight and unified
11879 Future API for sequential and parallel processing of R expression via futures.
11880 This package implements sequential, multicore, multisession, and cluster
11881 futures. With these, R expressions can be evaluated on the local machine, in
11882 parallel a set of local machines, or distributed on a mix of local and remote
11883 machines. Extensions to this package implement additional backends for
11884 processing futures via compute cluster schedulers etc. Because of its unified
11885 API, there is no need to modify any code in order to switch from sequential on
11886 the local machine to, say, distributed processing on a remote compute cluster.")
11887 (license license:lgpl2.1+)))
11889 (define-public r-future-apply
11891 (name "r-future-apply")
11896 (uri (cran-uri "future.apply" version))
11899 "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
11900 (properties `((upstream-name . "future.apply")))
11901 (build-system r-build-system)
11903 `(("r-future" ,r-future)
11904 ("r-globals" ,r-globals)))
11906 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11907 (home-page "https://github.com/HenrikBengtsson/future.apply")
11908 (synopsis "Apply function to elements in parallel using futures")
11910 "This package provides implementations of @code{apply()},
11911 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11912 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11913 can be resolved using any future-supported backend, e.g. parallel on the local
11914 machine or distributed on a compute cluster.")
11915 (license license:gpl2+)))
11917 (define-public r-rsvd
11924 (uri (cran-uri "rsvd" version))
11927 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
11928 (build-system r-build-system)
11930 `(("r-matrix" ,r-matrix)))
11931 (home-page "https://github.com/erichson/rSVD")
11932 (synopsis "Randomized singular value decomposition")
11934 "Low-rank matrix decompositions are fundamental tools and widely used for
11935 data analysis, dimension reduction, and data compression. Classically, highly
11936 accurate deterministic matrix algorithms are used for this task. However, the
11937 emergence of large-scale data has severely challenged our computational
11938 ability to analyze big data. The concept of randomness has been demonstrated
11939 as an effective strategy to quickly produce approximate answers to familiar
11940 problems such as the @dfn{singular value decomposition} (SVD). This package
11941 provides several randomized matrix algorithms such as the randomized singular
11942 value decomposition (@code{rsvd}), randomized principal component
11943 analysis (@code{rpca}), randomized robust principal component
11944 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11945 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11946 functions are provided.")
11947 (license license:gpl3+)))
11949 (define-public r-sloop
11956 (uri (cran-uri "sloop" version))
11959 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11960 (build-system r-build-system)
11962 `(("r-codetools" ,r-codetools)
11963 ("r-crayon" ,r-crayon)
11964 ("r-purrr" ,r-purrr)
11965 ("r-rlang" ,r-rlang)
11966 ("r-tibble" ,r-tibble)))
11967 (home-page "https://github.com/r-lib/sloop")
11968 (synopsis "Helpers for object-oriented programming in R")
11970 "This package provides a collection of helper functions designed to
11971 help you to better understand object oriented programming in R, particularly
11973 (license license:gpl3)))
11975 (define-public r-capushe
11982 (uri (cran-uri "capushe" version))
11985 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11986 (build-system r-build-system)
11987 (propagated-inputs `(("r-mass" ,r-mass)))
11988 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11989 (synopsis "Calibrating penalties using slope heuristics")
11991 "This package provides tools for the calibration of penalized criteria
11992 for model selection. The calibration methods available are based on the slope
11994 (license license:gpl2+)))
11996 (define-public r-dorng
12003 (uri (cran-uri "doRNG" version))
12006 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12007 (properties `((upstream-name . "doRNG")))
12008 (build-system r-build-system)
12010 `(("r-foreach" ,r-foreach)
12011 ("r-iterators" ,r-iterators)
12012 ("r-rngtools" ,r-rngtools)))
12013 (home-page "https://renozao.github.io/doRNG/")
12014 (synopsis "Generic reproducible parallel backend for foreach loops")
12016 "This package provides functions to perform reproducible parallel
12017 @code{foreach} loops, using independent random streams as generated by
12018 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12019 convert standard @code{%dopar%} loops into fully reproducible loops,
12020 independently of the number of workers, the task scheduling strategy, or the
12021 chosen parallel environment and associated foreach backend.")
12022 (license license:gpl2+)))
12024 (define-public r-blockmodeling
12026 (name "r-blockmodeling")
12031 (uri (cran-uri "blockmodeling" version))
12034 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
12035 (build-system r-build-system)
12037 `(("r-matrix" ,r-matrix)))
12038 (native-inputs `(("gfortran" ,gfortran)))
12039 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12040 (synopsis "Generalized and classical blockmodeling of valued networks")
12042 "This package is primarily meant as an implementation of generalized
12043 blockmodeling for valued networks. In addition, measures of similarity or
12044 dissimilarity based on structural equivalence and regular equivalence (REGE
12045 algorithms) can be computed and partitioned matrices can be plotted.")
12046 (license license:gpl2+)))
12048 (define-public r-upsetr
12055 (uri (cran-uri "UpSetR" version))
12058 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12059 (properties `((upstream-name . "UpSetR")))
12060 (build-system r-build-system)
12062 `(("r-ggplot2" ,r-ggplot2)
12063 ("r-gridextra" ,r-gridextra)
12065 ("r-scales" ,r-scales)))
12066 (home-page "https://github.com/hms-dbmi/UpSetR")
12067 (synopsis "Visualize intersecting sets")
12069 "This package provides a more scalable alternative to Venn and Euler
12070 diagrams for visualizing intersecting sets. Create visualizations of
12071 intersecting sets using a novel matrix design, along with visualizations of
12072 several common set, element and attribute related tasks.")
12073 (license license:expat)))
12075 ;; This package includes a JavaScript file, which is not minified. When
12076 ;; upgrading please check that there are no new minified JavaScript files.
12077 (define-public r-shinybs
12084 (uri (cran-uri "shinyBS" version))
12087 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12088 (properties `((upstream-name . "shinyBS")))
12089 (build-system r-build-system)
12090 ;; The tests spawn Shiny browser apps. They cannot be run
12091 ;; non-interactively.
12092 (arguments '(#:tests? #f))
12094 `(("r-htmltools" ,r-htmltools)
12095 ("r-shiny" ,r-shiny)))
12096 (home-page "https://ebailey78.github.io/shinyBS/")
12097 (synopsis "Twitter Bootstrap components for Shiny")
12099 "This package adds additional Twitter Bootstrap components to Shiny.")
12100 (license license:gpl3)))
12102 (define-public r-outliers
12104 (name "r-outliers")
12109 (uri (cran-uri "outliers" version))
12112 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12113 (build-system r-build-system)
12114 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12115 (synopsis "Tests for outliers")
12117 "This package provides a collection of some tests commonly used for
12118 identifying outliers.")
12119 (license license:gpl2+)))
12121 (define-public r-bayesm
12128 (uri (cran-uri "bayesm" version))
12130 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12131 (build-system r-build-system)
12133 `(("r-rcpp" ,r-rcpp)
12134 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12135 (home-page "http://www.perossi.org/home/bsm-1")
12136 (synopsis "Bayesian inference for marketing/micro-econometrics")
12138 "This package covers many important models used in marketing and
12139 micro-econometrics applications, including Bayes Regression (univariate or
12140 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12141 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12142 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12143 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12144 Estimation with normal base, Hierarchical Linear Models with normal prior and
12145 covariates, Hierarchical Linear Models with a mixture of normals prior and
12146 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12147 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12148 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12149 analysis of choice-based conjoint data, Bayesian treatment of linear
12150 instrumental variables models, Analysis of Multivariate Ordinal survey data
12151 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12152 Coefficient Logit Models.")
12153 (license license:gpl2+)))
12155 (define-public r-tensora
12162 (uri (cran-uri "tensorA" version))
12165 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12166 (properties `((upstream-name . "tensorA")))
12167 (build-system r-build-system)
12168 (home-page "http://www.stat.boogaart.de/tensorA")
12169 (synopsis "Advanced tensor arithmetic with named indices")
12171 "This package provides convenience functions for advanced linear algebra
12172 with tensors and computation with datasets of tensors on a higher level
12173 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12174 co- and contravariate indices, and parallel computations on sequences of
12176 (license license:gpl2+)))
12178 (define-public r-rarpack
12185 (uri (cran-uri "rARPACK" version))
12188 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12189 (properties `((upstream-name . "rARPACK")))
12190 (build-system r-build-system)
12191 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12192 (home-page "https://github.com/yixuan/rARPACK")
12193 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12195 "This package was previously an R wrapper of the ARPACK library, and now
12196 a shell of the R package RSpectra, an R interface to the Spectra library for
12197 solving large scale eigenvalue/vector problems. The current version of
12198 rARPACK simply imports and exports the functions provided by RSpectra. New
12199 users of rARPACK are advised to switch to the RSpectra package.")
12200 (license license:bsd-3)))
12202 (define-public r-compositions
12204 (name "r-compositions")
12209 (uri (cran-uri "compositions" version))
12212 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12213 (build-system r-build-system)
12215 `(("r-bayesm" ,r-bayesm)
12216 ("r-robustbase" ,r-robustbase)
12217 ("r-tensora" ,r-tensora)))
12218 (home-page "http://www.stat.boogaart.de/compositions")
12219 (synopsis "Compositional data analysis")
12221 "This package provides functions for the consistent analysis of
12222 compositional data (e.g. portions of substances) and positive
12223 numbers (e.g. concentrations).")
12224 (license license:gpl2+)))
12226 (define-public r-cobs
12233 (uri (cran-uri "cobs" version))
12236 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12237 (build-system r-build-system)
12239 `(("r-quantreg" ,r-quantreg)
12240 ("r-sparsem" ,r-sparsem)))
12241 (home-page "https://cran.r-project.org/web/packages/cobs")
12242 (synopsis "Constrained B-Splines (sparse matrix based)")
12244 "This package provides qualitatively constrained (regression) smoothing
12245 splines via linear programming and sparse matrices.")
12246 (license license:gpl2+)))
12248 (define-public r-drimpute
12250 (name "r-drimpute")
12255 (uri (cran-uri "DrImpute" version))
12258 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12259 (properties `((upstream-name . "DrImpute")))
12260 (build-system r-build-system)
12262 `(("r-rcpp" ,r-rcpp)
12263 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12264 (home-page "https://github.com/ikwak2/DrImpute")
12265 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12267 "This is an R package for imputing dropout events. Many statistical
12268 methods in cell type identification, visualization and lineage reconstruction
12269 do not account for dropout events. DrImpute can improve the performance of
12270 such software by imputing dropout events.")
12271 (license license:gpl3)))
12273 (define-public r-gamlss-dist
12275 (name "r-gamlss-dist")
12280 (uri (cran-uri "gamlss.dist" version))
12282 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12283 (properties `((upstream-name . "gamlss.dist")))
12284 (build-system r-build-system)
12285 (propagated-inputs `(("r-mass" ,r-mass)))
12286 (home-page "http://www.gamlss.org/")
12287 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12289 "This package provides a set of distributions which can be used for
12290 modelling the response variables in Generalized Additive Models for Location
12291 Scale and Shape. The distributions can be continuous, discrete or mixed
12292 distributions. Extra distributions can be created, by transforming, any
12293 continuous distribution defined on the real line, to a distribution defined on
12294 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12295 transformation, respectively.")
12296 ;; Either version of the GPL.
12297 (license (list license:gpl2 license:gpl3))))
12299 ;; This package includes JavaScript files, which are not minified. When
12300 ;; upgrading please check that there are no new minified JavaScript files.
12301 (define-public r-shinyjs
12308 (uri (cran-uri "shinyjs" version))
12311 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12312 (build-system r-build-system)
12314 `(("r-digest" ,r-digest)
12315 ("r-htmltools" ,r-htmltools)
12316 ("r-jsonlite" ,r-jsonlite)
12317 ("r-shiny" ,r-shiny)))
12318 (home-page "https://deanattali.com/shinyjs")
12319 (synopsis "Improve the user experience of your Shiny apps")
12321 "Perform common useful JavaScript operations in Shiny apps that will
12322 greatly improve your apps without having to know any JavaScript. Examples
12323 include: hiding an element, disabling an input, resetting an input back to its
12324 original value, delaying code execution by a few seconds, and many more useful
12325 functions for both the end user and the developer. Shinyjs can also be used
12326 to easily call your own custom JavaScript functions from R.")
12327 (license license:agpl3+)))
12329 ;; This package includes minified JavaScript files. When upgrading please
12330 ;; check that there are no new minified JavaScript files.
12331 (define-public r-colourpicker
12333 (name "r-colourpicker")
12338 (uri (cran-uri "colourpicker" version))
12341 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12342 (build-system r-build-system)
12344 `(#:modules ((guix build utils)
12345 (guix build r-build-system)
12349 (modify-phases %standard-phases
12350 (add-after 'unpack 'process-javascript
12351 (lambda* (#:key inputs #:allow-other-keys)
12352 (with-directory-excursion "inst"
12356 `((,(assoc-ref inputs "js-salvattore")
12357 "examples/colourInput/www/salvattore.min.js")
12358 (,(assoc-ref inputs "js-jquery")
12359 "htmlwidgets/lib/jquery/jquery.min.js")
12360 ("www/shared/colourpicker/js/colourpicker.js"
12361 "www/shared/colourpicker/js/colourpicker.min.js"))))
12362 (lambda (sources targets)
12363 (for-each (lambda (source target)
12364 (format #t "Processing ~a --> ~a~%"
12366 (delete-file target)
12367 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12368 (call-with-output-file target
12370 (dump-port minified port)))))
12371 sources targets))))
12374 `(("r-ggplot2" ,r-ggplot2)
12375 ("r-htmltools" ,r-htmltools)
12376 ("r-htmlwidgets" ,r-htmlwidgets)
12377 ("r-jsonlite" ,r-jsonlite)
12378 ("r-miniui" ,r-miniui)
12379 ("r-shiny" ,r-shiny)
12380 ("r-shinyjs" ,r-shinyjs)))
12382 `(("uglify-js" ,uglify-js)
12386 (uri "https://code.jquery.com/jquery-3.3.1.js")
12389 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12393 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12396 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12397 (home-page "https://github.com/daattali/colourpicker")
12398 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12400 "This package provides a color picker that can be used as an input in
12401 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12402 custom color palettes, and many more options. A plot color helper tool is
12403 available as an RStudio Addin, which helps you pick colors to use in your
12404 plots. A more generic color picker RStudio Addin is also provided to let you
12405 select colors to use in your R code.")
12406 (license license:expat)))
12408 (define-public r-ggextra
12415 (uri (cran-uri "ggExtra" version))
12418 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12419 (properties `((upstream-name . "ggExtra")))
12420 (build-system r-build-system)
12422 `(("r-colourpicker" ,r-colourpicker)
12423 ("r-ggplot2" ,r-ggplot2)
12424 ("r-gtable" ,r-gtable)
12425 ("r-miniui" ,r-miniui)
12427 ("r-scales" ,r-scales)
12428 ("r-shiny" ,r-shiny)
12429 ("r-shinyjs" ,r-shinyjs)))
12431 `(("r-knitr" ,r-knitr)))
12432 (home-page "https://github.com/daattali/ggExtra")
12433 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12435 "This package is a collection of functions and layers to enhance ggplot2.
12436 The flagship function is @code{ggMarginal()}, which can be used to add
12437 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12438 (license license:expat)))
12440 (define-public r-minpack-lm
12442 (name "r-minpack-lm")
12447 (uri (cran-uri "minpack.lm" version))
12450 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12451 (properties `((upstream-name . "minpack.lm")))
12452 (build-system r-build-system)
12453 (native-inputs `(("gfortran" ,gfortran)))
12454 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12455 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12457 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12458 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12459 problems by a modification of the Levenberg-Marquardt algorithm, with support
12460 for lower and upper parameter bounds. The implementation can be used via
12461 @code{nls}-like calls using the @code{nlsLM} function.")
12462 (license license:gpl3)))
12464 (define-public r-moments
12471 (uri (cran-uri "moments" version))
12474 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12475 (build-system r-build-system)
12476 (home-page "https://cran.r-project.org/web/packages/moments")
12477 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12479 "This package provides functions to calculate: moments, Pearson's
12480 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12481 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12482 (license license:gpl2+)))
12484 (define-public r-msir
12491 (uri (cran-uri "msir" version))
12494 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12495 (build-system r-build-system)
12497 `(("r-mclust" ,r-mclust)))
12498 (home-page "https://cran.r-project.org/web/packages/msir")
12499 (synopsis "Model-based sliced inverse regression")
12501 "This is an R package for dimension reduction based on finite Gaussian
12502 mixture modeling of inverse regression.")
12503 (license license:gpl2+)))
12505 (define-public r-pbivnorm
12507 (name "r-pbivnorm")
12512 (uri (cran-uri "pbivnorm" version))
12515 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12516 (build-system r-build-system)
12517 (native-inputs `(("gfortran" ,gfortran)))
12518 (home-page "https://github.com/brentonk/pbivnorm")
12519 (synopsis "Vectorized bivariate normal CDF")
12521 "This package provides a vectorized R function for calculating
12522 probabilities from a standard bivariate normal CDF.")
12523 (license license:gpl2+)))
12525 (define-public r-lavaan
12532 (uri (cran-uri "lavaan" version))
12535 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12536 (build-system r-build-system)
12538 `(("r-mass" ,r-mass)
12539 ("r-mnormt" ,r-mnormt)
12540 ("r-numderiv" ,r-numderiv)
12541 ("r-pbivnorm" ,r-pbivnorm)))
12542 (home-page "http://lavaan.ugent.be")
12543 (synopsis "Latent variable analysis")
12545 "This package provides tools to fit a variety of latent variable models,
12546 including confirmatory factor analysis, structural equation modeling and
12547 latent growth curve models.")
12548 (license license:gpl2+)))
12550 (define-public r-nonnest2
12552 (name "r-nonnest2")
12557 (uri (cran-uri "nonnest2" version))
12560 "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
12561 (build-system r-build-system)
12563 `(("r-compquadform" ,r-compquadform)
12564 ("r-lavaan" ,r-lavaan)
12565 ("r-mvtnorm" ,r-mvtnorm)
12566 ("r-sandwich" ,r-sandwich)))
12568 `(("r-knitr" ,r-knitr)))
12569 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12570 (synopsis "Tests of non-nested models")
12572 "This package allows for testing of non-nested models. It includes tests
12573 of model distinguishability and of model fit that can be applied to both
12574 nested and non-nested models. The package also includes functionality to
12575 obtain confidence intervals associated with AIC and BIC.")
12576 ;; Either version of the GPL.
12577 (license (list license:gpl2 license:gpl3))))
12579 (define-public r-penalized
12581 (name "r-penalized")
12586 (uri (cran-uri "penalized" version))
12589 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12590 (build-system r-build-system)
12592 `(("r-rcpp" ,r-rcpp)
12593 ("r-rcpparmadillo" ,r-rcpparmadillo)
12594 ("r-survival" ,r-survival)))
12595 (home-page "https://cran.r-project.org/web/packages/penalized/")
12596 (synopsis "Penalized estimation in GLMs and in the Cox model")
12598 "This package provides tools for fitting possibly high dimensional
12599 penalized regression models. The penalty structure can be any combination of
12600 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12601 constraint on the regression coefficients. The supported regression models
12602 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12603 model. Cross-validation routines allow optimization of the tuning
12605 (license license:gpl2+)))
12607 (define-public r-zim
12614 (uri (cran-uri "ZIM" version))
12617 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12618 (properties `((upstream-name . "ZIM")))
12619 (build-system r-build-system)
12620 (propagated-inputs `(("r-mass" ,r-mass)))
12621 (home-page "https://github.com/biostatstudio/ZIM")
12622 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12624 "Analyze count time series with excess zeros. Two types of statistical
12625 models are supported: Markov regression and state-space models. They are also
12626 known as observation-driven and parameter-driven models respectively in the
12627 time series literature. The functions used for Markov regression or
12628 observation-driven models can also be used to fit ordinary regression models
12629 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12630 negative binomial (ZINB) assumption. The package also contains miscellaneous
12631 functions to compute density, distribution, quantile, and generate random
12632 numbers from ZIP and ZINB distributions.")
12633 (license license:gpl3)))
12635 (define-public r-nor1mix
12642 (uri (cran-uri "nor1mix" version))
12645 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12646 (build-system r-build-system)
12647 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12648 (synopsis "Normal (1-d) mixture models")
12650 "This package provides S3 classes and methods for one-dimensional normal
12651 mixture models, for, e.g., density estimation or clustering algorithms
12652 research and teaching; it provides the widely used Marron-Wand densities. It
12653 also provides tools for efficient random number generation and graphics.")
12654 (license license:gpl2+)))
12656 (define-public r-beanplot
12658 (name "r-beanplot")
12663 (uri (cran-uri "beanplot" version))
12666 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12667 (build-system r-build-system)
12668 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12669 (synopsis "Visualization via beanplots")
12671 "This package provides beanplots, an alternative to
12672 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12674 (license license:gpl2)))
12676 (define-public r-pbdzmq
12683 (uri (cran-uri "pbdZMQ" version))
12686 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12687 (properties `((upstream-name . "pbdZMQ")))
12688 (build-system r-build-system)
12690 `(("zeromq" ,zeromq)
12693 `(("pkg-config" ,pkg-config)))
12694 (home-page "https://pbdr.org/")
12695 (synopsis "R interface to ZeroMQ")
12697 "ZeroMQ is a well-known library for high-performance asynchronous
12698 messaging in scalable, distributed applications. This package provides high
12699 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12700 interactive client/server programming frameworks. A few wrapper functions
12701 compatible with @code{rzmq} are also provided.")
12702 (license license:gpl3)))
12704 (define-public r-repr
12711 (uri (cran-uri "repr" version))
12714 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
12715 (build-system r-build-system)
12717 `(("r-base64enc" ,r-base64enc)
12718 ("r-htmltools" ,r-htmltools)
12719 ("r-jsonlite" ,r-jsonlite)
12720 ("r-pillar" ,r-pillar)))
12721 (home-page "https://cran.r-project.org/web/packages/repr/")
12722 (synopsis "Serializable representations")
12724 "This package provides string and binary representations of objects for
12725 several formats and MIME types.")
12726 (license license:gpl3)))
12728 (define-public r-irdisplay
12730 (name "r-irdisplay")
12735 (uri (cran-uri "IRdisplay" version))
12738 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12739 (properties `((upstream-name . "IRdisplay")))
12740 (build-system r-build-system)
12742 `(("r-repr" ,r-repr)))
12743 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12744 (synopsis "Jupyter display machinery")
12746 "This package provides an interface to the rich display capabilities of
12747 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12748 running IRkernel session.")
12749 (license license:expat)))
12751 (define-public r-irkernel
12753 (name "r-irkernel")
12758 (uri (cran-uri "IRkernel" version))
12761 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12762 (properties `((upstream-name . "IRkernel")))
12763 (build-system r-build-system)
12766 (modify-phases %standard-phases
12767 (add-after 'install 'install-kernelspec
12768 (lambda* (#:key outputs #:allow-other-keys)
12769 (let ((out (assoc-ref outputs "out")))
12770 (setenv "HOME" "/tmp")
12771 (invoke "jupyter" "kernelspec" "install"
12774 (string-append out "/site-library/IRkernel/kernelspec"))
12775 ;; Record the absolute file name of the 'R' executable in
12777 (substitute* (string-append out "/share/jupyter"
12778 "/kernels/ir/kernel.json")
12780 (string-append "[\"" (which "R") "\",")))
12783 `(("jupyter" ,jupyter)))
12785 `(("r-crayon" ,r-crayon)
12786 ("r-digest" ,r-digest)
12787 ("r-evaluate" ,r-evaluate)
12788 ("r-irdisplay" ,r-irdisplay)
12789 ("r-jsonlite" ,r-jsonlite)
12790 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12791 ("r-minimal" ,r-minimal)
12792 ("r-pbdzmq" ,r-pbdzmq)
12794 ("r-uuid" ,r-uuid)))
12795 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12796 (synopsis "Native R kernel for Jupyter")
12798 "The R kernel for the Jupyter environment executes R code which the
12799 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12801 (license license:expat)))
12803 (define-public r-gmodels
12810 (uri (cran-uri "gmodels" version))
12813 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12814 (build-system r-build-system)
12816 `(("r-gdata" ,r-gdata)
12817 ("r-mass" ,r-mass)))
12818 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12819 (synopsis "Various R programming tools for model fitting")
12821 "This package provides various R programming tools for model fitting.")
12822 (license license:gpl2)))
12824 (define-public r-apcluster
12826 (name "r-apcluster")
12831 (uri (cran-uri "apcluster" version))
12834 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12835 (build-system r-build-system)
12837 `(("r-matrix" ,r-matrix)
12838 ("r-rcpp" ,r-rcpp)))
12839 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12840 (synopsis "Affinity propagation clustering")
12842 "This package implements affinity propagation clustering introduced by
12843 Frey and Dueck (2007). The package further provides leveraged affinity
12844 propagation and an algorithm for exemplar-based agglomerative clustering that
12845 can also be used to join clusters obtained from affinity propagation. Various
12846 plotting functions are available for analyzing clustering results.")
12847 (license license:gpl2+)))
12849 (define-public r-valr
12856 (uri (cran-uri "valr" version))
12859 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12860 (build-system r-build-system)
12862 `(("r-broom" ,r-broom)
12863 ("r-dplyr" ,r-dplyr)
12864 ("r-ggplot2" ,r-ggplot2)
12866 ("r-readr" ,r-readr)
12867 ("r-rlang" ,r-rlang)
12868 ("r-stringr" ,r-stringr)
12869 ("r-tibble" ,r-tibble)))
12870 (home-page "http://github.com/rnabioco/valr")
12871 (synopsis "Genome interval arithmetic in R")
12873 "This package enables you to read and manipulate genome intervals and
12874 signals. It provides functionality similar to command-line tool suites within
12875 R, enabling interactive analysis and visualization of genome-scale data.")
12876 (license license:expat)))
12878 (define-public r-rematch2
12880 (name "r-rematch2")
12885 (uri (cran-uri "rematch2" version))
12888 "13siaa8s2ji9q6hykhb2r34ag76335ypmbqr90xaqilbir0klhnh"))))
12889 (build-system r-build-system)
12891 `(("r-tibble" ,r-tibble)))
12892 (home-page "https://github.com/r-lib/rematch2")
12893 (synopsis "Tidy output from regular expression matching")
12895 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12896 return the match results in tidy data frames.")
12897 (license license:expat)))
12899 (define-public r-picante
12906 (uri (cran-uri "picante" version))
12909 "1b16zm8zjjsl181b8krkdcrbcw347kf772c4w7y5332qmfi7jhz0"))))
12910 (build-system r-build-system)
12914 ("r-vegan" ,r-vegan)))
12915 (home-page "https://cran.r-project.org/web/packages/picante/")
12916 (synopsis "Integrating phylogenies and ecology")
12918 "This package provides functions for phylocom integration, community
12919 analyses, null-models, traits and evolution. It implements numerous
12920 ecophylogenetic approaches including measures of community phylogenetic and
12921 trait diversity, phylogenetic signal, estimation of trait values for
12922 unobserved taxa, null models for community and phylogeny randomizations, and
12923 utility functions for data input/output and phylogeny plotting. A full
12924 description of package functionality and methods are provided by Kembel et
12926 (license license:gpl2)))
12928 (define-public r-reinforcelearn
12930 (name "r-reinforcelearn")
12935 (uri (cran-uri "reinforcelearn" version))
12938 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12939 (build-system r-build-system)
12941 `(("r-checkmate" ,r-checkmate)
12943 ("r-purrr" ,r-purrr)
12945 (home-page "https://markusdumke.github.io/reinforcelearn")
12946 (synopsis "Reinforcement learning")
12948 "This package implements reinforcement learning environments and
12949 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12950 can be used with function approximation, eligibility traces (Singh & Sutton,
12951 1996) and experience replay (Mnih et al., 2013).")
12952 (license license:expat)))
12954 (define-public r-lemon
12961 (uri (cran-uri "lemon" version))
12964 "0m9hqwi709j9iwsxn8jh63741jiyr7ppwgqaw2zkv285p3m5wvd5"))))
12965 (build-system r-build-system)
12967 `(("r-ggplot2" ,r-ggplot2)
12968 ("r-gridextra" ,r-gridextra)
12969 ("r-gtable" ,r-gtable)
12970 ("r-knitr" ,r-knitr)
12971 ("r-lattice" ,r-lattice)
12973 ("r-rlang" ,r-rlang)
12974 ("r-scales" ,r-scales)))
12975 (home-page "https://github.com/stefanedwards/lemon")
12976 (synopsis "Freshen up your ggplot2 plots")
12978 "This package provides functions for working with legends and axis lines
12979 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12981 (license license:gpl3)))
12983 (define-public r-wgaim
12990 (uri (cran-uri "wgaim" version))
12992 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12993 (build-system r-build-system)
12995 `(("r-ggplot2" ,r-ggplot2)
12997 (home-page "https://cran.r-project.org/web/packages/wgaim")
12998 (synopsis "Whole genome average interval mapping for QTL detection")
13000 "This package integrates sophisticated mixed modelling methods with a
13001 whole genome approach to detecting significant QTL in linkage maps.")
13002 (license license:gpl2+)))
13004 (define-public r-bedr
13011 (uri (cran-uri "bedr" version))
13014 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13015 (build-system r-build-system)
13017 `(("r-data-table" ,r-data-table)
13018 ("r-r-utils" ,r-r-utils)
13019 ("r-testthat" ,r-testthat)
13020 ("r-venndiagram" ,r-venndiagram)
13023 ("bedtools" ,bedtools)
13024 ("htslib" ,htslib))) ; for tabix
13026 `(("r-knitr" ,r-knitr))) ; for vignettes
13027 (home-page "https://cran.r-project.org/web/packages/bedr")
13028 (synopsis "Genomic region processing")
13030 "This package is for genomic regions processing using command line tools
13031 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13032 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13033 The bedr package's API enhances access to these tools as well as offers
13034 additional utilities for genomic regions processing.")
13035 (license license:gpl2)))
13037 (define-public r-sets
13044 (uri (cran-uri "sets" version))
13047 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13048 (properties `((upstream-name . "sets")))
13049 (build-system r-build-system)
13050 (home-page "https://cran.r-project.org/web/packages/sets")
13051 (synopsis "Sets, generalized sets, customizable sets and intervals")
13053 "This package provides data structures and basic operations for ordinary
13054 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13055 customizable sets, and intervals.")
13056 (license license:gpl2)))
13058 (define-public r-partitions
13060 (name "r-partitions")
13065 (uri (cran-uri "partitions" version))
13068 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13069 (build-system r-build-system)
13072 ("r-polynom" ,r-polynom)
13073 ("r-sets" ,r-sets)))
13074 (home-page "https://cran.r-project.org/web/packages/partitions")
13075 (synopsis "Additive partitions of integers")
13077 "This package provides tools to enumerates the partitions, unequal
13078 partitions, and restricted partitions of an integer; the three corresponding
13079 partition functions are also given.")
13080 ;; Any version of the GPL
13081 (license license:gpl2+)))
13083 (define-public r-brobdingnag
13085 (name "r-brobdingnag")
13090 (uri (cran-uri "Brobdingnag" version))
13093 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13094 (properties `((upstream-name . "Brobdingnag")))
13095 (build-system r-build-system)
13096 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13097 (synopsis "Very large numbers in R")
13099 "This package handles very large numbers in R. Real numbers are held
13100 using their natural logarithms, plus a logical flag indicating sign. The
13101 package includes a vignette that gives a step-by-step introduction to using S4
13103 ;; Any version of the GPL
13104 (license license:gpl2+)))
13106 (define-public r-untb
13113 (uri (cran-uri "untb" version))
13116 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13117 (build-system r-build-system)
13119 `(("r-brobdingnag" ,r-brobdingnag)
13120 ("r-partitions" ,r-partitions)
13121 ("r-polynom" ,r-polynom)))
13122 (home-page "https://github.com/RobinHankin/untb.git")
13123 (synopsis "Ecological drift under the UNTB")
13125 "This package provides numerical simulations, and visualizations, of
13126 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13127 (license license:gpl2+)))
13129 (define-public r-stepwise
13131 (name "r-stepwise")
13136 (uri (cran-uri "stepwise" version))
13139 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13140 (build-system r-build-system)
13141 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13142 (synopsis "Stepwise detection of recombination breakpoints")
13144 "This package provides a stepwise approach to identifying recombination
13145 breakpoints in a genomic sequence alignment.")
13146 (license license:gpl2+)))
13148 (define-public r-snpmaxsel
13150 (name "r-snpmaxsel")
13155 (uri (cran-uri "SNPmaxsel" version))
13158 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13159 (properties `((upstream-name . "SNPmaxsel")))
13160 (build-system r-build-system)
13162 `(("r-combinat" ,r-combinat)
13163 ("r-mvtnorm" ,r-mvtnorm)))
13164 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13165 (synopsis "Maximally selected statistics for SNP data")
13167 "This package implements asymptotic methods related to maximally selected
13168 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13170 (license license:gpl2+)))
13172 (define-public r-acsnminer
13174 (name "r-acsnminer")
13175 (version "0.16.8.25")
13178 (uri (cran-uri "ACSNMineR" version))
13181 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13182 (properties `((upstream-name . "ACSNMineR")))
13183 (build-system r-build-system)
13185 `(("r-ggplot2" ,r-ggplot2)
13186 ("r-gridextra" ,r-gridextra)))
13187 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13188 (synopsis "Gene enrichment analysis")
13190 "This package provides tools to compute and represent gene set enrichment
13191 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13192 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13193 enrichment can be run with hypergeometric test or Fisher exact test, and can
13194 use multiple corrections. Visualization of data can be done either by
13195 barplots or heatmaps.")
13196 (license license:gpl2+)))
13198 (define-public r-seqinr
13205 (uri (cran-uri "seqinr" version))
13208 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13209 (build-system r-build-system)
13211 `(("r-ade4" ,r-ade4)
13212 ("r-segmented" ,r-segmented)))
13215 (home-page "http://seqinr.r-forge.r-project.org/")
13216 (synopsis "Biological sequences retrieval and analysis")
13218 "This package provides tools for exploratory data analysis and data
13219 visualization of biological sequence (DNA and protein) data. It also includes
13220 utilities for sequence data management under the ACNUC system.")
13221 (license license:gpl2+)))
13223 (define-public r-units
13230 (uri (cran-uri "units" version))
13233 "11x6xz1fbml28xmrhgn4sii9vfyj3gyfc1dfxahdg9cszdmcgdnh"))))
13234 (build-system r-build-system)
13236 `(("udunits" ,udunits)))
13238 `(("r-rcpp" ,r-rcpp)))
13240 `(("r-knitr" ,r-knitr)))
13241 (home-page "https://github.com/r-quantities/units/")
13242 (synopsis "Measurement Units for R Vectors")
13244 "This package provides support for measurement units in R vectors,
13245 matrices and arrays: automatic propagation, conversion, derivation and
13246 simplification of units; raising errors in case of unit incompatibility. It
13247 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13249 (license license:gpl2)))
13251 (define-public r-classint
13253 (name "r-classint")
13258 (uri (cran-uri "classInt" version))
13261 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13262 (properties `((upstream-name . "classInt")))
13263 (build-system r-build-system)
13265 `(("r-class" ,r-class)
13266 ("r-e1071" ,r-e1071)
13267 ("r-kernsmooth" ,r-kernsmooth)))
13269 `(("gfortran" ,gfortran)
13270 ("r-knitr" ,r-knitr)))
13271 (home-page "https://github.com/r-spatial/classInt/")
13272 (synopsis "Choose univariate class intervals")
13274 "This package provides selected commonly used methods for choosing
13275 univariate class intervals for mapping or other graphics purposes.")
13276 (license license:gpl2+)))
13278 (define-public r-spdata
13285 (uri (cran-uri "spData" version))
13288 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13289 (properties `((upstream-name . "spData")))
13290 (build-system r-build-system)
13292 `(("r-raster" ,r-raster)
13294 (home-page "https://github.com/Nowosad/spData")
13295 (synopsis "Datasets for spatial analysis")
13297 "This a package containing diverse spatial datasets for demonstrating,
13298 benchmarking and teaching spatial data analysis. It includes R data of class
13299 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13300 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13301 of the datasets are designed to illustrate specific analysis techniques.
13302 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13303 illustrate point pattern analysis techniques.")
13304 (license license:cc0)))
13306 (define-public r-learnbayes
13308 (name "r-learnbayes")
13313 (uri (cran-uri "LearnBayes" version))
13316 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13317 (properties `((upstream-name . "LearnBayes")))
13318 (build-system r-build-system)
13319 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13320 (synopsis "Functions for learning Bayesian inference")
13322 "This package provides a collection of functions helpful in learning the
13323 basic tenets of Bayesian statistical inference. It contains functions for
13324 summarizing basic one and two parameter posterior distributions and predictive
13325 distributions. It contains MCMC algorithms for summarizing posterior
13326 distributions defined by the user. It also contains functions for regression
13327 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13329 (license license:gpl2+)))
13331 (define-public r-deldir
13338 (uri (cran-uri "deldir" version))
13341 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13342 (build-system r-build-system)
13343 (native-inputs `(("gfortran" ,gfortran)))
13344 (home-page "https://cran.r-project.org/web/packages/deldir")
13345 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13347 "This package provides tools for calculating the Delaunay triangulation
13348 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13349 of a planar point set. It plots triangulations and tessellations in various
13350 ways, clips tessellations to sub-windows, calculates perimeters of
13351 tessellations, and summarizes information about the tiles of the
13353 (license license:gpl2+)))
13355 (define-public r-sf
13362 (uri (cran-uri "sf" version))
13365 "01xplgy5nlwy3ajfch4h1ssa1xhm7q0jzscpz04dmvgqfzwhhdfh"))))
13366 (build-system r-build-system)
13373 `(("r-classint" ,r-classint)
13375 ("r-magrittr" ,r-magrittr)
13377 ("r-units" ,r-units)))
13379 `(("pkg-config" ,pkg-config)
13380 ("r-knitr" ,r-knitr)))
13381 (home-page "https://github.com/r-spatial/sf/")
13382 (synopsis "Simple features for R")
13384 "This package provides support for simple features, a standardized way to
13385 encode spatial vector data. It binds to GDAL for reading and writing data, to
13386 GEOS for geometrical operations, and to PROJ for projection conversions and
13387 datum transformations.")
13388 ;; Either of these licenses
13389 (license (list license:gpl2 license:expat))))
13391 (define-public r-spdep
13398 (uri (cran-uri "spdep" version))
13401 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13402 (build-system r-build-system)
13404 `(("r-boot" ,r-boot)
13406 ("r-deldir" ,r-deldir)
13408 ("r-gmodels" ,r-gmodels)
13409 ("r-learnbayes" ,r-learnbayes)
13411 ("r-matrix" ,r-matrix)
13415 ("r-spdata" ,r-spdata)))
13416 (home-page "https://github.com/r-spatial/spdep/")
13417 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13419 "This package provides a collection of functions to create spatial
13420 weights matrix objects from polygon contiguities, from point patterns by
13421 distance and tessellations, for summarizing these objects, and for permitting
13422 their use in spatial data analysis, including regional aggregation by minimum
13424 (license license:gpl2+)))
13426 (define-public r-adegenet
13428 (name "r-adegenet")
13433 (uri (cran-uri "adegenet" version))
13436 "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
13437 (build-system r-build-system)
13439 `(("r-ade4" ,r-ade4)
13442 ("r-dplyr" ,r-dplyr)
13443 ("r-ggplot2" ,r-ggplot2)
13444 ("r-igraph" ,r-igraph)
13446 ("r-reshape2" ,r-reshape2)
13447 ("r-seqinr" ,r-seqinr)
13448 ("r-shiny" ,r-shiny)
13449 ("r-spdep" ,r-spdep)
13450 ("r-vegan" ,r-vegan)))
13451 (home-page "https://github.com/thibautjombart/adegenet")
13452 (synopsis "Exploratory analysis of genetic and genomic data")
13454 "This package provides a toolset for the exploration of genetic and
13455 genomic data. Adegenet provides formal (S4) classes for storing and handling
13456 various genetic data, including genetic markers with varying ploidy and
13457 hierarchical population structure (@code{genind} class), alleles counts by
13458 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13459 also implements original multivariate methods (DAPC, sPCA), graphics,
13460 statistical tests, simulation tools, distance and similarity measures, and
13461 several spatial methods. A range of both empirical and simulated datasets is
13462 also provided to illustrate various methods.")
13463 (license license:gpl2+)))
13465 (define-public r-pegas
13472 (uri (cran-uri "pegas" version))
13474 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13475 (build-system r-build-system)
13477 `(("r-adegenet" ,r-adegenet)
13479 (home-page "http://ape-package.ird.fr/pegas.html")
13480 (synopsis "Population and evolutionary genetics analysis system")
13482 "This package provides functions for reading, writing, plotting,
13483 analysing, and manipulating allelic and haplotypic data, including from VCF
13484 files, and for the analysis of population nucleotide sequences and
13485 micro-satellites including coalescent analyses, linkage disequilibrium,
13486 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13487 minimum spanning tree and network, and median-joining networks.")
13488 (license license:gpl2+)))
13490 (define-public r-rmetasim
13492 (name "r-rmetasim")
13497 (uri (cran-uri "rmetasim" version))
13500 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13501 (build-system r-build-system)
13503 `(("r-ade4" ,r-ade4)
13504 ("r-adegenet" ,r-adegenet)
13505 ("r-gtools" ,r-gtools)
13506 ("r-pegas" ,r-pegas)))
13507 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13508 (synopsis "Individual-based population genetic simulation environment")
13510 "This package provides an interface between R and the metasim simulation
13511 engine. The simulation environment is documented in: Strand, A.(2002),
13512 Metasim 1.0: an individual-based environment for simulating population
13513 genetics of complex population dynamics.")
13515 (license license:gpl2+)))
13517 (define-public r-genetics
13519 (name "r-genetics")
13520 (version "1.3.8.1.2")
13524 (uri (cran-uri "genetics" version))
13527 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13528 (build-system r-build-system)
13530 `(("r-combinat" ,r-combinat)
13531 ("r-gdata" ,r-gdata)
13532 ("r-gtools" ,r-gtools)
13534 ("r-mvtnorm" ,r-mvtnorm)))
13535 (home-page "https://cran.r-project.org/web/packages/genetics/")
13536 (synopsis "Population genetics")
13538 "This package provides classes and methods for handling genetic data.
13539 It includes classes to represent genotypes and haplotypes at single markers up
13540 to multiple markers on multiple chromosomes. Function include allele
13541 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13542 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13543 and testing for linkage disequilibrium, ...")
13544 ;; Any GPL version.
13545 (license license:gpl2+)))
13547 (define-public r-snp-plotter
13549 (name "r-snp-plotter")
13554 (uri (cran-uri "snp.plotter" version))
13557 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13558 (properties `((upstream-name . "snp.plotter")))
13559 (build-system r-build-system)
13560 (propagated-inputs `(("r-genetics" ,r-genetics)))
13561 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13562 (synopsis "Plot p-values using single SNP and/or haplotype data")
13564 "This package helps you create plots of p-values using single SNP and/or
13565 haplotype data. Main features of the package include options to display a
13566 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13567 datasets simultaneously. Plots can be created using global and/or individual
13568 haplotype p-values along with single SNP p-values. Images are created as
13569 either PDF/EPS files.")
13570 (license license:gpl2+)))
13572 (define-public r-polspline
13574 (name "r-polspline")
13579 (uri (cran-uri "polspline" version))
13581 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13582 (build-system r-build-system)
13583 (native-inputs `(("gfortran" ,gfortran)))
13584 (home-page "https://cran.r-project.org/web/packages/polspline/")
13585 (synopsis "Polynomial spline routines")
13587 "This package provides routines for the polynomial spline fitting
13588 routines hazard regression, hazard estimation with flexible tails, logspline,
13589 lspec, polyclass, and polymars.")
13590 (license license:gpl2+)))
13592 (define-public r-rms
13599 (uri (cran-uri "rms" version))
13601 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13602 (build-system r-build-system)
13604 `(("r-ggplot2" ,r-ggplot2)
13605 ("r-hmisc" ,r-hmisc)
13606 ("r-htmltable" ,r-htmltable)
13607 ("r-htmltools" ,r-htmltools)
13608 ("r-lattice" ,r-lattice)
13609 ("r-multcomp" ,r-multcomp)
13611 ("r-polspline" ,r-polspline)
13612 ("r-quantreg" ,r-quantreg)
13613 ("r-rpart" ,r-rpart)
13614 ("r-sparsem" ,r-sparsem)
13615 ("r-survival" ,r-survival)))
13616 (native-inputs `(("gfortran" ,gfortran)))
13617 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13618 (synopsis "Regression modeling strategies")
13620 "This is a package for regression modeling, testing, estimation,
13621 validation, graphics, prediction, and typesetting by storing enhanced model
13622 design attributes in the fit. The rms package is a collection of functions
13623 that assist with and streamline modeling. It also contains functions for
13624 binary and ordinal logistic regression models, ordinal models for continuous Y
13625 with a variety of distribution families, and the Buckley-James multiple
13626 regression model for right-censored responses, and implements penalized
13627 maximum likelihood estimation for logistic and ordinary linear models. The
13628 package works with almost any regression model, but it was especially written
13629 to work with binary or ordinal regression models, Cox regression, accelerated
13630 failure time models, ordinary linear models, the Buckley-James model,
13631 generalized least squares for serially or spatially correlated observations,
13632 generalized linear models, and quantile regression.")
13633 (license license:gpl2+)))
13635 (define-public r-haplo-stats
13637 (name "r-haplo-stats")
13642 (uri (cran-uri "haplo.stats" version))
13645 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13646 (properties `((upstream-name . "haplo.stats")))
13647 (build-system r-build-system)
13649 `(("r-rms" ,r-rms)))
13651 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13652 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13653 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13655 "This package provides routines for the analysis of indirectly measured
13656 haplotypes. The statistical methods assume that all subjects are unrelated
13657 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13658 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13659 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13660 examples in the vignette.")
13661 (license license:gpl2+)))
13663 (define-public r-bqtl
13670 (uri (cran-uri "bqtl" version))
13673 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13674 (build-system r-build-system)
13675 (native-inputs `(("gfortran" ,gfortran)))
13676 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13677 (synopsis "Bayesian QTL mapping toolkit")
13679 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13680 lines. It includes maximum likelihood and Bayesian tools.")
13681 (license license:gpl2+)))
13683 (define-public r-ibdreg
13690 (uri (cran-uri "ibdreg" version))
13693 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13694 (build-system r-build-system)
13695 (home-page "https://www.mayo.edu/research/labs/\
13696 statistical-genetics-genetic-epidemiology/software")
13697 (synopsis "Regression methods for IBD linkage with covariates")
13699 "This package provides a method to test genetic linkage with covariates
13700 by regression methods with response IBD sharing for relative pairs. Account
13701 for correlations of IBD statistics and covariates for relative pairs within
13702 the same pedigree.")
13703 (license license:gpl2+)))
13705 (define-public r-dlmap
13712 (uri (cran-uri "dlmap" version))
13715 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13716 (build-system r-build-system)
13718 `(("r-ibdreg" ,r-ibdreg)
13722 ("r-wgaim" ,r-wgaim)))
13723 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13724 (synopsis "Detection localization mapping for QTL")
13726 "This is package for QTL mapping in a mixed model framework with separate
13727 detection and localization stages. The first stage detects the number of QTL
13728 on each chromosome based on the genetic variation due to grouped markers on
13729 the chromosome; the second stage uses this information to determine the most
13730 likely QTL positions. The mixed model can accommodate general fixed and
13731 random effects, including spatial effects in field trials and pedigree
13732 effects. It is applicable to backcrosses, doubled haploids, recombinant
13733 inbred lines, F2 intercrosses, and association mapping populations.")
13734 (license license:gpl2)))
13736 (define-public r-ldheatmap
13738 (name "r-ldheatmap")
13743 (uri (cran-uri "LDheatmap" version))
13746 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13747 (properties `((upstream-name . "LDheatmap")))
13748 (build-system r-build-system)
13750 `(("r-genetics" ,r-genetics)
13752 ("r-snpstats" ,r-snpstats)))
13753 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
13754 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13756 "This package provides tools to produce a graphical display, as a heat
13757 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13758 optionally include the physical locations or genetic map distances of each SNP
13760 (license license:gpl3)))
13762 (define-public r-hwde
13769 (uri (cran-uri "hwde" version))
13772 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13773 (build-system r-build-system)
13774 (home-page "https://cran.r-project.org/web/packages/hwde/")
13775 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13777 "This package fits models for genotypic disequilibria, as described in
13778 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13779 terms are available that account for first order interactions between loci.
13780 It also implements, for a single locus in a single population, a conditional
13781 exact test for Hardy-Weinberg equilibrium.")
13782 (license license:gpl2+)))
13784 (define-public r-tdthap
13791 (uri (cran-uri "tdthap" version))
13794 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13795 (build-system r-build-system)
13796 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13797 (synopsis "TDT tests for extended haplotypes")
13799 "Functions and examples are provided for transmission/disequilibrium
13800 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13801 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13802 (license license:artistic2.0)))
13804 (define-public r-sparql
13810 (uri (cran-uri "SPARQL" version))
13813 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13814 (properties `((upstream-name . "SPARQL")))
13815 (build-system r-build-system)
13817 `(("r-rcurl" ,r-rcurl)
13819 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13820 (synopsis "SPARQL client for R")
13821 (description "This package provides an interface to use SPARQL to pose
13822 SELECT or UPDATE queries to an end-point.")
13823 ;; The only license indication is found in the DESCRIPTION file,
13824 ;; which states GPL-3. So we cannot assume GPLv3+.
13825 (license license:gpl3)))
13827 (define-public r-bookdown
13829 (name "r-bookdown")
13833 (uri (cran-uri "bookdown" version))
13836 "1my6g16phx21v5cvfqcnjibh3zcv02xkix347aafd6a7r3hnxpq5"))))
13837 (build-system r-build-system)
13839 `(("r-htmltools" ,r-htmltools)
13840 ("r-knitr" ,r-knitr)
13841 ("r-rmarkdown" ,r-rmarkdown)
13842 ("r-tinytex" ,r-tinytex)
13844 ("pandoc" ,ghc-pandoc)))
13845 (home-page "https://github.com/rstudio/bookdown")
13846 (synopsis "Authoring books and technical documents with R markdown")
13847 (description "This package provides output formats and utilities for
13848 authoring books and technical documents with R Markdown.")
13849 (license license:gpl3)))
13851 (define-public r-optparse
13853 (name "r-optparse")
13858 (uri (cran-uri "optparse" version))
13861 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
13862 (build-system r-build-system)
13864 `(("r-getopt" ,r-getopt)))
13866 `(("r-knitr" ,r-knitr)))
13867 (home-page "https://github.com/trevorld/optparse")
13868 (synopsis "Command line option parser")
13870 "This package provides a command line parser inspired by Python's
13871 @code{optparse} library to be used with Rscript to write shebang scripts
13872 that accept short and long options.")
13873 (license license:gpl2+)))
13875 (define-public r-wgcna
13882 (uri (cran-uri "WGCNA" version))
13885 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
13886 (properties `((upstream-name . "WGCNA")))
13887 (build-system r-build-system)
13889 `(("r-annotationdbi" ,r-annotationdbi)
13890 ("r-doparallel" ,r-doparallel)
13891 ("r-dynamictreecut" ,r-dynamictreecut)
13892 ("r-fastcluster" ,r-fastcluster)
13893 ("r-foreach" ,r-foreach)
13894 ("r-go-db" ,r-go-db)
13895 ("r-hmisc" ,r-hmisc)
13896 ("r-impute" ,r-impute)
13898 ("r-survival" ,r-survival)
13899 ("r-matrixstats" ,r-matrixstats)
13900 ("r-preprocesscore" ,r-preprocesscore)))
13902 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13903 (synopsis "Weighted correlation network analysis")
13905 "This package provides functions necessary to perform Weighted
13906 Correlation Network Analysis on high-dimensional data. It includes functions
13907 for rudimentary data cleaning, construction and summarization of correlation
13908 networks, module identification and functions for relating both variables and
13909 modules to sample traits. It also includes a number of utility functions for
13910 data manipulation and visualization.")
13911 (license license:gpl2+)))
13913 (define-public r-kernlab
13920 (uri (cran-uri "kernlab" version))
13922 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13923 (build-system r-build-system)
13924 (home-page "https://cran.r-project.org/web/packages/kernlab")
13925 (synopsis "Kernel-based machine learning tools")
13927 "This package provides kernel-based machine learning methods for
13928 classification, regression, clustering, novelty detection, quantile regression
13929 and dimensionality reduction. Among other methods @code{kernlab} includes
13930 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13932 (license license:gpl2)))
13934 (define-public r-hierfstat
13936 (name "r-hierfstat")
13937 (version "0.04-22")
13941 (uri (cran-uri "hierfstat" version))
13944 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13945 (build-system r-build-system)
13947 `(("r-ade4" ,r-ade4)
13948 ("r-adegenet" ,r-adegenet)
13949 ("r-gtools" ,r-gtools)))
13950 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13951 (synopsis "Estimation and tests of hierarchical F-statistics")
13953 "This package allows the estimation of hierarchical F-statistics from
13954 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13955 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13956 are also given to test via randomisations the significance of each F and
13957 variance components, using the likelihood-ratio statistics G.")
13958 (license license:gpl2+)))
13960 (define-public r-hapassoc
13962 (name "r-hapassoc")
13967 (uri (cran-uri "hapassoc" version))
13970 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13971 (build-system r-build-system)
13972 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
13973 (synopsis "Inference of trait associations with SNP haplotypes")
13975 "Hapassoc performs likelihood inference of trait associations with
13976 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13977 functions are developed primarily for data collected in cohort or
13978 cross-sectional studies. They can accommodate uncertain haplotype phase and
13979 handle missing genotypes at some SNPs.")
13980 (license license:gpl2)))
13982 (define-public r-sampling
13984 (name "r-sampling")
13989 (uri (cran-uri "sampling" version))
13992 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13993 (build-system r-build-system)
13995 `(("r-lpsolve" ,r-lpsolve)
13996 ("r-mass" ,r-mass)))
13997 (home-page "https://cran.r-project.org/web/packages/sampling/")
13998 (synopsis "Survey sampling")
14000 "This package provides functions for drawing and calibrating samples.")
14001 (license license:gpl2+)))
14003 (define-public r-r2html
14010 (uri (cran-uri "R2HTML" version))
14013 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14014 (properties `((upstream-name . "R2HTML")))
14015 (build-system r-build-system)
14016 (home-page "https://github.com/nalimilan/R2HTML")
14017 (synopsis "HTML export for R objects")
14019 "This package includes HTML functions and methods to write in an HTML
14020 file. Thus, making HTML reports is easy. It includes a function that allows
14021 redirection on the fly, which appears to be very useful for teaching purposes,
14022 as the student can keep a copy of the produced output to keep all that they
14023 did during the course. The package comes with a vignette describing how to
14024 write HTML reports for statistical analysis. Finally, a driver for Sweave
14025 parses HTML flat files containing R code and to automatically write
14026 the corresponding outputs (tables and graphs).")
14027 (license license:gpl2+)))
14029 (define-public r-rjava
14036 (uri (cran-uri "rJava" version))
14039 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
14040 (properties `((upstream-name . "rJava")))
14041 (build-system r-build-system)
14043 `(#:modules ((guix build utils)
14044 (guix build r-build-system)
14047 (modify-phases %standard-phases
14048 (add-after 'unpack 'set-JAVA_HOME
14049 (lambda* (#:key inputs #:allow-other-keys)
14050 (let ((jdk (assoc-ref inputs "jdk")))
14051 (setenv "JAVA_HOME" jdk)
14052 (setenv "JAVA" (which "java"))
14053 (setenv "JAR" (which "jar"))
14054 (setenv "JAVAC" (which "javac"))
14055 (setenv "JAVAH" (which "javah"))
14056 (setenv "JAVA_CPPFLAGS"
14057 (string-append "-I" jdk "/include "
14058 "-I" jdk "/include/linux"))
14059 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14060 ((lib) (setenv "JAVA_LIBS" lib))
14061 (_ (error "Could not find libjvm.so"))))
14065 ("jdk" ,icedtea-8 "jdk")
14068 (home-page "https://www.rforge.net/rJava/")
14069 (synopsis "Low-Level R to Java interface")
14071 "This package provides a low-level interface to the Java VM very much
14072 like .C/.Call and friends. It allows the creation of objects, calling methods
14073 and accessing fields.")
14074 (license license:gpl2)))
14076 (define-public r-svmisc
14083 (uri (cran-uri "svMisc" version))
14086 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14087 (properties `((upstream-name . "svMisc")))
14088 (build-system r-build-system)
14089 (home-page "https://github.com/SciViews/svMisc")
14090 (synopsis "Miscellaneous functions for SciViews")
14092 "This package provides miscellaneous functions for SciViews or general
14093 use, including tools to manage a temporary environment attached to the search
14094 path for temporary variables you do not want to @code{save()} or
14095 @code{load()}; test the current platform; showing progress bars, etc.")
14096 (license license:gpl2)))
14098 (define-public r-xyz
14105 (uri (cran-uri "xyz" version))
14108 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14109 (build-system r-build-system)
14111 `(("r-rcpp" ,r-rcpp)))
14112 (home-page "https://cran.r-project.org/web/packages/xyz/")
14113 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14115 "High dimensional interaction search by brute force requires a quadratic
14116 computational cost in the number of variables. The xyz algorithm provably
14117 finds strong interactions in almost linear time. For details of the algorithm
14118 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14119 interaction search in high-dimensional data.")
14120 ;; Any version of the GPL.
14121 (license license:gpl2+)))
14123 (define-public r-rttf2pt1
14125 (name "r-rttf2pt1")
14130 (uri (cran-uri "Rttf2pt1" version))
14133 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14134 (properties `((upstream-name . "Rttf2pt1")))
14135 (build-system r-build-system)
14136 (home-page "https://github.com/wch/Rttf2pt1")
14137 (synopsis "Font conversion utility")
14139 "This package contains the program @code{ttf2pt1}, for use with the
14140 @code{extrafont} package.")
14141 ;; Most of the files are covered under the Expat license. Some files are
14142 ;; covered under BSD-3. Deviations for individual files are recorded in
14143 ;; the LICENSE file.
14144 (license (list license:bsd-3 license:expat
14145 (license:non-copyleft "file://LICENSE")))))
14147 (define-public r-extrafontdb
14149 (name "r-extrafontdb")
14154 (uri (cran-uri "extrafontdb" version))
14157 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14158 (build-system r-build-system)
14159 (home-page "https://github.com/wch/extrafontdb")
14160 (synopsis "Database for the extrafont package")
14162 "This package holds the database for the @code{extrafont} package.")
14163 (license license:gpl2)))
14165 (define-public r-extrafont
14167 (name "r-extrafont")
14172 (uri (cran-uri "extrafont" version))
14175 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14176 (build-system r-build-system)
14178 `(("r-extrafontdb" ,r-extrafontdb)
14179 ("r-rttf2pt1" ,r-rttf2pt1)))
14180 (home-page "https://github.com/wch/extrafont")
14181 (synopsis "Tools for using fonts in R")
14183 "The extrafont package makes it easier to use fonts other than the basic
14184 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14185 used with PDF or PostScript output files. There are two hurdles for using
14186 fonts in PDF (or Postscript) output files:
14189 @item Making R aware of the font and the dimensions of the characters.
14190 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14191 properly on a device that doesn't have the font. This is usually needed if
14192 you want to print the PDF file or share it with others.
14195 The extrafont package makes both of these things easier.")
14196 (license license:gpl2)))
14198 (define-public r-xkcd
14205 (uri (cran-uri "xkcd" version))
14208 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14209 (build-system r-build-system)
14211 `(("r-extrafont" ,r-extrafont)
14212 ("r-ggplot2" ,r-ggplot2)
14213 ("r-hmisc" ,r-hmisc)))
14214 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14215 (synopsis "Plot ggplot2 graphics in the XKCD style")
14217 "This package provides the means to plot ggplot2 graphs in the style of
14218 the XKCD web comic.")
14219 (license license:gpl3)))
14221 (define-public r-msigdbr
14228 (uri (cran-uri "msigdbr" version))
14231 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14232 (build-system r-build-system)
14234 `(("r-dplyr" ,r-dplyr)
14235 ("r-magrittr" ,r-magrittr)
14236 ("r-rlang" ,r-rlang)
14237 ("r-tibble" ,r-tibble)))
14238 (home-page "https://github.com/igordot/msigdbr")
14239 (synopsis "MSigDB gene sets for multiple organisms")
14241 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14242 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14243 software in a standard R data frame with key-value pairs. Included are the
14244 original human gene symbols and Entrez IDs as well as the equivalents for
14245 various frequently studied model organisms such as mouse, rat, pig, fly, and
14247 ;; The package is covered under the Expat license, but the upstream MSigDB
14248 ;; files are made available under the Creative Commons Attribution 4.0
14249 ;; International license.
14250 (license (list license:expat license:cc-by4.0))))
14252 (define-public r-gridgraphics
14254 (name "r-gridgraphics")
14259 (uri (cran-uri "gridGraphics" version))
14262 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14263 (properties `((upstream-name . "gridGraphics")))
14264 (build-system r-build-system)
14265 (home-page "https://github.com/pmur002/gridgraphics")
14266 (synopsis "Redraw base graphics using @code{grid} graphics")
14268 "This package provides functions to convert a page of plots drawn with
14269 the @code{graphics} package into identical output drawn with the @code{grid}
14270 package. The result looks like the original @code{graphics}-based plot, but
14271 consists of @code{grid} grobs and viewports that can then be manipulated with
14272 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14273 (license license:gpl2+)))
14275 (define-public r-farver
14282 (uri (cran-uri "farver" version))
14285 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14286 (build-system r-build-system)
14287 (home-page "https://github.com/thomasp85/farver")
14288 (synopsis "Vectorized color conversion and comparison")
14290 "The encoding of color can be handled in many different ways, using
14291 different color spaces. As different color spaces have different uses,
14292 efficient conversion between these representations are important. This
14293 package provides a set of functions that gives access to very fast color space
14294 conversion and comparisons implemented in C++, and offers 100-fold speed
14295 improvements over the @code{convertColor} function in the @code{grDevices}
14297 (license license:expat)))
14299 (define-public r-ggplotify
14301 (name "r-ggplotify")
14306 (uri (cran-uri "ggplotify" version))
14309 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14310 (build-system r-build-system)
14312 `(("r-ggplot2" ,r-ggplot2)
14313 ("r-gridgraphics" ,r-gridgraphics)
14314 ("r-rvcheck" ,r-rvcheck)))
14316 `(("r-knitr" ,r-knitr)))
14317 (home-page "https://github.com/GuangchuangYu/ggplotify")
14318 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14320 "This package provides tools to convert plot function calls (using
14321 expression or formula) to @code{grob} or @code{ggplot} objects that are
14322 compatible with the @code{grid} and @code{ggplot2} environment. With this
14323 package, we are able to e.g. use @code{cowplot} to align plots produced by
14324 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14325 converting them to @code{ggplot} objects.")
14326 (license license:artistic2.0)))
14328 (define-public r-triebeard
14330 (name "r-triebeard")
14335 (uri (cran-uri "triebeard" version))
14338 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14339 (build-system r-build-system)
14340 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14341 (home-page "https://github.com/Ironholds/triebeard/")
14342 (synopsis "Radix trees in Rcpp")
14344 "Radix trees, or tries, are key-value data structures optimized for
14345 efficient lookups, similar in purpose to hash tables. This package provides
14346 an implementation of radix trees for use in R programming and in developing
14347 packages with Rcpp.")
14348 (license license:expat)))
14350 (define-public r-tweenr
14357 (uri (cran-uri "tweenr" version))
14360 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14361 (build-system r-build-system)
14363 `(("r-farver" ,r-farver)
14364 ("r-magrittr" ,r-magrittr)
14366 ("r-rlang" ,r-rlang)))
14367 (home-page "https://github.com/thomasp85/tweenr")
14368 (synopsis "Interpolate data for smooth animations")
14370 "In order to create smooth animation between states of data, tweening is
14371 necessary. This package provides a range of functions for creating tweened
14372 data that can be used as basis for animation. Furthermore it adds a number of
14373 vectorized interpolaters for common R data types such as numeric, date and
14375 (license license:expat)))
14377 (define-public r-polyclip
14379 (name "r-polyclip")
14384 (uri (cran-uri "polyclip" version))
14387 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14388 (build-system r-build-system)
14389 (native-inputs `(("pkg-config" ,pkg-config)))
14390 (home-page "http://www.angusj.com/delphi/clipper.php")
14391 (synopsis "Polygon clipping")
14393 "This package provides an R port of the library Clipper. It performs
14394 polygon clipping operations (intersection, union, set minus, set difference)
14395 for polygonal regions of arbitrary complexity, including holes. It computes
14396 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14397 dilations) for polygonal regions and polygonal lines. It computes the
14398 Minkowski Sum of general polygons. There is a function for removing
14399 self-intersections from polygon data.")
14400 (license license:boost1.0)))
14402 (define-public r-urltools
14404 (name "r-urltools")
14409 (uri (cran-uri "urltools" version))
14412 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14413 (build-system r-build-system)
14415 `(("r-rcpp" ,r-rcpp)
14416 ("r-triebeard" ,r-triebeard)))
14417 (home-page "https://github.com/Ironholds/urltools/")
14418 (synopsis "Vectorized tools for URL handling and parsing")
14420 "This package provides a toolkit for all URL-handling needs, including
14421 encoding and decoding, parsing, parameter extraction and modification. All
14422 functions are designed to be both fast and entirely vectorized. It is
14423 intended to be useful for people dealing with web-related datasets, such as
14424 server-side logs, although may be useful for other situations involving large
14426 (license license:expat)))
14428 (define-public r-ggforce
14435 (uri (cran-uri "ggforce" version))
14438 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14439 (build-system r-build-system)
14441 `(("r-ggplot2" ,r-ggplot2)
14442 ("r-gtable" ,r-gtable)
14444 ("r-polyclip" ,r-polyclip)
14446 ("r-rcppeigen" ,r-rcppeigen)
14447 ("r-rlang" ,r-rlang)
14448 ("r-scales" ,r-scales)
14449 ("r-tidyselect" ,r-tidyselect)
14450 ("r-tweenr" ,r-tweenr)
14451 ("r-withr" ,r-withr)))
14452 (home-page "https://ggforce.data-imaginist.com")
14453 (synopsis "Accelerating ggplot2")
14455 "The aim of the ggplot2 package is to aid in visual data investigations.
14456 This focus has led to a lack of facilities for composing specialized plots.
14457 Thi package aims to be a collection of mainly new statistics and geometries
14458 that fills this gap.")
14459 (license license:expat)))
14461 (define-public r-europepmc
14463 (name "r-europepmc")
14468 (uri (cran-uri "europepmc" version))
14471 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14472 (build-system r-build-system)
14474 `(("r-dplyr" ,r-dplyr)
14476 ("r-jsonlite" ,r-jsonlite)
14478 ("r-progress" ,r-progress)
14479 ("r-purrr" ,r-purrr)
14480 ("r-urltools" ,r-urltools)
14481 ("r-xml2" ,r-xml2)))
14482 (home-page "https://github.com/ropensci/europepmc/")
14483 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14485 "This package provides an R Client for the
14486 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14487 Service}. It gives access to both metadata on life science literature and
14488 open access full texts. Europe PMC indexes all PubMed content and other
14489 literature sources including Agricola, a bibliographic database of citations
14490 to the agricultural literature, or Biological Patents. In addition to
14491 bibliographic metadata, the client allows users to fetch citations and
14492 reference lists. Links between life-science literature and other EBI
14493 databases, including ENA, PDB or ChEMBL are also accessible.")
14494 (license license:gpl3)))
14496 (define-public r-ggraph
14503 (uri (cran-uri "ggraph" version))
14506 "1ckq82hg52vr2wydkqv2wrppgjyvddd6bwqzrngqlm7j71xapjl0"))))
14507 (build-system r-build-system)
14509 `(("r-digest" ,r-digest)
14510 ("r-dplyr" ,r-dplyr)
14511 ("r-ggforce" ,r-ggforce)
14512 ("r-ggplot2" ,r-ggplot2)
14513 ("r-ggrepel" ,r-ggrepel)
14514 ("r-graphlayouts" ,r-graphlayouts)
14515 ("r-gtable" ,r-gtable)
14516 ("r-igraph" ,r-igraph)
14519 ("r-rlang" ,r-rlang)
14520 ("r-scales" ,r-scales)
14521 ("r-tidygraph" ,r-tidygraph)
14522 ("r-viridis" ,r-viridis)))
14524 `(("r-knitr" ,r-knitr)))
14525 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14526 (synopsis "Implementation of grammar of graphics for graphs and networks")
14528 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14529 graph and network visualizations due to its reliance on tabular data input.
14530 The ggraph package is an extension of the ggplot2 API tailored to graph
14531 visualizations and provides the same flexible approach to building up plots
14533 (license license:gpl3)))
14535 (define-public r-varselrf
14537 (name "r-varselrf")
14542 (uri (cran-uri "varSelRF" version))
14545 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14546 (properties `((upstream-name . "varSelRF")))
14547 (build-system r-build-system)
14549 `(("r-randomforest" ,r-randomforest)))
14550 (home-page "https://www.ligarto.org/rdiaz/software/software")
14551 (synopsis "Variable selection using random forests")
14553 "This package provides tools for the variable selection from random
14554 forests using both backwards variable elimination (for the selection of small
14555 sets of non-redundant variables) and selection based on the importance
14556 spectrum (somewhat similar to scree plots; for the selection of large,
14557 potentially highly-correlated variables). The main applications are in
14558 high-dimensional data (e.g., microarray data, and other genomics and
14559 proteomics applications).")
14560 (license license:gpl2+)))
14562 (define-public r-pamr
14569 (uri (cran-uri "pamr" version))
14572 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14573 (build-system r-build-system)
14575 `(("r-cluster" ,r-cluster)
14576 ("r-survival" ,r-survival)))
14577 (native-inputs `(("gfortran" ,gfortran)))
14578 (home-page "https://cran.r-project.org/web/packages/pamr/")
14579 (synopsis "Prediction Analysis for Microarrays")
14581 "This package provides some functions for sample classification in
14583 (license license:gpl2)))
14585 (define-public r-rda
14588 (version "1.0.2-2.1")
14592 (uri (cran-uri "rda" version))
14595 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14596 (build-system r-build-system)
14597 (home-page "https://cran.r-project.org/web/packages/rda/")
14598 (synopsis "Shrunken centroids regularized discriminant analysis")
14600 "This package provides tools for shrunken centroids regularized
14601 discriminant analysis for the purpose of classifying high dimensional data.")
14602 (license license:gpl2+)))
14604 (define-public r-ggvis
14611 (uri (cran-uri "ggvis" version))
14614 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14615 (build-system r-build-system)
14617 `(("r-assertthat" ,r-assertthat)
14618 ("r-dplyr" ,r-dplyr)
14619 ("r-htmltools" ,r-htmltools)
14620 ("r-jsonlite" ,r-jsonlite)
14621 ("r-lazyeval" ,r-lazyeval)
14622 ("r-magrittr" ,r-magrittr)
14623 ("r-shiny" ,r-shiny)))
14624 (home-page "https://ggvis.rstudio.com/")
14625 (synopsis "Interactive grammar of graphics")
14627 "This package is a data visualization package for R providing an
14628 implementation of an interactive grammar of graphics, taking the best parts of
14629 ggplot2, combining them with the reactive framework of Shiny and drawing web
14630 graphics using Vega.")
14631 (license license:gpl2)))
14633 (define-public r-gbm
14640 (uri (cran-uri "gbm" version))
14643 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14644 (build-system r-build-system)
14646 `(("r-gridextra" ,r-gridextra)
14647 ("r-lattice" ,r-lattice)
14648 ("r-survival" ,r-survival)))
14649 (home-page "https://github.com/gbm-developers/gbm")
14650 (synopsis "Generalized boosted regression models")
14652 "This package is an implementation of extensions to Freund and Schapire's
14653 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14654 regression methods for least squares, absolute loss, t-distribution loss,
14655 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14656 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14657 and Learning to Rank measures (LambdaMart).")
14658 (license license:gpl2+)))
14660 (define-public r-threejs
14667 (uri (cran-uri "threejs" version))
14670 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14671 (build-system r-build-system)
14673 `(#:modules ((guix build utils)
14674 (guix build r-build-system)
14678 (modify-phases %standard-phases
14679 (add-after 'unpack 'process-javascript
14680 (lambda* (#:key inputs #:allow-other-keys)
14681 (with-directory-excursion "inst"
14685 `((,(assoc-ref inputs "js-jquery")
14686 "htmlwidgets/lib/jquery/jquery.min.js")
14687 (,(assoc-ref inputs "js-threejs-111")
14688 "htmlwidgets/lib/threejs-111/three.min.js"))))
14689 (lambda (sources targets)
14690 (for-each (lambda (source target)
14691 (format #t "Processing ~a --> ~a~%"
14693 (delete-file target)
14694 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14695 (call-with-output-file target
14697 (dump-port minified port)))))
14698 sources targets))))
14701 `(("r-base64enc" ,r-base64enc)
14702 ("r-crosstalk" ,r-crosstalk)
14703 ("r-htmlwidgets" ,r-htmlwidgets)
14704 ("r-igraph" ,r-igraph)))
14706 `(("uglify-js" ,uglify-js)
14710 (uri "https://code.jquery.com/jquery-1.12.4.js")
14713 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
14717 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
14720 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
14721 (home-page "https://bwlewis.github.io/rthreejs")
14722 (synopsis "Interactive 3D scatter plots, networks and globes")
14724 "Create interactive 3D scatter plots, network plots, and globes in R
14725 using the three.js visualization library.")
14726 (license license:expat)))
14728 (define-public r-mlbench
14735 (uri (cran-uri "mlbench" version))
14738 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14739 (build-system r-build-system)
14740 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14741 (synopsis "Machine learning benchmark problems")
14743 "This package provides a collection of artificial and real-world machine
14744 learning benchmark problems, including, e.g., several data sets from the UCI
14746 (license license:gpl2)))
14748 (define-public r-mpm
14755 (uri (cran-uri "mpm" version))
14758 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14759 (build-system r-build-system)
14761 `(("r-kernsmooth" ,r-kernsmooth)
14762 ("r-mass" ,r-mass)))
14763 (home-page "http://mpm.r-forge.r-project.org")
14764 (synopsis "Multivariate projection methods")
14766 "This is a package for exploratory graphical analysis of multivariate
14767 data, specifically gene expression data with different projection methods:
14768 principal component analysis, correspondence analysis, spectral map
14770 (license license:gpl2+)))
14772 (define-public r-png
14778 (uri (cran-uri "png" version))
14781 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14782 (build-system r-build-system)
14784 `(("libpng" ,libpng)
14786 (home-page "https://www.rforge.net/png/")
14787 (synopsis "Read and write PNG images")
14789 "This package provides an easy and simple way to read, write and display
14790 bitmap images stored in the PNG format. It can read and write both files and
14791 in-memory raw vectors.")
14792 ;; Any of these GPL versions.
14793 (license (list license:gpl2 license:gpl3))))
14795 (define-public r-ggcorrplot
14797 (name "r-ggcorrplot")
14802 (uri (cran-uri "ggcorrplot" version))
14805 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14806 (build-system r-build-system)
14808 `(("r-ggplot2" ,r-ggplot2)
14809 ("r-reshape2" ,r-reshape2)))
14810 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14811 (synopsis "Visualization of a correlation matrix using ggplot2")
14813 "The ggcorrplot package can be used to visualize easily a correlation
14814 matrix using ggplot2. It provides a solution for reordering the correlation
14815 matrix and displays the significance level on the plot. It also includes a
14816 function for computing a matrix of correlation p-values.")
14817 (license license:gpl2)))
14819 (define-public r-flexdashboard
14821 (name "r-flexdashboard")
14822 (version "0.5.1.1")
14826 (uri (cran-uri "flexdashboard" version))
14829 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14830 (build-system r-build-system)
14832 `(#:modules ((guix build utils)
14833 (guix build r-build-system)
14837 (ice-9 textual-ports))
14839 (modify-phases %standard-phases
14840 (add-after 'unpack 'process-javascript
14841 (lambda* (#:key inputs #:allow-other-keys)
14842 (with-directory-excursion "inst"
14843 ;; Concatenate all components of prism.js
14844 (let ((contents (string-join
14845 (map (lambda (name)
14846 (call-with-input-file
14847 (assoc-ref inputs name)
14851 "js-prism-line-numbers"))
14853 (call-with-output-file "prism-src.js"
14854 (cut display contents <>)))
14858 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14859 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14861 "www/sly/sly.min.js")
14863 "www/prism/prism.js")
14864 (,(assoc-ref inputs "js-raphael")
14865 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14866 (,(assoc-ref inputs "js-featherlight")
14867 "www/featherlight/featherlight.min.js"))))
14868 (lambda (sources targets)
14869 (for-each (lambda (source target)
14870 (format #t "Processing ~a --> ~a~%"
14872 (delete-file target)
14873 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14874 (call-with-output-file target
14876 (dump-port minified port)))))
14877 sources targets))))
14880 `(("r-htmltools" ,r-htmltools)
14881 ("r-htmlwidgets" ,r-htmlwidgets)
14882 ("r-jsonlite" ,r-jsonlite)
14883 ("r-knitr" ,r-knitr)
14884 ("r-rmarkdown" ,r-rmarkdown)
14885 ("r-shiny" ,r-shiny)))
14887 `(("uglify-js" ,uglify-js)
14891 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14894 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14898 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14901 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14905 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14908 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14909 ("js-prism-line-numbers"
14912 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14915 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14919 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14922 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14923 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14924 (synopsis "R Markdown format for flexible dashboards")
14926 "This package provides an R Markdown format for converting an R Markdown
14927 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14928 of its components to the containing web page.")
14929 (license license:expat)))
14931 (define-public r-preseqr
14938 (uri (cran-uri "preseqR" version))
14941 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14942 (properties `((upstream-name . "preseqR")))
14943 (build-system r-build-system)
14945 `(("r-polynom" ,r-polynom)))
14946 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14947 (synopsis "Predicting species accumulation curves")
14949 "This package can be used to predict the r-species accumulation
14950 curve (r-SAC), which is the number of species represented at least r times as
14951 a function of the sampling effort. When r = 1, the curve is known as the
14952 species accumulation curve, or the library complexity curve in high-throughput
14953 genomic sequencing. The package includes both parametric and nonparametric
14954 methods, as described by Deng C, et al. (2018).")
14955 (license license:gpl3)))
14957 (define-public r-mapplots
14959 (name "r-mapplots")
14964 (uri (cran-uri "mapplots" version))
14967 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14968 (build-system r-build-system)
14969 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14970 (synopsis "Data visualization on maps")
14972 "This package helps you create simple maps; add sub-plots like pie plots
14973 to a map or any other plot; format, plot and export gridded data. The package
14974 was developed for displaying fisheries data but most functions can be used for
14975 more generic data visualisation.")
14976 (license license:gpl2+)))
14978 (define-public r-pmcmr
14985 (uri (cran-uri "PMCMR" version))
14988 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14989 (properties `((upstream-name . "PMCMR")))
14990 (build-system r-build-system)
14991 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14992 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14994 "This is a deprecated package for calculating pairwise multiple
14995 comparisons of mean rank sums. This package is superseded by the novel
14996 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14997 compatibility of dependent packages for some time.")
14998 (license license:gpl3+)))
15000 (define-public r-downloader
15002 (name "r-downloader")
15007 (uri (cran-uri "downloader" version))
15010 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15011 (build-system r-build-system)
15013 `(("r-digest" ,r-digest)))
15014 (home-page "https://github.com/wch/downloader")
15015 (synopsis "Download files over HTTP and HTTPS")
15017 "This package provides a wrapper for the @code{download.file} function,
15018 making it possible to download files over HTTPS across platforms. The
15019 @code{RCurl} package provides this functionality (and much more) but has
15020 external dependencies. This package has is implemented purely in R.")
15021 (license license:gpl2)))
15023 (define-public r-rex
15030 (uri (cran-uri "rex" version))
15033 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15034 (build-system r-build-system)
15036 `(("r-lazyeval" ,r-lazyeval)))
15038 `(("r-knitr" ,r-knitr)))
15039 (home-page "https://github.com/kevinushey/rex")
15040 (synopsis "Friendly regular expressions")
15042 "This package provides a friendly interface for the construction of
15043 regular expressions. Regular expressions are a very powerful feature, however
15044 they are often difficult to interpret. Rex allows you to build complex
15045 regular expressions from human readable expressions")
15046 (license license:expat)))
15048 (define-public r-xmlparsedata
15050 (name "r-xmlparsedata")
15055 (uri (cran-uri "xmlparsedata" version))
15058 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15059 (properties `((upstream-name . "xmlparsedata")))
15060 (build-system r-build-system)
15061 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15062 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15064 "This package provides tools to convert the output of
15065 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15066 @code{XPath}, and is easier to manipulate in general.")
15067 (license license:expat)))
15069 (define-public r-cyclocomp
15071 (name "r-cyclocomp")
15076 (uri (cran-uri "cyclocomp" version))
15079 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15080 (properties `((upstream-name . "cyclocomp")))
15081 (build-system r-build-system)
15083 `(("r-callr" ,r-callr)
15084 ("r-crayon" ,r-crayon)
15086 ("r-remotes" ,r-remotes)
15087 ("r-withr" ,r-withr)))
15088 (home-page "https://github.com/MangoTheCat/cyclocomp")
15089 (synopsis "Cyclomatic complexity of R code")
15091 "Cyclomatic complexity is a software metric, used to indicate the
15092 complexity of a program. It is a quantitative measure of the number of
15093 linearly independent paths through a program's source code. This package
15094 provides tools to compute this metric.")
15095 (license license:expat)))
15097 (define-public r-lintr
15104 (uri (cran-uri "lintr" version))
15107 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15108 (properties `((upstream-name . "lintr")))
15109 (build-system r-build-system)
15111 `(("r-codetools" ,r-codetools)
15112 ("r-crayon" ,r-crayon)
15113 ("r-cyclocomp" ,r-cyclocomp)
15114 ("r-digest" ,r-digest)
15116 ("r-jsonlite" ,r-jsonlite)
15117 ("r-knitr" ,r-knitr)
15119 ("r-rstudioapi" ,r-rstudioapi)
15120 ("r-testthat" ,r-testthat)
15122 ("r-xmlparsedata" ,r-xmlparsedata)))
15123 (home-page "https://github.com/jimhester/lintr")
15124 (synopsis "Linter for R code")
15125 (description "This package checks adherence to a given style, syntax
15126 errors and possible semantic issues. It supports on the fly checking of R
15127 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15128 (license license:expat)))
15130 (define-public r-sctransform
15132 (name "r-sctransform")
15137 (uri (cran-uri "sctransform" version))
15140 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15141 (build-system r-build-system)
15143 `(("r-future-apply" ,r-future-apply)
15144 ("r-ggplot2" ,r-ggplot2)
15145 ("r-gridextra" ,r-gridextra)
15147 ("r-matrix" ,r-matrix)
15149 ("r-rcppeigen" ,r-rcppeigen)
15150 ("r-reshape2" ,r-reshape2)))
15151 (home-page "https://github.com/ChristophH/sctransform")
15152 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15154 "This package provides a normalization method for single-cell UMI count
15155 data using a variance stabilizing transformation. The transformation is based
15156 on a negative binomial regression model with regularized parameters. As part
15157 of the same regression framework, this package also provides functions for
15158 batch correction, and data correction.")
15159 (license license:gpl3)))
15161 (define-public r-styler
15168 (uri (cran-uri "styler" version))
15171 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15172 (build-system r-build-system)
15174 `(("r-backports" ,r-backports)
15176 ("r-magrittr" ,r-magrittr)
15177 ("r-purrr" ,r-purrr)
15178 ("r-r-cache" ,r-r-cache)
15179 ("r-rematch2" ,r-rematch2)
15180 ("r-rlang" ,r-rlang)
15181 ("r-rprojroot" ,r-rprojroot)
15182 ("r-tibble" ,r-tibble)
15183 ("r-withr" ,r-withr)
15184 ("r-xfun" ,r-xfun)))
15185 (home-page "https://github.com/r-lib/styler")
15186 (synopsis "Non-invasive pretty printing of R code")
15188 "This is a package for pretty-printing R code without changing the user's
15189 formatting intent.")
15190 (license license:gpl3)))
15192 (define-public r-scrime
15199 (uri (cran-uri "scrime" version))
15202 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15203 (build-system r-build-system)
15204 (home-page "https://cran.r-project.org/web/packages/scrime/")
15205 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15207 "This package provides tools for the analysis of high-dimensional data
15208 developed/implemented at the group \"Statistical Complexity Reduction In
15209 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15210 the functions can also be applied to other types of categorical data.")
15211 (license license:gpl2)))
15213 (define-public r-pbmcapply
15215 (name "r-pbmcapply")
15220 (uri (cran-uri "pbmcapply" version))
15223 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15224 (build-system r-build-system)
15225 (home-page "https://github.com/kvnkuang/pbmcapply")
15226 (synopsis "Track the progress of apply procedures with a progress bar")
15228 "This light-weight package helps you track and visualize the progress of
15229 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15230 (license license:expat)))
15232 (define-public r-blme
15239 (uri (cran-uri "blme" version))
15242 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15243 (build-system r-build-system)
15244 (propagated-inputs `(("r-lme4" ,r-lme4)))
15245 (home-page "https://github.com/vdorie/blme")
15246 (synopsis "Bayesian linear mixed-effects models")
15248 "This package provides tools for maximum a posteriori estimation for
15249 linear and generalized linear mixed-effects models in a Bayesian setting. It
15250 extends the lme4 package.")
15251 (license license:gpl2+)))
15253 (define-public r-batchtools
15255 (name "r-batchtools")
15260 (uri (cran-uri "batchtools" version))
15263 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15264 (build-system r-build-system)
15266 `(("r-backports" ,r-backports)
15267 ("r-base64url" ,r-base64url)
15269 ("r-checkmate" ,r-checkmate)
15270 ("r-data-table" ,r-data-table)
15271 ("r-digest" ,r-digest)
15273 ("r-progress" ,r-progress)
15275 ("r-rappdirs" ,r-rappdirs)
15276 ("r-stringi" ,r-stringi)
15277 ("r-withr" ,r-withr)))
15279 `(("r-knitr" ,r-knitr)))
15280 (home-page "https://github.com/mllg/batchtools")
15281 (synopsis "Tools for computation on batch systems")
15283 "As a successor of the packages BatchJobs and BatchExperiments, this
15284 package provides a parallel implementation of the Map function for high
15285 performance computing systems managed by various schedulers. A multicore and
15286 socket mode allow the parallelization on a local machines, and multiple
15287 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15288 the package provides an abstraction mechanism to define large-scale computer
15289 experiments in a well-organized and reproducible way.")
15290 (license license:lgpl3)))
15292 (define-public r-clue
15299 (uri (cran-uri "clue" version))
15302 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15303 (build-system r-build-system)
15304 (propagated-inputs `(("r-cluster" ,r-cluster)))
15305 (home-page "https://cran.r-project.org/web/packages/clue/")
15306 (synopsis "Tools for analyzing cluster ensembles")
15307 (description "Cluster ensembles are collections of individual solutions to
15308 a given clustering problem which are useful or necessary to consider in a wide
15309 range of applications. This R package provides an extensible computational
15310 environment for creating and analyzing cluster ensembles, with basic data
15311 structures for representing partitions and hierarchies, and facilities for
15312 computing on them, including methods for measuring proximity and obtaining
15313 consensus and secondary clusterings.")
15314 (license license:gpl2)))
15316 (define-public r-sitmo
15323 (uri (cran-uri "sitmo" version))
15326 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15327 (build-system r-build-system)
15328 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15329 (home-page "https://github.com/coatless/sitmo/")
15330 (synopsis "Parallel pseudo random number generator header files")
15332 "This package provides two high quality and fast PPRNGs that may be used
15333 in an OpenMP parallel environment. In addition, there is a generator for one
15334 dimensional low-discrepancy sequence.")
15335 (license license:expat)))
15337 (define-public r-dqrng
15344 (uri (cran-uri "dqrng" version))
15347 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15348 (build-system r-build-system)
15352 ("r-sitmo" ,r-sitmo)))
15353 (home-page "https://www.daqana.org/dqrng")
15354 (synopsis "Fast pseudo random number generators")
15356 "Several fast random number generators are provided as C++ header-only
15357 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15358 Additionally, fast functions for generating random numbers according to a
15359 uniform, normal and exponential distribution are included. The latter two use
15360 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15361 functions are exported to R and as a C++ interface and are enabled for use
15362 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15363 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15364 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15365 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15366 ;; whole is distributed under the terms of the AGPL 3.
15367 (license license:agpl3)))
15369 (define-public r-ingredients
15371 (name "r-ingredients")
15376 (uri (cran-uri "ingredients" version))
15379 "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
15380 (properties `((upstream-name . "ingredients")))
15381 (build-system r-build-system)
15383 `(("r-ggplot2" ,r-ggplot2)
15384 ("r-gridextra" ,r-gridextra)
15385 ("r-scales" ,r-scales)))
15386 (native-inputs `(("r-knitr" ,r-knitr)))
15387 (home-page "https://ModelOriented.github.io/ingredients/")
15388 (synopsis "Effects and importances of model ingredients")
15390 "This is a collection of tools for assessment of feature importance and
15391 feature effects. Key functions are:
15394 @item @code{feature_importance()} for assessment of global level feature
15396 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15397 @item @code{partial_dependence()} for partial dependence plots,
15398 @item @code{conditional_dependence()} for conditional dependence plots,
15399 @item @code{accumulated_dependence()} for accumulated local effects plots,
15400 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15401 aggregation of ceteris paribus profiles,
15402 @item generic @code{print()} and @code{plot()} for better usability of
15403 selected explainers,
15404 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15405 @item generic @code{describe()} for explanations in natural language.
15407 (license license:gpl3)))
15409 (define-public r-ibreakdown
15411 (name "r-ibreakdown")
15416 (uri (cran-uri "iBreakDown" version))
15419 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15420 (properties `((upstream-name . "iBreakDown")))
15421 (build-system r-build-system)
15422 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15423 (native-inputs `(("r-knitr" ,r-knitr)))
15424 (home-page "https://ModelOriented.github.io/iBreakDown/")
15425 (synopsis "Model agnostic instance level variable attributions")
15427 "This package provides a model agnostic tool for decomposition of
15428 predictions from black boxes. It supports additive attributions and
15429 attributions with interactions. The Break Down Table shows contributions of
15430 every variable to a final prediction. The Break Down Plot presents variable
15431 contributions in a concise graphical way. This package works for
15432 classification and regression models.")
15433 (license license:gpl3)))
15435 (define-public r-dalex
15442 (uri (cran-uri "DALEX" version))
15445 "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
15446 (properties `((upstream-name . "DALEX")))
15447 (build-system r-build-system)
15449 `(("r-ggplot2" ,r-ggplot2)
15450 ("r-ibreakdown" ,r-ibreakdown)
15451 ("r-ingredients" ,r-ingredients)))
15452 (home-page "https://pbiecek.github.io/DALEX/")
15453 (synopsis "Descriptive machine learning explanations")
15455 "Machine Learning models are widely used and have various applications in
15456 classification or regression. Models created with boosting, bagging, stacking
15457 or similar techniques are often used due to their high performance, but such
15458 black-box models usually lack interpretability. The DALEX package contains
15459 various explainers that help to understand the link between input variables
15460 and model output.")
15461 ;; Any version of the GPL
15462 (license license:gpl3+)))
15464 (define-public r-enrichr
15471 (uri (cran-uri "enrichR" version))
15474 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15475 (properties `((upstream-name . "enrichR")))
15476 (build-system r-build-system)
15478 `(("r-httr" ,r-httr)
15479 ("r-rjson" ,r-rjson)))
15480 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15481 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15483 "This package provides an R interface to all Enrichr databases, a
15484 web-based tool for analyzing gene sets and returns any enrichment of common
15485 annotated biological functions.")
15486 (license license:gpl2+)))
15488 (define-public r-plot3d
15495 (uri (cran-uri "plot3D" version))
15498 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15499 (properties `((upstream-name . "plot3D")))
15500 (build-system r-build-system)
15501 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15502 (home-page "https://cran.r-project.org/web/packages/plot3D")
15503 (synopsis "Plot multi-dimensional data")
15505 "This package provides functions for viewing 2D and 3D data, including
15506 perspective plots, slice plots, surface plots, scatter plots, etc. It
15507 includes data sets from oceanography.")
15508 (license license:gpl3+)))
15510 (define-public r-ggfortify
15512 (name "r-ggfortify")
15517 (uri (cran-uri "ggfortify" version))
15520 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15521 (build-system r-build-system)
15523 `(("r-dplyr" ,r-dplyr)
15524 ("r-ggplot2" ,r-ggplot2)
15525 ("r-gridextra" ,r-gridextra)
15526 ("r-scales" ,r-scales)
15527 ("r-stringr" ,r-stringr)
15528 ("r-tibble" ,r-tibble)
15529 ("r-tidyr" ,r-tidyr)))
15531 `(("r-knitr" ,r-knitr)))
15532 (home-page "https://github.com/sinhrks/ggfortify")
15533 (synopsis "Data visualization tools for statistical analysis results")
15535 "This package provides unified plotting tools for statistics commonly
15536 used, such as GLM, time series, PCA families, clustering and survival
15537 analysis. The package offers a single plotting interface for these analysis
15538 results and plots in a unified style using the @code{ggplot2} package.")
15539 (license license:gpl2)))
15541 (define-public r-refmanager
15543 (name "r-refmanager")
15548 (uri (cran-uri "RefManageR" version))
15551 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15552 (properties `((upstream-name . "RefManageR")))
15553 (build-system r-build-system)
15555 `(("r-bibtex" ,r-bibtex)
15557 ("r-jsonlite" ,r-jsonlite)
15558 ("r-lubridate" ,r-lubridate)
15560 ("r-stringr" ,r-stringr)
15561 ("r-xml2" ,r-xml2)))
15562 (home-page "https://github.com/ropensci/RefManageR/")
15563 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15565 "This package provides tools for importing and working with bibliographic
15566 references. It greatly enhances the @code{bibentry} class by providing a
15567 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15568 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15569 by various formats for name lists (author by last names, translator by full
15570 names, etc.). Entries can be updated, combined, sorted, printed in a number
15571 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15572 into R and converted to @code{BibEntry} objects.")
15573 ;; Any of these licenses may be picked.
15574 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15576 (define-public r-citr
15583 (uri (cran-uri "citr" version))
15586 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15587 (build-system r-build-system)
15589 `(("r-assertthat" ,r-assertthat)
15592 ("r-miniui" ,r-miniui)
15593 ("r-refmanager" ,r-refmanager)
15594 ("r-rstudioapi" ,r-rstudioapi)
15595 ("r-shiny" ,r-shiny)
15596 ("r-shinyjs" ,r-shinyjs)
15597 ("r-yaml" ,r-yaml)))
15598 (home-page "https://github.com/crsh/citr")
15599 (synopsis "RStudio add-in to insert Markdown citations")
15601 "This package provides functions and an RStudio add-in that search a
15602 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15603 the current document.")
15604 (license license:expat)))
15606 (define-public r-xgboost
15609 (version "1.0.0.2")
15613 (uri (cran-uri "xgboost" version))
15616 "1ld2w51c5fy3bl0kvjn1iplffc4lmin9s9zz5xx7xsm44d6j6kzd"))))
15617 (build-system r-build-system)
15619 `(("r-data-table" ,r-data-table)
15620 ("r-magrittr" ,r-magrittr)
15621 ("r-matrix" ,r-matrix)
15622 ("r-stringi" ,r-stringi)))
15624 `(("r-knitr" ,r-knitr)))
15625 (home-page "https://github.com/dmlc/xgboost")
15626 (synopsis "Extreme gradient boosting")
15628 "This package provides an R interface to Extreme Gradient Boosting, which
15629 is an efficient implementation of the gradient boosting framework from Chen
15630 and Guestrin (2016). The package includes efficient linear model solver and
15631 tree learning algorithms. The package can automatically do parallel
15632 computation on a single machine. It supports various objective functions,
15633 including regression, classification and ranking. The package is made to be
15634 extensible, so that users are also allowed to define their own objectives
15636 (license license:asl2.0)))
15638 (define-public r-umap
15641 (version "0.2.5.0")
15645 (uri (cran-uri "umap" version))
15648 "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
15649 (build-system r-build-system)
15651 `(("r-openssl" ,r-openssl)
15653 ("r-reticulate" ,r-reticulate)
15654 ("r-rspectra" ,r-rspectra)))
15656 `(("r-knitr" ,r-knitr)))
15657 (home-page "https://github.com/tkonopka/umap")
15658 (synopsis "Uniform manifold approximation and projection")
15660 "Uniform manifold approximation and projection is a technique for
15661 dimension reduction. This package provides an interface to the UMAP algorithm
15662 in R, including a translation of the original algorithm into R.")
15663 (license license:expat)))
15665 (define-public r-uwot
15672 (uri (cran-uri "uwot" version))
15675 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
15676 (build-system r-build-system)
15678 `(("r-dqrng" ,r-dqrng)
15680 ("r-irlba" ,r-irlba)
15681 ("r-matrix" ,r-matrix)
15683 ("r-rcppannoy" ,r-rcppannoy)
15684 ("r-rcppprogress" ,r-rcppprogress)
15685 ("r-rspectra" ,r-rspectra)))
15686 (home-page "https://github.com/jlmelville/uwot")
15687 (synopsis "Uniform manifold approximation and projection")
15689 "This package provides an implementation of the Uniform Manifold
15690 Approximation and Projection dimensionality reduction by McInnes et
15691 al. (2018). It also provides means to transform new data and to carry out
15692 supervised dimensionality reduction. An implementation of the related
15693 LargeVis method of Tang et al. (2016) is also provided.")
15694 (license license:gpl3)))
15696 (define-public r-kableextra
15698 (name "r-kableextra")
15703 (uri (cran-uri "kableExtra" version))
15706 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15707 (properties `((upstream-name . "kableExtra")))
15708 (build-system r-build-system)
15710 `(("r-digest" ,r-digest)
15712 ("r-htmltools" ,r-htmltools)
15713 ("r-knitr" ,r-knitr)
15714 ("r-magrittr" ,r-magrittr)
15715 ("r-readr" ,r-readr)
15716 ("r-rmarkdown" ,r-rmarkdown)
15717 ("r-rstudioapi" ,r-rstudioapi)
15718 ("r-rvest" ,r-rvest)
15719 ("r-scales" ,r-scales)
15720 ("r-stringr" ,r-stringr)
15721 ("r-viridislite" ,r-viridislite)
15722 ("r-webshot" ,r-webshot)
15723 ("r-xml2" ,r-xml2)))
15724 (home-page "https://haozhu233.github.io/kableExtra/")
15725 (synopsis "Construct complex tables with pipe syntax")
15727 "Build complex HTML or LaTeX tables using @code{kable()} from
15728 @code{knitr} and the piping syntax from @code{magrittr}. The function
15729 @code{kable()} is a light weight table generator coming from @code{knitr}.
15730 This package simplifies the way to manipulate the HTML or LaTeX codes
15731 generated by @code{kable()} and allows users to construct complex tables and
15732 customize styles using a readable syntax.")
15733 (license license:expat)))
15735 (define-public r-glasso
15742 (uri (cran-uri "glasso" version))
15744 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15745 (build-system r-build-system)
15746 (native-inputs `(("gfortran" ,gfortran)))
15747 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
15748 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15750 "This is a package for estimation of a sparse inverse covariance matrix
15751 using a lasso (L1) penalty. Facilities are provided for estimates along a
15752 path of values for the regularization parameter.")
15753 (license license:gpl2)))
15755 (define-public r-rhpcblasctl
15757 (name "r-rhpcblasctl")
15758 (version "0.20-17")
15762 (uri (cran-uri "RhpcBLASctl" version))
15765 "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
15766 (properties `((upstream-name . "RhpcBLASctl")))
15767 (build-system r-build-system)
15768 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
15769 (synopsis "Control the number of threads on BLAS")
15771 "This package allows you to control the number of threads the BLAS
15772 library uses. It is also possible to control the number of threads in
15774 (license license:agpl3+)))
15776 (define-public r-lda
15783 (uri (cran-uri "lda" version))
15786 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15787 (build-system r-build-system)
15788 (home-page "https://cran.r-project.org/web/packages/lda/")
15789 (synopsis "Collapsed Gibbs sampling methods for topic models")
15791 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15792 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15793 mixed-membership stochastic blockmodel. Inference for all of these models is
15794 implemented via a fast collapsed Gibbs sampler written in C. Utility
15795 functions for reading/writing data typically used in topic models, as well as
15796 tools for examining posterior distributions are also included.")
15797 ;; Any version of the LGPL
15798 (license license:lgpl3+)))
15800 (define-public r-rann-l1
15807 (uri (cran-uri "RANN.L1" version))
15810 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15811 (properties `((upstream-name . "RANN.L1")))
15812 (build-system r-build-system)
15813 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15814 (synopsis "Fast nearest neighbour search using L1 metric")
15816 "This package provides tools to find the k nearest neighbours for every
15817 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15818 library. There is support for approximate as well as exact searches, fixed
15819 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15820 computed using the L1 (Manhattan, taxicab) metric.")
15821 (license license:gpl3+)))
15823 (define-public r-leiden
15830 (uri (cran-uri "leiden" version))
15833 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
15834 (properties `((upstream-name . "leiden")))
15835 (build-system r-build-system)
15837 `(("r-igraph" ,r-igraph)
15838 ("r-matrix" ,r-matrix)
15839 ("r-reticulate" ,r-reticulate)))
15840 (home-page "https://github.com/TomKellyGenetics/leiden")
15841 (synopsis "R implementation of Leiden clustering algorithm")
15843 "This package implements the Python @code{leidenalg} module to be called
15844 in R. It enables clustering using the Leiden algorithm for partitioning a
15845 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15846 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15847 (license license:gpl3)))
15849 (define-public r-patchwork
15851 (name "r-patchwork")
15856 (uri (cran-uri "patchwork" version))
15859 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
15860 (build-system r-build-system)
15862 `(("r-ggplot2" ,r-ggplot2)
15863 ("r-gtable" ,r-gtable)))
15865 `(("r-knitr" ,r-knitr)))
15866 (home-page "https://github.com/thomasp85/patchwork")
15867 (synopsis "Compose ggplot2 plots")
15869 "The @code{ggplot2} package provides a strong API for sequentially
15870 building up a plot, but does not concern itself with composition of multiple
15871 plots. Patchwork is a package that expands the API to allow for arbitrarily
15872 complex composition of plots by providing mathmatical operators for combining
15874 (license license:expat)))
15876 (define-public r-liger
15883 (uri (git-reference
15884 (url "https://github.com/MacoskoLab/liger.git")
15885 (commit (string-append "v" version))))
15886 (file-name (git-file-name name version))
15889 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15890 (modules '((guix build utils)))
15893 (delete-file "inst/java/ModularityOptimizer.jar")
15895 (build-system r-build-system)
15898 (modify-phases %standard-phases
15899 (add-after 'unpack 'build-java-part
15900 (lambda* (#:key inputs #:allow-other-keys)
15901 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15902 (for-each (lambda (file) (invoke "javac" file))
15903 (find-files "." "\\.java$"))
15904 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15905 (find-files "." "\\.class$"))
15908 `(("r-cowplot" ,r-cowplot)
15909 ("r-dosnow" ,r-dosnow)
15910 ("r-dplyr" ,r-dplyr)
15912 ("r-foreach" ,r-foreach)
15913 ("r-ggplot2" ,r-ggplot2)
15914 ("r-ggrepel" ,r-ggrepel)
15915 ("r-hmisc" ,r-hmisc)
15917 ("r-irlba" ,r-irlba)
15918 ("r-matrix" ,r-matrix)
15919 ("r-mclust" ,r-mclust)
15920 ("r-patchwork" ,r-patchwork)
15922 ("r-rann-l1" ,r-rann-l1)
15924 ("r-rcpparmadillo" ,r-rcpparmadillo)
15925 ("r-riverplot" ,r-riverplot)
15926 ("r-rtsne" ,r-rtsne)
15927 ("r-snow" ,r-snow)))
15929 `(("jdk" ,icedtea "jdk")
15930 ;; See https://github.com/MacoskoLab/liger/issues/96
15931 ;; The optimizer is released under the Expat license.
15935 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15938 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15940 ("r-knitr" ,r-knitr))) ; for vignettes
15941 (home-page "https://github.com/MacoskoLab/liger")
15942 (synopsis "Integrate and analyze multiple single-cell datasets")
15944 "LIGER is a package for integrating and analyzing multiple single-cell
15945 datasets, developed and maintained by the Macosko lab. It relies on
15946 integrative non-negative matrix factorization to identify shared and
15947 dataset-specific factors.")
15948 (license license:gpl3)))
15950 (define-public r-harmony
15957 (uri (git-reference
15958 (url "https://github.com/immunogenomics/harmony")
15960 (file-name (git-file-name name version))
15963 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
15964 (modules '((guix build utils)))
15967 (for-each delete-file '("config.status" "configure"))
15969 (build-system r-build-system)
15971 `(("r-cowplot" ,r-cowplot)
15972 ("r-dplyr" ,r-dplyr)
15973 ("r-ggplot2" ,r-ggplot2)
15974 ("r-irlba" ,r-irlba)
15975 ("r-matrix" ,r-matrix)
15977 ("r-rcpparmadillo" ,r-rcpparmadillo)
15978 ("r-rcppprogress" ,r-rcppprogress)
15979 ("r-rlang" ,r-rlang)
15980 ("r-tibble" ,r-tibble)
15981 ("r-tidyr" ,r-tidyr)))
15983 `(("autoconf" ,autoconf)))
15984 (home-page "https://github.com/immunogenomics/harmony")
15985 (synopsis "Integration of single cell sequencing data")
15987 "This package provides an implementation of the Harmony algorithm for
15988 single cell integration, described in Korsunsky et al
15989 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15990 function and interfaces to external frameworks.")
15991 (license license:gpl3)))
15993 (define-public r-covr
16000 (uri (cran-uri "covr" version))
16002 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16003 (properties `((upstream-name . "covr")))
16004 (build-system r-build-system)
16006 `(("r-crayon" ,r-crayon)
16007 ("r-digest" ,r-digest)
16009 ("r-jsonlite" ,r-jsonlite)
16011 ("r-withr" ,r-withr)
16012 ("r-yaml" ,r-yaml)))
16014 `(("r-knitr" ,r-knitr))) ; for vignettes
16015 (home-page "https://github.com/r-lib/covr")
16016 (synopsis "Test coverage for R packages")
16018 "Thisp package enables you to track and report code coverage for your
16019 package and (optionally) upload the results to a coverage service. Code
16020 coverage is a measure of the amount of code being exercised by a set of tests.
16021 It is an indirect measure of test quality and completeness. This package is
16022 compatible with any testing methodology or framework and tracks coverage of
16023 both R code and compiled C/C++/FORTRAN code.")
16024 (license license:gpl3)))
16026 (define-public r-systemfonts
16028 (name "r-systemfonts")
16033 (uri (cran-uri "systemfonts" version))
16036 "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
16037 (properties `((upstream-name . "systemfonts")))
16038 (build-system r-build-system)
16040 `(("fontconfig" ,fontconfig)
16043 `(("pkg-config" ,pkg-config)
16044 ("r-knitr" ,r-knitr)))
16045 (home-page "https://github.com/r-lib/systemfonts")
16046 (synopsis "System native font finding")
16048 "This package provides system native access to the font catalogue. As
16049 font handling varies between systems it is difficult to correctly locate
16050 installed fonts across different operating systems. The 'systemfonts' package
16051 provides bindings to the native libraries for finding font files that can then
16052 be used further by e.g. graphic devices.")
16053 (license license:expat)))
16055 (define-public r-graphlayouts
16057 (name "r-graphlayouts")
16062 (uri (cran-uri "graphlayouts" version))
16065 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16066 (properties `((upstream-name . "graphlayouts")))
16067 (build-system r-build-system)
16069 `(("r-igraph" ,r-igraph)
16071 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16072 (home-page "https://github.com/schochastics/graphlayouts")
16073 (synopsis "Additional layout algorithms for network visualizations")
16075 "This package provides several layout algorithms to visualize networks
16076 which are not part of the igraph library. Most are based on the concept of
16077 stress majorization by Gansner et al. (2004)
16078 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16079 emphasize hidden group structures in networks or focus on specific nodes.")
16080 (license license:expat)))
16082 (define-public r-tidygraph
16084 (name "r-tidygraph")
16089 (uri (cran-uri "tidygraph" version))
16092 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
16093 (properties `((upstream-name . "tidygraph")))
16094 (build-system r-build-system)
16096 `(("r-dplyr" ,r-dplyr)
16097 ("r-igraph" ,r-igraph)
16098 ("r-magrittr" ,r-magrittr)
16099 ("r-pillar" ,r-pillar)
16102 ("r-rlang" ,r-rlang)
16103 ("r-tibble" ,r-tibble)
16104 ("r-tidyr" ,r-tidyr)))
16105 (home-page "https://github.com/thomasp85/tidygraph")
16106 (synopsis "Tidy API for graph manipulation")
16108 "This package provides a graph implementation that can be thought of as
16109 two tidy data frames describing node and edge data respectively. It provides
16110 an approach to manipulate these two virtual data frames using the API defined
16111 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16112 common graph algorithms.")
16113 (license license:expat)))
16115 (define-public r-soupx
16116 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16120 (version (git-version "0.3.1" revision commit))
16124 (uri (git-reference
16125 (url "https://github.com/constantAmateur/SoupX")
16127 (file-name (git-file-name name version))
16130 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16131 (properties `((upstream-name . "SoupX")))
16132 (build-system r-build-system)
16134 `(("r-ggplot2" ,r-ggplot2)
16135 ("r-matrix" ,r-matrix)
16136 ("r-seurat" ,r-seurat)))
16137 (home-page "https://github.com/constantAmateur/SoupX")
16138 (synopsis "Single cell mRNA Soup eXterminator")
16140 "This package provides a package for quantifying, profiling and
16141 removing cell free mRNA contamination (the \"soup\") from droplet based single
16142 cell RNA-seq experiments.")
16143 (license license:gpl2))))
16145 (define-public r-assertr
16152 (uri (cran-uri "assertr" version))
16155 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16156 (build-system r-build-system)
16158 `(("r-dplyr" ,r-dplyr)
16160 ("r-rlang" ,r-rlang)))
16162 `(("r-knitr" ,r-knitr))) ; needed for vignette
16163 (home-page "https://github.com/ropensci/assertr")
16164 (synopsis "Assertive programming for R analysis pipelines")
16166 "This package provides functionality to assert conditions that have to be
16167 met so that errors in data used in analysis pipelines can fail quickly. It is
16168 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16170 (license license:expat)))
16172 (define-public r-parameters
16174 (name "r-parameters")
16179 (uri (cran-uri "parameters" version))
16182 "0mylxkf1y6mk4kf6c57x102sf4c800pfasjcfbf1hnsh6ya0m6dy"))))
16183 (properties `((upstream-name . "parameters")))
16184 (build-system r-build-system)
16186 `(("r-bayestestr" ,r-bayestestr)
16187 ("r-insight" ,r-insight)))
16189 `(("r-knitr" ,r-knitr)))
16190 (home-page "https://cran.r-project.org/web/packages/parameters")
16191 (synopsis "Processing of model parameters")
16193 "This package provides utilities for processing the parameters of various
16194 statistical models. Beyond computing p values, CIs, and other indices for a
16195 wide variety of models, this package implements features like standardization
16196 or bootstrapping of parameters and models, feature reduction (feature
16197 extraction and variable selection) as well as conversion between indices of
16199 (license license:gpl3)))
16201 (define-public r-rgdal
16208 (uri (cran-uri "rgdal" version))
16210 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
16211 (properties `((upstream-name . "rgdal")))
16212 (build-system r-build-system)
16220 `(("pkg-config" ,pkg-config)))
16221 (home-page "http://rgdal.r-forge.r-project.org")
16222 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16224 "This package provides bindings to the Geospatial Data Abstraction
16225 Library (GDAL) and access to projection/transformation operations from the
16227 (license license:gpl2+)))
16229 (define-public r-insol
16236 (uri (cran-uri "insol" version))
16239 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16240 (properties `((upstream-name . "insol")))
16241 (build-system r-build-system)
16243 `(("r-raster" ,r-raster)))
16245 `(("gfortran" ,gfortran)))
16246 (home-page "https://meteoexploration.com/R/insol/index.html")
16247 (synopsis "Tools for calculating solar radiation")
16249 "This package provides functions to compute insolation on tilted
16250 surfaces, computes atmospheric transmittance and related parameters such as:
16251 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16252 time, vector in the direction of the sun, vector normal to surface, and some
16253 atmospheric physics.")
16254 (license license:gpl2+)))
16256 (define-public r-lifecycle
16258 (name "r-lifecycle")
16263 (uri (cran-uri "lifecycle" version))
16266 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16267 (properties `((upstream-name . "lifecycle")))
16268 (build-system r-build-system)
16270 `(("r-glue" ,r-glue)
16271 ("r-rlang" ,r-rlang)))
16273 `(("r-knitr" ,r-knitr))) ; for vignettes
16274 (home-page "https://github.com/r-lib/lifecycle")
16275 (synopsis "Manage the life cycle of your package functions")
16277 "Manage the life cycle of your exported functions with shared
16278 conventions, documentation badges, and non-invasive deprecation warnings. The
16279 lifecycle package defines four development stages (experimental, maturing,
16280 stable, and questioning) and three deprecation stages (soft-deprecated,
16281 deprecated, and defunct). It makes it easy to insert badges corresponding to
16282 these stages in your documentation. Usage of deprecated functions are
16283 signalled with increasing levels of non-invasive verbosity.")
16284 (license license:gpl3)))
16286 (define-public r-assertable
16288 (name "r-assertable")
16293 (uri (cran-uri "assertable" version))
16296 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16297 (build-system r-build-system)
16299 `(("r-data-table" ,r-data-table)))
16300 (home-page "https://cran.r-project.org/web/packages/assertable/")
16301 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16302 (description "This package provides simple, flexible assertions on
16303 data.frame or data.table objects with verbose output for vetting. While other
16304 assertion packages apply towards more general use-cases, @code{assertable} is
16305 tailored towards tabular data. It includes functions to check variable names
16306 and values, whether the dataset contains all combinations of a given set of
16307 unique identifiers, and whether it is a certain length. In addition,
16308 @code{assertable} includes utility functions to check the existence of target
16309 files and to efficiently import multiple tabular data files into one
16311 (license license:gpl3)))
16313 (define-public r-quadprog
16315 (name "r-quadprog")
16320 (uri (cran-uri "quadprog" version))
16322 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16323 (build-system r-build-system)
16325 `(("gfortran" ,gfortran)))
16326 (home-page "https://cran.r-project.org/web/packages/quadprog")
16327 (synopsis "Functions to solve quadratic programming problems")
16329 "This package contains routines and documentation for solving quadratic
16330 programming problems.")
16331 (license license:gpl3+)))
16333 (define-public r-desolve
16340 (uri (cran-uri "deSolve" version))
16342 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16343 (properties `((upstream-name . "deSolve")))
16344 (build-system r-build-system)
16346 `(("gfortran" ,gfortran)))
16347 (home-page "https://desolve.r-forge.r-project.org/")
16348 (synopsis "Solvers for initial value problems of differential equations")
16349 (description "This package provides functions that solve initial value
16350 problems of a system of first-order @dfn{ordinary differential
16351 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16352 @dfn{differential algebraic equations} (DAE), and of delay differential
16353 equations. The functions provide an interface to the FORTRAN functions
16354 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16355 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16356 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16357 time steps. The package contains routines designed for solving ODEs resulting
16358 from 1-D, 2-D and 3-D partial differential equations that have been converted
16359 to ODEs by numerical differencing.")
16360 (license license:gpl2+)))
16362 (define-public r-pracma
16368 (uri (cran-uri "pracma" version))
16370 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16371 (build-system r-build-system)
16372 (home-page "https://cran.r-project.org/web/packages/pracma/")
16373 (synopsis "Practical numerical math functions")
16374 (description "This package provides functions for numerical analysis and
16375 linear algebra, numerical optimization, differential equations, plus some
16376 special functions. It uses Matlab function names where appropriate to simplify
16378 (license license:gpl3+)))
16380 (define-public r-subplex
16387 (uri (cran-uri "subplex" version))
16390 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16391 (build-system r-build-system)
16393 `(("gfortran" ,gfortran)))
16394 (home-page "https://cran.r-project.org/web/packages/subplex")
16395 (synopsis "Unconstrained optimization using the subplex algorithm")
16397 "This package implements the Subplex optimization algorithm.
16398 It solves unconstrained optimization problems using a simplex method on
16399 subspaces. The method is well suited for optimizing objective functions that
16400 are noisy or are discontinuous at the solution.")
16401 (license license:gpl3+)))
16403 (define-public r-txtplot
16410 (uri (cran-uri "txtplot" version))
16413 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16414 (build-system r-build-system)
16415 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16416 (synopsis "Text-based plotting")
16417 (description "This package provides functions to produce rudimentary ASCII
16418 graphics directly in the terminal window. This package provides a basic
16419 plotting function (and equivalents of curve, density, acf and barplot) as well
16420 as a boxplot function.")
16421 (license license:lgpl3+)))
16423 (define-public r-bio3d
16430 (uri (cran-uri "bio3d" version))
16433 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16434 (properties `((upstream-name . "bio3d")))
16435 (build-system r-build-system)
16436 (inputs `(("zlib" ,zlib)))
16437 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16438 (home-page "http://thegrantlab.org/bio3d/")
16439 (synopsis "Biological structure analysis")
16441 "This package provides utilities to process, organize and explore protein
16442 structure, sequence and dynamics data. Features include the ability to read
16443 and write structure, sequence and dynamic trajectory data, perform sequence
16444 and structure database searches, data summaries, atom selection, alignment,
16445 superposition, rigid core identification, clustering, torsion analysis,
16446 distance matrix analysis, structure and sequence conservation analysis, normal
16447 mode analysis, principal component analysis of heterogeneous structure data,
16448 and correlation network analysis from normal mode and molecular dynamics data.
16449 In addition, various utility functions are provided to enable the statistical
16450 and graphical power of the R environment to work with biological sequence and
16452 (license license:gpl2+)))
16454 (define-public r-bios2cor
16456 (name "r-bios2cor")
16461 (uri (cran-uri "Bios2cor" version))
16464 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16465 (properties `((upstream-name . "Bios2cor")))
16466 (build-system r-build-system)
16468 `(("r-bigmemory" ,r-bigmemory)
16469 ("r-bio3d" ,r-bio3d)
16470 ("r-circular" ,r-circular)
16471 ("r-igraph" ,r-igraph)))
16472 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16473 (synopsis "From biological sequences and simulations to correlation analysis")
16475 "This package provides utilities for computation and analysis of
16476 correlation/covariation in multiple sequence alignments and in side chain
16477 motions during molecular dynamics simulations. Features include the
16478 computation of correlation/covariation scores using a variety of scoring
16479 functions between either sequence positions in alignments or side chain
16480 dihedral angles in molecular dynamics simulations and utilities to analyze the
16481 correlation/covariation matrix through a variety of tools including network
16482 representation and principal components analysis. In addition, several
16483 utility functions are based on the R graphical environment to provide friendly
16484 tools for help in data interpretation.")
16485 (license license:gpl2+)))
16487 ;; This package includes minified JavaScript files. When upgrading please
16488 ;; check that there are no new minified JavaScript files.
16489 (define-public r-networkd3
16491 (name "r-networkd3")
16496 (uri (cran-uri "networkD3" version))
16499 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16502 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16504 (properties `((upstream-name . "networkD3")))
16505 (build-system r-build-system)
16507 `(#:modules ((guix build utils)
16508 (guix build r-build-system)
16512 (modify-phases %standard-phases
16513 (add-after 'unpack 'process-javascript
16514 (lambda* (#:key inputs #:allow-other-keys)
16515 (with-directory-excursion "inst/htmlwidgets/lib/"
16519 `((,(assoc-ref inputs "d3.v4.js")
16520 "d3-4.5.0/d3.min.js"))))
16521 (lambda (sources targets)
16522 (for-each (lambda (source target)
16523 (format #t "Processing ~a --> ~a~%"
16525 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16526 (call-with-output-file target
16528 (dump-port minified port)))))
16529 sources targets))))
16532 `(("uglify-js" ,uglify-js)
16533 ;; NOTE: Make sure that this version of d3 is still valid when
16534 ;; upgrading the package.
16538 (uri "https://d3js.org/d3.v4.js")
16541 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16543 `(("r-htmlwidgets" ,r-htmlwidgets)
16544 ("r-igraph" ,r-igraph)
16545 ("r-magrittr" ,r-magrittr)))
16546 (home-page "https://cran.r-project.org/package=networkD3")
16547 (synopsis "D3 JavaScript network graphs from R")
16549 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16551 (license license:gpl3+)))
16553 (define-public r-aasea
16560 (uri (cran-uri "aaSEA" version))
16563 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16564 (properties `((upstream-name . "aaSEA")))
16565 (build-system r-build-system)
16567 `(("r-bios2cor" ,r-bios2cor)
16569 ("r-hmisc" ,r-hmisc)
16570 ("r-magrittr" ,r-magrittr)
16571 ("r-networkd3" ,r-networkd3)
16572 ("r-plotly" ,r-plotly)
16573 ("r-seqinr" ,r-seqinr)
16574 ("r-shiny" ,r-shiny)
16575 ("r-shinydashboard" ,r-shinydashboard)))
16576 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16577 (synopsis "Amino acid substitution effect analyzer")
16579 "Given a protein multiple sequence alignment, it is a daunting task to
16580 assess the effects of substitutions along sequence length. The aaSEA package
16581 is intended to help researchers to rapidly analyze property changes caused by
16582 single, multiple and correlated amino acid substitutions in proteins.")
16583 (license license:gpl3)))
16585 (define-public r-abacus
16592 (uri (cran-uri "ABACUS" version))
16595 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16596 (properties `((upstream-name . "ABACUS")))
16597 (build-system r-build-system)
16599 `(("r-ggplot2" ,r-ggplot2)
16600 ("r-shiny" ,r-shiny)))
16601 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16602 (synopsis "Apps-based activities for communicating and understanding statistics")
16604 "This package provides a set of Shiny apps for effective communication
16605 and understanding in statistics. The current version includes properties of
16606 normal distribution, properties of sampling distribution, one-sample z and t
16607 tests, two samples independent (unpaired) t test and analysis of variance.")
16608 (license license:gpl3)))
16610 (define-public r-abc-rap
16617 (uri (cran-uri "ABC.RAP" version))
16620 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16621 (properties `((upstream-name . "ABC.RAP")))
16622 (build-system r-build-system)
16623 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16624 (synopsis "Array-based CpG region analysis pipeline")
16626 "This package aims to identify candidate genes that are differentially
16627 methylated between cases and controls. It applies Student's t-test and delta
16628 beta analysis to identify candidate genes containing multiple CpG sites.")
16629 (license license:gpl3)))
16631 (define-public r-abcadm
16638 (uri (cran-uri "abcADM" version))
16641 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16642 (properties `((upstream-name . "abcADM")))
16643 (build-system r-build-system)
16646 ("r-rcpp" ,r-rcpp)))
16647 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16648 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16650 "This package provides tools to estimate parameters of accumulated
16651 damage (load duration) models based on failure time data under a Bayesian
16652 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16653 long-term reliability under stochastic load profiles.")
16654 (license license:gpl3)))
16656 (define-public r-rglpk
16663 (uri (cran-uri "Rglpk" version))
16666 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16667 (properties `((upstream-name . "Rglpk")))
16668 (build-system r-build-system)
16670 `(("r-slam" ,r-slam)))
16673 (home-page "https://r-forge.r-project.org/projects/rglp/")
16674 (synopsis "R interface to the GNU Linear Programming Kit")
16676 "This package provides an R interface to the GNU Linear Programming Kit,
16677 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16678 integer linear programming} (MILP) and other related problems.")
16680 (license (list license:gpl2 license:gpl3))))
16682 (define-public r-abcdefba
16684 (name "r-abcdefba")
16689 (uri (cran-uri "abcdeFBA" version))
16692 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16693 (properties `((upstream-name . "abcdeFBA")))
16694 (build-system r-build-system)
16696 `(("r-corrplot" ,r-corrplot)
16697 ("r-lattice" ,r-lattice)
16699 ("r-rglpk" ,r-rglpk)))
16700 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16701 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16703 "This package provides functions for Constraint Based Simulation using
16704 Flux Balance Analysis and informative analysis of the data generated during
16706 (license license:gpl2)))
16708 (define-public r-abcrlda
16715 (uri (cran-uri "abcrlda" version))
16718 "0zjdrbg3zx0znqnh0dvmifs9c12b8vjhbaf3nbwab9xh25nsmg75"))))
16719 (properties `((upstream-name . "abcrlda")))
16720 (build-system r-build-system)
16721 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16722 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16724 "This package offers methods to perform @dfn{asymptotically
16725 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16726 cost-sensitive binary classification. The bias-correction is an estimate of
16727 the bias term added to regularized discriminant analysis that minimizes the
16729 (license license:gpl3)))
16731 (define-public r-abemus
16738 (uri (cran-uri "abemus" version))
16741 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16742 (properties `((upstream-name . "abemus")))
16743 (build-system r-build-system)
16745 `(("r-data-table" ,r-data-table)))
16746 (home-page "https://cran.r-project.org/web/packages/abemus/")
16747 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16749 "This package provides an implementation of @dfn{Adaptive Base Error
16750 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16751 platform-specific genetic knowledge and empirical signal to readily detect and
16752 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16753 cell free DNA} (cfDNA).")
16754 (license license:gpl3)))
16756 ;; This package includes minified JavaScript files. When upgrading please
16757 ;; check that there are no new minified JavaScript files.
16758 (define-public r-rintrojs
16760 (name "r-rintrojs")
16765 (uri (cran-uri "rintrojs" version))
16768 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16769 (properties `((upstream-name . "rintrojs")))
16770 (build-system r-build-system)
16772 `(#:modules ((guix build utils)
16773 (guix build r-build-system)
16777 (modify-phases %standard-phases
16778 (add-after 'unpack 'process-javascript
16779 (lambda* (#:key inputs #:allow-other-keys)
16780 (with-directory-excursion "inst/javascript/introjs/"
16784 `((,(assoc-ref inputs "intro.js")
16786 (lambda (sources targets)
16787 (for-each (lambda (source target)
16788 (format #t "Processing ~a --> ~a~%"
16790 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16791 (call-with-output-file target
16793 (dump-port minified port)))))
16794 sources targets))))
16797 `(("uglify-js" ,uglify-js)
16801 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16804 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16806 `(("r-jsonlite" ,r-jsonlite)
16807 ("r-shiny" ,r-shiny)))
16808 (home-page "https://github.com/carlganz/rintrojs")
16809 (synopsis "Wrapper for the Intro.js library")
16811 "This package provides a wrapper for the @url{http://www.introjs.com,
16812 Intro.js} library. This package makes it easy to include step-by-step
16813 introductions, and clickable hints in a Shiny application. It supports both
16814 static introductions in the UI, and programmatic introductions from the
16816 (license license:agpl3+)))
16818 (define-public r-sysfonts
16820 (name "r-sysfonts")
16825 (uri (cran-uri "sysfonts" version))
16828 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16829 (properties `((upstream-name . "sysfonts")))
16830 (build-system r-build-system)
16832 `(("freetype" ,freetype)
16836 `(("pkg-config" ,pkg-config)))
16837 (home-page "https://github.com/yixuan/sysfonts")
16838 (synopsis "Loading fonts into R")
16840 "This is a package to simplify loading of system fonts and Google Fonts
16841 into R, in order to support other packages.")
16842 (license license:gpl2)))
16844 (define-public r-showtextdb
16846 (name "r-showtextdb")
16851 (uri (cran-uri "showtextdb" version))
16854 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16855 (properties `((upstream-name . "showtextdb")))
16856 (build-system r-build-system)
16858 `(("r-sysfonts" ,r-sysfonts)))
16859 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16860 (synopsis "Font files for the 'showtext' package")
16862 "This package provides font files that can be used by the @code{showtext}
16864 (license license:asl2.0)))
16866 (define-public r-showtext
16868 (name "r-showtext")
16873 (uri (cran-uri "showtext" version))
16876 "0a5gg72bfrc7wm0phj1aflj1wc08kfi81ac32na6ya9s2ivyimw5"))))
16877 (properties `((upstream-name . "showtext")))
16878 (build-system r-build-system)
16880 `(("freetype" ,freetype)
16884 `(("r-showtextdb" ,r-showtextdb)
16885 ("r-sysfonts" ,r-sysfonts)))
16886 (native-inputs `(("pkg-config" ,pkg-config)))
16887 (home-page "https://github.com/yixuan/showtext")
16888 (synopsis "Using fonts more easily in R graphs")
16890 "This package aims to make it easy to use various types of
16891 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16892 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16893 will be converted into polygons or raster images, hence after the plot has
16894 been created, it no longer relies on the font files. No external software
16895 such as Ghostscript is needed to use this package.")
16896 (license license:asl2.0)))
16898 (define-public r-emojifont
16900 (name "r-emojifont")
16905 (uri (cran-uri "emojifont" version))
16908 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16909 (properties `((upstream-name . "emojifont")))
16910 (build-system r-build-system)
16912 `(("r-ggplot2" ,r-ggplot2)
16913 ("r-proto" ,r-proto)
16914 ("r-showtext" ,r-showtext)
16915 ("r-sysfonts" ,r-sysfonts)))
16916 (home-page "https://guangchuangyu.github.io/emojifont")
16917 (synopsis "Emoji and Font Awesome in R graphics")
16919 "This package enables the use of emoji and the Font Awesome glyphs in
16920 both base and ggplot2 graphics.")
16921 (license license:artistic2.0)))
16923 (define-public r-abstractr
16925 (name "r-abstractr")
16930 (uri (cran-uri "abstractr" version))
16933 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16934 (properties `((upstream-name . "abstractr")))
16935 (build-system r-build-system)
16937 `(("r-colourpicker" ,r-colourpicker)
16938 ("r-emojifont" ,r-emojifont)
16939 ("r-ggplot2" ,r-ggplot2)
16940 ("r-gridextra" ,r-gridextra)
16941 ("r-rintrojs" ,r-rintrojs)
16942 ("r-shiny" ,r-shiny)
16943 ("r-shinythemes" ,r-shinythemes)))
16944 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16945 (synopsis "R-Shiny application for creating visual abstracts")
16947 "This package provides an R Shiny application to create visual abstracts
16948 for original research. A variety of user defined options and formatting are
16950 (license license:gpl3)))
16952 (define-public r-qgam
16959 (uri (cran-uri "qgam" version))
16962 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
16963 (properties `((upstream-name . "qgam")))
16964 (build-system r-build-system)
16966 `(("r-doparallel" ,r-doparallel)
16969 ("r-shiny" ,r-shiny)))
16970 (native-inputs `(("r-knitr" ,r-knitr)))
16971 (home-page "https://cran.r-project.org/web/packages/qgam/")
16972 (synopsis "Smooth additive quantile regression models")
16974 "This package provides smooth additive quantile regression models, fitted
16975 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
16976 the smoothing parameters are estimated automatically by marginal loss
16977 minimization, while the regression coefficients are estimated using either
16978 PIRLS or Newton algorithm. The learning rate is determined so that the
16979 Bayesian credible intervals of the estimated effects have approximately the
16980 correct coverage. The main function is @code{qgam()} which is similar to
16981 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
16982 regression models.")
16983 (license license:gpl2+)))
16985 (define-public r-abtest
16992 (uri (cran-uri "abtest" version))
16995 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
16996 (properties `((upstream-name . "abtest")))
16997 (build-system r-build-system)
16999 `(("r-matrix" ,r-matrix)
17000 ("r-mvtnorm" ,r-mvtnorm)
17001 ("r-plotrix" ,r-plotrix)
17003 ("r-rcolorbrewer" ,r-rcolorbrewer)
17006 ("r-truncnorm" ,r-truncnorm)))
17007 (home-page "https://cran.r-project.org/web/packages/abtest/")
17008 (synopsis "Bayesian A/B testing")
17010 "This package provides functions for Bayesian A/B testing including prior
17011 elicitation options based on Kass and Vaidyanathan (1992)
17012 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17013 (license license:gpl2+)))
17015 (define-public r-accept
17022 (uri (cran-uri "accept" version))
17025 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17026 (properties `((upstream-name . "accept")))
17027 (build-system r-build-system)
17029 `(("r-dplyr" ,r-dplyr)
17030 ("r-extrafont" ,r-extrafont)
17032 ("r-plotly" ,r-plotly)
17033 ("r-stringr" ,r-stringr)
17034 ("r-viridis" ,r-viridis)))
17035 (home-page "https://cran.r-project.org/web/packages/accept/")
17036 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17038 "This package allows clinicians to predict the rate and severity of
17039 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17040 Disease} (COPD) patients, based on the clinical prediction model published in
17041 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17042 (license license:gpl3)))
17044 (define-public r-smpracticals
17046 (name "r-smpracticals")
17051 (uri (cran-uri "SMPracticals" version))
17054 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17055 (properties `((upstream-name . "SMPracticals")))
17056 (build-system r-build-system)
17058 `(("r-ellipse" ,r-ellipse)
17061 ("r-survival" ,r-survival)))
17062 (home-page "http://statwww.epfl.ch/davison/SM/")
17063 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17065 "This package contains the datasets and a few functions for use with the
17066 practicals outlined in Appendix A of the book Statistical Models (Davison,
17067 2003, Cambridge University Press). The practicals themselves can be found at
17068 @url{http://statwww.epfl.ch/davison/SM/}.")
17069 (license license:gpl2+)))
17071 (define-public r-fgui
17078 (uri (cran-uri "fgui" version))
17081 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17082 (properties `((upstream-name . "fgui")))
17083 (build-system r-build-system)
17085 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17086 (synopsis "Create GUI for R functions")
17088 "Rapidly create a GUI for a function you created by automatically
17089 creating widgets for arguments of the function. This package automatically
17090 parses help routines for context-sensitive help to these arguments. The
17091 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17092 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17093 incorporated into the interface for greater customization for the more
17095 ;; Any version of the GPL.
17096 (license (list license:gpl2+ license:gpl3+))))
17098 (define-public r-tcltk2
17105 (uri (cran-uri "tcltk2" version))
17108 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17109 (properties `((upstream-name . "tcltk2")))
17110 (build-system r-build-system)
17114 (home-page "https://www.sciviews.org/SciViews-R")
17115 (synopsis "Tcl/Tk additions")
17117 "This package provides a series of additional Tcl commands and Tk widgets
17118 with style and various functions to supplement the tcltk package")
17119 (license license:lgpl3)))
17121 (define-public r-accrual
17128 (uri (cran-uri "accrual" version))
17131 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17132 (properties `((upstream-name . "accrual")))
17133 (build-system r-build-system)
17135 `(("r-fgui" ,r-fgui)
17136 ("r-smpracticals" ,r-smpracticals)
17137 ("r-tcltk2" ,r-tcltk2)))
17138 (home-page "https://cran.r-project.org/web/packages/accrual/")
17139 (synopsis "Bayesian accrual prediction")
17141 "Subject recruitment for medical research is challenging. Slow patient
17142 accrual leads to delay in research. Accrual monitoring during the process of
17143 recruitment is critical. Researchers need reliable tools to manage the
17144 accrual rate. This package provides an implementation of a Bayesian method
17145 that integrates researcher's experience on previous trials and data from the
17146 current study, providing reliable prediction on accrual rate for clinical
17147 studies. It provides functions for Bayesian accrual prediction which can be
17148 easily used by statisticians and clinical researchers.")
17149 (license license:gpl2)))
17151 (define-public r-accrued
17158 (uri (cran-uri "accrued" version))
17161 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17162 (properties `((upstream-name . "accrued")))
17163 (build-system r-build-system)
17164 (home-page "https://cran.r-project.org/web/packages/accrued/")
17165 (synopsis "Data quality visualization tools for partially accruing data")
17167 "This is a package for visualizing data quality of partially accruing
17169 (license license:gpl3)))
17171 (define-public r-mda
17178 (uri (cran-uri "mda" version))
17181 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
17182 (properties `((upstream-name . "mda")))
17183 (build-system r-build-system)
17184 (propagated-inputs `(("r-class" ,r-class)))
17185 (native-inputs `(("gfortran" ,gfortran)))
17186 (home-page "https://cran.r-project.org/web/packages/mda/")
17187 (synopsis "Mixture and flexible discriminant analysis")
17189 "This is a package for mixture and flexible discriminant analysis,
17190 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17191 (license license:gpl2)))
17193 (define-public r-elasticnet
17195 (name "r-elasticnet")
17200 (uri (cran-uri "elasticnet" version))
17203 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
17204 (properties `((upstream-name . "elasticnet")))
17205 (build-system r-build-system)
17207 `(("r-lars" ,r-lars)))
17208 (home-page "http://users.stat.umn.edu/~zouxx019/")
17209 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17211 "This package provides functions for fitting the entire solution path of
17212 the Elastic-Net and also provides functions for estimating sparse Principal
17213 Components. The Lasso solution paths can be computed by the same function.")
17214 (license license:gpl2+)))
17216 (define-public r-sparselda
17218 (name "r-sparselda")
17223 (uri (cran-uri "sparseLDA" version))
17226 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17227 (properties `((upstream-name . "sparseLDA")))
17228 (build-system r-build-system)
17230 `(("r-elasticnet" ,r-elasticnet)
17233 (home-page "https://www.imm.dtu.dk/~lkhc/")
17234 (synopsis "Sparse discriminant analysis")
17236 "This package performs sparse linear discriminant analysis for Gaussians
17237 and mixture of Gaussian models.")
17238 (license license:gpl2+)))
17240 (define-public r-accsda
17247 (uri (cran-uri "accSDA" version))
17250 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17251 (properties `((upstream-name . "accSDA")))
17252 (build-system r-build-system)
17254 `(("r-ggplot2" ,r-ggplot2)
17255 ("r-ggthemes" ,r-ggthemes)
17256 ("r-gridextra" ,r-gridextra)
17258 ("r-rarpack" ,r-rarpack)
17259 ("r-sparselda" ,r-sparselda)))
17260 (home-page "https://github.com/gumeo/accSDA/wiki")
17261 (synopsis "Accelerated sparse discriminant analysis")
17263 "This package provides an implementation of sparse linear discriminant
17264 analysis, which is a supervised classification method for multiple classes.
17265 Various novel optimization approaches to this problem are implemented
17266 including @dfn{alternating direction method of multipliers} (ADMM),
17267 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17268 Functions for performing cross validation are also supplied along with basic
17269 prediction and plotting functions. @dfn{Sparse zero variance
17270 discriminant} (SZVD) analysis is also included in the package.")
17271 (license license:gpl2+)))
17273 (define-public r-ace2fastq
17275 (name "r-ace2fastq")
17280 (uri (cran-uri "ace2fastq" version))
17283 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17284 (properties `((upstream-name . "ace2fastq")))
17285 (build-system r-build-system)
17287 `(("r-stringr" ,r-stringr)))
17288 (home-page "https://github.com/c5sire/ace2fastq")
17289 (synopsis "ACE file to FASTQ converter")
17291 "The ACE file format is used in genomics to store contigs from sequencing
17292 machines. This tools converts it into FASTQ format. Both formats contain the
17293 sequence characters and their corresponding quality information. Unlike the
17294 FASTQ file, the ACE file stores the quality values numerically. The
17295 conversion algorithm uses the standard Sanger formula. The package
17296 facilitates insertion into pipelines, and content inspection.")
17297 (license license:gpl3)))
17299 (define-public r-rngwell
17306 (uri (cran-uri "rngWELL" version))
17309 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17310 (properties `((upstream-name . "rngWELL")))
17311 (build-system r-build-system)
17312 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17313 (synopsis "Toolbox for WELL random number generators")
17315 "This is a dedicated package to WELL pseudo random generators, which were
17316 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17317 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17318 (license license:bsd-3)))
17320 (define-public r-randtoolbox
17322 (name "r-randtoolbox")
17327 (uri (cran-uri "randtoolbox" version))
17330 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17331 (properties `((upstream-name . "randtoolbox")))
17332 (build-system r-build-system)
17334 `(("r-rngwell" ,r-rngwell)))
17336 `(("gfortran" ,gfortran)))
17337 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17338 (synopsis "Toolbox for pseudo and quasi random number generation")
17340 "This package provides
17343 @item pseudo random generators, such as general linear
17344 congruential generators, multiple recursive generators and generalized
17345 feedback shift register (SF-Mersenne Twister algorithm and WELL
17348 @item quasi random generators, such as the Torus algorithm, the Sobol
17349 sequence, the Halton sequence (including the Van der Corput sequence), and
17351 @item some generator tests: the gap test, the serial test, the poker test.
17354 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17355 (license license:bsd-3)))
17357 (define-public r-lhs
17364 (uri (cran-uri "lhs" version))
17367 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17368 (properties `((upstream-name . "lhs")))
17369 (build-system r-build-system)
17370 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17372 `(("r-knitr" ,r-knitr)))
17373 (home-page "https://github.com/bertcarnell/lhs")
17374 (synopsis "Latin Hypercube Samples")
17376 "This package provides a number of methods for creating and augmenting
17377 Latin Hypercube Samples.")
17378 (license license:gpl3)))
17380 (define-public r-acebayes
17382 (name "r-acebayes")
17387 (uri (cran-uri "acebayes" version))
17390 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17391 (properties `((upstream-name . "acebayes")))
17392 (build-system r-build-system)
17394 `(("r-compare" ,r-compare)
17396 ("r-randtoolbox" ,r-randtoolbox)
17398 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17399 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17400 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17402 "Finding an optimal Bayesian experimental design involves maximizing an
17403 objective function given by the expectation of some appropriately chosen
17404 utility function with respect to the joint distribution of unknown
17405 quantities (including responses). This objective function is usually not
17406 available in closed form and the design space can be continuous and of high
17407 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17408 to maximise an approximation to the expectation of the utility function.")
17409 (license license:gpl2)))
17411 (define-public r-acet
17418 (uri (cran-uri "ACEt" version))
17421 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17422 (properties `((upstream-name . "ACEt")))
17423 (build-system r-build-system)
17428 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17429 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17430 (synopsis "Estimating dynamic heritability and twin model comparison")
17432 "This package supports twin models that are able to estimate the dynamic
17433 behaviour of the variance components in the classical twin models with respect
17434 to age using B-splines and P-splines.")
17435 (license license:gpl2+)))
17437 (define-public r-acfmperiod
17439 (name "r-acfmperiod")
17444 (uri (cran-uri "acfMPeriod" version))
17447 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17448 (properties `((upstream-name . "acfMPeriod")))
17449 (build-system r-build-system)
17451 `(("r-mass" ,r-mass)))
17452 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17453 (synopsis "Estimation of the ACF from the M-periodogram")
17455 "This package support non-robust and robust computations of the sample
17456 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17457 univariate and multivariate processes. The methodology consists in reversing
17458 the diagonalization procedure involving the periodogram or the
17459 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17460 ACOVF or the ACF as discussed in Fuller (1995)
17461 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17462 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17463 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17464 (license license:gpl2+)))
17466 (define-public r-gamlss-data
17468 (name "r-gamlss-data")
17473 (uri (cran-uri "gamlss.data" version))
17476 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17477 (properties `((upstream-name . "gamlss.data")))
17478 (build-system r-build-system)
17479 (home-page "http://www.gamlss.org/")
17480 (synopsis "GAMLSS data")
17482 "This package provides data used as examples to demonstrate GAMLSS
17484 ;; Either version of the license
17485 (license (list license:gpl2 license:gpl3))))
17487 (define-public r-gamlss
17494 (uri (cran-uri "gamlss" version))
17497 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17498 (properties `((upstream-name . "gamlss")))
17499 (build-system r-build-system)
17501 `(("r-gamlss-data" ,r-gamlss-data)
17502 ("r-gamlss-dist" ,r-gamlss-dist)
17505 ("r-survival" ,r-survival)))
17506 (home-page "http://www.gamlss.org/")
17507 (synopsis "Generalized additive models for location scale and shape")
17509 "This package provides functions for fitting the generalized additive
17510 models for location scale and shape introduced by Rigby and
17511 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17512 use a distributional regression approach where all the parameters of the
17513 conditional distribution of the response variable are modelled using
17514 explanatory variables.")
17515 ;; Either version of the license
17516 (license (list license:gpl2 license:gpl3))))
17518 (define-public r-acid
17525 (uri (cran-uri "acid" version))
17528 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17529 (properties `((upstream-name . "acid")))
17530 (build-system r-build-system)
17532 `(("r-gamlss" ,r-gamlss)
17533 ("r-gamlss-dist" ,r-gamlss-dist)
17534 ("r-hmisc" ,r-hmisc)))
17535 (home-page "https://cran.r-project.org/web/packages/acid/")
17536 (synopsis "Analysing conditional income distributions")
17538 "This package provides functions for the analysis of income distributions
17539 for subgroups of the population as defined by a set of variables like age,
17540 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17541 distribution as well as functions for moments, inequality measures, entropy
17542 measures and polarisation measures of income distributions. This package thus
17543 aides the analysis of income inequality by offering tools for the exploratory
17544 analysis of income distributions at the disaggregated level.")
17545 (license license:gpl3)))
17547 (define-public r-acm4r
17554 (uri (cran-uri "acm4r" version))
17557 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17558 (properties `((upstream-name . "acm4r")))
17559 (build-system r-build-system)
17560 (propagated-inputs `(("r-mass" ,r-mass)))
17561 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17562 (synopsis "Align-and-count method comparisons of RFLP data")
17564 "This is a package to compare sequence fragment lengths or molecular
17565 weights from pairs of lanes. The number of matching bands in the
17566 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17567 the align-and-count method.")
17568 ;; Any version of the GPL
17569 (license (list license:gpl2+ license:gpl3+))))
17571 (define-public r-filematrix
17573 (name "r-filematrix")
17578 (uri (cran-uri "filematrix" version))
17581 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17582 (properties `((upstream-name . "filematrix")))
17583 (build-system r-build-system)
17584 ;; These inputs are needed for vignettes
17586 `(("r-knitr" ,r-knitr)
17587 ("r-rmarkdown" ,r-rmarkdown)
17588 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17589 (home-page "https://github.com/andreyshabalin/filematrix")
17590 (synopsis "File-backed matrix class with convenient read and write access")
17592 "This package provides an interface for working with large matrices
17593 stored in files, not in computer memory. It supports multiple non-character
17594 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17595 byte real values). Access to parts of the matrix is done by indexing, exactly
17596 as with usual R matrices. It supports very large matrices; the package has
17597 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17598 columns, ad allows for quick addition of extra columns to a filematrix.")
17599 (license license:lgpl3)))
17601 (define-public r-acmeeqtl
17603 (name "r-acmeeqtl")
17608 (uri (cran-uri "ACMEeqtl" version))
17611 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17612 (properties `((upstream-name . "ACMEeqtl")))
17613 (build-system r-build-system)
17615 `(("r-filematrix" ,r-filematrix)))
17616 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17617 (synopsis "Estimation of interpretable eQTL effect sizes")
17619 "This package provides a non-linear model, termed ACME, that reflects a
17620 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17621 With non-linear least-squares algorithm the maximum likelihood parameters can
17622 be estimated. The ACME model provides interpretable effect size estimates and
17623 p-values with well controlled Type-I error.")
17624 (license license:lgpl3)))
17626 (define-public r-acmer
17633 (uri (cran-uri "acmeR" version))
17636 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17637 (properties `((upstream-name . "acmeR")))
17638 (build-system r-build-system)
17639 (propagated-inputs `(("r-foreign" ,r-foreign)))
17640 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17641 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17643 "This package provides an implementation of the ACME estimator, described
17644 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17645 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17646 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17647 as carcasses age; variable bleed-through at successive searches; and interval
17648 mortality estimates. The package provides, based on search data, functions
17649 for estimating the mortality inflation factor in Frequentist and Bayesian
17651 (license license:expat)))
17653 (define-public r-r-huge
17660 (uri (cran-uri "R.huge" version))
17663 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17664 (properties `((upstream-name . "R.huge")))
17665 (build-system r-build-system)
17667 `(("r-r-methodss3" ,r-r-methodss3)
17669 ("r-r-utils" ,r-r-utils)))
17670 (home-page "https://github.com/HenrikBengtsson/R.huge")
17671 (synopsis "Methods for accessing huge amounts of data")
17673 "This is a deprecated package for accessing huge amounts of data.
17674 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17675 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17676 the @code{aroma.affymetrix} package.")
17677 (license license:lgpl2.1+)))
17679 (define-public r-r-filesets
17681 (name "r-r-filesets")
17686 (uri (cran-uri "R.filesets" version))
17689 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17690 (properties `((upstream-name . "R.filesets")))
17691 (build-system r-build-system)
17693 `(("r-digest" ,r-digest)
17694 ("r-r-cache" ,r-r-cache)
17695 ("r-r-methodss3" ,r-r-methodss3)
17697 ("r-r-utils" ,r-r-utils)))
17698 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17699 (synopsis "Easy handling of and access to files")
17701 "This package provides classes and methods to locate, setup, subset,
17702 navigate and iterate file sets, i.e. sets of files located in one or more
17703 directories on the file system. The API is designed such that these classes
17704 can be extended via inheritance to provide a richer API for special file
17705 formats. Moreover, a specific name format is defined such that filenames and
17706 directories can be considered to have full names which consists of a name
17707 followed by comma-separated tags. This adds additional flexibility to
17708 identify file sets and individual files.")
17709 (license license:lgpl2.1+)))
17711 (define-public r-r-devices
17713 (name "r-r-devices")
17718 (uri (cran-uri "R.devices" version))
17721 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17722 (properties `((upstream-name . "R.devices")))
17723 (build-system r-build-system)
17725 `(("r-base64enc" ,r-base64enc)
17726 ("r-r-methodss3" ,r-r-methodss3)
17728 ("r-r-utils" ,r-r-utils)))
17729 (home-page "https://github.com/HenrikBengtsson/R.devices")
17730 (synopsis "Unified handling of graphics devices")
17732 "This package provides functions for creating plots and image files in a
17733 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17734 Default device options as well as scales and aspect ratios are controlled in a
17735 uniform way across all device types. Switching output format requires minimal
17736 changes in code. This package is ideal for large-scale batch processing,
17737 because it will never leave open graphics devices or incomplete image files
17738 behind, even on errors or user interrupts.")
17739 (license license:lgpl2.1+)))
17741 (define-public r-acnr
17748 (uri (cran-uri "acnr" version))
17751 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17752 (properties `((upstream-name . "acnr")))
17753 (build-system r-build-system)
17754 (home-page "https://github.com/mpierrejean/acnr")
17755 (synopsis "Annotated copy-number regions")
17757 "This package provides SNP array data from different types of copy-number
17758 regions. These regions were identified manually by the authors of the package
17759 and may be used to generate realistic data sets with known truth.")
17760 (license license:lgpl2.1+)))
17762 (define-public r-acopula
17769 (uri (cran-uri "acopula" version))
17772 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17773 (properties `((upstream-name . "acopula")))
17774 (build-system r-build-system)
17775 (home-page "https://cran.r-project.org/web/packages/acopula/")
17776 (synopsis "Modelling dependence with multivariate Archimax copulas")
17778 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17779 package provides definitions of several parametric families of generator and
17780 dependence function, computes CDF and PDF, estimates parameters, tests for
17781 goodness of fit, generates random sample and checks copula properties for
17782 custom constructs. In the 2-dimensional case explicit formulas for density
17783 are used, contrary to higher dimensions when all derivatives are linearly
17784 approximated. Several non-archimax families (normal, FGM, Plackett) are
17785 provided as well.")
17786 (license license:gpl2)))
17788 (define-public r-tuner
17795 (uri (cran-uri "tuneR" version))
17798 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17799 (properties `((upstream-name . "tuneR")))
17800 (build-system r-build-system)
17801 (propagated-inputs `(("r-signal" ,r-signal)))
17802 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17803 (synopsis "Analysis of music and speech")
17805 "This is a package for the analysis of music and speech. Analyze music
17806 and speech, extract features like MFCCs, handle wave files and their
17807 representation in various ways, read MP3, read MIDI, perform steps of a
17808 transcription, ...")
17809 ;; Either of these versions.
17810 (license (list license:gpl2 license:gpl3))))
17812 (define-public r-seewave
17819 (uri (cran-uri "seewave" version))
17822 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17823 (properties `((upstream-name . "seewave")))
17824 (build-system r-build-system)
17826 `(("r-tuner" ,r-tuner)))
17827 (home-page "http://rug.mnhn.fr/seewave")
17828 (synopsis "Sound analysis and synthesis")
17830 "This package provides functions for analysing, manipulating, displaying,
17831 editing and synthesizing time waves (particularly sound). This package
17832 processes time analysis (oscillograms and envelopes), spectral content,
17833 resonance quality factor, entropy, cross correlation and autocorrelation,
17834 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17835 and 3D spectrograms and many other analyses.")
17836 (license license:gpl2+)))
17838 (define-public r-acousticndlcoder
17840 (name "r-acousticndlcoder")
17845 (uri (cran-uri "AcousticNDLCodeR" version))
17848 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17850 `((upstream-name . "AcousticNDLCodeR")))
17851 (build-system r-build-system)
17853 `(("r-seewave" ,r-seewave)
17854 ("r-tuner" ,r-tuner)
17856 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17857 (synopsis "Coding sound files for use with NDL")
17859 "Make acoustic cues to use with the R package @code{ndl}.
17860 The package implements functions used in the PLoS ONE paper \"Words from
17861 spontaneous conversational speech can be recognized with human-like accuracy
17862 by an error-driven learning algorithm that discriminates between meanings
17863 straight from smart acoustic features, bypassing the phoneme as recognition
17864 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17865 (license license:gpl2+)))
17867 (define-public r-acp
17874 (uri (cran-uri "acp" version))
17877 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17878 (properties `((upstream-name . "acp")))
17879 (build-system r-build-system)
17881 `(("r-quantmod" ,r-quantmod)
17882 ("r-tseries" ,r-tseries)))
17883 (home-page "https://cran.r-project.org/web/packages/acp/")
17884 (synopsis "Autoregressive conditional Poisson")
17886 "This package supports the analysis of count data exhibiting
17887 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17888 model (ACP(p,q)) proposed by Heinen (2003).")
17889 (license license:gpl2)))
17891 (define-public r-ada
17898 (uri (cran-uri "ada" version))
17901 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17902 (properties `((upstream-name . "ada")))
17903 (build-system r-build-system)
17904 (propagated-inputs `(("r-rpart" ,r-rpart)))
17905 (home-page "https://cran.r-project.org/web/packages/ada/")
17906 (synopsis "Stochastic boosting")
17908 "This package provides a straightforward, well-documented, and broad
17909 boosting routine for classification, ideally suited for small to
17910 moderate-sized data sets. It performs discrete, real, and gentle boost under
17911 both exponential and logistic loss on a given data set.")
17912 ;; Any version of the GPL.
17913 (license (list license:gpl2+ license:gpl3+))))
17915 (define-public r-genalg
17922 (uri (cran-uri "genalg" version))
17925 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17926 (properties `((upstream-name . "genalg")))
17927 (build-system r-build-system)
17928 (home-page "https://github.com/egonw/genalg")
17929 (synopsis "R based genetic algorithm")
17931 "This package provides an R based genetic algorithm for binary and
17932 floating point chromosomes.")
17933 (license license:gpl2)))
17935 (define-public r-kernelfactory
17937 (name "r-kernelfactory")
17942 (uri (cran-uri "kernelFactory" version))
17945 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17946 (properties `((upstream-name . "kernelFactory")))
17947 (build-system r-build-system)
17950 ("r-genalg" ,r-genalg)
17951 ("r-kernlab" ,r-kernlab)
17952 ("r-randomforest" ,r-randomforest)))
17953 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17954 (synopsis "Ensemble of kernel machines")
17956 "Kernel factory is an ensemble method where each base classifier (random
17957 forest) is fit on the kernel matrix of a subset of the training data.")
17958 (license license:gpl2+)))
17960 (define-public r-dummies
17967 (uri (cran-uri "dummies" version))
17970 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17971 (properties `((upstream-name . "dummies")))
17972 (build-system r-build-system)
17973 (home-page "https://decisionpatterns.com")
17974 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17976 "This package lets you expand factors, characters and other eligible
17977 classes into dummy/indicator variables.")
17978 (license license:gpl2+)))
17980 (define-public r-acrm
17987 (uri (cran-uri "aCRM" version))
17990 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17991 (properties `((upstream-name . "aCRM")))
17992 (build-system r-build-system)
17995 ("r-dummies" ,r-dummies)
17996 ("r-kernelfactory" ,r-kernelfactory)
17997 ("r-randomforest" ,r-randomforest)))
17998 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17999 (synopsis "Convenience functions for analytical customer relationship management")
18001 "This package provides convenience functions for data preparation and
18002 modeling often used in @dfn{analytical customer relationship
18003 management} (aCRM).")
18004 (license license:gpl2+)))
18006 (define-public r-treeclust
18008 (name "r-treeclust")
18013 (uri (cran-uri "treeClust" version))
18016 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18017 (properties `((upstream-name . "treeClust")))
18018 (build-system r-build-system)
18020 `(("r-cluster" ,r-cluster)
18021 ("r-rpart" ,r-rpart)))
18022 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18023 (synopsis "Cluster distances through trees")
18025 "This package provides tools to create a measure of inter-point
18026 dissimilarity useful for clustering mixed data, and, optionally, perform the
18028 (license license:gpl2+)))
18030 (define-public r-acrosstic
18032 (name "r-acrosstic")
18037 (uri (cran-uri "AcrossTic" version))
18040 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18041 (properties `((upstream-name . "AcrossTic")))
18042 (build-system r-build-system)
18044 `(("r-lpsolve" ,r-lpsolve)
18045 ("r-treeclust" ,r-treeclust)))
18046 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18047 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18049 "This is a package for constructing minimum-cost regular spanning
18050 subgraph as part of a non-parametric two-sample test for equality of
18052 (license license:gpl2+)))
18054 (define-public r-acrt
18061 (uri (cran-uri "acrt" version))
18064 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18065 (properties `((upstream-name . "acrt")))
18066 (build-system r-build-system)
18068 `(("r-rcpp" ,r-rcpp)
18069 ("r-rcppeigen" ,r-rcppeigen)
18070 ("r-sandwich" ,r-sandwich)))
18071 (home-page "https://cran.r-project.org/web/packages/acrt/")
18072 (synopsis "Autocorrelation robust testing")
18074 "This package provides functions for testing affine hypotheses on the
18075 regression coefficient vector in regression models with autocorrelated
18077 (license license:gpl2)))
18079 (define-public r-acs
18086 (uri (cran-uri "acs" version))
18089 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18090 (properties `((upstream-name . "acs")))
18091 (build-system r-build-system)
18093 `(("r-httr" ,r-httr)
18096 ("r-stringr" ,r-stringr)
18098 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18099 (synopsis "Work with data from the US Census")
18101 "This package provides a general toolkit for downloading, managing,
18102 analyzing, and presenting data from the
18103 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18104 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18105 American Community Survey (ACS). Confidence intervals provided with ACS data
18106 are converted to standard errors to be bundled with estimates in complex
18107 @code{acs} objects. The package provides new methods to conduct standard
18108 operations on @code{acs} objects and present/plot data in statistically
18109 appropriate ways.")
18110 (license license:gpl3)))
18112 (define-public r-acss-data
18114 (name "r-acss-data")
18119 (uri (cran-uri "acss.data" version))
18122 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18123 (properties `((upstream-name . "acss.data")))
18124 (build-system r-build-system)
18125 (home-page "http://complexitycalculator.com/methodology.html")
18126 (synopsis "Data for algorithmic complexity of short strings")
18128 "This is a data only package providing the algorithmic complexity of
18129 short strings, computed using the coding theorem method. For a given set of
18130 symbols in a string, all possible or a large number of random samples of
18131 Turing machines with a given number of states (e.g., 5) and number of symbols
18132 corresponding to the number of symbols in the strings were simulated until
18133 they reached a halting state or failed to end. This package contains data on
18134 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18135 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18136 distribution of the halting states.")
18137 (license license:gpl2+)))
18139 (define-public r-acss
18146 (uri (cran-uri "acss" version))
18149 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18150 (properties `((upstream-name . "acss")))
18151 (build-system r-build-system)
18153 `(("r-acss-data" ,r-acss-data)
18155 (home-page "http://complexitycalculator.com/methodology.html")
18156 (synopsis "Algorithmic complexity for short strings")
18158 "The main purpose of this package is to provide the algorithmic
18159 complexity for short strings, an approximation of the Kolmogorov Complexity of
18160 a short string using the coding theorem method. While the database containing
18161 the complexity is provided in the data only package @code{acss.data}, this
18162 package provides functions accessing the data such as @code{prob_random}
18163 returning the posterior probability that a given string was produced by a
18164 random process. In addition, two traditional (but problematic) measures of
18165 complexity are also provided: entropy and change complexity.")
18166 (license license:gpl2+)))
18168 (define-public r-acswr
18175 (uri (cran-uri "ACSWR" version))
18178 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18179 (properties `((upstream-name . "ACSWR")))
18180 (build-system r-build-system)
18182 `(("r-mass" ,r-mass)))
18183 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18184 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18186 "This is a companion package for the book \"A Course in Statistics with
18187 R\" (ISBN 978-1-119-15272-9.)")
18188 (license license:gpl2)))
18190 (define-public r-alabama
18193 (version "2015.3-1")
18197 (uri (cran-uri "alabama" version))
18200 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18201 (properties `((upstream-name . "alabama")))
18202 (build-system r-build-system)
18203 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18204 (home-page "https://cran.r-project.org/web/packages/alabama/")
18205 (synopsis "Constrained nonlinear optimization")
18207 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18208 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18209 constraints. Linear or nonlinear equality and inequality constraints are
18211 (license license:gpl2+)))
18213 (define-public r-gdina
18220 (uri (cran-uri "GDINA" version))
18223 "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx"))))
18224 (properties `((upstream-name . "GDINA")))
18225 (build-system r-build-system)
18227 `(("r-alabama" ,r-alabama)
18228 ("r-ggplot2" ,r-ggplot2)
18230 ("r-nloptr" ,r-nloptr)
18231 ("r-numderiv" ,r-numderiv)
18233 ("r-rcpparmadillo" ,r-rcpparmadillo)
18234 ("r-rsolnp" ,r-rsolnp)
18235 ("r-shiny" ,r-shiny)
18236 ("r-shinydashboard" ,r-shinydashboard)))
18238 `(("r-knitr" ,r-knitr)))
18239 (home-page "https://github.com/Wenchao-Ma/GDINA")
18240 (synopsis "Generalized DINA model framework")
18242 "This package provides a set of psychometric tools for cognitive
18243 diagnosis modeling based on the generalized deterministic inputs, noisy and
18244 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18245 and its extensions, including the sequential G-DINA model by Ma and de la
18246 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18247 polytomous G-DINA model by Chen and de la Torre
18248 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18249 distribution can be independent, saturated, higher-order, loglinear smoothed
18250 or structured. Q-matrix validation, item and model fit statistics, model
18251 comparison at test and item level and differential item functioning can also
18252 be conducted. A graphical user interface is also provided.")
18253 (license license:gpl3)))
18255 (define-public r-actcd
18262 (uri (cran-uri "ACTCD" version))
18265 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18266 (properties `((upstream-name . "ACTCD")))
18267 (build-system r-build-system)
18269 `(("r-gdina" ,r-gdina)
18270 ("r-r-methodss3" ,r-r-methodss3)))
18272 `(("gfortran" ,gfortran)))
18273 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18274 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18276 "This is a package supporting cluster analysis for cognitive diagnosis
18277 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18278 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18279 sum-scores, cluster analysis techniques can be used to classify examinees into
18280 latent classes based on their attribute patterns. In addition to the
18281 algorithms used to classify data, three labeling approaches are proposed to
18282 label clusters so that examinees' attribute profiles can be obtained.")
18283 (license license:gpl2+)))
18285 (define-public r-ineq
18292 (uri (cran-uri "ineq" version))
18295 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18296 (properties `((upstream-name . "ineq")))
18297 (build-system r-build-system)
18298 (home-page "https://cran.r-project.org/web/packages/ineq/")
18299 (synopsis "Measuring inequality, concentration, and poverty")
18301 "This package provides tools for measuring inequality, concentration, and
18302 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18303 ;; Either of these two versions.
18304 (license (list license:gpl2 license:gpl3))))
18306 (define-public r-actfrag
18313 (uri (cran-uri "ActFrag" version))
18316 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18317 (properties `((upstream-name . "ActFrag")))
18318 (build-system r-build-system)
18320 `(("r-accelerometry" ,r-accelerometry)
18321 ("r-dplyr" ,r-dplyr)
18323 ("r-survival" ,r-survival)
18324 ("r-tidyr" ,r-tidyr)))
18325 (home-page "https://github.com/junruidi/ActFrag")
18326 (synopsis "Activity fragmentation metrics extraction")
18328 "This package provides functions to extract commonly used fragmentation
18329 metrics to quantify time accumulation strategies based on minute level
18330 actigraphy-measured activity counts data.")
18331 (license license:gpl3)))
18333 (define-public r-fda
18340 (uri (cran-uri "fda" version))
18343 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18344 (properties `((upstream-name . "fda")))
18345 (build-system r-build-system)
18347 `(("r-matrix" ,r-matrix)))
18348 (home-page "https://www.functionaldata.org")
18349 (synopsis "Functional data analysis")
18351 "These functions were developed to support functional data analysis as
18352 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18353 Analysis. The package includes data sets and script files working many
18355 (license license:gpl2+)))
18357 (define-public r-actigraphy
18359 (name "r-actigraphy")
18364 (uri (cran-uri "Actigraphy" version))
18367 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18368 (properties `((upstream-name . "Actigraphy")))
18369 (build-system r-build-system)
18371 `(("r-fda" ,r-fda)))
18372 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18373 (synopsis "Actigraphy data analysis")
18375 "This package provides tools for functional linear modeling and analysis
18376 of actigraphy data.")
18377 (license license:asl2.0)))
18379 (define-public r-activedriver
18381 (name "r-activedriver")
18386 (uri (cran-uri "ActiveDriver" version))
18389 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18390 (properties `((upstream-name . "ActiveDriver")))
18391 (build-system r-build-system)
18393 `(("r-mass" ,r-mass)))
18394 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18395 (synopsis "Tools for finding cancer driver proteins")
18397 "This package provides a mutation analysis tool that discovers cancer
18398 driver genes with frequent mutations in protein signalling sites such as
18399 post-translational modifications (phosphorylation, ubiquitination, etc). The
18400 Poisson generalized linear regression model identifies genes where cancer
18401 mutations in signalling sites are more frequent than expected from the
18402 sequence of the entire gene. Integration of mutations with signalling
18403 information helps find new driver genes and propose candidate mechanisms to
18405 (license license:gpl2+)))
18407 (define-public r-activitycounts
18409 (name "r-activitycounts")
18414 (uri (cran-uri "activityCounts" version))
18417 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18419 `((upstream-name . "activityCounts")))
18420 (build-system r-build-system)
18422 `(("r-lubridate" ,r-lubridate)
18423 ("r-magrittr" ,r-magrittr)
18424 ("r-seewave" ,r-seewave)
18425 ("r-signal" ,r-signal)
18426 ("r-tibble" ,r-tibble)))
18427 (home-page "https://github.com/walkabillylab/activityCounts")
18428 (synopsis "Generate ActiLife counts")
18430 "ActiLife generates activity counts from data collected by Actigraph
18431 accelerometers. Actigraph is one of the most common research-grade
18432 accelerometers. There is considerable research validating and developing
18433 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18434 counts are proprietary and difficult to implement if researchers use different
18435 accelerometer brands. The code creates ActiLife counts from raw acceleration
18436 data for different accelerometer brands.")
18437 (license license:gpl3)))
18439 (define-public r-activityindex
18441 (name "r-activityindex")
18446 (uri (cran-uri "ActivityIndex" version))
18449 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18450 (properties `((upstream-name . "ActivityIndex")))
18451 (build-system r-build-system)
18453 `(("r-data-table" ,r-data-table)
18454 ("r-matrixstats" ,r-matrixstats)
18455 ("r-r-utils" ,r-r-utils)))
18456 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18457 (synopsis "Activity Index calculation using raw accelerometry data")
18459 "This is a package to read raw accelerometry from GT3X+ accelerometry
18460 data and plain table data to calculate the Activity Index from Bai et
18461 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18462 (license license:gpl3)))
18464 (define-public r-activpal
18466 (name "r-activpal")
18471 (uri (cran-uri "activPAL" version))
18474 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18475 (properties `((upstream-name . "activPAL")))
18476 (build-system r-build-system)
18478 `(("r-devtools" ,r-devtools)
18479 ("r-dplyr" ,r-dplyr)
18480 ("r-ggplot2" ,r-ggplot2)
18481 ("r-lubridate" ,r-lubridate)
18482 ("r-magrittr" ,r-magrittr)
18483 ("r-tidyr" ,r-tidyr)))
18484 (home-page "https://cran.r-project.org/web/packages/activPAL")
18485 (synopsis "Processing and chart generation from activPAL events files")
18487 "This package contains functions to generate pre-defined summary
18488 statistics from activPAL events files. The package also contains functions to
18489 produce informative graphics that visualize physical activity behaviour and
18490 trends. This includes generating graphs that align physical activity
18491 behaviour with additional time based observations described by other data
18492 sets, such as sleep diaries and continuous glucose monitoring data.")
18493 (license license:gpl3)))
18495 (define-public r-activpalprocessing
18497 (name "r-activpalprocessing")
18502 (uri (cran-uri "activpalProcessing" version))
18505 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18507 `((upstream-name . "activpalProcessing")))
18508 (build-system r-build-system)
18510 `(("r-chron" ,r-chron)))
18511 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18512 (synopsis "Process activPAL events files")
18514 "This package performs estimation of physical activity and sedentary
18515 behavior variables from activPAL events files.")
18516 ;; Either version of the GPL.
18517 (license (list license:gpl2 license:gpl3))))
18519 (define-public r-actogrammr
18521 (name "r-actogrammr")
18526 (uri (cran-uri "actogrammr" version))
18529 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18530 (properties `((upstream-name . "actogrammr")))
18531 (build-system r-build-system)
18533 `(("r-dplyr" ,r-dplyr)
18534 ("r-ggplot2" ,r-ggplot2)
18535 ("r-lubridate" ,r-lubridate)
18536 ("r-readr" ,r-readr)
18537 ("r-tidyr" ,r-tidyr)))
18538 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18539 (synopsis "Read in activity data and plot actograms")
18541 "Read in activity measurements from standard file formats used by
18542 circadian rhythm researchers, currently only ClockLab format, and process and
18543 plot the data. The central type of plot is the actogram, as first described
18544 in \"Activity and distribution of certain wild mice in relation to biotic
18545 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18546 (license license:gpl3)))
18548 (define-public r-expint
18555 (uri (cran-uri "expint" version))
18558 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18559 (properties `((upstream-name . "expint")))
18560 (build-system r-build-system)
18561 (home-page "https://gitlab.com/vigou3/expint")
18562 (synopsis "Exponential integral and incomplete Gamma function")
18564 "This package provides the exponential integrals @code{E_1(x)},
18565 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18566 function @code{G(a, x)} defined for negative values of its first argument.
18567 The package also gives easy access to the underlying C routines through an
18568 API; see the package vignette for details.")
18569 (license license:gpl2+)))
18571 (define-public r-actuar
18578 (uri (cran-uri "actuar" version))
18581 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18582 (properties `((upstream-name . "actuar")))
18583 (build-system r-build-system)
18584 (propagated-inputs `(("r-expint" ,r-expint)))
18585 (home-page "https://gitlab.com/vigou3/actuar")
18586 (synopsis "Actuarial functions and heavy tailed distributions")
18588 "This package provides functions and data sets for actuarial science:
18589 modeling of loss distributions; risk theory and ruin theory; simulation of
18590 compound models, discrete mixtures and compound hierarchical models;
18591 credibility theory. It boasts support for many additional probability
18592 distributions to model insurance loss amounts and loss frequency: 19
18593 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18594 distribution; zero-truncated and zero-modified extensions of the standard
18595 discrete distributions. It also supports phase-type distributions commonly
18596 used to compute ruin probabilities.")
18597 (license license:gpl2+)))
18599 (define-public r-bmp
18606 (uri (cran-uri "bmp" version))
18609 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18610 (properties `((upstream-name . "bmp")))
18611 (build-system r-build-system)
18612 (home-page "https://cran.r-project.org/web/packages/bmp/")
18613 (synopsis "Read Bitmap (BMP) images")
18615 "This package provides pure R tools to read BMP format images. It is
18616 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18617 (license license:gpl2+)))
18619 (define-public r-readbitmap
18621 (name "r-readbitmap")
18626 (uri (cran-uri "readbitmap" version))
18629 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18630 (properties `((upstream-name . "readbitmap")))
18631 (build-system r-build-system)
18633 `(("libjpeg" ,libjpeg-turbo)
18634 ("libpng" ,libpng)))
18639 ("r-tiff" ,r-tiff)))
18640 (home-page "https://github.com/jefferis/readbitmap")
18641 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18643 "This package provides tools to identify and read BMP, JPEG, PNG, and
18644 TIFF format bitmap images. Identification defaults to the use of the magic
18645 number embedded in the file rather than the file extension.")
18646 (license license:gpl2+)))
18648 (define-public r-imager
18655 (uri (cran-uri "imager" version))
18658 "1d7a49lcna77wyfjf5q1b89jck3p3vnysnkgz4drb0qkpy6hz76b"))))
18659 (properties `((upstream-name . "imager")))
18660 (build-system r-build-system)
18663 ("libtiff" ,libtiff)
18667 `(("r-downloader" ,r-downloader)
18668 ("r-igraph" ,r-igraph)
18670 ("r-magrittr" ,r-magrittr)
18672 ("r-purrr" ,r-purrr)
18674 ("r-readbitmap" ,r-readbitmap)
18675 ("r-stringr" ,r-stringr)))
18676 (native-inputs `(("pkg-config" ,pkg-config)))
18677 (home-page "https://dahtah.github.io/imager/")
18678 (synopsis "Image processing library")
18680 "This is a package for fast image processing for images in up to 4
18681 dimensions (two spatial dimensions, one time/depth dimension, one color
18682 dimension). It provides most traditional image processing tools (filtering,
18683 morphology, transformations, etc.) as well as various functions for easily
18684 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18685 simple, modern C++ library for image processing.")
18686 (license license:lgpl3)))
18688 (define-public r-acuityview
18690 (name "r-acuityview")
18695 (uri (cran-uri "AcuityView" version))
18698 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18699 (properties `((upstream-name . "AcuityView")))
18700 (build-system r-build-system)
18702 `(("r-fftwtools" ,r-fftwtools)
18703 ("r-imager" ,r-imager)
18704 ("r-plotrix" ,r-plotrix)))
18705 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18706 (synopsis "Display scenes as seen by an animal with less acute vision")
18708 "This package provides a simple method for representing a visual scene as
18709 it may be seen by an animal with less acute vision.")
18710 (license license:gpl2+)))
18712 (define-public r-caret
18719 (uri (cran-uri "caret" version))
18722 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
18723 (build-system r-build-system)
18725 `(("r-foreach" ,r-foreach)
18726 ("r-ggplot2" ,r-ggplot2)
18727 ("r-lattice" ,r-lattice)
18728 ("r-modelmetrics" ,r-modelmetrics)
18732 ("r-recipes" ,r-recipes)
18733 ("r-reshape2" ,r-reshape2)
18734 ("r-withr" ,r-withr)))
18736 `(("r-knitr" ,r-knitr)))
18737 (home-page "https://github.com/topepo/caret")
18738 (synopsis "Classification and regression training")
18740 "This package provides miscellaneous functions for training and plotting
18741 classification and regression models.")
18742 (license license:gpl2+)))
18744 (define-public r-adabag
18751 (uri (cran-uri "adabag" version))
18754 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18755 (properties `((upstream-name . "adabag")))
18756 (build-system r-build-system)
18758 `(("r-caret" ,r-caret)
18759 ("r-doparallel" ,r-doparallel)
18760 ("r-foreach" ,r-foreach)
18761 ("r-rpart" ,r-rpart)))
18762 (home-page "https://cran.r-project.org/web/packages/adabag/")
18763 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18765 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18766 Breiman's Bagging algorithm using classification trees as individual
18767 classifiers. Once these classifiers have been trained, they can be used to
18768 predict on new data. Also, cross validation estimation of the error can be
18770 (license license:gpl2+)))
18772 (define-public r-adagio
18779 (uri (cran-uri "adagio" version))
18782 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18783 (properties `((upstream-name . "adagio")))
18784 (build-system r-build-system)
18785 (native-inputs `(("gfortran" ,gfortran)))
18786 (home-page "https://cran.r-project.org/web/packages/adagio/")
18787 (synopsis "Discrete and global optimization routines")
18789 "This package provides methods and algorithms for discrete optimization,
18790 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18791 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18793 (license license:gpl3+)))
18795 (define-public r-univoutl
18797 (name "r-univoutl")
18802 (uri (cran-uri "univOutl" version))
18805 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
18806 (properties `((upstream-name . "univOutl")))
18807 (build-system r-build-system)
18809 `(("r-hmisc" ,r-hmisc)
18810 ("r-robustbase" ,r-robustbase)))
18811 (home-page "https://github.com/marcellodo/univOutl")
18812 (synopsis "Detection of univariate outliers")
18814 "This package provides well-known outlier detection techniques in the
18815 univariate case. Methods to deal with skewed distribution are included too.
18816 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18817 historical data is implemented as well. When available, survey weights can be
18818 used in outliers detection.")
18819 (license license:gpl2+)))
18821 (define-public r-tolerance
18823 (name "r-tolerance")
18828 (uri (cran-uri "tolerance" version))
18831 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
18832 (properties `((upstream-name . "tolerance")))
18833 (build-system r-build-system)
18835 `(("r-mass" ,r-mass)
18837 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18838 (synopsis "Statistical tolerance intervals and regions")
18840 "This package provides functions for estimating tolerance
18841 limits (intervals) for various univariate distributions (binomial, Cauchy,
18842 discrete Pareto, exponential, two-parameter exponential, extreme value,
18843 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18844 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18845 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18846 nonparametric tolerance intervals, tolerance bands for regression
18847 settings (linear regression, nonlinear regression, nonparametric regression,
18848 and multivariate regression), and analysis of variance tolerance intervals.
18849 Visualizations are also available for most of these settings.")
18850 (license license:gpl2+)))
18852 (define-public r-additivitytests
18854 (name "r-additivitytests")
18859 (uri (cran-uri "additivityTests" version))
18862 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18864 `((upstream-name . "additivityTests")))
18865 (build-system r-build-system)
18866 (home-page "https://github.com/simecek/additivityTests")
18867 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18869 "This package provides an implementation of the Tukey, Mandel,
18870 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18871 (license license:gpl3)))
18873 (define-public r-flexclust
18875 (name "r-flexclust")
18880 (uri (cran-uri "flexclust" version))
18883 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18884 (properties `((upstream-name . "flexclust")))
18885 (build-system r-build-system)
18887 `(("r-class" ,r-class)
18888 ("r-lattice" ,r-lattice)
18889 ("r-modeltools" ,r-modeltools)))
18890 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18891 (synopsis "Flexible cluster algorithms")
18893 "The main function @code{kcca} implements a general framework for
18894 k-centroids cluster analysis supporting arbitrary distance measures and
18895 centroid computation. Further cluster methods include hard competitive
18896 learning, neural gas, and QT clustering. There are numerous visualization
18897 methods for cluster results (neighborhood graphs, convex cluster hulls,
18898 barcharts of centroids, ...), and bootstrap methods for the analysis of
18899 cluster stability.")
18900 (license license:gpl2)))
18902 (define-public r-biclust
18909 (uri (cran-uri "biclust" version))
18912 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
18913 (properties `((upstream-name . "biclust")))
18914 (build-system r-build-system)
18916 `(("r-additivitytests" ,r-additivitytests)
18917 ("r-colorspace" ,r-colorspace)
18918 ("r-flexclust" ,r-flexclust)
18919 ("r-ggplot2" ,r-ggplot2)
18920 ("r-lattice" ,r-lattice)
18922 ("r-tidyr" ,r-tidyr)))
18923 (home-page "https://cran.r-project.org/web/packages/biclust/")
18924 (synopsis "BiCluster algorithms")
18926 "The main function @code{biclust()} provides several algorithms to find
18927 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18928 In addition, the package provides methods for data
18929 preprocessing (normalization and discretization), visualization, and
18930 validation of bicluster solutions.")
18931 (license license:gpl3)))
18933 (define-public r-icge
18940 (uri (cran-uri "ICGE" version))
18943 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18944 (properties `((upstream-name . "ICGE")))
18945 (build-system r-build-system)
18947 `(("r-cluster" ,r-cluster)
18948 ("r-mass" ,r-mass)))
18949 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18950 (synopsis "Cluster estimation and identification of atypical units")
18952 "ICGE is a package that helps to estimate the number of real clusters in
18953 data as well as to identify atypical units. The underlying methods are based
18954 on distances rather than on unit x variables.")
18955 (license license:gpl2+)))
18957 (define-public r-depth
18960 (version "2.1-1.1")
18964 (uri (cran-uri "depth" version))
18967 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18968 (properties `((upstream-name . "depth")))
18969 (build-system r-build-system)
18971 `(("r-abind" ,r-abind)
18972 ("r-circular" ,r-circular)
18975 `(("gfortran" ,gfortran)))
18976 (home-page "https://cran.r-project.org/web/packages/depth/")
18977 (synopsis "Nonparametric depth functions for multivariate analysis")
18979 "This package provides tools for depth functions methodology applied to
18980 multivariate analysis. Besides allowing calculation of depth values and
18981 depth-based location estimators, the package includes functions or drawing
18982 contour plots and perspective plots of depth functions. Euclidian and
18983 spherical depths are supported.")
18984 (license license:gpl2)))
18986 (define-public r-archetypes
18988 (name "r-archetypes")
18989 (version "2.2-0.1")
18993 (uri (cran-uri "archetypes" version))
18996 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18997 (properties `((upstream-name . "archetypes")))
18998 (build-system r-build-system)
19000 `(("r-modeltools" ,r-modeltools)
19001 ("r-nnls" ,r-nnls)))
19002 (home-page "https://cran.r-project.org/web/packages/archetypes")
19003 (synopsis "Archetypal analysis")
19005 "The main function @code{archetypes} implements a framework for
19006 archetypal analysis supporting arbitrary problem solving mechanisms for the
19007 different conceptual parts of the algorithm.")
19008 (license license:gpl2+)))
19010 (define-public r-shapes
19017 (uri (cran-uri "shapes" version))
19020 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19021 (properties `((upstream-name . "shapes")))
19022 (build-system r-build-system)
19024 `(("r-mass" ,r-mass)
19025 ("r-minpack-lm" ,r-minpack-lm)
19027 ("r-scatterplot3d" ,r-scatterplot3d)))
19028 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19029 (synopsis "Statistical shape analysis")
19031 "This package provides routines for the statistical analysis of landmark
19032 shapes, including Procrustes analysis, graphical displays, principal
19033 components analysis, permutation and bootstrap tests, thin-plate spline
19034 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19035 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19036 Edition), John Wiley and Sons.")
19037 (license license:gpl2)))
19039 (define-public r-anthropometry
19041 (name "r-anthropometry")
19046 (uri (cran-uri "Anthropometry" version))
19049 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19050 (properties `((upstream-name . "Anthropometry")))
19051 (build-system r-build-system)
19053 `(("r-archetypes" ,r-archetypes)
19054 ("r-biclust" ,r-biclust)
19055 ("r-cluster" ,r-cluster)
19056 ("r-depth" ,r-depth)
19061 ("r-shapes" ,r-shapes)))
19063 `(("r-knitr" ,r-knitr)))
19064 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19065 (synopsis "Statistical methods for anthropometric data")
19067 "This package provides statistical methods especially developed to
19068 analyze anthropometric data. These methods are aimed at providing effective
19069 solutions to some commons problems related to Ergonomics and Anthropometry.
19070 They are based on clustering, the statistical concept of data depth,
19071 statistical shape analysis and archetypal analysis.")
19072 (license license:gpl2+)))
19074 (define-public r-adamethods
19076 (name "r-adamethods")
19081 (uri (cran-uri "adamethods" version))
19084 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19085 (properties `((upstream-name . "adamethods")))
19086 (build-system r-build-system)
19088 `(("r-anthropometry" ,r-anthropometry)
19089 ("r-archetypes" ,r-archetypes)
19091 ("r-foreach" ,r-foreach)
19093 ("r-tolerance" ,r-tolerance)
19094 ("r-univoutl" ,r-univoutl)))
19095 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19096 (synopsis "Archetypoid algorithms and anomaly detection")
19098 "This package is a collection of several algorithms to obtain
19099 archetypoids with small and large databases and with both classical
19100 multivariate data and functional data (univariate and multivariate). Some of
19101 these algorithms also allow to detect anomalies (outliers).")
19102 (license license:gpl2+)))
19104 (define-public r-idpmisc
19111 (uri (cran-uri "IDPmisc" version))
19114 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19115 (properties `((upstream-name . "IDPmisc")))
19116 (build-system r-build-system)
19118 `(("r-lattice" ,r-lattice)))
19119 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19120 (synopsis "Functions for data analyses and visualization")
19122 "This package provides different high-level graphics functions for
19123 displaying large datasets, displaying circular data in a very flexible way,
19124 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19125 2D-plots, creating figures with differently colored margin and plot region.
19126 In addition, the package contains auxiliary functions for data manipulation
19127 like omitting observations with irregular values or selecting data by logical
19128 vectors, which include NAs. Other functions are especially useful in
19129 spectroscopy and analyses of environmental data: robust baseline fitting,
19130 finding peaks in spectra, converting humidity measures.")
19131 (license license:gpl3+)))
19133 (define-public r-qqman
19140 (uri (cran-uri "qqman" version))
19143 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19144 (properties `((upstream-name . "qqman")))
19145 (build-system r-build-system)
19147 `(("r-calibrate" ,r-calibrate)))
19148 (home-page "https://cran.r-project.org/web/packages/qqman/")
19149 (synopsis "Q-Q and Manhattan plots for GWAS data")
19151 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19152 from PLINK results.")
19153 (license license:gpl3)))
19155 (define-public r-ggplot-multistats
19157 (name "r-ggplot-multistats")
19162 (uri (cran-uri "ggplot.multistats" version))
19165 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19167 `((upstream-name . "ggplot.multistats")))
19168 (build-system r-build-system)
19170 `(("r-ggplot2" ,r-ggplot2)
19171 ("r-hexbin" ,r-hexbin)
19172 ("r-rlang" ,r-rlang)
19173 ("r-scales" ,r-scales)))
19174 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19175 (synopsis "Multiple summary statistics for binned stats/geometries")
19177 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19178 which functions similar to its singular form, but allows the use of multiple
19179 statistics per bin. Those statistics can be mapped to multiple bin
19181 (license license:gpl3)))
19183 (define-public r-knn-covertree
19185 (name "r-knn-covertree")
19190 (uri (cran-uri "knn.covertree" version))
19193 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19194 (properties `((upstream-name . "knn.covertree")))
19195 (build-system r-build-system)
19197 `(("r-matrix" ,r-matrix)
19199 ("r-rcppeigen" ,r-rcppeigen)))
19200 (home-page "https://github.com/flying-sheep/knn.covertree")
19201 (synopsis "Accurate kNN Implementation with multiple distance measures")
19203 "Similarly to the FNN package, this package allows calculation of the k
19204 nearest neighbors (kNN) of a data matrix. The implementation is based on
19205 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19206 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19207 (license license:agpl3+)))
19209 (define-public r-poibin
19216 (uri (cran-uri "poibin" version))
19219 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19220 (properties `((upstream-name . "poibin")))
19221 (build-system r-build-system)
19222 (home-page "https://cran.r-project.org/web/packages/poibin/")
19223 (synopsis "Poisson binomial distribution")
19225 "This package provides an implementation of both the exact and
19226 approximation methods for computing the @dfn{cumulative distribution
19227 function} (CDF) of the Poisson binomial distribution. It also provides the
19228 @dfn{probability mass function} (PMF), quantile function, and random number
19229 generation for the Poisson binomial distribution.")
19230 (license license:gpl2)))
19232 (define-public r-diagram
19239 (uri (cran-uri "diagram" version))
19242 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19243 (properties `((upstream-name . "diagram")))
19244 (build-system r-build-system)
19246 `(("r-shape" ,r-shape)))
19247 (home-page "https://cran.r-project.org/web/packages/diagram/")
19248 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19250 "This package provides tools to visualize simple graphs (networks) based
19251 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19252 electrical networks, etc. It also includes supporting material for the book
19253 \"A practical guide to ecological modelling - using R as a simulation
19254 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19255 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19256 Francesca Mazzia (2012).")
19257 (license license:gpl2+)))
19259 (define-public r-lim
19266 (uri (cran-uri "LIM" version))
19269 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19270 (properties `((upstream-name . "LIM")))
19271 (build-system r-build-system)
19273 `(("r-diagram" ,r-diagram)
19274 ("r-limsolve" ,r-limsolve)))
19275 (home-page "https://cran.r-project.org/web/packages/LIM/")
19276 (synopsis "Linear inverse model examples and solution methods")
19278 "This package provides functions that read and solve linear inverse
19279 problems (food web problems, linear programming problems).")
19280 (license license:gpl2+)))
19282 (define-public r-shinycssloaders
19284 (name "r-shinycssloaders")
19289 (uri (cran-uri "shinycssloaders" version))
19292 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19294 `((upstream-name . "shinycssloaders")))
19295 (build-system r-build-system)
19297 `(("r-digest" ,r-digest)
19299 ("r-shiny" ,r-shiny)))
19300 (home-page "https://github.com/andrewsali/shinycssloaders")
19301 (synopsis "Add CSS loading animations to Shiny outputs")
19303 "This package provides tools to create a lightweight Shiny wrapper for
19304 the css-loaders created by Luke Hass
19305 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19306 automatically show a loader when the output is (re)calculating.")
19307 (license license:gpl3)))
19309 (define-public r-rsvg
19316 (uri (cran-uri "rsvg" version))
19319 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
19320 (properties `((upstream-name . "rsvg")))
19321 (build-system r-build-system)
19323 `(("librsvg" ,librsvg)
19326 `(("pkg-config" ,pkg-config)))
19327 (home-page "https://github.com/jeroen/rsvg#readme")
19328 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19330 "This package allows you to render vector-based SVG images into
19331 high-quality custom-size bitmap arrays using the librsvg2 library. The
19332 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19333 addition, the package can convert images directly to various formats such as
19334 PDF or PostScript.")
19335 (license license:expat)))
19337 (define-public r-influencer
19339 (name "r-influencer")
19344 (uri (cran-uri "influenceR" version))
19347 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19348 (properties `((upstream-name . "influenceR")))
19349 (build-system r-build-system)
19351 `(("r-igraph" ,r-igraph)
19352 ("r-matrix" ,r-matrix)))
19353 (home-page "https://github.com/rcc-uchicago/influenceR")
19354 (synopsis "Tools to quantify structural importance of nodes in a network")
19356 "This package provides functionality to compute various node centrality
19357 measures on networks. Included are functions to compute betweenness
19358 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19359 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19360 algorithm to identify key players, and Valente's bridging metric. The
19361 betweenness, Key Players, and bridging implementations are parallelized with
19363 (license license:gpl2)))
19365 (define-public r-emplik
19368 (version "1.0-4.3")
19372 (uri (cran-uri "emplik" version))
19375 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19376 (properties `((upstream-name . "emplik")))
19377 (build-system r-build-system)
19379 `(("r-quantreg" ,r-quantreg)))
19380 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19381 (synopsis "Empirical likelihood ratio for censored/truncated data")
19383 "This package provides empirical likelihood ratio tests for
19384 means/quantiles/hazards from possibly censored and/or truncated data. It also
19386 (license license:gpl2+)))
19388 (define-public r-imputeyn
19390 (name "r-imputeyn")
19395 (uri (cran-uri "imputeYn" version))
19398 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19399 (properties `((upstream-name . "imputeYn")))
19400 (build-system r-build-system)
19402 `(("r-boot" ,r-boot)
19403 ("r-emplik" ,r-emplik)
19404 ("r-mvtnorm" ,r-mvtnorm)
19405 ("r-quadprog" ,r-quadprog)
19406 ("r-survival" ,r-survival)))
19407 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19408 (synopsis "Impute last largest censored observation under weighted least squares")
19410 "This package allows for the imputation of the last largest censored
19411 observantions. This method brings less bias and more efficient estimates for
19413 (license license:gpl2)))
19415 (define-public r-adapenetclass
19417 (name "r-adapenetclass")
19422 (uri (cran-uri "AdapEnetClass" version))
19425 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19426 (properties `((upstream-name . "AdapEnetClass")))
19427 (build-system r-build-system)
19429 `(("r-glmnet" ,r-glmnet)
19430 ("r-imputeyn" ,r-imputeyn)
19432 ("r-quadprog" ,r-quadprog)))
19433 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19434 (synopsis "Class of adaptive elastic net methods for censored data")
19436 "This package provides methods for variable selection for AFT models.")
19437 (license license:gpl2)))
19439 (define-public r-flock
19446 (uri (cran-uri "flock" version))
19449 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19450 (properties `((upstream-name . "flock")))
19451 (build-system r-build-system)
19452 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19453 (home-page "https://cran.r-project.org/web/packages/flock/")
19454 (synopsis "Process synchronization using file locks")
19456 "This package implements synchronization between R processes (spawned by
19457 using the @code{parallel} package for instance) using file locks. It supports
19458 both exclusive and shared locking.")
19459 (license license:asl2.0)))
19461 (define-public r-archivist
19463 (name "r-archivist")
19468 (uri (cran-uri "archivist" version))
19471 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19472 (properties `((upstream-name . "archivist")))
19473 (build-system r-build-system)
19476 ("r-digest" ,r-digest)
19477 ("r-flock" ,r-flock)
19479 ("r-lubridate" ,r-lubridate)
19480 ("r-magrittr" ,r-magrittr)
19481 ("r-rcurl" ,r-rcurl)
19482 ("r-rsqlite" ,r-rsqlite)))
19483 (home-page "https://pbiecek.github.io/archivist/")
19484 (synopsis "Tools for storing, restoring and searching for R objects")
19486 "Data exploration and modelling is a process in which a lot of data
19487 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19488 statistical models, different versions of data sets and different versions of
19489 results. Archivist helps to store and manage artifacts created in R. It
19490 allows you to store selected artifacts as binary files together with their
19491 metadata and relations. Archivist allows sharing artifacts with others. It
19492 can look for already created artifacts by using its class, name, date of the
19493 creation or other properties. It also makes it easy to restore such
19495 (license license:gpl2)))
19497 (define-public r-versions
19499 (name "r-versions")
19504 (uri (cran-uri "versions" version))
19507 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19508 (properties `((upstream-name . "versions")))
19509 (build-system r-build-system)
19510 (home-page "https://cran.r-project.org/web/packages/versions/")
19511 (synopsis "Query and install specific versions of CRAN packages")
19513 "This package allows you to install specified versions of R packages
19514 hosted on CRAN and provides functions to list available versions and the
19515 versions of currently installed packages.")
19516 (license license:bsd-3)))
19518 (define-public r-adapr
19525 (uri (cran-uri "adapr" version))
19528 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19529 (properties `((upstream-name . "adapr")))
19530 (build-system r-build-system)
19532 `(("r-archivist" ,r-archivist)
19533 ("r-devtools" ,r-devtools)
19534 ("r-digest" ,r-digest)
19535 ("r-doparallel" ,r-doparallel)
19536 ("r-gdata" ,r-gdata)
19537 ("r-ggplot2" ,r-ggplot2)
19538 ("r-git2r" ,r-git2r)
19539 ("r-igraph" ,r-igraph)
19540 ("r-knitr" ,r-knitr)
19541 ("r-plotly" ,r-plotly)
19543 ("r-rmarkdown" ,r-rmarkdown)
19544 ("r-shiny" ,r-shiny)
19545 ("r-shinydashboard" ,r-shinydashboard)
19546 ("r-versions" ,r-versions)))
19547 (home-page "https://cran.r-project.org/web/packages/adapr/")
19548 (synopsis "Implementation of an accountable data analysis process")
19550 "This package tracks reading and writing within R scripts that are
19551 organized into a directed acyclic graph. It contains an interactive Shiny
19552 application @code{adaprApp()}. It uses Git and file hashes to track version
19553 histories of inputs and outputs.")
19554 (license license:lgpl2.0)))
19556 (define-public r-adapsamp
19558 (name "r-adapsamp")
19563 (uri (cran-uri "AdapSamp" version))
19566 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19567 (properties `((upstream-name . "AdapSamp")))
19568 (build-system r-build-system)
19569 (propagated-inputs `(("r-pracma" ,r-pracma)))
19570 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19571 (synopsis "Adaptive sampling algorithms")
19573 "For distributions whose probability density functions are log-concave,
19574 the adaptive rejection sampling algorithm can be used to build envelope
19575 functions for sampling. For others, the modified adaptive rejection sampling
19576 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19577 adaptive slice sampling algorithm can be used. This R package mainly includes
19578 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19579 @code{rASS()}. These functions can realize sampling based on the algorithms
19581 (license license:gpl2)))
19583 (define-public r-adaptalint
19585 (name "r-adaptalint")
19590 (uri (cran-uri "adaptalint" version))
19593 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19594 (properties `((upstream-name . "adaptalint")))
19595 (build-system r-build-system)
19597 `(("r-dplyr" ,r-dplyr)
19598 ("r-lintr" ,r-lintr)
19599 ("r-purrr" ,r-purrr)))
19600 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19601 (synopsis "Check R code style")
19603 "This package provides tools to infer the code style (which style rules
19604 are followed and which ones are not) from one package and use it to check
19605 another. This makes it easier to find and correct the most important problems
19607 (license license:gpl3)))
19609 (define-public r-fracdiff
19611 (name "r-fracdiff")
19616 (uri (cran-uri "fracdiff" version))
19619 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19620 (properties `((upstream-name . "fracdiff")))
19621 (build-system r-build-system)
19622 (home-page "https://github.com/mmaechler/fracdiff")
19624 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19626 "This package provides tools for the maximum likelihood estimation of the
19627 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19628 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19629 (license license:gpl2+)))
19631 (define-public r-forecast
19633 (name "r-forecast")
19638 (uri (cran-uri "forecast" version))
19641 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19642 (properties `((upstream-name . "forecast")))
19643 (build-system r-build-system)
19645 `(("r-colorspace" ,r-colorspace)
19646 ("r-fracdiff" ,r-fracdiff)
19647 ("r-ggplot2" ,r-ggplot2)
19648 ("r-lmtest" ,r-lmtest)
19649 ("r-magrittr" ,r-magrittr)
19652 ("r-rcpparmadillo" ,r-rcpparmadillo)
19653 ("r-timedate" ,r-timedate)
19654 ("r-tseries" ,r-tseries)
19658 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19659 (home-page "https://pkg.robjhyndman.com/forecast/")
19660 (synopsis "Forecasting functions for time series and linear models")
19662 "This package provides methods and tools for displaying and analysing
19663 univariate time series forecasts including exponential smoothing via state
19664 space models and automatic ARIMA modelling.")
19665 (license license:gpl3)))
19667 (define-public r-xmisc
19674 (uri (cran-uri "Xmisc" version))
19677 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
19678 (properties `((upstream-name . "Xmisc")))
19679 (build-system r-build-system)
19680 (home-page "https://cran.r-project.org/package=Xmisc")
19682 "Xiaobei's miscellaneous classes and functions")
19684 "This package provides Xiaobei's miscellaneous classes and functions,
19685 which are useful when developing R packages for @dfn{object oriented
19686 programming} (OOP) using R Reference Class.")
19687 (license license:gpl2+)))
19689 (define-public r-proxyc
19696 (uri (cran-uri "proxyC" version))
19699 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
19700 (properties `((upstream-name . "proxyC")))
19701 (build-system r-build-system)
19703 `(("r-matrix" ,r-matrix)
19705 ("r-rcpparmadillo" ,r-rcpparmadillo)
19706 ("r-rcppparallel" ,r-rcppparallel)))
19707 (home-page "https://cran.r-project.org/package=proxyC")
19708 (synopsis "Compute proximity in large sparse matrices")
19710 "This package provides efficient tools to compute the proximity between
19711 rows or columns of large matrices. Functions are optimised for large sparse
19712 matrices using the Armadillo and Intel TBB libraries. Among several built-in
19713 similarity/distance measures, computation of correlation, cosine similarity
19714 and Euclidean distance is particularly fast.")
19715 (license license:gpl3)))
19717 (define-public r-isocodes
19719 (name "r-isocodes")
19720 (version "2020.03.16")
19724 (uri (cran-uri "ISOcodes" version))
19727 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
19728 (properties `((upstream-name . "ISOcodes")))
19729 (build-system r-build-system)
19730 (home-page "https://cran.r-project.org/package=ISOcodes")
19731 (synopsis "Selected ISO codes")
19733 "This package provides ISO language, territory, currency, script and
19734 character codes. It provides ISO 639 language codes, ISO 3166 territory
19735 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
19736 character codes as well as the UN M.49 area codes.")
19737 (license license:gpl2)))
19739 (define-public r-stopwords
19741 (name "r-stopwords")
19746 (uri (cran-uri "stopwords" version))
19749 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
19750 (properties `((upstream-name . "stopwords")))
19751 (build-system r-build-system)
19753 `(("r-desc" ,r-desc)
19754 ("r-isocodes" ,r-isocodes)
19755 ("r-usethis" ,r-usethis)))
19756 (home-page "https://github.com/quanteda/stopwords")
19757 (synopsis "Multilingual stopword lists")
19759 "This package provides multiple sources of stopwords, for use in text
19760 analysis and natural language processing.")
19761 (license license:expat)))
19763 (define-public r-spacyr
19770 (uri (cran-uri "spacyr" version))
19773 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
19774 (properties `((upstream-name . "spacyr")))
19775 (build-system r-build-system)
19777 `(("r-data-table" ,r-data-table)
19778 ("r-reticulate" ,r-reticulate)))
19779 (home-page "https://spacyr.quanteda.io")
19780 (synopsis "R wrapper for the spaCy NLP library")
19782 "This package provides an R wrapper to the Python @dfn{natural language
19783 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
19784 (license license:gpl3)))
19786 (define-public r-snowballc
19788 (name "r-snowballc")
19793 (uri (cran-uri "SnowballC" version))
19796 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
19797 (properties `((upstream-name . "SnowballC")))
19798 (build-system r-build-system)
19799 (home-page "https://r-forge.r-project.org/projects/r-temis/")
19800 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
19802 "This package provides an R interface to the C @code{libstemmer} library
19803 that implements Porter's word stemming algorithm for collapsing words to a
19804 common root to aid comparison of vocabulary. Currently supported languages
19805 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
19806 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
19807 (license license:bsd-3)))
19809 (define-public r-quanteda
19811 (name "r-quanteda")
19816 (uri (cran-uri "quanteda" version))
19819 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
19820 (properties `((upstream-name . "quanteda")))
19821 (build-system r-build-system)
19823 `(("r-data-table" ,r-data-table)
19824 ("r-extrafont" ,r-extrafont)
19825 ("r-fastmatch" ,r-fastmatch)
19826 ("r-ggplot2" ,r-ggplot2)
19827 ("r-ggrepel" ,r-ggrepel)
19828 ("r-jsonlite" ,r-jsonlite)
19829 ("r-magrittr" ,r-magrittr)
19830 ("r-matrix" ,r-matrix)
19831 ("r-network" ,r-network)
19832 ("r-proxyc" ,r-proxyc)
19834 ("r-rcpparmadillo" ,r-rcpparmadillo)
19835 ("r-rcppparallel" ,r-rcppparallel)
19837 ("r-snowballc" ,r-snowballc)
19838 ("r-stopwords" ,r-stopwords)
19839 ("r-stringi" ,r-stringi)
19841 ("r-yaml" ,r-yaml)))
19843 `(("r-knitr" ,r-knitr)))
19844 (home-page "https://quanteda.io")
19845 (synopsis "Quantitative analysis of textual data")
19847 "This package provides a fast, flexible, and comprehensive framework for
19848 quantitative text analysis in R. It provides functionality for corpus
19849 management, creating and manipulating tokens and ngrams, exploring keywords in
19850 context, forming and manipulating sparse matrices of documents by features and
19851 feature co-occurrences, analyzing keywords, computing feature similarities and
19852 distances, applying content dictionaries, applying supervised and unsupervised
19853 machine learning, visually representing text and text analyses, and more.")
19854 (license license:gpl3)))
19856 (define-public r-topicmodels
19858 (name "r-topicmodels")
19863 (uri (cran-uri "topicmodels" version))
19866 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
19867 (properties `((upstream-name . "topicmodels")))
19868 (build-system r-build-system)
19872 `(("r-modeltools" ,r-modeltools)
19875 (home-page "https://cran.r-project.org/package=topicmodels")
19876 (synopsis "Topic models")
19878 "This package provides an interface to the C code for @dfn{Latent
19879 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
19880 David M. Blei and co-authors and the C++ code for fitting LDA models using
19881 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
19882 (license license:gpl2)))
19884 (define-public r-stm
19891 (uri (cran-uri "stm" version))
19894 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
19895 (properties `((upstream-name . "stm")))
19896 (build-system r-build-system)
19898 `(("r-data-table" ,r-data-table)
19899 ("r-glmnet" ,r-glmnet)
19901 ("r-matrix" ,r-matrix)
19902 ("r-matrixstats" ,r-matrixstats)
19903 ("r-quadprog" ,r-quadprog)
19904 ("r-quanteda" ,r-quanteda)
19906 ("r-rcpparmadillo" ,r-rcpparmadillo)
19908 ("r-stringr" ,r-stringr)))
19909 (home-page "http://www.structuraltopicmodel.com/")
19910 (synopsis "Estimation of the Structural Topic Model")
19912 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
19913 topic models with document-level covariates. The package also includes tools
19914 for model selection, visualization, and estimation of topic-covariate
19916 (license license:expat)))
19918 (define-public r-polycor
19925 (uri (cran-uri "polycor" version))
19928 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
19929 (properties `((upstream-name . "polycor")))
19930 (build-system r-build-system)
19932 `(("r-matrix" ,r-matrix)
19933 ("r-mvtnorm" ,r-mvtnorm)))
19934 (home-page "https://r-forge.r-project.org/projects/polycor/")
19935 (synopsis "Polychoric and polyserial correlations")
19937 "This package provides tools to compute polychoric and polyserial
19938 correlations by quick \"two-step\" methods or ML, optionally with standard
19939 errors; tetrachoric and biserial correlations are special cases.")
19940 (license license:gpl2+)))
19942 (define-public r-msm
19949 (uri (cran-uri "msm" version))
19952 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
19953 (properties `((upstream-name . "msm")))
19954 (build-system r-build-system)
19956 `(("r-expm" ,r-expm)
19957 ("r-mvtnorm" ,r-mvtnorm)
19958 ("r-survival" ,r-survival)))
19959 (home-page "https://github.com/chjackson/msm")
19960 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
19962 "This package provides functions for fitting continuous-time Markov and
19963 hidden Markov multi-state models to longitudinal data. It was designed for
19964 processes observed at arbitrary times in continuous time (panel data) but some
19965 other observation schemes are supported. Both Markov transition rates and the
19966 hidden Markov output process can be modelled in terms of covariates, which may
19967 be constant or piecewise-constant in time.")
19968 (license license:gpl2+)))
19970 (define-public r-ltm
19977 (uri (cran-uri "ltm" version))
19980 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
19981 (properties `((upstream-name . "ltm")))
19982 (build-system r-build-system)
19984 `(("r-mass" ,r-mass)
19986 ("r-polycor" ,r-polycor)))
19987 (home-page "https://github.com/drizopoulos/ltm")
19988 (synopsis "Latent trait models under IRT")
19990 "This is a package supporting the analysis of multivariate dichotomous
19991 and polytomous data using latent trait models under the Item Response Theory
19992 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
19993 Three-Parameter, the Graded Response, and the Generalized Partial Credit
19995 (license license:gpl2+)))
19997 (define-public r-mi
20004 (uri (cran-uri "mi" version))
20007 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20008 (properties `((upstream-name . "mi")))
20009 (build-system r-build-system)
20012 ("r-matrix" ,r-matrix)))
20013 (home-page "http://www.stat.columbia.edu/~gelman/")
20014 (synopsis "Missing data imputation and model checking")
20016 "This package provides functions for data manipulation, imputing missing
20017 values in an approximate Bayesian framework, diagnostics of the models used to
20018 generate the imputations, confidence-building mechanisms to validate some of
20019 the assumptions of the imputation algorithm, and functions to analyze multiply
20020 imputed data sets with the appropriate degree of sampling uncertainty.")
20021 (license license:gpl2+)))
20023 (define-public r-matrixcalc
20025 (name "r-matrixcalc")
20030 (uri (cran-uri "matrixcalc" version))
20033 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20034 (properties `((upstream-name . "matrixcalc")))
20035 (build-system r-build-system)
20036 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20037 (synopsis "Collection of functions for matrix calculations")
20039 "This package provides a collection of functions to support matrix
20040 calculations for probability, econometric and numerical analysis. There are
20041 additional functions that are comparable to APL functions which are useful for
20042 actuarial models such as pension mathematics.")
20043 (license license:gpl2+)))
20045 (define-public r-sem
20052 (uri (cran-uri "sem" version))
20055 "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
20056 (properties `((upstream-name . "sem")))
20057 (build-system r-build-system)
20059 `(("r-boot" ,r-boot)
20061 ("r-matrixcalc" ,r-matrixcalc)
20063 (home-page "https://cran.r-project.org/package=sem")
20064 (synopsis "Structural equation models")
20066 "This package provides functions for fitting general linear structural
20067 equation models (with observed and latent variables) using the RAM approach,
20068 and for fitting structural equations in observed-variable models by two-stage
20070 (license license:gpl2+)))
20072 (define-public r-semtools
20074 (name "r-semtools")
20079 (uri (cran-uri "semTools" version))
20082 "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
20083 (properties `((upstream-name . "semTools")))
20084 (build-system r-build-system)
20086 `(("r-lavaan" ,r-lavaan)))
20087 (home-page "https://github.com/simsem/semTools/wiki")
20088 (synopsis "Useful tools for structural equation modeling")
20090 "This package provides useful tools for structural equation modeling.")
20091 (license license:gpl2+)))
20093 (define-public r-regsem
20100 (uri (cran-uri "regsem" version))
20103 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20104 (properties `((upstream-name . "regsem")))
20105 (build-system r-build-system)
20107 `(("r-lavaan" ,r-lavaan)
20109 ("r-rcpparmadillo" ,r-rcpparmadillo)
20110 ("r-rsolnp" ,r-rsolnp)))
20111 (home-page "https://cran.r-project.org/package=regsem")
20112 (synopsis "Regularized structural equation modeling")
20114 "This package uses both ridge and lasso penalties (and extensions) to
20115 penalize specific parameters in structural equation models. The package
20116 offers additional cost functions, cross validation, and other extensions
20117 beyond traditional structural equation models. It also contains a function to
20118 perform @dfn{exploratory mediation} (XMed).")
20119 (license license:gpl2+)))
20121 (define-public r-stanheaders
20123 (name "r-stanheaders")
20128 (uri (cran-uri "StanHeaders" version))
20131 "0cmk0fzczx7dcywcw1dhm6gfq84qlsx77qrsk4z3bf3dhr4bznam"))))
20132 (properties `((upstream-name . "StanHeaders")))
20133 (build-system r-build-system)
20134 (inputs `(("pandoc" ,ghc-pandoc)))
20136 `(("gfortran" ,gfortran)
20137 ("r-knitr" ,r-knitr))) ; for vignettes
20138 (home-page "https://mc-stan.org/")
20139 (synopsis "C++ header files for Stan")
20141 "The C++ header files of the Stan project are provided by this package.
20142 There is a shared object containing part of the @code{CVODES} library, but it
20143 is not accessible from R. @code{r-stanheaders} is only useful for developers
20144 who want to utilize the @code{LinkingTo} directive of their package's
20145 DESCRIPTION file to build on the Stan library without incurring unnecessary
20148 The Stan project develops a probabilistic programming language that implements
20149 full or approximate Bayesian statistical inference via Markov Chain Monte
20150 Carlo or variational methods and implements (optionally penalized) maximum
20151 likelihood estimation via optimization. The Stan library includes an advanced
20152 automatic differentiation scheme, templated statistical and linear algebra
20153 functions that can handle the automatically differentiable scalar types (and
20154 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20155 package provides user-facing R functions to parse, compile, test, estimate,
20156 and analyze Stan models.")
20157 (license license:bsd-3)))
20159 (define-public r-rpf
20166 (uri (cran-uri "rpf" version))
20169 "1i2kqd7nx55nn35qnw89xmnqk23x9c8xhkh736c2xg7k2ai84ybl"))))
20170 (properties `((upstream-name . "rpf")))
20171 (build-system r-build-system)
20173 `(("r-lifecycle" ,r-lifecycle)
20174 ("r-mvtnorm" ,r-mvtnorm)
20176 ("r-rcppeigen" ,r-rcppeigen)))
20177 (home-page "https://github.com/jpritikin/rpf")
20178 (synopsis "Response probability functions")
20180 "The purpose of this package is to factor out logic and math common to
20181 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20182 core support code suitable for more specialized IRT packages to build upon.
20183 Complete access to optimized C functions is made available with
20184 @code{R_RegisterCCallable()}.")
20185 (license license:gpl3+)))
20187 (define-public r-openmx
20194 (uri (cran-uri "OpenMx" version))
20197 "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc"))))
20198 (properties `((upstream-name . "OpenMx")))
20199 (build-system r-build-system)
20202 ("r-digest" ,r-digest)
20204 ("r-matrix" ,r-matrix)
20206 ("r-rcppeigen" ,r-rcppeigen)
20208 ("r-stanheaders" ,r-stanheaders)))
20209 (native-inputs `(("gfortran" ,gfortran)))
20210 (home-page "http://openmx.ssri.psu.edu")
20211 (synopsis "Extended structural equation modelling")
20213 "This package allows for the estimation of a wide variety of advanced
20214 multivariate statistical models. It consists of a library of functions and
20215 optimizers that allow you to quickly and flexibly define an SEM model and
20216 estimate parameters given observed data.")
20217 (license license:asl2.0)))
20219 (define-public r-kutils
20226 (uri (cran-uri "kutils" version))
20229 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20230 (properties `((upstream-name . "kutils")))
20231 (build-system r-build-system)
20233 `(("r-foreign" ,r-foreign)
20234 ("r-openxlsx" ,r-openxlsx)
20236 ("r-runit" ,r-runit)
20237 ("r-xtable" ,r-xtable)))
20238 (home-page "https://cran.r-project.org/package=kutils")
20239 (synopsis "Project management tools")
20241 "This package provides tools for data importation, recoding, and
20242 inspection. There are functions to create new project folders, R code
20243 templates, create uniquely named output directories, and to quickly obtain a
20244 visual summary for each variable in a data frame. The main feature here is
20245 the systematic implementation of the \"variable key\" framework for data
20246 importation and recoding.")
20247 (license license:gpl2)))
20249 (define-public r-rockchalk
20251 (name "r-rockchalk")
20252 (version "1.8.144")
20256 (uri (cran-uri "rockchalk" version))
20259 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20260 (properties `((upstream-name . "rockchalk")))
20261 (build-system r-build-system)
20263 `(("r-cardata" ,r-cardata)
20264 ("r-kutils" ,r-kutils)
20266 ("r-mass" ,r-mass)))
20267 (home-page "https://cran.r-project.org/package=rockchalk")
20268 (synopsis "Regression estimation and presentation")
20270 "This package provides a collection of functions for interpretation and
20271 presentation of regression analysis. These functions are used to produce the
20272 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20273 includes regression diagnostics, regression tables, and plots of interactions
20274 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20275 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20276 fairly comprehensive overview.")
20277 (license license:gpl3+)))
20279 (define-public r-lisreltor
20281 (name "r-lisreltor")
20286 (uri (cran-uri "lisrelToR" version))
20289 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20290 (properties `((upstream-name . "lisrelToR")))
20291 (build-system r-build-system)
20292 (home-page "https://cran.r-project.org/package=lisrelToR")
20293 (synopsis "Import output from LISREL into R")
20295 "This is an unofficial package aimed at automating the import of LISREL
20297 (license license:gpl2)))
20299 (define-public r-bdgraph
20306 (uri (cran-uri "BDgraph" version))
20309 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20310 (properties `((upstream-name . "BDgraph")))
20311 (build-system r-build-system)
20313 `(("r-igraph" ,r-igraph)))
20314 (home-page "https://www.uva.nl/profile/a.mohammadi")
20315 (synopsis "Bayesian structure learning in graphical models")
20317 "This package provides statistical tools for Bayesian structure learning
20318 in undirected graphical models for continuous, discrete, and mixed data. It
20319 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20320 on a continuous-time birth-death process.")
20321 (license license:gpl2+)))
20323 (define-public r-d3network
20325 (name "r-d3network")
20326 (version "0.5.2.1")
20330 (uri (cran-uri "d3Network" version))
20333 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20334 (properties `((upstream-name . "d3Network")))
20335 (build-system r-build-system)
20337 `(("r-plyr" ,r-plyr)
20338 ("r-rjson" ,r-rjson)
20339 ("r-whisker" ,r-whisker)))
20340 (home-page "http://christophergandrud.github.io/d3Network/")
20341 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20343 "This package is intended to make it easy to create D3 JavaScript
20344 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20345 (license license:gpl3+)))
20347 (define-public r-qgraph
20354 (uri (cran-uri "qgraph" version))
20357 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20358 (properties `((upstream-name . "qgraph")))
20359 (build-system r-build-system)
20361 `(("r-abind" ,r-abind)
20362 ("r-bdgraph" ,r-bdgraph)
20363 ("r-colorspace" ,r-colorspace)
20364 ("r-corpcor" ,r-corpcor)
20365 ("r-d3network" ,r-d3network)
20366 ("r-dplyr" ,r-dplyr)
20367 ("r-fdrtool" ,r-fdrtool)
20368 ("r-ggplot2" ,r-ggplot2)
20369 ("r-ggraph" ,r-ggraph)
20370 ("r-glasso" ,r-glasso)
20371 ("r-gtools" ,r-gtools)
20372 ("r-hmisc" ,r-hmisc)
20374 ("r-igraph" ,r-igraph)
20376 ("r-lavaan" ,r-lavaan)
20377 ("r-matrix" ,r-matrix)
20378 ("r-pbapply" ,r-pbapply)
20381 ("r-psych" ,r-psych)
20383 ("r-reshape2" ,r-reshape2)
20384 ("r-tidygraph" ,r-tidygraph)))
20385 (home-page "http://sachaepskamp.com/qgraph/")
20386 (synopsis "Weighted network visualization and analysis")
20388 "This package implements tools for weighted network visualization and
20389 analysis, as well as Gaussian graphical model computation. It contains graph
20390 plotting methods, and tools for psychometric data visualization and graphical
20391 model estimation. See Epskamp et al. (2012)
20392 @url{doi:10.18637/jss.v048.i04}.")
20393 (license license:gpl2)))
20395 (define-public r-semplot
20402 (uri (cran-uri "semPlot" version))
20405 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20406 (properties `((upstream-name . "semPlot")))
20407 (build-system r-build-system)
20409 `(("r-colorspace" ,r-colorspace)
20410 ("r-corpcor" ,r-corpcor)
20411 ("r-igraph" ,r-igraph)
20412 ("r-lavaan" ,r-lavaan)
20413 ("r-lisreltor" ,r-lisreltor)
20414 ("r-openmx" ,r-openmx)
20416 ("r-qgraph" ,r-qgraph)
20417 ("r-regsem" ,r-regsem)
20418 ("r-rockchalk" ,r-rockchalk)
20421 (home-page "https://github.com/SachaEpskamp/semPlot")
20422 (synopsis "Unified visualizations of structural equation models")
20424 "Structural equation modeling (SEM) has a long history of representing
20425 models graphically as path diagrams. The semPlot package for R fills the gap
20426 between advanced, but time-consuming, graphical software and the limited
20427 graphics produced automatically by SEM software. In addition, semPlot offers
20428 more functionality than drawing path diagrams: it can act as a common ground
20429 for importing SEM results into R. Any result usable as input to semPlot can
20430 also be represented in any of the three popular SEM frame-works, as well as
20431 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20432 (license license:gpl2)))
20434 (define-public r-cdm
20441 (uri (cran-uri "CDM" version))
20444 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20445 (properties `((upstream-name . "CDM")))
20446 (build-system r-build-system)
20448 `(("r-mvtnorm" ,r-mvtnorm)
20449 ("r-polycor" ,r-polycor)
20451 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20453 "https://github.com/alexanderrobitzsch/CDM")
20454 (synopsis "Cognitive diagnosis modeling")
20456 "This package provides functions for cognitive diagnosis modeling and
20457 multidimensional item response modeling for dichotomous and polytomous item
20458 responses. It enables the estimation of the DINA and DINO model, the multiple
20459 group (polytomous) GDINA model, the multiple choice DINA model, the general
20460 diagnostic model (GDM), the structured latent class model (SLCA), and
20461 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20462 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20463 estimation and the package structure. For tutorials on how to use the CDM
20464 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20465 well as Ravand and Robitzsch (2015).")
20466 (license license:gpl2+)))
20468 (define-public r-tam
20475 (uri (cran-uri "TAM" version))
20478 "111d7qkxhwh1lfvldyh9d61pdb5vb6x8lr8n9h95ssvw07vjqvk9"))))
20479 (properties `((upstream-name . "TAM")))
20480 (build-system r-build-system)
20484 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20485 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20486 (synopsis "Test analysis modules")
20488 "This package includes tools for marginal maximum likelihood estimation
20489 and joint maximum likelihood estimation for unidimensional and
20490 multidimensional item response models. The package functionality covers the
20491 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20492 multi-faceted Rasch model, nominal item response model, structured latent
20493 class model, mixture distribution IRT models, and located latent class models.
20494 Latent regression models and plausible value imputation are also supported.")
20495 (license license:gpl2+)))
20497 (define-public r-erm
20504 (uri (cran-uri "eRm" version))
20507 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20508 (properties `((upstream-name . "eRm")))
20509 (build-system r-build-system)
20511 `(("r-colorspace" ,r-colorspace)
20512 ("r-lattice" ,r-lattice)
20514 ("r-matrix" ,r-matrix)
20515 ("r-psych" ,r-psych)))
20516 (native-inputs `(("gfortran" ,gfortran)))
20517 (home-page "https://cran.r-project.org/package=eRm")
20518 (synopsis "Extended Rasch modeling")
20520 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20521 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20522 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20523 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20524 data matrix. Additional features are the ML estimation of the person
20525 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20526 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20527 infit and outfit measures, ICC and other plots, automated stepwise item
20528 elimination, and a simulation module for various binary data matrices.")
20529 (license license:gpl3)))
20531 (define-public r-irtoys
20538 (uri (cran-uri "irtoys" version))
20541 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20542 (properties `((upstream-name . "irtoys")))
20543 (build-system r-build-system)
20547 (home-page "https://cran.r-project.org/package=irtoys")
20548 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20550 "This package provides a collection of functions useful in learning and
20551 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20552 programs. It provides basic CTT analysis, a simple common interface to the
20553 estimation of item parameters in IRT models for binary responses with three
20554 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20555 EAP, WLE, plausible values), item and person fit statistics, scaling
20556 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20557 array of parametric and non-parametric (kernel) plots. It estimates and plots
20558 Haberman's interaction model when all items are dichotomously scored.")
20559 (license license:gpl2+)))
20561 (define-public r-iheatmapr
20563 (name "r-iheatmapr")
20568 (uri (cran-uri "iheatmapr" version))
20571 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20572 (properties `((upstream-name . "iheatmapr")))
20573 (build-system r-build-system)
20575 `(("r-fastcluster" ,r-fastcluster)
20576 ("r-ggdendro" ,r-ggdendro)
20577 ("r-htmlwidgets" ,r-htmlwidgets)
20578 ("r-jsonlite" ,r-jsonlite)
20579 ("r-knitr" ,r-knitr)
20580 ("r-magrittr" ,r-magrittr)
20582 ("r-rcolorbrewer" ,r-rcolorbrewer)
20583 ("r-s4vectors" ,r-s4vectors)
20584 ("r-scales" ,r-scales)))
20585 (home-page "https://docs.ropensci.org/iheatmapr")
20586 (synopsis "Interactive, Complex Heatmaps")
20588 "iheatmapr is an R package for building complex, interactive heatmaps
20589 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20590 subplots along the rows or columns of the main heatmap add more information
20591 about each row or column. For example, a one column additional heatmap may
20592 indicate what group a particular row or column belongs to. Complex heatmaps
20593 may also include multiple side by side heatmaps which show different types of
20594 data for the same conditions. Interactivity can improve complex heatmaps by
20595 providing tooltips with information about each cell and enabling zooming into
20596 interesting features. iheatmapr uses the plotly library for interactivity.")
20597 (license license:expat)))
20599 (define-public r-packrat
20606 (uri (cran-uri "packrat" version))
20609 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20610 (properties `((upstream-name . "packrat")))
20611 (build-system r-build-system)
20612 (home-page "https://github.com/rstudio/packrat/")
20613 (synopsis "Dependency management R projects")
20615 "This package provides a dependency manager for R projects that allows
20616 you to manage the R packages your project depends on in an isolated, portable,
20617 and reproducible way.")
20618 (license license:gpl2)))
20620 (define-public r-rsconnect
20622 (name "r-rsconnect")
20627 (uri (cran-uri "rsconnect" version))
20630 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20631 (properties `((upstream-name . "rsconnect")))
20632 (build-system r-build-system)
20634 `(("r-curl" ,r-curl)
20635 ("r-digest" ,r-digest)
20636 ("r-jsonlite" ,r-jsonlite)
20637 ("r-openssl" ,r-openssl)
20638 ("r-packrat" ,r-packrat)
20639 ("r-rstudioapi" ,r-rstudioapi)
20640 ("r-yaml" ,r-yaml)))
20641 (home-page "https://github.com/rstudio/rsconnect")
20642 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20644 "This package provides a programmatic deployment interface for RPubs,
20645 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20646 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20647 (license license:gpl2)))
20649 ;; This package includes minified JavaScript files. When upgrading please
20650 ;; check that there are no new minified JavaScript files.
20651 (define-public r-dygraphs
20653 (name "r-dygraphs")
20654 (version "1.1.1.6")
20658 (uri (cran-uri "dygraphs" version))
20661 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20662 (properties `((upstream-name . "dygraphs")))
20663 (build-system r-build-system)
20665 `(#:modules ((guix build utils)
20666 (guix build r-build-system)
20670 (modify-phases %standard-phases
20671 (add-after 'unpack 'process-javascript
20672 (lambda* (#:key inputs #:allow-other-keys)
20673 (with-directory-excursion "inst/htmlwidgets/lib/"
20677 `(("dygraphs/dygraph-combined-dev.js"
20678 "dygraph-combined.js")
20679 (,(assoc-ref inputs "js-jquery")
20680 "jquery/jquery.min.js")
20681 (,(assoc-ref inputs "js-fquarter")
20682 "fquarter/moment-fquarter.min.js"))))
20683 (lambda (sources targets)
20684 (for-each (lambda (source target)
20685 (format #t "Processing ~a --> ~a~%"
20687 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
20688 (call-with-output-file target
20690 (dump-port minified port)))))
20691 sources targets))))
20694 `(("uglify-js" ,uglify-js)
20695 ;; They actually use version 1.11.1, but this more recent version
20696 ;; should be just fine.
20700 (uri "https://code.jquery.com/jquery-1.12.4.js")
20703 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
20707 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
20708 "moment-fquarter/1.0.1/moment-fquarter.js"))
20711 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
20713 `(("r-htmltools" ,r-htmltools)
20714 ("r-htmlwidgets" ,r-htmlwidgets)
20715 ("r-magrittr" ,r-magrittr)
20718 (home-page "https://github.com/rstudio/dygraphs")
20719 (synopsis "Interface to Dygraphs interactive time series charting library")
20721 "This package provides an R interface to the dygraphs JavaScript charting
20722 library (a copy of which is included in the package). It provides rich
20723 facilities for charting time-series data in R, including highly configurable
20724 series- and axis-display and interactive features like zoom/pan and
20725 series/point highlighting.")
20726 (license license:expat)))
20728 (define-public r-shinystan
20730 (name "r-shinystan")
20735 (uri (cran-uri "shinystan" version))
20738 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
20739 (properties `((upstream-name . "shinystan")))
20740 (build-system r-build-system)
20742 `(("r-bayesplot" ,r-bayesplot)
20743 ("r-colourpicker" ,r-colourpicker)
20745 ("r-dygraphs" ,r-dygraphs)
20746 ("r-ggplot2" ,r-ggplot2)
20747 ("r-gridextra" ,r-gridextra)
20748 ("r-gtools" ,r-gtools)
20749 ("r-markdown" ,r-markdown)
20750 ("r-reshape2" ,r-reshape2)
20751 ("r-rsconnect" ,r-rsconnect)
20752 ("r-rstan" ,r-rstan)
20753 ("r-shiny" ,r-shiny)
20754 ("r-shinyjs" ,r-shinyjs)
20755 ("r-shinythemes" ,r-shinythemes)
20756 ("r-threejs" ,r-threejs)
20757 ("r-xtable" ,r-xtable)
20759 (home-page "https://mc-stan.org/")
20760 (synopsis "Interactive visual and numerical analysis for Bayesian models")
20762 "This package provides a graphical user interface for interactive
20763 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
20764 for analyzing a posterior sample. The interface is powered by the Shiny web
20765 application framework and works with the output of MCMC programs written in
20766 any programming language (and has extended functionality for Stan models fit
20767 using the @code{rstan} and @code{rstanarm} packages).")
20768 (license license:gpl3+)))
20770 (define-public r-rstantools
20772 (name "r-rstantools")
20777 (uri (cran-uri "rstantools" version))
20780 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
20781 (properties `((upstream-name . "rstantools")))
20782 (build-system r-build-system)
20783 (inputs `(("pandoc" ,ghc-pandoc)))
20785 `(("r-desc" ,r-desc)
20786 ("r-rcpp" ,r-rcpp)))
20787 (home-page "https://mc-stan.org/rstantools/")
20788 (synopsis "Tools for developing R packages interfacing with Stan")
20790 "This package provides various tools for developers of R packages
20791 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
20792 up the required package structure, S3 generics and default methods to unify
20793 function naming across Stan-based R packages, and vignettes with
20794 recommendations for developers.")
20795 (license license:gpl3+)))
20797 (define-public r-loo
20804 (uri (cran-uri "loo" version))
20807 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
20808 (properties `((upstream-name . "loo")))
20809 (build-system r-build-system)
20811 `(("pandoc" ,ghc-pandoc)
20812 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20814 `(("r-checkmate" ,r-checkmate)
20815 ("r-matrixstats" ,r-matrixstats)))
20816 (home-page "https://mc-stan.org/loo/")
20817 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
20819 "This package provides an implementation of efficient approximate
20820 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
20821 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
20822 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
20823 procedure for regularizing importance weights. As a byproduct of the
20824 calculations, we also obtain approximate standard errors for estimated
20825 predictive errors and for the comparison of predictive errors between models.
20826 The package also provides methods for using stacking and other model weighting
20827 techniques to average Bayesian predictive distributions.")
20828 (license license:gpl3+)))
20830 (define-public r-rstan
20837 (uri (cran-uri "rstan" version))
20840 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
20841 (properties `((upstream-name . "rstan")))
20842 (build-system r-build-system)
20845 (modify-phases %standard-phases
20846 (add-before 'install 'set-timezone
20847 ;; This package is picky about timezones.
20848 (lambda* (#:key inputs #:allow-other-keys)
20849 (setenv "TZ" "UTC+1")
20851 (string-append (assoc-ref inputs "tzdata")
20852 "/share/zoneinfo"))
20855 `(("tzdata" ,tzdata-for-tests)
20856 ("pandoc" ,ghc-pandoc)))
20859 ("r-ggplot2" ,r-ggplot2)
20860 ("r-gridextra" ,r-gridextra)
20861 ("r-inline" ,r-inline)
20863 ("r-pkgbuild" ,r-pkgbuild)
20865 ("r-rcppeigen" ,r-rcppeigen)
20866 ("r-stanheaders" ,r-stanheaders)))
20867 (home-page "https://discourse.mc-stan.org/")
20868 (synopsis "R interface to Stan")
20870 "User-facing R functions are provided to parse, compile, test, estimate,
20871 and analyze Stan models by accessing the header-only Stan library provided by
20872 the StanHeaders package. The Stan project develops a probabilistic
20873 programming language that implements full Bayesian statistical inference via
20874 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
20875 approximation, and (optionally penalized) maximum likelihood estimation via
20876 optimization. In all three cases, automatic differentiation is used to
20877 quickly and accurately evaluate gradients without burdening the user with the
20878 need to derive the partial derivatives.")
20879 (license license:gpl3+)))
20881 (define-public r-rstanarm
20883 (name "r-rstanarm")
20888 (uri (cran-uri "rstanarm" version))
20891 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
20892 (properties `((upstream-name . "rstanarm")))
20893 (build-system r-build-system)
20895 `(("pandoc" ,ghc-pandoc)
20896 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20898 `(("r-bayesplot" ,r-bayesplot)
20900 ("r-ggplot2" ,r-ggplot2)
20903 ("r-matrix" ,r-matrix)
20906 ("r-rcppeigen" ,r-rcppeigen)
20907 ("r-rcppparallel" ,r-rcppparallel)
20908 ("r-rstan" ,r-rstan)
20909 ("r-rstantools" ,r-rstantools)
20910 ("r-shinystan" ,r-shinystan)
20911 ("r-stanheaders" ,r-stanheaders)
20912 ("r-survival" ,r-survival)))
20913 (home-page "https://mc-stan.org/rstanarm/")
20914 (synopsis "Bayesian applied regression modeling via Stan")
20916 "This package estimates previously compiled regression models using the
20917 @code{rstan} package, which provides the R interface to the Stan C++ library
20918 for Bayesian estimation. Users specify models via the customary R syntax with
20919 a formula and @code{data.frame} plus some additional arguments for priors.")
20920 (license license:gpl3+)))
20922 (define-public r-kendall
20929 (uri (cran-uri "Kendall" version))
20932 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
20933 (properties `((upstream-name . "Kendall")))
20934 (build-system r-build-system)
20936 `(("r-boot" ,r-boot)))
20938 `(("gfortran" ,gfortran)))
20939 (home-page "https://cran.r-project.org/web/packages/Kendall/")
20940 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
20942 "This package computes the Kendall rank correlation and Mann-Kendall
20944 (license license:gpl2+)))
20946 (define-public r-zyp
20949 (version "0.10-1.1")
20953 (uri (cran-uri "zyp" version))
20956 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
20957 (properties `((upstream-name . "zyp")))
20958 (build-system r-build-system)
20960 `(("r-kendall" ,r-kendall)))
20961 (home-page "https://cran.r-project.org/web/packages/zyp/")
20962 (synopsis "Zhang + Yue-Pilon Trends Package")
20964 "This package contains an efficient implementation of Sen's slope
20965 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
20966 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
20968 (license license:lgpl2.1)))
20970 (define-public r-zvcv
20977 (uri (cran-uri "ZVCV" version))
20980 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
20981 (properties `((upstream-name . "ZVCV")))
20982 (build-system r-build-system)
20984 `(("r-abind" ,r-abind)
20985 ("r-glmnet" ,r-glmnet)
20986 ("r-mvtnorm" ,r-mvtnorm)
20987 ("r-partitions" ,r-partitions)
20989 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20990 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
20991 (synopsis "Zero-Variance Control Variates")
20993 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
20994 to reduce the variance of Monte Carlo estimators of expectations using the
20995 derivatives of the log target. Once the derivatives are available, the only
20996 additional computational effort is in solving a linear regression problem.
20997 This method has been extended to higher dimensions using regularisation. This
20998 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
20999 samples, derivatives and function evaluations are available. Additional
21000 functions for applying ZV-CV to two estimators for the normalising constant of
21001 the posterior distribution in Bayesian statistics are also supplied.")
21002 (license license:gpl2+)))
21004 (define-public r-ztype
21011 (uri (cran-uri "ztype" version))
21014 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21015 (properties `((upstream-name . "ztype")))
21016 (build-system r-build-system)
21018 `(("r-assertthat" ,r-assertthat)
21019 ("r-dplyr" ,r-dplyr)
21020 ("r-ggplot2" ,r-ggplot2)
21021 ("r-lubridate" ,r-lubridate)
21022 ("r-magrittr" ,r-magrittr)
21023 ("r-rvest" ,r-rvest)
21024 ("r-stringr" ,r-stringr)))
21025 (home-page "https://cran.r-project.org/web/packages/ztype/")
21026 (synopsis "Run a Ztype game loaded with R functions")
21028 "How fast can you type R functions on your keyboard? Find out by running
21029 a @code{zty.pe} game: export R functions as instructions to type to destroy
21030 opponents' vessels.")
21031 (license license:gpl3)))
21033 (define-public r-zseq
21040 (uri (cran-uri "Zseq" version))
21043 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21044 (properties `((upstream-name . "Zseq")))
21045 (build-system r-build-system)
21047 `(("r-gmp" ,r-gmp)))
21048 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21049 (synopsis "Integer sequence generator")
21051 "This package generates well-known integer sequences. The @code{gmp}
21052 package is adopted for computing with arbitrarily large numbers. Every
21053 function has a hyperlink to its corresponding item in the @dfn{On-Line
21054 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21055 (license license:gpl3+)))
21057 (define-public r-isoband
21064 (uri (cran-uri "isoband" version))
21067 "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
21068 (properties `((upstream-name . "isoband")))
21069 (build-system r-build-system)
21071 `(("r-rcpp" ,r-rcpp)
21072 ("r-testthat" ,r-testthat)))
21074 `(("r-knitr" ,r-knitr)))
21075 (home-page "https://github.com/wilkelab/isoband")
21076 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21078 "This package provides a fast C++ implementation to generate contour
21079 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21080 containing elevation data.")
21081 (license license:expat)))
21083 (define-public r-ppcor
21090 (uri (cran-uri "ppcor" version))
21093 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21094 (properties `((upstream-name . "ppcor")))
21095 (build-system r-build-system)
21097 `(("r-mass" ,r-mass)))
21098 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21099 (synopsis "Partial and semi-partial correlation")
21101 "This package provides users not only with a function to readily
21102 calculate the higher-order partial and semi-partial correlations but also with
21103 statistics and p-values of the correlation coefficients.")
21104 (license license:gpl2)))
21106 (define-public r-hrbrthemes
21108 (name "r-hrbrthemes")
21113 (uri (cran-uri "hrbrthemes" version))
21115 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21116 (properties `((upstream-name . "hrbrthemes")))
21117 (build-system r-build-system)
21119 `(("r-extrafont" ,r-extrafont)
21120 ("r-gdtools" ,r-gdtools)
21121 ("r-ggplot2" ,r-ggplot2)
21122 ("r-htmltools" ,r-htmltools)
21123 ("r-knitr" ,r-knitr)
21124 ("r-magrittr" ,r-magrittr)
21125 ("r-rmarkdown" ,r-rmarkdown)
21126 ("r-scales" ,r-scales)))
21128 `(("r-knitr" ,r-knitr)))
21129 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21130 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21132 "This package provides a compilation of extra @code{ggplot2} themes,
21133 scales and utilities, including a spell check function for plot label fields
21134 and an overall emphasis on typography.")
21135 (license license:expat)))
21137 (define-public r-crochet
21144 (uri (cran-uri "crochet" version))
21147 "1cbv79nyycxk6f8ldcsnn2pvgxqlnrj0qs19nhafnq2clxy863k6"))))
21148 (build-system r-build-system)
21149 (home-page "https://github.com/agrueneberg/crochet")
21150 (synopsis "Implementation Helper for Matrix-Like Types")
21152 "Functions to help implement the extraction / subsetting / indexing
21153 function @code{[} and replacement function @code{[<-} of custom matrix-like
21154 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21155 as possible (with tests to prove it).")
21156 (license license:expat)))
21158 (define-public r-boa
21161 (version "1.1.8-2")
21165 (uri (cran-uri "boa" version))
21168 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21169 (properties `((upstream-name . "boa")))
21170 (build-system r-build-system)
21171 (home-page "http://www.jstatsoft.org/v21/i11")
21172 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21174 "This package provides a menu-driven program and library of functions for
21175 carrying out convergence diagnostics and statistical and graphical analysis of
21176 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21177 (license license:gpl2+)))
21179 (define-public r-httpcode
21181 (name "r-httpcode")
21185 (uri (cran-uri "httpcode" version))
21188 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21189 (build-system r-build-system)
21190 (home-page "https://github.com/sckott/httpcode")
21191 (synopsis "HTTP status code helper")
21192 (description "@code{httpcode} provides functionality for finding and
21193 explaining the meaning of @code{HTTP} status codes. Functions are included for
21194 searching for codes by full or partial number, by message, and to get
21195 appropriate dog and cat images for many status codes.")
21196 (license license:expat)))
21198 (define-public r-latex2exp
21200 (name "r-latex2exp")
21204 (uri (cran-uri "latex2exp" version))
21207 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21208 (build-system r-build-system)
21210 `(("r-stringr" ,r-stringr)
21211 ("r-magrittr", r-magrittr)))
21212 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21213 (synopsis "Use LaTeX expressions in plots")
21214 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21215 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21216 rendered as text, axis labels, etc. throughout R's plotting system.")
21217 (license license:expat)))
21219 (define-public r-oai
21225 (uri (cran-uri "oai" version))
21228 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21229 (build-system r-build-system)
21231 `(("r-xml2" ,r-xml2)
21234 ("r-stringr" ,r-stringr)
21235 ("r-tibble" ,r-tibble)))
21236 (home-page "https://github.com/ropensci/oai/")
21237 (synopsis "General purpose OAI-PMH services client")
21238 (description "@code{oai} provides a general purpose client to work with
21239 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21240 service. Functions are provided to work with the OAI-PMH verbs:
21241 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21242 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21243 (license license:expat)))
21245 (define-public r-argon2
21252 (uri (cran-uri "argon2" version))
21255 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21256 (properties `((upstream-name . "argon2")))
21257 (build-system r-build-system)
21258 (home-page "https://github.com/wrathematics/argon2")
21259 (synopsis "Secure password hashing based on the argon2 algorithm")
21261 "This package provides utilities for secure password hashing via the
21262 argon2 algorithm.")
21263 (license license:bsd-2)))
21265 (define-public r-getpass
21272 (uri (cran-uri "getPass" version))
21275 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21276 (properties `((upstream-name . "getPass")))
21277 (build-system r-build-system)
21279 `(("r-rstudioapi" ,r-rstudioapi)))
21280 (home-page "https://github.com/wrathematics/getPass")
21281 (synopsis "Masked user input")
21283 "This package provides a micro-package for reading \"passwords\", i.e.
21284 reading user input with masking, so that the input is not displayed as it is
21285 typed. Currently, RStudio, the command line (every OS), and any platform
21286 where tcltk is present are supported.")
21287 (license license:bsd-2)))
21289 (define-public r-remoter
21296 (uri (cran-uri "remoter" version))
21299 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21300 (properties `((upstream-name . "remoter")))
21301 (build-system r-build-system)
21303 `(("r-argon2" ,r-argon2)
21304 ("r-getpass" ,r-getpass)
21305 ("r-pbdzmq" ,r-pbdzmq)
21307 (home-page "https://github.com/RBigData/remoter")
21308 (synopsis "Control a remote R session from a local one")
21310 "This package provides a set of utilities for client/server computing
21311 with R, controlling a remote R session (the server) from a local one (the
21313 (license license:bsd-2)))
21315 (define-public r-asd
21322 (uri (cran-uri "asd" version))
21325 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21326 (properties `((upstream-name . "asd")))
21327 (build-system r-build-system)
21329 `(("r-mvtnorm" ,r-mvtnorm)))
21330 (home-page "https://cran.r-project.org/web/packages/asd")
21331 (synopsis "Simulations for Adaptive Seamless Designs")
21333 "This package provdes means to run simulations for adaptive seamless
21334 designs with and without early outcomes for treatment selection and
21335 subpopulation type designs.")
21336 (license license:gpl3)))
21338 (define-public r-nbconvertr
21340 (name "r-nbconvertr")
21345 (uri (cran-uri "nbconvertR" version))
21348 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21349 (properties `((upstream-name . "nbconvertR")))
21350 (build-system r-build-system)
21352 `(("jupyter" ,python-nbconvert)
21353 ("pandoc" ,ghc-pandoc)))
21354 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21355 (synopsis "Vignette engine wrapping Jupyter notebooks")
21357 "This package calls the Jupyter script @code{nbconvert} to create
21358 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21359 containing rich text, code, and its output. Code cells can be edited and
21360 evaluated interactively.")
21361 (license license:gpl3)))
21363 (define-public r-bridgesampling
21365 (name "r-bridgesampling")
21370 (uri (cran-uri "bridgesampling" version))
21373 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21375 `((upstream-name . "bridgesampling")))
21376 (build-system r-build-system)
21378 `(("r-brobdingnag" ,r-brobdingnag)
21380 ("r-matrix" ,r-matrix)
21381 ("r-mvtnorm" ,r-mvtnorm)
21382 ("r-scales" ,r-scales)
21383 ("r-stringr" ,r-stringr)))
21385 `(("r-knitr" ,r-knitr)))
21386 (home-page "https://github.com/quentingronau/bridgesampling")
21387 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21389 "This package provides functions for estimating marginal likelihoods,
21390 Bayes factors, posterior model probabilities, and normalizing constants in
21391 general, via different versions of bridge sampling.")
21392 (license license:gpl2+)))
21394 (define-public r-tea
21401 (uri (cran-uri "tea" version))
21404 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21406 `((upstream-name . "tea")))
21407 (build-system r-build-system)
21409 `(("r-matrix" ,r-matrix)))
21410 (home-page "https://cran.r-project.org/web/packages/tea/")
21411 (synopsis "Threshold estimation approaches")
21413 "This package provides different approaches for selecting the threshold
21414 in generalized Pareto distributions. Most of them are based on minimizing the
21415 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21416 Others are heuristically motivated by searching for stable sample paths, i.e.
21417 a nearly constant region of the tail index estimator with respect to k, which
21418 is the number of data in the tail. The third class is motivated by graphical
21419 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21420 is also implemented here.")
21421 (license license:gpl3)))
21423 (define-public r-awsmethods
21425 (name "r-awsmethods")
21430 (uri (cran-uri "awsMethods" version))
21433 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21435 `((upstream-name . "awsMethods")))
21436 (build-system r-build-system)
21437 (home-page "http://www.wias-berlin.de/software/imaging/")
21438 (synopsis "Class and methods definitions")
21440 "This package defines the generic method @code{extract} and provides
21441 @code{openMP} support as needed in several packages like
21442 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21443 (license license:gpl2+)))
21445 (define-public r-aws
21452 (uri (cran-uri "aws" version))
21455 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21457 `((upstream-name . "aws")))
21458 (build-system r-build-system)
21460 `(("r-awsmethods" ,r-awsmethods)
21463 `(("gfortran" ,gfortran)))
21464 (home-page "https://cran.r-project.org/web/packages/aws/")
21465 (synopsis "Adaptive weights smoothing")
21467 "This package provides a collection of R-functions implementing adaptive
21468 smoothing procedures in 1D, 2D and 3D. This includes the
21469 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21470 Confidence Intervals} (ICI), variational approaches, and a non-local means
21472 (license license:gpl2+)))
21474 (define-public r-sgloptim
21476 (name "r-sgloptim")
21481 (uri (cran-uri "sglOptim" version))
21484 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21486 `((upstream-name . "sglOptim")))
21487 (build-system r-build-system)
21490 ("r-doparallel" ,r-doparallel)
21491 ("r-foreach" ,r-foreach)
21492 ("r-matrix" ,r-matrix)
21494 ("r-rcpparmadillo" ,r-rcpparmadillo)
21495 ("r-rcppprogress" ,r-rcppprogress)))
21497 `(("r-knitr" ,r-knitr)))
21498 (home-page "https://github.com/nielsrhansen/sglOptim")
21499 (synopsis "Generic sparse group Lasso solver")
21501 "This package provides a fast generic solver for sparse group lasso
21502 optimization problems. The loss (objective) function must be defined in a C++
21503 module. The optimization problem is solved using a coordinate gradient
21504 descent algorithm. Convergence of the algorithm is established and the
21505 algorithm is applicable to a broad class of loss functions. Use of parallel
21506 computing for cross validation and subsampling is supported through the
21507 @code{foreach} and @code{doParallel} packages.")
21508 (license license:gpl2+)))
21510 (define-public r-grouped
21517 (uri (cran-uri "grouped" version))
21520 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
21522 `((upstream-name . "grouped")))
21523 (build-system r-build-system)
21525 `(("r-mass" ,r-mass)))
21526 (home-page "https://cran.r-project.org/web/packages/grouped/")
21527 (synopsis "Regression analysis of grouped and coarse data")
21529 "This package provides regression models for grouped and coarse data,
21530 under the coarsened at random assumption.")
21531 (license license:gpl2+)))
21533 (define-public r-stam
21540 (uri (cran-uri "stam" version))
21543 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
21545 `((upstream-name . "stam")))
21546 (build-system r-build-system)
21550 (home-page "https://cran.r-project.org/web/packages/stam")
21551 (synopsis "Spatio-temporal analysis and modelling")
21553 "This package provides various methods to conduct Spatio-Temporal
21554 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
21555 Inferred Spatio-Temporal Modelling.")
21556 (license license:gpl2+)))
21558 (define-public r-dcv
21565 (uri (cran-uri "dcv" version))
21568 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
21570 `((upstream-name . "dcv")))
21571 (build-system r-build-system)
21573 `(("r-lmtest" ,r-lmtest)))
21574 (home-page "https://cran.r-project.org/web/packages/dcv/")
21575 (synopsis "Conventional cross-validation statistics for climate-growth model")
21577 "This package performs several conventional cross-validation statistical
21578 methods for climate-growth model in the climate reconstruction from tree
21579 rings, including Sign Test statistic, Reduction of Error statistic, Product
21580 Mean Test, Durbin-Watson statistic etc.")
21581 (license license:gpl2)))
21583 (define-public r-rcdd
21590 (uri (cran-uri "rcdd" version))
21593 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
21595 `((upstream-name . "rcdd")))
21596 (build-system r-build-system)
21599 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
21600 (synopsis "Computational geometry")
21602 "This package converts back and forth between two representations of a
21603 convex polytope: as solution of a set of linear equalities and inequalities
21604 and as convex hull of set of points and rays. Also does linear programming
21605 and redundant generator elimination. All functions can use exact
21606 infinite-precision rational arithmetic.")
21607 (license license:gpl2)))
21609 (define-public r-rxnat
21616 (uri (cran-uri "Rxnat" version))
21619 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
21621 `((upstream-name . "Rxnat")))
21622 (build-system r-build-system)
21624 `(("r-httr" ,r-httr)
21625 ("r-rcurl" ,r-rcurl)))
21627 `(("r-knitr" ,r-knitr)))
21628 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
21629 (synopsis "Queries and extracts images from neuroimaging datasets")
21631 "This package allows communication with the Extensible Neuroimaging
21632 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
21634 (license license:gpl2)))
21636 (define-public r-rserve
21643 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
21644 version ".tar.gz"))
21647 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
21648 (build-system r-build-system)
21650 `(("r-checkmate" ,r-checkmate)
21652 ("r-jsonlite" ,r-jsonlite)
21653 ("r-knitr" ,r-knitr)
21656 ("r-uuid" ,r-uuid)))
21658 `(("openssl" ,openssl)
21660 (home-page "https://github.com/s-u/Rserve")
21662 "Server providing access to R from many languages and systems")
21664 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
21665 binary requests to be sent to R. Every connection has a separate workspace
21666 and working directory. Client-side implementations are available for popular
21667 languages such as C/C++ and Java, allowing any application to use facilities
21668 of R without the need of linking to R code. Rserve supports remote
21669 connection, user authentication and file transfer. A simple R client is
21670 included in this package as well.")
21671 (license license:gpl2)))