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 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 Eric Brown <brown@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
22 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
23 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
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-clipr
93 (uri (cran-uri "clipr" version))
96 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
97 (build-system r-build-system)
98 (home-page "https://github.com/mdlincoln/clipr")
99 (synopsis "Read and write from the system clipboard")
101 "This package provides simple utility functions to read from and write to
102 the system clipboards.")
103 (license license:gpl3)))
105 (define-public r-oenb
112 (uri (cran-uri "oenb" version))
115 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
116 (properties `((upstream-name . "oenb")))
117 (build-system r-build-system)
119 `(("r-dplyr" ,r-dplyr)
121 (native-inputs `(("r-knitr" ,r-knitr)))
122 (home-page "https://github.com/franzmohr/oenb")
123 (synopsis "Tools for the OeNB Data Web Service")
125 "Tools to access data from the data web service of the
126 @acronym{OeNB, Oesterreichische Nationalbank},
127 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
128 (license license:gpl2+)))
130 (define-public r-scales
137 (uri (cran-uri "scales" version))
139 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
140 (build-system r-build-system)
142 `(("r-farver" ,r-farver)
143 ("r-labeling" ,r-labeling)
144 ("r-lifecycle" ,r-lifecycle)
145 ("r-munsell" ,r-munsell)
146 ("r-rcolorbrewer" ,r-rcolorbrewer)
148 ("r-viridislite" ,r-viridislite)))
149 (home-page "https://github.com/hadley/scales")
150 (synopsis "Scale functions for visualization")
152 "This package provides graphical scales that map data to aesthetics, and
153 provides methods for automatically determining breaks and labels for axes and
155 (license license:expat)))
157 (define-public r-pheatmap
164 (uri (cran-uri "pheatmap" version))
167 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
168 (build-system r-build-system)
170 `(("r-gtable" ,r-gtable)
171 ("r-rcolorbrewer" ,r-rcolorbrewer)
172 ("r-scales" ,r-scales)))
173 (home-page "https://cran.r-project.org/web/packages/pheatmap")
174 (synopsis "Pretty heatmaps")
176 "This package provides an implementation of heatmaps that offers more
177 control over dimensions and appearance.")
178 (license license:gpl2+)))
180 (define-public r-ellipsis
187 (uri (cran-uri "ellipsis" version))
190 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
191 (build-system r-build-system)
193 `(("r-rlang" ,r-rlang)))
194 (home-page "https://github.com/hadley/ellipsis")
195 (synopsis "Tools for working with additional arguments")
197 "In S3 generics, it's useful to take @code{...} so that methods can have
198 additional arguments. But this flexibility comes at a cost: misspelled
199 arguments will be silently ignored. The @code{ellipsis} package is an
200 experiment that allows a generic to warn if any arguments passed in @code{...}
202 (license license:gpl3)))
211 (uri (cran-uri "grr" version))
214 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
215 (build-system r-build-system)
216 (home-page "https://cran.r-project.org/web/packages/grr")
217 (synopsis "Alternative implementations of base R functions")
219 "This package provides alternative implementations of some base R
220 functions, including @code{sort}, @code{order}, and @code{match}. The
221 functions are simplified but can be faster or have other advantages.")
222 (license license:gpl3)))
224 (define-public r-matrix-utils
226 (name "r-matrix-utils")
231 (uri (cran-uri "Matrix.utils" version))
234 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
235 (properties `((upstream-name . "Matrix.utils")))
236 (build-system r-build-system)
239 ("r-matrix" ,r-matrix)))
240 (home-page "https://github.com/cvarrichio/Matrix.utils")
242 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
244 "This package implements data manipulation methods such as @code{cast},
245 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
247 (license license:gpl3)))
256 (uri (cran-uri "sys" version))
259 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
260 (build-system r-build-system)
261 (home-page "https://github.com/jeroen/sys")
262 (synopsis "Powerful and reliable tools for running system commands in R")
264 "This package provides drop-in replacements for the base @code{system2()}
265 function with fine control and consistent behavior across platforms. It
266 supports clean interruption, timeout, background tasks, and streaming STDIN /
267 STDOUT / STDERR over binary or text connections. The package also provides
268 functions for evaluating expressions inside a temporary fork. Such
269 evaluations have no side effects on the main R process, and support reliable
270 interrupts and timeouts. This provides the basis for a sandboxing
272 (license license:expat)))
274 (define-public r-askpass
281 (uri (cran-uri "askpass" version))
284 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
285 (build-system r-build-system)
286 (propagated-inputs `(("r-sys" ,r-sys)))
287 (home-page "https://github.com/jeroen/askpass")
288 (synopsis "Safe password entry for R")
290 "This package provides cross-platform utilities for prompting the user
291 for credentials or a passphrase, for example to authenticate with a server or
292 read a protected key.")
293 (license license:expat)))
295 (define-public r-vegan
302 (uri (cran-uri "vegan" version))
305 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
306 (build-system r-build-system)
308 `(("gfortran" ,gfortran)))
310 `(("r-cluster" ,r-cluster)
311 ("r-knitr" ,r-knitr) ; needed for vignettes
312 ("r-lattice" ,r-lattice)
315 ("r-permute" ,r-permute)))
316 (home-page "https://cran.r-project.org/web/packages/vegan")
317 (synopsis "Functions for community ecology")
319 "The vegan package provides tools for descriptive community ecology. It
320 has most basic functions of diversity analysis, community ordination and
321 dissimilarity analysis. Most of its multivariate tools can be used for other
322 data types as well.")
323 (license license:gpl2+)))
325 (define-public r-tidyverse
332 (uri (cran-uri "tidyverse" version))
335 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
336 (build-system r-build-system)
338 `(("r-broom" ,r-broom)
340 ("r-crayon" ,r-crayon)
341 ("r-dbplyr" ,r-dbplyr)
343 ("r-forcats" ,r-forcats)
344 ("r-ggplot2" ,r-ggplot2)
348 ("r-jsonlite" ,r-jsonlite)
349 ("r-lubridate" ,r-lubridate)
350 ("r-magrittr" ,r-magrittr)
351 ("r-modelr" ,r-modelr)
352 ("r-pillar" ,r-pillar)
355 ("r-readxl" ,r-readxl)
356 ("r-reprex" ,r-reprex)
358 ("r-rstudioapi" ,r-rstudioapi)
360 ("r-stringr" ,r-stringr)
361 ("r-tibble" ,r-tibble)
364 (home-page "https://tidyverse.tidyverse.org")
365 (synopsis "Install and load packages from the \"Tidyverse\"")
367 "The @code{tidyverse} is a set of packages that work in harmony because
368 they share common data representations and API design. This package is
369 designed to make it easy to install and load multiple tidyverse packages in a
371 (license license:gpl3)))
373 (define-public r-rvest
380 (uri (cran-uri "rvest" version))
382 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
383 (build-system r-build-system)
386 ("r-magrittr" ,r-magrittr)
387 ("r-selectr" ,r-selectr)
389 (home-page "https://github.com/hadley/rvest")
390 (synopsis "Simple web scraping for R")
392 "@code{r-rvest} helps you scrape information from web pages. It is
393 designed to work with @code{magrittr} to make it easy to express common web
394 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
395 (license license:gpl3)))
397 (define-public r-selectr
404 (uri (cran-uri "selectr" version))
406 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
407 (build-system r-build-system)
409 `(("r-stringr" ,r-stringr)
411 (home-page "https://sjp.co.nz/projects/selectr/")
412 (synopsis "Translate CSS selectors to XPath expressions")
414 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
415 expression. This allows you to use CSS selectors when working with the XML
416 package as it can only evaluate XPath expressions. Also provided are
417 convenience functions useful for using CSS selectors on XML nodes. This
418 package is a port of the Python package @code{cssselect}.")
419 (license license:bsd-3)))
421 (define-public r-reprex
428 (uri (cran-uri "reprex" version))
431 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
432 (build-system r-build-system)
434 `(("r-callr" ,r-callr)
438 ("r-rmarkdown" ,r-rmarkdown)
439 ("r-whisker" ,r-whisker)
440 ("r-withr" ,r-withr)))
441 (home-page "https://github.com/tidyverse/reprex")
442 (synopsis "Prepare reproducible R code examples for sharing")
444 "This package provides a convenience wrapper that uses the
445 @code{rmarkdown} package to render small snippets of code to target formats
446 that include both code and output. The goal is to encourage the sharing of
447 small, reproducible, and runnable examples on code-oriented websites or email.
448 @code{reprex} also extracts clean, runnable R code from various common formats,
449 such as copy/paste from an R session.")
450 (license license:expat)))
452 (define-public r-callr
459 (uri (cran-uri "callr" version))
462 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
463 (build-system r-build-system)
466 ("r-processx" ,r-processx)))
467 (home-page "https://github.com/r-lib/callr#readme")
468 (synopsis "Call R from R")
470 "It is sometimes useful to perform a computation in a separate R process,
471 without affecting the current R process at all. This package does exactly
473 (license license:expat)))
475 (define-public r-readxl
482 (uri (cran-uri "readxl" version))
485 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
486 (build-system r-build-system)
488 `(("r-cellranger" ,r-cellranger)
489 ("r-progress" ,r-progress)
491 ("r-tibble" ,r-tibble)))
492 (home-page "https://readxl.tidyverse.org")
493 (synopsis "Read Excel files")
495 "This package lets you import Excel files into R. It supports
496 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
497 the embedded @code{RapidXML} C++ library.")
498 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
499 ;; 'rapidxml' which is Boost.
500 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
502 (define-public r-modelr
509 (uri (cran-uri "modelr" version))
512 "1x2m34m4qirb401krmgc5wg3g7ndbcglfab2l0655rmky3fz7rfp"))))
513 (build-system r-build-system)
515 `(("r-broom" ,r-broom)
517 ("r-magrittr" ,r-magrittr)
520 ("r-tibble" ,r-tibble)
522 ("r-tidyselect" ,r-tidyselect)))
523 (home-page "https://github.com/tidyverse/modelr")
524 (synopsis "Helper functions for modelling in pipelines")
526 "Functions for modelling that help you seamlessly integrate modelling
527 into a pipeline of data manipulation and visualisation.")
528 (license license:gpl3)))
530 (define-public r-httpuv
536 (uri (cran-uri "httpuv" version))
539 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
540 (build-system r-build-system)
544 ("r-promises" ,r-promises)
547 (home-page "https://github.com/rstudio/httpuv")
548 (synopsis "HTTP and WebSocket server library for R")
550 "The httpuv package provides low-level socket and protocol support for
551 handling HTTP and WebSocket requests directly from within R. It is primarily
552 intended as a building block for other packages, rather than making it
553 particularly easy to create complete web applications using httpuv alone.")
554 ;; This package includes third-party code that was originally released
555 ;; under various non-copyleft licenses. Full licensing information can be
556 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
557 (license license:gpl3+)))
559 (define-public r-jsonlite
565 (uri (cran-uri "jsonlite" version))
568 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
569 (build-system r-build-system)
570 (home-page "https://arxiv.org/abs/1403.2805")
571 (synopsis "Robust, high performance JSON parser and generator for R")
573 "The jsonlite package provides a fast JSON parser and generator optimized
574 for statistical data and the web. It offers flexible, robust, high
575 performance tools for working with JSON in R and is particularly powerful for
576 building pipelines and interacting with a web API. In addition to converting
577 JSON data from/to R objects, jsonlite contains functions to stream, validate,
578 and prettify JSON data. The unit tests included with the package verify that
579 all edge cases are encoded and decoded consistently for use with dynamic data
580 in systems and applications.")
581 (license license:expat)))
583 (define-public r-servr
589 (uri (cran-uri "servr" version))
592 "106skz04iq4dkblr17idxsxfcfqic6rcaz8mahydkwjjppnhp5fc"))))
593 (build-system r-build-system)
595 `(("r-httpuv" ,r-httpuv)
596 ("r-jsonlite" ,r-jsonlite)
599 (home-page "https://github.com/yihui/servr")
600 (synopsis "Simple HTTP server to serve static files or dynamic documents")
602 "Servr provides an HTTP server in R to serve static files, or dynamic
603 documents that can be converted to HTML files (e.g., R Markdown) under a given
605 (license license:expat)))
607 (define-public r-htmltools
613 (uri (cran-uri "htmltools" version))
616 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
617 (build-system r-build-system)
619 `(("r-digest" ,r-digest)
621 ("r-rlang" ,r-rlang)))
622 (home-page "https://cran.r-project.org/web/packages/htmltools")
623 (synopsis "R tools for HTML")
625 "This package provides tools for HTML generation and output in R.")
626 (license license:expat)))
628 (define-public r-htmlwidgets
630 (name "r-htmlwidgets")
634 (uri (cran-uri "htmlwidgets" version))
637 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
638 (build-system r-build-system)
640 `(("r-htmltools" ,r-htmltools)
641 ("r-jsonlite" ,r-jsonlite)
643 (home-page "https://github.com/ramnathv/htmlwidgets")
644 (synopsis "HTML Widgets for R")
646 "HTML widgets is a framework for creating HTML widgets that render in
647 various contexts including the R console, R Markdown documents, and Shiny web
649 (license license:expat)))
651 (define-public r-htmltable
658 (uri (cran-uri "htmlTable" version))
661 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
662 (properties `((upstream-name . "htmlTable")))
663 (build-system r-build-system)
665 `(("r-checkmate" ,r-checkmate)
666 ("r-htmltools" ,r-htmltools)
667 ("r-htmlwidgets" ,r-htmlwidgets)
669 ("r-magrittr" ,r-magrittr)
670 ("r-rstudioapi" ,r-rstudioapi)
671 ("r-stringr" ,r-stringr)))
672 (home-page "http://gforge.se/packages/")
673 (synopsis "Advanced tables for Markdown/HTML")
675 "This package provides functions to build tables with advanced layout
676 elements such as row spanners, column spanners, table spanners, zebra
677 striping, and more. While allowing advanced layout, the underlying
678 CSS-structure is simple in order to maximize compatibility with word
679 processors such as LibreOffice. The package also contains a few text
680 formatting functions that help outputting text compatible with HTML or
682 (license license:gpl3+)))
684 (define-public r-curl
690 (uri (cran-uri "curl" version))
693 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
694 (build-system r-build-system)
697 (modify-phases %standard-phases
698 ;; The environment variable CURL_CA_BUNDLE is only respected when
699 ;; running Windows, so we disable the platform checks.
700 ;; This can be removed once the libcurl has been patched.
701 (add-after 'unpack 'allow-CURL_CA_BUNDLE
703 (substitute* "R/onload.R"
704 (("if \\(!grepl\\(\"mingw\".*")
706 (substitute* "src/handle.c"
709 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
710 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
717 `(("pkg-config" ,pkg-config)))
718 (home-page "https://github.com/jeroenooms/curl")
719 (synopsis "HTTP client for R")
721 "The @code{curl()} and @code{curl_download()} functions provide highly
722 configurable drop-in replacements for base @code{url()} and
723 @code{download.file()} with better performance, support for encryption, gzip
724 compression, authentication, and other @code{libcurl} goodies. The core of
725 the package implements a framework for performing fully customized requests
726 where data can be processed either in memory, on disk, or streaming via the
727 callback or connection interfaces.")
728 (license license:expat)))
730 (define-public r-hwriter
737 (uri (cran-uri "hwriter" version))
740 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
741 (build-system r-build-system)
742 (home-page "https://cran.r-project.org/web/packages/hwriter")
743 (synopsis "Output R objects in HTML format")
745 "This package provides easy-to-use and versatile functions to output R
746 objects in HTML format.")
747 (license license:lgpl2.1+)))
749 (define-public r-rjson
756 (uri (cran-uri "rjson" version))
759 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
760 (build-system r-build-system)
761 (home-page "https://cran.r-project.org/web/packages/rjson")
762 (synopsis "JSON library for R")
764 "This package provides functions to convert R objects into JSON objects
766 (license license:gpl2+)))
768 (define-public r-fastmap
775 (uri (cran-uri "fastmap" version))
778 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
779 (properties `((upstream-name . "fastmap")))
780 (build-system r-build-system)
781 (home-page "https://r-lib.github.io/fastmap/")
782 (synopsis "Fast implementation of a key-value store")
784 "This package provides a fast implementation of a key-value store.
785 Environments are commonly used as key-value stores, but every time a new key
786 is used, it is added to R's global symbol table, causing a small amount of
787 memory leakage. This can be problematic in cases where many different keys
788 are used. Fastmap avoids this memory leak issue by implementing the map using
789 data structures in C++.")
790 (license license:expat)))
792 (define-public r-shiny
800 (url "https://github.com/rstudio/shiny.git")
801 (commit (string-append "v" version))))
802 (file-name (git-file-name name version))
805 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
806 (build-system r-build-system)
808 `(#:modules ((guix build r-build-system)
809 (guix build minify-build-system)
812 #:imported-modules (,@%r-build-system-modules
813 (guix build minify-build-system))
815 (modify-phases (@ (guix build r-build-system) %standard-phases)
816 (add-after 'unpack 'replace-bundled-minified-JavaScript
817 (lambda* (#:key inputs #:allow-other-keys)
818 (let ((replace-file (lambda (old new)
819 (format #t "replacing ~a with ~a\n" old new)
822 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
823 ;; contain just data. They are not minified code, so we don't
825 (with-directory-excursion "inst/www/shared"
826 (replace-file "bootstrap/shim/respond.min.js"
827 (string-append (assoc-ref inputs "js-respond")
828 "/share/javascript/respond.min.js"))
829 (replace-file "bootstrap/shim/html5shiv.min.js"
830 (string-append (assoc-ref inputs "js-html5shiv")
831 "/share/javascript/html5shiv.min.js"))
832 (replace-file "json2-min.js"
833 (string-append (assoc-ref inputs "js-json2")
834 "/share/javascript/json2-min.js"))
835 (replace-file "strftime/strftime-min.js"
836 (string-append (assoc-ref inputs "js-strftime")
837 "/share/javascript/strftime.min.js"))
838 (replace-file "highlight/highlight.pack.js"
839 (string-append (assoc-ref inputs "js-highlight")
840 "/share/javascript/highlight.min.js"))
841 (replace-file "datatables/js/jquery.dataTables.min.js"
842 (string-append (assoc-ref inputs "js-datatables")
843 "/share/javascript/jquery.dataTables.min.js"))
844 (replace-file "selectize/js/selectize.min.js"
845 (string-append (assoc-ref inputs "js-selectize")
846 "/share/javascript/selectize.min.js"))
847 (replace-file "selectize/js/es5-shim.min.js"
848 (string-append (assoc-ref inputs "js-es5-shim")
849 "/share/javascript/es5-shim.min.js"))
850 (for-each (match-lambda
853 (minify source #:target target)))
854 '(("jqueryui/jquery-ui.js" .
855 "jqueryui/jquery-ui.min.js")
856 ("datepicker/js/bootstrap-datepicker.js" .
857 "datepicker/js/bootstrap-datepicker.min.js")
858 ("ionrangeslider/js/ion.rangeSlider.js" .
859 "ionrangeslider/js/ion.rangeSlider.min.js")
860 ("bootstrap/js/bootstrap.js" .
861 "bootstrap/js/bootstrap.min.js")
866 ("legacy/jquery.js" .
867 "legacy/jquery.min.js")
868 ("showdown/src/showdown.js" .
869 "showdown/compressed/showdown.js")))))
872 `(("r-crayon" ,r-crayon)
873 ("r-digest" ,r-digest)
874 ("r-fastmap" ,r-fastmap)
875 ("r-htmltools" ,r-htmltools)
876 ("r-httpuv" ,r-httpuv)
877 ("r-jsonlite" ,r-jsonlite)
880 ("r-promises" ,r-promises)
883 ("r-sourcetools" ,r-sourcetools)
885 ("r-xtable" ,r-xtable)))
887 `(("js-datatables" ,js-datatables)
888 ("js-html5shiv" ,js-html5shiv)
889 ("js-json2" ,js-json2)
890 ("js-respond" ,js-respond)
891 ("js-selectize" ,js-selectize)
892 ("js-strftime" ,js-strftime)
893 ("js-highlight" ,js-highlight)
894 ("js-es5-shim" ,js-es5-shim)))
896 `(("uglify-js" ,uglify-js)
897 ("gfortran" ,gfortran)))
898 (home-page "http://shiny.rstudio.com")
899 (synopsis "Easy interactive web applications with R")
901 "Makes it incredibly easy to build interactive web applications
902 with R. Automatic \"reactive\" binding between inputs and outputs and
903 extensive prebuilt widgets make it possible to build beautiful,
904 responsive, and powerful applications with minimal effort.")
905 (license license:artistic2.0)))
907 ;; This package includes minified JavaScript files. When upgrading please
908 ;; check that there are no new minified JavaScript files.
909 (define-public r-shinytree
916 (uri (cran-uri "shinyTree" version))
919 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
920 (modules '((guix build utils)))
923 ;; Delete minified JavaScript
924 (for-each delete-file
925 '("inst/www/jsTree-3.3.7/libs/require.js"
926 "inst/www/jsTree-3.3.7/libs/jquery.js"
927 "inst/www/jsTree-3.3.7/jstree.min.js"))
929 (properties `((upstream-name . "shinyTree")))
930 (build-system r-build-system)
932 `(#:modules ((guix build utils)
933 (guix build r-build-system)
937 (modify-phases %standard-phases
938 (add-after 'unpack 'replace-minified-javascript
939 (lambda* (#:key inputs #:allow-other-keys)
940 (with-directory-excursion "inst/www/jsTree-3.3.7/"
941 (symlink (string-append (assoc-ref inputs "js-requirejs")
942 "/share/javascript/require.min.js")
947 `((,(assoc-ref inputs "js-jquery")
951 (lambda (sources targets)
952 (for-each (lambda (source target)
953 (format #t "Processing ~a --> ~a~%"
955 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
956 (call-with-output-file target
958 (dump-port minified port)))))
962 `(("r-htmlwidgets" ,r-htmlwidgets)
963 ("r-jsonlite" ,r-jsonlite)
964 ("r-promises" ,r-promises)
966 ("r-stringr" ,r-stringr)))
968 `(("js-requirejs" ,js-requirejs)))
970 `(("uglify-js" ,uglify-js)
974 (uri "https://code.jquery.com/jquery-3.3.1.js")
977 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
978 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
979 (synopsis "jsTree bindings for Shiny")
981 "This package exposes R bindings to jsTree, a JavaScript library that
982 supports interactive trees, to enable rich, editable trees in Shiny.")
983 (license license:expat)))
985 (define-public r-shinydashboard
987 (name "r-shinydashboard")
991 (uri (cran-uri "shinydashboard" version))
994 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
995 (build-system r-build-system)
996 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
997 ;; Regenerate it from the included sources.
999 `(#:modules ((guix build utils)
1000 (guix build r-build-system)
1003 (modify-phases %standard-phases
1004 (add-after 'unpack 'generate-minified-javascript
1006 (with-directory-excursion "inst/AdminLTE"
1007 (delete-file "app.min.js")
1008 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1009 (call-with-output-file "app.min.js"
1011 (dump-port minified port))))))))))
1013 `(("r-htmltools" ,r-htmltools)
1014 ("r-promises" ,r-promises)
1015 ("r-shiny" ,r-shiny)))
1017 `(("uglify-js" ,uglify-js)))
1018 (home-page "https://rstudio.github.io/shinydashboard/")
1019 (synopsis "Create dashboards with shiny")
1020 (description "This package provides an extension to the Shiny web
1021 application framework for R, making it easy to create attractive dashboards.")
1022 ;; This package includes software that was released under the Expat
1023 ;; license, but the whole package is released under GPL version 2 or
1025 (license license:gpl2+)))
1027 (define-public r-shinyfiles
1029 (name "r-shinyfiles")
1034 (uri (cran-uri "shinyFiles" version))
1036 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
1037 (properties `((upstream-name . "shinyFiles")))
1038 (build-system r-build-system)
1041 ("r-htmltools" ,r-htmltools)
1042 ("r-jsonlite" ,r-jsonlite)
1043 ("r-shiny" ,r-shiny)
1044 ("r-tibble" ,r-tibble)))
1045 (home-page "https://github.com/thomasp85/shinyFiles")
1046 (synopsis "Server-side file system viewer for Shiny")
1048 "This package provides functionality for client-side navigation of the
1049 server side file system in shiny apps. In case the app is running locally
1050 this gives the user direct access to the file system without the need to
1051 \"download\" files to a temporary location. Both file and folder selection as
1052 well as file saving is available.")
1053 (license license:gpl2+)))
1055 (define-public r-shinythemes
1057 (name "r-shinythemes")
1062 (uri (cran-uri "shinythemes" version))
1065 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1066 (properties `((upstream-name . "shinythemes")))
1067 (build-system r-build-system)
1068 (propagated-inputs `(("r-shiny" ,r-shiny)))
1069 (home-page "https://rstudio.github.io/shinythemes/")
1070 (synopsis "Themes for Shiny")
1072 "This package provides themes for use with Shiny. It includes several
1073 Bootstrap themes, which are packaged for use with Shiny applications.")
1074 ;; The package is released under version 3 of the GPL, but it includes
1075 ;; source files that are covered by the Expat license. It also includes
1076 ;; fonts under SIL or the ASL.
1077 (license (list license:gpl3 license:expat
1078 license:silofl1.1 license:asl2.0))))
1080 ;; The package sources include minified variants of d3.js and non-minified
1081 ;; source code of d3-jetpack.
1082 (define-public r-d3r
1089 (uri (cran-uri "d3r" version))
1092 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1093 (build-system r-build-system)
1095 `(#:modules ((guix build utils)
1096 (guix build r-build-system)
1100 (modify-phases %standard-phases
1101 (add-after 'unpack 'process-javascript
1102 (lambda* (#:key inputs #:allow-other-keys)
1103 (with-directory-excursion "inst/www/d3/"
1107 `((,(assoc-ref inputs "d3.v3.js")
1108 "v3/dist/d3.min.js")
1109 (,(assoc-ref inputs "d3.v4.js")
1110 "v4/dist/d3.min.js")
1111 (,(assoc-ref inputs "d3.v5.js")
1112 "v5/dist/d3.min.js"))))
1113 (lambda (sources targets)
1114 (for-each (lambda (source target)
1115 (format #t "Processing ~a --> ~a~%"
1117 (delete-file target)
1118 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1119 (call-with-output-file target
1121 (dump-port minified port)))))
1125 `(("r-dplyr" ,r-dplyr)
1126 ("r-htmltools" ,r-htmltools)
1127 ("r-tidyr" ,r-tidyr)))
1129 `(("uglify-js" ,uglify-js)
1133 (uri "https://d3js.org/d3.v3.js")
1136 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1140 (uri "https://d3js.org/d3.v4.js")
1143 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1147 (uri "https://d3js.org/d3.v5.js")
1150 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1151 (home-page "https://github.com/timelyportfolio/d3r")
1152 (synopsis "d3.js utilities for R")
1154 "This package provides a suite of functions to help ease the use of the
1155 d3.js visualization library in R. These helpers include
1156 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1157 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1158 R objects into the JSON format that the d3.js library expects.")
1159 (license license:bsd-3)))
1161 ;; We use the latest commit here because the last release was in 2016 while
1162 ;; the latest commit was in 2018.
1163 (define-public r-sankeyd3
1164 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1168 (version (git-version "0.3.2" revision commit))
1173 (url "https://github.com/fbreitwieser/sankeyD3.git")
1175 (file-name (git-file-name name version))
1178 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1179 (build-system r-build-system)
1182 ("r-htmlwidgets" ,r-htmlwidgets)
1183 ("r-shiny" ,r-shiny)
1184 ("r-magrittr" ,r-magrittr)))
1185 (home-page "https://github.com/fbreitwieser/sankeyD3")
1186 (synopsis "Sankey network graphs from R")
1188 "This package provides an R library to generate Sankey network graphs
1189 in R and Shiny via the D3 visualization library.")
1190 ;; The R code is licensed under GPLv3+. It includes the non-minified
1191 ;; JavaScript source code of d3-sankey, which is released under the
1192 ;; 3-clause BSD license.
1193 (license (list license:gpl3+ license:bsd-3)))))
1195 (define-public r-crosstalk
1197 (name "r-crosstalk")
1202 (uri (cran-uri "crosstalk" version))
1205 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1206 (build-system r-build-system)
1208 `(("r-htmltools" ,r-htmltools)
1209 ("r-jsonlite" ,r-jsonlite)
1210 ("r-lazyeval" ,r-lazyeval)
1212 (home-page "https://rstudio.github.io/crosstalk/")
1213 (synopsis "Inter-widget interactivity for HTML widgets")
1215 "This package provides building blocks for allowing HTML widgets to
1216 communicate with each other, with Shiny or without (i.e. static @code{.html}
1217 files). It currently supports linked brushing and filtering.")
1218 (license license:expat)))
1220 (define-public r-rook
1227 (uri (cran-uri "Rook" version))
1230 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1231 (properties `((upstream-name . "Rook")))
1232 (build-system r-build-system)
1233 (propagated-inputs `(("r-brew" ,r-brew)))
1234 (home-page "https://cran.r-project.org/web/packages/Rook")
1235 (synopsis "Web server interface for R")
1237 "This package contains the Rook specification and convenience software
1238 for building and running Rook applications. A Rook application is an R
1239 reference class object that implements a @code{call} method or an R closure
1240 that takes exactly one argument, an environment, and returns a list with three
1241 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1242 (license license:gpl2)))
1244 (define-public r-miniui
1251 (uri (cran-uri "miniUI" version))
1254 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1255 (properties `((upstream-name . "miniUI")))
1256 (build-system r-build-system)
1258 `(("r-htmltools" ,r-htmltools)
1259 ("r-shiny" ,r-shiny)))
1260 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1261 (synopsis "Shiny UI widgets for small screens")
1263 "This package provides UI widget and layout functions for writing Shiny apps that
1264 work well on small screens.")
1265 (license license:gpl3)))
1267 (define-public r-feather
1274 (uri (cran-uri "feather" version))
1277 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1278 (build-system r-build-system)
1282 ("r-tibble" ,r-tibble)))
1283 (home-page "https://github.com/wesm/feather")
1284 (synopsis "R Bindings to the Feather API")
1285 (description "Read and write feather files, a lightweight binary columnar
1286 data store designed for maximum speed.")
1287 (license license:asl2.0)))
1289 (define-public r-maps
1296 (uri (cran-uri "maps" version))
1299 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1300 (build-system r-build-system)
1301 (home-page "https://cran.r-project.org/web/packages/maps")
1302 (synopsis "Draw geographical maps")
1303 (description "This package provides an R module for display of maps.
1304 Projection code and larger maps are in separate packages (@code{mapproj} and
1306 (license license:gpl2)))
1308 (define-public r-mapproj
1315 (uri (cran-uri "mapproj" version))
1318 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1319 (build-system r-build-system)
1320 (propagated-inputs `(("r-maps" ,r-maps)))
1321 (home-page "https://cran.r-project.org/web/packages/mapproj")
1322 (synopsis "Map projection in R")
1323 (description "This package converts latitude/longitude into projected
1325 (license (list license:gpl2 ; The R interface
1326 (license:non-copyleft ; The C code
1327 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1328 "Lucent Public License Version 1.02")))))
1330 (define-public r-rgooglemaps
1332 (name "r-rgooglemaps")
1337 (uri (cran-uri "RgoogleMaps" version))
1340 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1341 (properties `((upstream-name . "RgoogleMaps")))
1342 (build-system r-build-system)
1346 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1347 (synopsis "Use Google Maps in R")
1348 (description "This package serves two purposes:
1350 @item Provide a comfortable R interface to query the Google server for static
1352 @item Use the map as a background image to overlay plots within R. This
1353 requires proper coordinate scaling.
1355 (license license:gpl2+)))
1357 (define-public r-geosphere
1359 (name "r-geosphere")
1364 (uri (cran-uri "geosphere" version))
1367 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1368 (build-system r-build-system)
1369 (propagated-inputs `(("r-sp" ,r-sp)))
1370 (home-page "https://cran.r-project.org/web/packages/geosphere")
1371 (synopsis "Spherical trigonometry")
1372 (description "This package computes spherical trigonometry for geographic
1373 applications. That is, compute distances and related measures for angular
1374 (longitude/latitude) locations.")
1375 (license license:gpl3+)))
1377 (define-public r-jpeg
1384 (uri (cran-uri "jpeg" version))
1387 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1388 (build-system r-build-system)
1389 (inputs `(("libjpeg" ,libjpeg-turbo)))
1390 (home-page "https://www.rforge.net/jpeg/")
1391 (synopsis "Read and write JPEG images with R")
1392 (description "This package provides a way to read, write and display
1393 bitmap images stored in the JPEG format with R. It can read and write both
1394 files and in-memory raw vectors.")
1395 (license license:gpl2+)))
1397 (define-public r-ggmap
1404 (uri (cran-uri "ggmap" version))
1407 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1408 (build-system r-build-system)
1410 `(("r-bitops" ,r-bitops)
1411 ("r-digest" ,r-digest)
1412 ("r-dplyr" ,r-dplyr)
1413 ("r-ggplot2" ,r-ggplot2)
1417 ("r-magrittr" ,r-magrittr)
1420 ("r-purrr" ,r-purrr)
1421 ("r-rgooglemaps" ,r-rgooglemaps)
1422 ("r-rjson" ,r-rjson)
1423 ("r-scales" ,r-scales)
1424 ("r-stringr" ,r-stringr)
1425 ("r-tibble" ,r-tibble)
1426 ("r-tidyr" ,r-tidyr)))
1427 (home-page "https://github.com/dkahle/ggmap")
1428 (synopsis "Spatial visualization with ggplot2")
1429 (description "This package provides a collection of functions to visualize
1430 spatial data and models on top of static maps from various online sources (e.g
1431 Google Maps and Stamen Maps). It includes tools common to those tasks,
1432 including functions for geolocation and routing.")
1433 (license license:gpl2)))
1435 (define-public r-haven
1442 (uri (cran-uri "haven" version))
1445 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1446 (build-system r-build-system)
1450 `(("r-forcats" ,r-forcats)
1453 ("r-rlang" ,r-rlang)
1454 ("r-readr" ,r-readr)
1455 ("r-tibble" ,r-tibble)
1456 ("r-tidyselect" ,r-tidyselect)))
1457 (home-page "https://haven.tidyverse.org")
1458 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1460 "This package lets you mport foreign statistical formats into R via the
1461 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1462 (license license:expat)))
1464 (define-public r-amap
1470 (uri (cran-uri "amap" version))
1473 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1474 (build-system r-build-system)
1476 `(("gfortran" ,gfortran)))
1477 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1478 (synopsis "Another multidimensional analysis package")
1479 (description "This package provides tools for clustering and principal
1480 component analysis (with robust methods, and parallelized functions).")
1481 (license license:gpl2+)))
1483 (define-public r-ape
1490 (uri (cran-uri "ape" version))
1493 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1494 (build-system r-build-system)
1496 `(("r-lattice" ,r-lattice)
1498 ("r-rcpp" ,r-rcpp)))
1499 (home-page "http://ape-package.ird.fr/")
1500 (synopsis "Analyses of phylogenetics and evolution")
1502 "This package provides functions for reading, writing, plotting, and
1503 manipulating phylogenetic trees, analyses of comparative data in a
1504 phylogenetic framework, ancestral character analyses, analyses of
1505 diversification and macroevolution, computing distances from DNA sequences,
1506 and several other tools.")
1507 (license license:gpl2+)))
1509 (define-public r-abbyyr
1516 (uri (cran-uri "abbyyR" version))
1519 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1520 (properties `((upstream-name . "abbyyR")))
1521 (build-system r-build-system)
1523 `(("r-curl" ,r-curl)
1526 ("r-progress" ,r-progress)
1527 ("r-readr" ,r-readr)
1529 (home-page "https://github.com/soodoku/abbyyR")
1530 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1532 "This package provides tools to get text from images of text using Abbyy
1533 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1534 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1535 passports and get the results in a variety of formats including plain text and
1536 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1537 (license license:expat)))
1539 (define-public r-colorspace
1541 (name "r-colorspace")
1546 (uri (cran-uri "colorspace" version))
1548 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1549 (build-system r-build-system)
1550 (home-page "https://cran.r-project.org/web/packages/colorspace")
1551 (synopsis "Color space manipulation")
1553 "This package carries out a mapping between assorted color spaces
1554 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1555 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1556 colors are provided.")
1557 (license license:bsd-3)))
1559 (define-public r-glue
1566 (uri (cran-uri "glue" version))
1569 "1hb9j2519jv9zgkgjb25hnqi22i7zxnaksqd16m4nxa1f6gl0v7a"))))
1570 (build-system r-build-system)
1571 ;; knitr depends on glue, so we can't add knitr here to build the
1575 `(("r-knitr" ,r-knitr)))
1576 (home-page "https://github.com/tidyverse/glue")
1577 (synopsis "Interpreted string literals")
1579 "This package provides an implementation of interpreted string literals,
1580 inspired by Python's Literal String Interpolation (PEP-0498) and
1581 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1582 (license license:expat)))
1584 (define-public r-pastecs
1590 (uri (cran-uri "pastecs" version))
1593 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1594 (build-system r-build-system)
1596 `(("r-boot" ,r-boot)))
1597 (home-page "http://www.sciviews.org/pastecs")
1598 (synopsis "Analysis of space-time ecological series")
1600 "This package provides functions for regulation, decomposition and analysis
1601 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1602 initiative to bring PASSTEC 2000 functionalities to R.")
1603 (license license:gpl2+)))
1605 (define-public r-plogr
1612 (uri (cran-uri "plogr" version))
1615 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1616 (build-system r-build-system)
1617 (home-page "https://github.com/krlmlr/plogr")
1618 (synopsis "R bindings for the plog C++ logging library")
1620 "This package provides the header files for a stripped-down version of
1621 the plog header-only C++ logging library, and a method to log to R's standard
1623 (license license:expat)))
1625 (define-public r-pls
1632 (uri (cran-uri "pls" version))
1634 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1635 (build-system r-build-system)
1636 (home-page "https://mevik.net/work/software/pls.html")
1637 (synopsis "Partial Least Squares and Principal Component Regression")
1639 "The pls package implements multivariate regression methods: Partial Least
1640 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1641 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1644 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1645 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1646 @item multi-response models (or @dfn{PLS2})
1647 @item flexible cross-validation
1648 @item Jackknife variance estimates of regression coefficients
1649 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1650 (R)MSEP, R², and correlation loadings
1651 @item formula interface, modelled after @code{lm()}, with methods for predict,
1652 print, summary, plot, update, etc.
1653 @item extraction functions for coefficients, scores, and loadings
1654 @item MSEP, RMSEP, and R² estimates
1655 @item multiplicative scatter correction (@dfn{MSC})
1657 (license license:gpl2)))
1666 (uri (cran-uri "ps" version))
1668 (base32 "0127q6pw9iw8hhcfp231gmdh29nahh2n5jzc38avrzy7yrm4bwl9"))))
1669 (build-system r-build-system)
1670 (home-page "https://ps.r-lib.org")
1671 (synopsis "List, query, and manipulate system processes")
1673 "The ps package implements an API to list, query, and manipulate system
1674 processes. Most of its code is based on the @code{psutil} Python package.")
1675 (license license:bsd-3)))
1677 (define-public r-pkgbuild
1684 (uri (cran-uri "pkgbuild" version))
1686 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1687 (build-system r-build-system)
1689 `(("r-callr" ,r-callr)
1691 ("r-crayon" ,r-crayon)
1693 ("r-prettyunits" ,r-prettyunits)
1695 ("r-rprojroot" ,r-rprojroot)
1696 ("r-withr" ,r-withr)))
1697 (home-page "https://github.com/r-pkgs/pkgbuild")
1698 (synopsis "Find tools needed to build R packages")
1700 "This package provides functions used to build R packages. It locates
1701 compilers needed to build R packages on various platforms and ensures the PATH
1702 is configured appropriately so R can use them.")
1703 (license license:gpl3)))
1705 (define-public r-pkgload
1712 (uri (cran-uri "pkgload" version))
1715 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1716 (build-system r-build-system)
1718 `(("r-desc" ,r-desc)
1719 ("r-pkgbuild" ,r-pkgbuild)
1720 ("r-rlang" ,r-rlang)
1721 ("r-rprojroot" ,r-rprojroot)
1722 ("r-rstudioapi" ,r-rstudioapi)
1723 ("r-withr" ,r-withr)))
1724 (home-page "https://github.com/r-lib/pkgload")
1725 (synopsis "Simulate package installation and attach")
1727 "This package simulates the process of installing a package and then
1728 attaching it. This is a key part of the @code{devtools} package as it allows
1729 you to rapidly iterate while developing a package.")
1730 (license license:gpl3)))
1732 (define-public r-rcpp
1739 (uri (cran-uri "Rcpp" version))
1741 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
1742 (build-system r-build-system)
1743 (home-page "http://www.rcpp.org")
1744 (synopsis "Seamless R and C++ integration")
1746 "The Rcpp package provides R functions as well as C++ classes which offer
1747 a seamless integration of R and C++. Many R data types and objects can be
1748 mapped back and forth to C++ equivalents which facilitates both writing of new
1749 code as well as easier integration of third-party libraries. Documentation
1750 about Rcpp is provided by several vignettes included in this package, via the
1751 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1752 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1753 @code{citation(\"Rcpp\")} for details on these last two.")
1754 (license license:gpl2+)))
1756 (define-public r-bindr
1763 (uri (cran-uri "bindr" version))
1766 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1767 (build-system r-build-system)
1768 (home-page "https://github.com/krlmlr/bindr")
1769 (synopsis "Parametrized active bindings")
1771 "This package provides a simple interface for creating active bindings
1772 where the bound function accepts additional arguments.")
1773 (license license:expat)))
1775 (define-public r-bindrcpp
1782 (uri (cran-uri "bindrcpp" version))
1785 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1786 (build-system r-build-system)
1788 `(("r-bindr" ,r-bindr)
1789 ("r-plogr" ,r-plogr)
1790 ("r-rcpp" ,r-rcpp)))
1791 (home-page "https://github.com/krlmlr/bindrcpp")
1792 (synopsis "Rcpp interface to active bindings")
1794 "This package provides an easy way to fill an environment with active
1795 bindings that call a C++ function.")
1796 (license license:expat)))
1798 (define-public r-auc
1805 (uri (cran-uri "AUC" version))
1808 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1809 (properties `((upstream-name . "AUC")))
1810 (build-system r-build-system)
1811 (home-page "https://cran.r-project.org/web/packages/AUC")
1812 (synopsis "Compute the area under the curve of selected measures")
1814 "This package includes functions to compute the area under the curve of
1815 selected measures: the area under the sensitivity curve (AUSEC), the area
1816 under the specificity curve (AUSPC), the area under the accuracy
1817 curve (AUACC), and the area under the receiver operating characteristic
1818 curve (AUROC). The curves can also be visualized. Support for partial areas
1820 (license license:gpl2+)))
1822 (define-public r-calibrate
1824 (name "r-calibrate")
1829 (uri (cran-uri "calibrate" version))
1831 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1832 (build-system r-build-system)
1834 `(("r-mass" ,r-mass)))
1835 (home-page "https://cran.r-project.org/web/packages/calibrate")
1836 (synopsis "Calibration of scatterplot and biplot axes")
1838 "This is a package for drawing calibrated scales with tick marks
1839 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1840 (license license:gpl2)))
1842 (define-public r-shape
1849 (uri (cran-uri "shape" version))
1852 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1853 (build-system r-build-system)
1854 (home-page "https://cran.r-project.org/web/packages/shape")
1855 (synopsis "Functions for plotting graphical shapes")
1857 "This package provides functions for plotting graphical shapes such as
1858 ellipses, circles, cylinders, arrows, ...")
1859 (license license:gpl3+)))
1861 (define-public r-globaloptions
1863 (name "r-globaloptions")
1868 (uri (cran-uri "GlobalOptions" version))
1870 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1871 (properties `((upstream-name . "GlobalOptions")))
1872 (build-system r-build-system)
1873 (home-page "https://github.com/jokergoo/GlobalOptions")
1874 (synopsis "Generate functions to get or set global options")
1876 "This package provides more controls on the option values such as
1877 validation and filtering on the values, making options invisible or private.")
1878 (license license:gpl2+)))
1880 (define-public r-circlize
1887 (uri (cran-uri "circlize" version))
1890 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1891 (build-system r-build-system)
1893 `(("r-colorspace" ,r-colorspace)
1894 ("r-globaloptions" ,r-globaloptions)
1895 ("r-shape" ,r-shape)))
1896 (home-page "https://github.com/jokergoo/circlize")
1897 (synopsis "Circular visualization")
1899 "Circular layout is an efficient way to visualise huge amounts of
1900 information. This package provides an implementation of circular layout
1901 generation in R as well as an enhancement of available software. Its
1902 flexibility is based on the usage of low-level graphics functions such that
1903 self-defined high-level graphics can be easily implemented by users for
1904 specific purposes. Together with the seamless connection between the powerful
1905 computational and visual environment in R, it gives users more convenience and
1906 freedom to design figures for better understanding complex patterns behind
1907 multi-dimensional data.")
1908 (license license:gpl2+)))
1910 (define-public r-powerlaw
1917 (uri (cran-uri "poweRlaw" version))
1919 (base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
1920 (properties `((upstream-name . "poweRlaw")))
1921 (build-system r-build-system)
1923 `(("r-vgam" ,r-vgam)))
1924 (home-page "https://github.com/csgillespie/poweRlaw")
1925 (synopsis "Tools for the analysis of heavy tailed distributions")
1927 "This package provides an implementation of maximum likelihood estimators
1928 for a variety of heavy tailed distributions, including both the discrete and
1929 continuous power law distributions. Additionally, a goodness-of-fit based
1930 approach is used to estimate the lower cut-off for the scaling region.")
1931 ;; Any of these GPL versions.
1932 (license (list license:gpl2 license:gpl3))))
1934 (define-public r-compare
1941 (uri (cran-uri "compare" version))
1944 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1945 (build-system r-build-system)
1946 (home-page "https://cran.r-project.org/web/packages/compare")
1947 (synopsis "Comparing objects for differences")
1949 "This package provides functions to compare a model object to a
1950 comparison object. If the objects are not identical, the functions can be
1951 instructed to explore various modifications of the objects (e.g., sorting
1952 rows, dropping names) to see if the modified versions are identical.")
1953 (license license:gpl2+)))
1955 (define-public r-dendextend
1957 (name "r-dendextend")
1962 (uri (cran-uri "dendextend" version))
1965 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
1966 (build-system r-build-system)
1968 `(("r-ggplot2" ,r-ggplot2)
1969 ("r-magrittr" ,r-magrittr)
1970 ("r-viridis" ,r-viridis)))
1971 (home-page "https://cran.r-project.org/web/packages/dendextend")
1972 (synopsis "Extending 'dendrogram' functionality in R")
1974 "This package offers a set of functions for extending @code{dendrogram}
1975 objects in R, letting you visualize and compare trees of hierarchical
1976 clusterings. You can adjust a tree's graphical parameters (the color, size,
1977 type, etc of its branches, nodes and labels) and visually and statistically
1978 compare different dendrograms to one another.")
1979 ;; Any of these versions
1980 (license (list license:gpl2 license:gpl3))))
1982 (define-public r-getoptlong
1984 (name "r-getoptlong")
1989 (uri (cran-uri "GetoptLong" version))
1992 "1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
1993 (properties `((upstream-name . "GetoptLong")))
1994 (build-system r-build-system)
1998 `(("r-globaloptions" ,r-globaloptions)
1999 ("r-rjson" ,r-rjson)))
2000 (home-page "https://github.com/jokergoo/GetoptLong")
2001 (synopsis "Parsing command-line arguments and variable interpolation")
2003 "This is yet another command-line argument parser which wraps the
2004 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2005 use in R. It also provides a simple way for variable interpolation in R.")
2006 (license license:gpl2+)))
2008 (define-public r-fastmatch
2010 (name "r-fastmatch")
2015 (uri (cran-uri "fastmatch" version))
2018 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2019 (build-system r-build-system)
2020 (home-page "https://www.rforge.net/fastmatch")
2021 (synopsis "Fast match function")
2023 "This package provides a fast @code{match} replacement for cases that
2024 require repeated look-ups. It is slightly faster that R's built-in
2025 @code{match} function on first match against a table, but extremely fast on
2026 any subsequent lookup as it keeps the hash table in memory.")
2027 (license license:gpl2)))
2036 (uri (cran-uri "ff" version))
2039 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
2040 (build-system r-build-system)
2041 (propagated-inputs `(("r-bit" ,r-bit)))
2042 (home-page "http://ff.r-forge.r-project.org/")
2043 (synopsis "Memory-efficient storage of large data on disk and access functions")
2045 "This package provides data structures that are stored on disk but
2046 behave (almost) as if they were in RAM by transparently mapping only a section
2048 ;; error Architecture not supported.
2049 (supported-systems (delete "aarch64-linux" %supported-systems))
2050 (license license:gpl2)))
2052 (define-public r-ffbase
2059 (uri (cran-uri "ffbase" version))
2062 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2063 (build-system r-build-system)
2066 ("r-fastmatch" ,r-fastmatch)
2068 (home-page "http://github.com/edwindj/ffbase")
2069 (synopsis "Basic statistical functions for package 'ff'")
2071 "This package extends the out of memory vectors of @code{ff} with
2072 statistical functions and other utilities to ease their usage.")
2073 (license license:gpl3)))
2075 (define-public r-prettyunits
2077 (name "r-prettyunits")
2082 (uri (cran-uri "prettyunits" version))
2085 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2086 (build-system r-build-system)
2087 (home-page "https://github.com/gaborcsardi/prettyunits")
2088 (synopsis "Pretty, human readable formatting of quantities")
2090 "This package provides tools for pretty, human readable formatting of
2092 (license license:expat)))
2094 (define-public r-reshape
2101 (uri (cran-uri "reshape" version))
2104 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2105 (build-system r-build-system)
2107 `(("r-plyr" ,r-plyr)
2108 ("r-rcpp" ,r-rcpp)))
2109 (home-page "http://had.co.nz/reshape")
2110 (synopsis "Flexibly reshape data")
2112 "Flexibly restructure and aggregate data using just two functions:
2113 @code{melt} and @code{cast}. This package provides them.")
2114 (license license:expat)))
2116 (define-public r-progress
2123 (uri (cran-uri "progress" version))
2126 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2127 (build-system r-build-system)
2129 `(("r-crayon" ,r-crayon)
2131 ("r-prettyunits" ,r-prettyunits)
2133 (home-page "https://github.com/gaborcsardi/progress")
2134 (synopsis "Terminal progress bars")
2136 "This package provides configurable progress bars. They may include
2137 percentage, elapsed time, and/or the estimated completion time. They work in
2138 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2139 package also provides a C++ API, that works with or without Rcpp.")
2140 (license license:expat)))
2142 (define-public r-ggally
2149 (uri (cran-uri "GGally" version))
2152 "082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
2153 (properties `((upstream-name . "GGally")))
2154 (build-system r-build-system)
2156 `(("libressl" ,libressl)))
2158 `(("r-ggplot2" ,r-ggplot2)
2159 ("r-gtable" ,r-gtable)
2161 ("r-progress" ,r-progress)
2162 ("r-rcolorbrewer" ,r-rcolorbrewer)
2163 ("r-reshape" ,r-reshape)
2164 ("r-rlang" ,r-rlang)))
2165 (home-page "https://ggobi.github.io/ggally")
2166 (synopsis "Extension to ggplot2")
2168 "The R package ggplot2 is a plotting system based on the grammar of
2169 graphics. GGally extends ggplot2 by adding several functions to reduce the
2170 complexity of combining geometric objects with transformed data. Some of
2171 these functions include a pairwise plot matrix, a two group pairwise plot
2172 matrix, a parallel coordinates plot, a survival plot, and several functions to
2174 (license license:gpl2+)))
2176 (define-public r-proxy
2183 (uri (cran-uri "proxy" version))
2186 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2187 (build-system r-build-system)
2188 (home-page "https://cran.r-project.org/web/packages/proxy")
2189 (synopsis "Distance and similarity measures")
2191 "This package provides an extensible framework for the efficient
2192 calculation of auto- and cross-proximities, along with implementations of the
2193 most popular ones.")
2194 (license license:gpl2)))
2203 (uri (cran-uri "sp" version))
2205 (base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg"))))
2206 (build-system r-build-system)
2208 `(("r-lattice" ,r-lattice)))
2209 (home-page "https://cran.r-project.org/web/packages/sp")
2210 (synopsis "Classes and methods for spatial data")
2212 "This package provides classes and methods for spatial data; the classes
2213 document where the spatial location information resides, for 2D or 3D data.
2214 Utility functions are provided, e.g. for plotting data as maps, spatial
2215 selection, as well as methods for retrieving coordinates, for subsetting,
2216 print, summary, etc.")
2217 (license license:gpl2+)))
2219 (define-public r-rmtstat
2226 (uri (cran-uri "RMTstat" version))
2229 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2230 (properties `((upstream-name . "RMTstat")))
2231 (build-system r-build-system)
2232 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2233 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2235 "This package provides functions for working with the Tracy-Widom laws
2236 and other distributions related to the eigenvalues of large Wishart
2238 (license license:bsd-3)))
2240 (define-public r-rmpi
2246 (uri (cran-uri "Rmpi" version))
2249 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2250 (properties `((upstream-name . "Rmpi")))
2251 (build-system r-build-system)
2253 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2254 #:phases (modify-phases %standard-phases
2255 (add-before 'install 'mpi-setup
2258 `(("openmpi" ,openmpi)))
2260 `(("pkg-config" ,pkg-config)))
2261 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2262 (synopsis "R interface to message-passing interface (MPI)")
2264 "This package provides an interface (wrapper) to MPI APIs. It also
2265 provides an interactive R manager and worker environment.")
2266 (license license:gpl2+)))
2268 (define-public r-lmoments
2275 (uri (cran-uri "Lmoments" version))
2278 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2279 (properties `((upstream-name . "Lmoments")))
2280 (build-system r-build-system)
2282 `(("r-rcpp" ,r-rcpp)
2283 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2284 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2285 (synopsis "L-moments and quantile mixtures")
2287 "This package contains functions to estimate L-moments and trimmed
2288 L-moments from the data. It also contains functions to estimate the
2289 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2290 quantile mixture from L-moments and trimmed L-moments.")
2291 (license license:gpl2)))
2293 (define-public r-distillery
2295 (name "r-distillery")
2300 (uri (cran-uri "distillery" version))
2303 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2304 (build-system r-build-system)
2305 (home-page "https://ral.ucar.edu/staff/ericg/")
2306 (synopsis "Functions for confidence intervals and object information")
2308 "This package provides some very simple method functions for confidence
2309 interval calculation and to distill pertinent information from a potentially
2310 complex object; primarily used in common with the packages extRemes and
2312 (license license:gpl2+)))
2314 (define-public r-extremes
2321 (uri (cran-uri "extRemes" version))
2324 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2325 (properties `((upstream-name . "extRemes")))
2326 (build-system r-build-system)
2328 `(("r-distillery" ,r-distillery)
2329 ("r-lmoments" ,r-lmoments)))
2330 (home-page "https://www.assessment.ucar.edu/toolkit/")
2331 (synopsis "Extreme value analysis")
2333 "ExtRemes is a suite of functions for carrying out analyses on the
2334 extreme values of a process of interest; be they block maxima over long blocks
2335 or excesses over a high threshold.")
2336 (license license:gpl2+)))
2338 (define-public r-lmtest
2345 (uri (cran-uri "lmtest" version))
2348 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2349 (build-system r-build-system)
2351 `(("r-zoo" ,r-zoo)))
2353 `(("gfortran" ,gfortran)))
2354 (home-page "https://cran.r-project.org/web/packages/lmtest")
2355 (synopsis "Testing linear regression models")
2357 "This package provides a collection of tests, data sets, and examples for
2358 diagnostic checking in linear regression models. Furthermore, some generic
2359 tools for inference in parametric models are provided.")
2360 ;; Either version is okay
2361 (license (list license:gpl2 license:gpl3))))
2363 (define-public r-idr
2369 (uri (cran-uri "idr" version))
2372 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2373 (build-system r-build-system)
2374 (home-page "https://cran.r-project.org/web/packages/idr/")
2375 (synopsis "Irreproducible discovery rate")
2377 "This is a package for estimating the copula mixture model and plotting
2378 correspondence curves in \"Measuring reproducibility of high-throughput
2379 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2380 by Li, Brown, Huang, and Bickel")
2381 (license license:gpl2+)))
2383 (define-public r-inline
2389 (uri (cran-uri "inline" version))
2392 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2393 (build-system r-build-system)
2394 (home-page "https://cran.r-project.org/web/packages/inline")
2395 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2397 "This package provides functionality to dynamically define R functions
2398 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2399 @code{.Call} calling conventions.")
2400 ;; Any version of the LGPL.
2401 (license license:lgpl3+)))
2403 (define-public r-bdsmatrix
2405 (name "r-bdsmatrix")
2410 (uri (cran-uri "bdsmatrix" version))
2413 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2414 (properties `((upstream-name . "bdsmatrix")))
2415 (build-system r-build-system)
2416 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2417 (synopsis "Routines for block diagonal symmetric matrices")
2419 "This package provides procedures to work with block diagonal symmetric
2420 matrices, a special case of sparse matrices.")
2421 (license license:lgpl2.0)))
2423 (define-public r-bbmle
2426 (version "1.0.23.1")
2430 (uri (cran-uri "bbmle" version))
2433 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2434 (build-system r-build-system)
2436 `(("r-bdsmatrix" ,r-bdsmatrix)
2437 ("r-lattice" ,r-lattice)
2439 ("r-matrix" ,r-matrix)
2440 ("r-mvtnorm" ,r-mvtnorm)
2441 ("r-numderiv" ,r-numderiv)))
2442 (home-page "https://cran.r-project.org/web/packages/bbmle")
2443 (synopsis "Tools for General Maximum Likelihood Estimation")
2445 "This package provides methods and functions for fitting maximum
2446 likelihood models in R. This package modifies and extends the @code{mle}
2447 classes in the @code{stats4} package.")
2448 ;; Any version of the GPL
2449 (license license:gpl2+)))
2451 (define-public r-emdbook
2458 (uri (cran-uri "emdbook" version))
2461 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2462 (build-system r-build-system)
2464 `(("r-bbmle" ,r-bbmle)
2466 ("r-lattice" ,r-lattice)
2468 ("r-plyr" ,r-plyr)))
2469 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2470 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2472 "This package provides auxiliary functions and data sets for \"Ecological
2473 Models and Data\", a book presenting maximum likelihood estimation and related
2474 topics for ecologists (ISBN 978-0-691-12522-0).")
2476 (license (list license:gpl2 license:gpl3))))
2478 (define-public r-lpsolve
2485 (uri (cran-uri "lpSolve" version))
2488 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2489 (properties `((upstream-name . "lpSolve")))
2490 (build-system r-build-system)
2491 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2492 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2494 "Lp_solve is software for solving linear, integer and mixed integer
2495 programs. This implementation supplies a \"wrapper\" function in C and some R
2496 functions that solve general linear/integer problems, assignment problems, and
2497 transportation problems.")
2498 (license license:lgpl2.0)))
2500 (define-public r-limsolve
2507 (uri (cran-uri "limSolve" version))
2510 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2511 (properties `((upstream-name . "limSolve")))
2512 (build-system r-build-system)
2514 `(("r-lpsolve" ,r-lpsolve)
2516 ("r-quadprog" ,r-quadprog)))
2517 (native-inputs `(("gfortran" ,gfortran)))
2518 (home-page "https://cran.r-project.org/web/packages/limSolve")
2519 (synopsis "Solving linear inverse models")
2521 "This package provides functions that:
2524 @item find the minimum/maximum of a linear or quadratic function,
2525 @item sample an underdetermined or overdetermined system,
2526 @item solve a linear system Ax=B for the unknown x.
2529 It includes banded and tridiagonal linear systems. The package calls Fortran
2530 functions from LINPACK.")
2532 (license (list license:gpl2+ license:gpl3+))))
2534 (define-public r-fitdistrplus
2536 (name "r-fitdistrplus")
2541 (uri (cran-uri "fitdistrplus" version))
2544 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2545 (build-system r-build-system)
2547 `(("r-mass" ,r-mass)
2548 ("r-npsurv" ,r-npsurv)
2549 ("r-survival" ,r-survival)))
2550 (home-page "http://riskassessment.r-forge.r-project.org")
2551 (synopsis "Fitting a parametric distribution from data")
2553 "This package extends the @code{fitdistr} function of the MASS package
2554 with several functions to help the fit of a parametric distribution to
2555 non-censored or censored data. Censored data may contain left-censored,
2556 right-censored and interval-censored values, with several lower and upper
2557 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2558 provides moment matching (MME), quantile matching (QME) and maximum
2559 goodness-of-fit estimation (MGE) methods (available only for non-censored
2560 data). Weighted versions of MLE, MME and QME are available.")
2561 (license license:gpl2+)))
2563 (define-public r-energy
2570 (uri (cran-uri "energy" version))
2573 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2574 (build-system r-build-system)
2576 `(("r-boot" ,r-boot)
2577 ("r-rcpp" ,r-rcpp)))
2578 (home-page "https://cran.r-project.org/web/packages/energy")
2579 (synopsis "Multivariate inference via the energy of data")
2581 "This package provides e-statistics (energy) tests and statistics for
2582 multivariate and univariate inference, including distance correlation,
2583 one-sample, two-sample, and multi-sample tests for comparing multivariate
2584 distributions, are implemented. Measuring and testing multivariate
2585 independence based on distance correlation, partial distance correlation,
2586 multivariate goodness-of-fit tests, clustering based on energy distance,
2587 testing for multivariate normality, distance components (disco) for
2588 non-parametric analysis of structured data, and other energy
2589 statistics/methods are implemented.")
2590 (license license:gpl2+)))
2592 (define-public r-suppdists
2594 (name "r-suppdists")
2599 (uri (cran-uri "SuppDists" version))
2602 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2603 (properties `((upstream-name . "SuppDists")))
2604 (build-system r-build-system)
2605 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2606 (synopsis "Supplementary distributions")
2608 "This package provides ten distributions supplementing those built into
2609 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2610 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2611 coefficient, Johnson distributions, normal scores and generalized
2612 hypergeometric distributions. In addition two random number generators of
2613 George Marsaglia are included.")
2614 (license license:gpl2+)))
2616 (define-public r-ksamples
2623 (uri (cran-uri "kSamples" version))
2626 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2627 (properties `((upstream-name . "kSamples")))
2628 (build-system r-build-system)
2630 `(("r-suppdists" ,r-suppdists)))
2631 (home-page "https://cran.r-project.org/web/packages/kSamples")
2632 (synopsis "K-Sample rank tests and their combinations")
2634 "This package provides tools to compares k samples using the
2635 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2636 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2637 test. It computes asymptotic, simulated or (limited) exact P-values, all
2638 valid under randomization, with or without ties, or conditionally under random
2639 sampling from populations, given the observed tie pattern. Except for Steel's
2640 test and the JT test it also combines these tests across several blocks of
2642 (license license:gpl2+)))
2644 (define-public r-cvst
2651 (uri (cran-uri "CVST" version))
2654 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2655 (properties `((upstream-name . "CVST")))
2656 (build-system r-build-system)
2658 `(("r-kernlab" ,r-kernlab)
2659 ("r-matrix" ,r-matrix)))
2660 (home-page "https://cran.r-project.org/web/packages/CVST")
2661 (synopsis "Fast cross-validation via sequential testing")
2663 "This package implements the fast cross-validation via sequential
2664 testing (CVST) procedure. CVST is an improved cross-validation procedure
2665 which uses non-parametric testing coupled with sequential analysis to
2666 determine the best parameter set on linearly increasing subsets of the data.
2667 Additionally to the CVST the package contains an implementation of the
2668 ordinary k-fold cross-validation with a flexible and powerful set of helper
2669 objects and methods to handle the overall model selection process. The
2670 implementations of the Cochran's Q test with permutations and the sequential
2671 testing framework of Wald are generic and can therefore also be used in other
2673 (license license:gpl2+)))
2675 (define-public r-squarem
2682 (uri (cran-uri "SQUAREM" version))
2685 "1j6sa93xjvynnzx9jx79a3fysbykmbqyknknsqif5bcha6xp6cvf"))))
2686 (properties `((upstream-name . "SQUAREM")))
2687 (build-system r-build-system)
2688 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2689 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2691 "This package provides algorithms for accelerating the convergence of
2692 slow, monotone sequences from smooth, contraction mapping such as the EM
2693 algorithm. It can be used to accelerate any smooth, linearly convergent
2694 acceleration scheme. A tutorial style introduction to this package is
2695 available in a vignette.")
2696 (license license:gpl2+)))
2698 (define-public r-lava
2705 (uri (cran-uri "lava" version))
2708 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2709 (build-system r-build-system)
2711 `(("r-numderiv" ,r-numderiv)
2712 ("r-squarem" ,r-squarem)
2713 ("r-survival" ,r-survival)))
2714 (home-page "https://github.com/kkholst/lava")
2715 (synopsis "Latent variable models")
2717 "This package provides tools for the estimation and simulation of latent
2719 (license license:gpl3)))
2721 (define-public r-drr
2728 (uri (cran-uri "DRR" version))
2731 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
2732 (properties `((upstream-name . "DRR")))
2733 (build-system r-build-system)
2735 `(("r-cvst" ,r-cvst)
2736 ("r-kernlab" ,r-kernlab)
2737 ("r-matrix" ,r-matrix)))
2738 (home-page "https://cran.r-project.org/web/packages/DRR")
2739 (synopsis "Dimensionality reduction via regression")
2741 "This package provides an implementation of dimensionality reduction via
2742 regression using Kernel Ridge Regression.")
2743 (license license:gpl3)))
2745 (define-public r-prodlim
2748 (version "2019.11.13")
2752 (uri (cran-uri "prodlim" version))
2755 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2756 (build-system r-build-system)
2758 `(("r-kernsmooth" ,r-kernsmooth)
2761 ("r-survival" ,r-survival)))
2762 (home-page "https://cran.r-project.org/web/packages/prodlim")
2763 (synopsis "Product-limit estimation for censored event history analysis")
2765 "This package provides a fast and user-friendly implementation of
2766 nonparametric estimators for censored event history (survival) analysis with
2767 the Kaplan-Meier and Aalen-Johansen methods.")
2768 (license license:gpl2+)))
2770 (define-public r-dimred
2777 (uri (cran-uri "dimRed" version))
2780 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2781 (properties `((upstream-name . "dimRed")))
2782 (build-system r-build-system)
2785 ("r-magrittr" ,r-magrittr)))
2786 (home-page "https://github.com/gdkrmr/dimRed")
2787 (synopsis "Framework for dimensionality reduction")
2789 "This package provides a collection of dimensionality reduction
2790 techniques from R packages and provides a common interface for calling the
2792 (license license:gpl3)))
2794 (define-public r-timedate
2797 (version "3043.102")
2801 (uri (cran-uri "timeDate" version))
2804 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2805 (properties `((upstream-name . "timeDate")))
2806 (build-system r-build-system)
2807 (home-page "https://www.rmetrics.org")
2808 (synopsis "Chronological and calendar objects")
2810 "This package provides an environment for teaching \"Financial
2811 Engineering and Computational Finance\" and for managing chronological and
2813 (license license:gpl2+)))
2815 (define-public r-magic
2822 (uri (cran-uri "magic" version))
2825 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2826 (build-system r-build-system)
2828 `(("r-abind" ,r-abind)))
2829 (home-page "https://github.com/RobinHankin/magic.git")
2830 (synopsis "Create and investigate magic squares")
2832 "This package provides a collection of efficient, vectorized algorithms
2833 for the creation and investigation of magic squares and hypercubes, including
2834 a variety of functions for the manipulation and analysis of arbitrarily
2835 dimensioned arrays.")
2836 (license license:gpl2)))
2838 (define-public r-rmysql
2845 (uri (cran-uri "RMySQL" version))
2848 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
2849 (properties `((upstream-name . "RMySQL")))
2850 (build-system r-build-system)
2852 `(("mariadb" ,mariadb "lib")
2853 ("mariadb-dev" ,mariadb "dev")
2856 `(("r-dbi" ,r-dbi)))
2857 (home-page "https://github.com/r-dbi/RMySQL")
2858 (synopsis "Database interface and MySQL driver for R")
2860 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2861 package contains an old implementation based on legacy code from S-PLUS which
2862 is being phased out. A modern MySQL client based on Rcpp is available from
2863 the RMariaDB package.")
2864 (license license:gpl2)))
2866 (define-public r-rpostgresql
2868 (name "r-rpostgresql")
2873 (uri (cran-uri "RPostgreSQL" version))
2876 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2877 (properties `((upstream-name . "RPostgreSQL")))
2878 (build-system r-build-system)
2880 `(("postgresql" ,postgresql)))
2882 `(("r-dbi" ,r-dbi)))
2883 (home-page "https://github.com/tomoakin/RPostgreSQL")
2884 (synopsis "R interface to the PostgreSQL database system")
2886 "This package provides a Database Interface (DBI) compliant driver for R
2887 to access PostgreSQL database systems.")
2888 ;; The whole package is released under GPL version 2. It includes code
2889 ;; under the PostgreSQL license.
2890 (license license:gpl2)))
2892 (define-public r-linprog
2899 (uri (cran-uri "linprog" version))
2902 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2903 (build-system r-build-system)
2904 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2905 (home-page "http://linprog.r-forge.r-project.org/")
2906 (synopsis "Linear programming and optimization")
2908 "This package can be used to solve Linear Programming / Linear
2909 Optimization problems by using the simplex algorithm.")
2910 (license license:gpl2+)))
2912 (define-public r-geometry
2919 (uri (cran-uri "geometry" version))
2922 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2923 (build-system r-build-system)
2925 `(("r-magic" ,r-magic)
2926 ("r-linprog" ,r-linprog)
2927 ("r-lpsolve" ,r-lpsolve)
2929 ("r-rcppprogress" ,r-rcppprogress)))
2930 (home-page "http://geometry.r-forge.r-project.org/")
2931 (synopsis "Mesh generation and surface tesselation")
2933 "This package makes the qhull library available in R, in a similar manner
2934 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2935 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2936 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2937 and higher dimensions. It implements the Quickhull algorithm for computing
2938 the convex hull. Qhull does not support constrained Delaunay triangulations,
2939 or mesh generation of non-convex objects, but the package does include some R
2940 functions that allow for this. Currently the package only gives access to
2941 Delaunay triangulation and convex hull computation.")
2942 ;; The Qhull sources are included and are distributed under a custom
2943 ;; non-copyleft license. The R sources are released under GPL version 2.
2944 (license (list license:gpl2
2945 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2947 (define-public r-ddalpha
2954 (uri (cran-uri "ddalpha" version))
2957 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
2958 (build-system r-build-system)
2961 ("r-class" ,r-class)
2962 ("r-geometry" ,r-geometry)
2965 ("r-robustbase" ,r-robustbase)
2966 ("r-sfsmisc" ,r-sfsmisc)))
2968 `(("gfortran" ,gfortran)))
2969 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2970 (synopsis "Depth-Based classification and calculation of data depth")
2972 "This package contains procedures for depth-based supervised learning,
2973 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2974 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2975 statistical depth function to a compact low-dimensional space, where the final
2976 classification is done. It also offers an extension to functional data and
2977 routines for calculating certain notions of statistical depth functions. 50
2978 multivariate and 5 functional classification problems are included.")
2979 (license license:gpl2)))
2981 (define-public r-gower
2988 (uri (cran-uri "gower" version))
2991 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2992 (build-system r-build-system)
2993 (home-page "https://github.com/markvanderloo/gower")
2994 (synopsis "Gower's distance")
2996 "This package provides tools to compute Gower's distance (or similarity)
2997 coefficient between records, and to compute the top-n matches between records.
2998 Core algorithms are executed in parallel on systems supporting OpenMP.")
2999 (license license:gpl3)))
3001 (define-public r-rcpproll
3008 (uri (cran-uri "RcppRoll" version))
3011 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3012 (properties `((upstream-name . "RcppRoll")))
3013 (build-system r-build-system)
3015 `(("r-rcpp" ,r-rcpp)))
3016 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3017 (synopsis "Efficient rolling and windowed operations")
3019 "This package provides fast and efficient routines for common rolling /
3020 windowed operations. Routines for the efficient computation of windowed mean,
3021 median, sum, product, minimum, maximum, standard deviation and variance are
3023 (license license:gpl2+)))
3025 (define-public r-ipred
3032 (uri (cran-uri "ipred" version))
3035 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3036 (build-system r-build-system)
3038 `(("r-class" ,r-class)
3041 ("r-prodlim" ,r-prodlim)
3042 ("r-rpart" ,r-rpart)
3043 ("r-survival" ,r-survival)))
3044 (home-page "https://cran.r-project.org/web/packages/ipred")
3045 (synopsis "Improved predictors")
3047 "This package provides improved predictive models by indirect
3048 classification and bagging for classification, regression and survival
3049 problems as well as resampling based estimators of prediction error.")
3050 (license license:gpl2+)))
3052 (define-public r-psych
3055 (version "1.9.12.31")
3059 (uri (cran-uri "psych" version))
3062 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3063 (build-system r-build-system)
3065 `(("r-lattice" ,r-lattice)
3066 ("r-mnormt" ,r-mnormt)
3067 ("r-nlme" ,r-nlme)))
3068 (home-page "https://cran.r-project.org/web/packages/psych/")
3069 (synopsis "Procedures for psychological, psychometric, and personality research")
3071 "This package provides a general purpose toolbox for personality,
3072 psychometric theory and experimental psychology. Functions are primarily for
3073 multivariate analysis and scale construction using factor analysis, principal
3074 component analysis, cluster analysis and reliability analysis, although others
3075 provide basic descriptive statistics. Item Response Theory is done using
3076 factor analysis of tetrachoric and polychoric correlations. Functions for
3077 analyzing data at multiple levels include within and between group statistics,
3078 including correlations and factor analysis. Functions for simulating and
3079 testing particular item and test structures are included. Several functions
3080 serve as a useful front end for structural equation modeling. Graphical
3081 displays of path diagrams, factor analysis and structural equation models are
3082 created using basic graphics.")
3083 (license license:gpl2+)))
3085 (define-public r-generics
3092 (uri (cran-uri "generics" version))
3095 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3096 (build-system r-build-system)
3097 (home-page "https://github.com/r-lib/generics")
3098 (synopsis "Common S3 generics not provided by base R methods")
3100 "In order to reduce potential package dependencies and conflicts,
3101 generics provides a number of commonly used S3 generics that are not provided
3102 by base R methods related to model fitting.")
3103 (license license:gpl2)))
3105 (define-public r-broom
3112 (uri (cran-uri "broom" version))
3115 "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
3116 (build-system r-build-system)
3118 `(("r-backports" ,r-backports)
3119 ("r-dplyr" ,r-dplyr)
3120 ("r-generics" ,r-generics)
3122 ("r-purrr" ,r-purrr)
3123 ("r-reshape2" ,r-reshape2)
3124 ("r-stringr" ,r-stringr)
3125 ("r-tibble" ,r-tibble)
3126 ("r-tidyr" ,r-tidyr)))
3127 (home-page "https://github.com/tidyverse/broom")
3128 (synopsis "Convert statistical analysis objects into tidy data frames")
3130 "This package provides tools to convert statistical analysis objects from
3131 R into tidy data frames, so that they can more easily be combined, reshaped
3132 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3133 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3134 summarizes a model's statistical findings such as coefficients of a
3135 regression; @code{augment}, which adds columns to the original data such as
3136 predictions, residuals and cluster assignments; and @code{glance}, which
3137 provides a one-row summary of model-level statistics.")
3138 (license license:expat)))
3140 (define-public r-recipes
3147 (uri (cran-uri "recipes" version))
3150 "11f96aanrzi2v6cn49fhvf9y4cmhra63wcy6nvpv6hcfaqqmwd2g"))))
3151 (build-system r-build-system)
3153 `(("r-dplyr" ,r-dplyr)
3154 ("r-generics" ,r-generics)
3156 ("r-gower" ,r-gower)
3157 ("r-ipred" ,r-ipred)
3158 ("r-lubridate" ,r-lubridate)
3159 ("r-magrittr" ,r-magrittr)
3160 ("r-matrix" ,r-matrix)
3161 ("r-purrr" ,r-purrr)
3162 ("r-rlang" ,r-rlang)
3163 ("r-tibble" ,r-tibble)
3164 ("r-tidyr" ,r-tidyr)
3165 ("r-tidyselect" ,r-tidyselect)
3166 ("r-timedate" ,r-timedate)
3167 ("r-withr" ,r-withr)))
3169 `(("r-knitr" ,r-knitr)))
3170 (home-page "https://github.com/topepo/recipes")
3171 (synopsis "Preprocessing tools to create design matrices")
3173 "Recipes is an extensible framework to create and preprocess design
3174 matrices. Recipes consist of one or more data manipulation and analysis
3175 \"steps\". Statistical parameters for the steps can be estimated from an
3176 initial data set and then applied to other data sets. The resulting design
3177 matrices can then be used as inputs into statistical or machine learning
3179 (license license:gpl2)))
3181 (define-public r-pdist
3188 (uri (cran-uri "pdist" version))
3191 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3192 (build-system r-build-system)
3193 (home-page "https://github.com/jeffwong/pdist")
3194 (synopsis "Partitioned distance function")
3196 "Pdist computes the euclidean distance between rows of a matrix X and
3197 rows of another matrix Y. Previously, this could be done by binding the two
3198 matrices together and calling @code{dist}, but this creates unnecessary
3199 computation by computing the distances between a row of X and another row of
3200 X, and likewise for Y. Pdist strictly computes distances across the two
3201 matrices, not within the same matrix, making computations significantly faster
3202 for certain use cases.")
3203 (license license:gpl3+)))
3205 (define-public r-ggrepel
3212 (uri (cran-uri "ggrepel" version))
3215 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3216 (build-system r-build-system)
3218 `(("r-ggplot2" ,r-ggplot2)
3220 ("r-scales" ,r-scales)))
3222 `(("r-knitr" ,r-knitr))) ; for vignettes
3223 (home-page "http://github.com/slowkow/ggrepel")
3224 (synopsis "Repulsive text and label geometries for ggplot2")
3226 "This package provides text and label geometries for ggplot2 that help to
3227 avoid overlapping text labels. Labels repel away from each other and away
3228 from the data points.")
3229 (license license:gpl3)))
3231 (define-public r-corrplot
3238 (uri (cran-uri "corrplot" version))
3241 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3242 (build-system r-build-system)
3243 (home-page "https://github.com/taiyun/corrplot")
3244 (synopsis "Visualization of a correlation matrix")
3246 "This package provides a graphical display of a correlation matrix or
3247 general matrix. It also contains some algorithms to do matrix reordering. In
3248 addition, corrplot is good at details, including choosing color, text labels,
3249 color labels, layout, etc.")
3250 ;; Any version of the GPL
3251 (license license:gpl2+)))
3253 (define-public r-stringdist
3255 (name "r-stringdist")
3260 (uri (cran-uri "stringdist" version))
3262 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3263 (build-system r-build-system)
3264 (home-page "https://github.com/markvanderloo/stringdist")
3265 (synopsis "Approximate string matching and string distance functions")
3267 "This package implements an approximate string matching version of R's
3268 native @code{match} function. It can calculate various string distances based
3269 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3270 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3271 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3272 can be computed between character vectors while taking proper care of encoding
3273 or between integer vectors representing generic sequences.")
3274 (license license:gpl3+)))
3276 (define-public r-ucminf
3283 (uri (cran-uri "ucminf" version))
3286 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3287 (build-system r-build-system)
3288 (native-inputs `(("gfortran" ,gfortran)))
3289 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3290 (synopsis "General-purpose unconstrained non-linear optimization")
3292 "This package provides an implementation of an algorithm for
3293 general-purpose unconstrained non-linear optimization. The algorithm is of
3294 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3295 search with a trust region type monitoring of the input to the line search
3296 algorithm. The interface of @code{ucminf} is designed for easy interchange
3297 with the package @code{optim}.")
3298 (license license:gpl2+)))
3300 (define-public r-ordinal
3303 (version "2019.12-10")
3307 (uri (cran-uri "ordinal" version))
3310 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3311 (build-system r-build-system)
3313 `(("r-mass" ,r-mass)
3314 ("r-matrix" ,r-matrix)
3315 ("r-numderiv" ,r-numderiv)
3316 ("r-ucminf" ,r-ucminf)))
3317 (home-page "https://github.com/runehaubo/ordinal")
3318 (synopsis "Regression models for ordinal data")
3320 "This package provides an implementation of cumulative link (mixed)
3321 models also known as ordered regression models, proportional odds models,
3322 proportional hazards models for grouped survival times and ordered models.
3323 Estimation is via maximum likelihood and mixed models are fitted with the
3324 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3325 (license license:gpl2+)))
3327 (define-public r-jomo
3334 (uri (cran-uri "jomo" version))
3337 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3338 (build-system r-build-system)
3340 `(("r-lme4" ,r-lme4)
3342 ("r-ordinal" ,r-ordinal)
3343 ("r-survival" ,r-survival)))
3344 (home-page "https://cran.r-project.org/web/packages/jomo/")
3345 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3347 "Similarly to Schafer's package pan, jomo is a package for multilevel
3348 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3349 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3350 possibility of handling binary and categorical data through latent normal
3351 variables, the option to use cluster-specific covariance matrices and to
3352 impute compatibly with the substantive model.")
3353 (license license:gpl2)))
3355 (define-public r-pan
3362 (uri (cran-uri "pan" version))
3365 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3366 (build-system r-build-system)
3367 (native-inputs `(("gfortran" ,gfortran)))
3368 (home-page "https://cran.r-project.org/web/packages/pan/")
3369 (synopsis "Multiple imputation for multivariate panel or clustered data")
3371 "This package implements multiple imputation for multivariate panel or
3373 (license license:gpl3)))
3375 (define-public r-mitml
3382 (uri (cran-uri "mitml" version))
3385 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3386 (build-system r-build-system)
3388 `(("r-haven" ,r-haven)
3391 (home-page "https://cran.r-project.org/web/packages/mitml/")
3392 (synopsis "Tools for multiple imputation in multilevel modeling")
3394 "This package provides tools for multiple imputation of missing data in
3395 multilevel modeling. It includes a user-friendly interface to the packages
3396 pan and jomo, and several functions for visualization, data management and the
3397 analysis of multiply imputed data sets.")
3398 (license license:gpl2+)))
3400 (define-public r-mice
3407 (uri (cran-uri "mice" version))
3410 "1ibybvigqkkla4xwhqs2w4m6c68alfcdsljx99nn4p92rzb1ig04"))))
3411 (build-system r-build-system)
3413 `(("r-broom" ,r-broom)
3414 ("r-dplyr" ,r-dplyr)
3415 ("r-lattice" ,r-lattice)
3417 ("r-tidyr" ,r-tidyr)))
3418 (home-page "https://cran.r-project.org/web/packages/mice/")
3419 (synopsis "Multivariate imputation by chained equations")
3421 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3422 implemented by the MICE algorithm as described in @url{Van Buuren and
3423 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3424 variable has its own imputation model. Built-in imputation models are
3425 provided for continuous data (predictive mean matching, normal), binary
3426 data (logistic regression), unordered categorical data (polytomous logistic
3427 regression) and ordered categorical data (proportional odds). MICE can also
3428 impute continuous two-level data (normal model, pan, second-level variables).
3429 Passive imputation can be used to maintain consistency between variables.
3430 Various diagnostic plots are available to inspect the quality of the
3432 ;; Any of these two versions.
3433 (license (list license:gpl2 license:gpl3))))
3435 (define-public r-truncnorm
3437 (name "r-truncnorm")
3442 (uri (cran-uri "truncnorm" version))
3445 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3446 (build-system r-build-system)
3447 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3448 (synopsis "Truncated normal distribution")
3449 (description "This package provides functions for the truncated normal
3450 distribution with mean equal to @code{mean} and standard deviation equal to
3451 @code{sd}. It includes density, distribution, quantile, and expected value
3452 functions, as well as a random generation function.")
3453 (license license:gpl2)))
3455 (define-public r-rsolnp
3462 (uri (cran-uri "Rsolnp" version))
3465 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3466 (properties `((upstream-name . "Rsolnp")))
3467 (build-system r-build-system)
3469 `(("r-truncnorm" ,r-truncnorm)))
3470 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3471 (synopsis "General non-linear optimization")
3472 (description "The Rsolnp package implements a general non-linear augmented
3473 Lagrange multiplier method solver, a @dfn{sequential quadratic
3474 programming} (SQP) based solver).")
3475 ;; Any version of the GPL.
3476 (license license:gpl2+)))
3478 (define-public r-hardyweinberg
3480 (name "r-hardyweinberg")
3485 (uri (cran-uri "HardyWeinberg" version))
3488 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3489 (properties `((upstream-name . "HardyWeinberg")))
3490 (build-system r-build-system)
3492 `(("r-mice" ,r-mice)
3494 ("r-rsolnp" ,r-rsolnp)))
3495 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3496 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3498 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3499 diallelic genetic marker data. All classical tests (chi-square, exact,
3500 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3501 included in the package, as well as functions for power computation and for
3502 the simulation of marker data under equilibrium and disequilibrium. Routines
3503 for dealing with markers on the X-chromosome are included. Functions for
3504 testing equilibrium in the presence of missing data by using multiple
3505 imputation are also provided. Implements several graphics for exploring the
3506 equilibrium status of a large set of diallelic markers: ternary plots with
3507 acceptance regions, log-ratio plots and Q-Q plots.")
3508 (license license:gpl2+)))
3517 (uri (cran-uri "sm" version))
3520 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3521 (build-system r-build-system)
3522 (native-inputs `(("gfortran" ,gfortran)))
3523 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3524 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3526 "This is software accompanying the book 'Applied Smoothing Techniques for
3527 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3528 University Press. It provides smoothing methods for nonparametric regression
3529 and density estimation")
3530 (license license:gpl2+)))
3532 (define-public r-venndiagram
3534 (name "r-venndiagram")
3538 (uri (cran-uri "VennDiagram" version))
3541 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3542 (properties `((upstream-name . "VennDiagram")))
3543 (build-system r-build-system)
3545 `(("r-futile-logger" ,r-futile-logger)))
3546 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3547 (synopsis "Generate High-Resolution Venn and Euler Plots")
3549 "This package provides a set of functions to generate high-resolution
3550 Venn and Euler plots. It includes handling for several special cases,
3551 including two-case scaling, and extensive customization of plot shape and
3553 (license license:gpl2+)))
3555 (define-public r-vioplot
3562 (uri (cran-uri "vioplot" version))
3565 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3566 (build-system r-build-system)
3570 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3571 (synopsis "Violin plot")
3573 "This package provides a violin plot, which is a combination of a box
3574 plot and a kernel density plot.")
3575 (license license:bsd-3)))
3577 (define-public r-rsofia
3583 ;; This package has been removed from CRAN, so we can
3584 ;; only fetch it from the archives.
3585 (uri (string-append "https://cran.r-project.org/src/"
3586 "contrib/Archive/RSofia/RSofia_"
3590 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3591 (properties `((upstream-name . "RSofia")))
3592 (build-system r-build-system)
3594 `(("r-rcpp" ,r-rcpp)))
3595 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3596 (synopsis "Port of sofia-ml to R")
3597 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3598 suite of fast incremental algorithms for machine learning that can be used for
3599 training models for classification or ranking.")
3600 (license license:asl2.0)))
3602 (define-public r-xts
3609 (uri (cran-uri "xts" version))
3612 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3613 (build-system r-build-system)
3614 (propagated-inputs `(("r-zoo" ,r-zoo)))
3615 (home-page "https://github.com/joshuaulrich/xts")
3616 (synopsis "Extensible time series")
3618 "This package provides for uniform handling of R's different time-based
3619 data classes by extending @code{zoo}, maximizing native format information
3620 preservation and allowing for user-level customization and extension, while
3621 simplifying cross-class interoperability.")
3622 (license license:gpl2+)))
3624 (define-public r-performanceanalytics
3626 (name "r-performanceanalytics")
3631 (uri (cran-uri "PerformanceAnalytics" version))
3634 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3636 `((upstream-name . "PerformanceAnalytics")))
3637 (build-system r-build-system)
3639 `(("r-quadprog" ,r-quadprog)
3642 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3643 (synopsis "Econometric tools for performance and risk analysis")
3644 (description "This is a collection of econometric functions for
3645 performance and risk analysis. This package aims to aid practitioners and
3646 researchers in utilizing the latest research in analysis of non-normal return
3647 streams. In general, it is most tested on return (rather than price) data on
3648 a regular scale, but most functions will work with irregular return data as
3649 well, and increasing numbers of functions will work with P&L or price data
3651 ;; Either version may be picked.
3652 (license (list license:gpl2 license:gpl3))))
3654 (define-public r-laeken
3661 (uri (cran-uri "laeken" version))
3664 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3665 (build-system r-build-system)
3667 `(("r-boot" ,r-boot)
3668 ("r-mass" ,r-mass)))
3669 (home-page "https://cran.r-project.org/web/packages/laeken/")
3670 (synopsis "Estimation of indicators on social exclusion and poverty")
3671 (description "This package provides tools for the estimation of indicators
3672 on social exclusion and poverty, as well as an implementation of Pareto tail
3673 modeling for empirical income distributions.")
3674 (license license:gpl2+)))
3676 (define-public r-vcd
3683 (uri (cran-uri "vcd" version))
3686 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3687 (build-system r-build-system)
3689 `(("r-colorspace" ,r-colorspace)
3690 ("r-lmtest" ,r-lmtest)
3691 ("r-mass" ,r-mass)))
3692 (home-page "https://cran.r-project.org/web/packages/vcd/")
3693 (synopsis "Visualizing categorical data")
3694 (description "This package provides visualization techniques, data sets,
3695 summary and inference procedures aimed particularly at categorical data.
3696 Special emphasis is given to highly extensible grid graphics. The package was
3697 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3698 Friendly and is now the main support package for a new book, \"Discrete Data
3699 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3700 (license license:gpl2)))
3702 (define-public r-ica
3709 (uri (cran-uri "ica" version))
3712 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3713 (build-system r-build-system)
3714 (home-page "https://cran.r-project.org/web/packages/ica/")
3715 (synopsis "Independent component analysis")
3716 (description "This package provides tools for @dfn{Independent Component
3717 Analysis} (ICA) using various algorithms: FastICA,
3718 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3719 of Eigenmatrices} (JADE).")
3720 (license license:gpl2+)))
3722 (define-public r-dtw
3729 (uri (cran-uri "dtw" version))
3732 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3733 (build-system r-build-system)
3734 (propagated-inputs `(("r-proxy" ,r-proxy)))
3735 (home-page "http://dtw.r-forge.r-project.org/")
3736 (synopsis "Dynamic Time Warping Algorithms")
3737 (description "This package provides a comprehensive implementation of
3738 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3739 optimal (least cumulative distance) alignment between points of two time
3740 series. Common DTW variants covered include local (slope) and global (window)
3741 constraints, subsequence matches, arbitrary distance definitions,
3742 normalizations, minimum variance matching, and so on.")
3743 (license license:gpl2+)))
3745 (define-public r-sdmtools
3748 (version "1.1-221.2")
3752 (uri (cran-uri "SDMTools" version))
3755 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3756 (properties `((upstream-name . "SDMTools")))
3757 (build-system r-build-system)
3758 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3759 (home-page "https://www.rforge.net/SDMTools/")
3760 (synopsis "Species distribution modelling tools")
3761 (description "This package provides a set of tools for post processing
3762 the outcomes of species distribution modeling exercises. It includes novel
3763 methods for comparing models and tracking changes in distributions through
3764 time. It further includes methods for visualizing outcomes, selecting
3765 thresholds, calculating measures of accuracy and landscape fragmentation
3767 (license license:gpl3+)))
3769 (define-public r-scatterplot3d
3771 (name "r-scatterplot3d")
3776 (uri (cran-uri "scatterplot3d" version))
3779 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3780 (build-system r-build-system)
3781 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3782 (synopsis "3D scatter plot")
3783 (description "This package provides an implementation of scatter plots for
3784 plotting. a three dimensional point cloud.")
3785 (license license:gpl2)))
3787 (define-public r-ggridges
3794 (uri (cran-uri "ggridges" version))
3797 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
3798 (build-system r-build-system)
3800 `(("r-ggplot2" ,r-ggplot2)
3802 ("r-scales" ,r-scales)
3803 ("r-withr" ,r-withr)))
3804 (home-page "https://github.com/clauswilke/ggridges")
3805 (synopsis "Ridgeline plots in ggplot2")
3807 "Ridgeline plots provide a convenient way of visualizing changes in
3808 distributions over time or space. This package enables the creation of such
3809 plots in @code{ggplot2}.")
3810 (license license:gpl2)))
3812 (define-public r-ggjoy
3819 (uri (cran-uri "ggjoy" version))
3822 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3823 (build-system r-build-system)
3825 `(("r-ggplot2" ,r-ggplot2)
3826 ("r-ggridges" ,r-ggridges)))
3827 (home-page "https://github.com/clauswilke/ggjoy")
3828 (synopsis "Joyplots in ggplot2")
3829 (description "Joyplots provide a convenient way of visualizing changes in
3830 distributions over time or space. This package enables the creation of such
3831 plots in @code{ggplot2}.")
3832 (license license:gpl2)))
3834 (define-public r-cli
3841 (uri (cran-uri "cli" version))
3844 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
3845 (build-system r-build-system)
3847 `(("r-assertthat" ,r-assertthat)
3848 ("r-crayon" ,r-crayon)
3849 ("r-fansi" ,r-fansi)
3850 ("r-glue" ,r-glue)))
3851 (home-page "https://github.com/r-lib/cli#readme")
3852 (synopsis "Helpers for developing command line interfaces")
3853 (description "This package provides a suite of tools designed to build
3854 attractive command line interfaces (CLIs). It includes tools for drawing
3855 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3856 (license license:expat)))
3858 (define-public r-argparser
3860 (name "r-argparser")
3865 (uri (cran-uri "argparser" version))
3868 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3869 (build-system r-build-system)
3870 (home-page "https://bitbucket.org/djhshih/argparser")
3871 (synopsis "Command-line argument parser")
3873 "This package provides a cross-platform command-line argument parser
3874 written purely in R with no external dependencies. It is useful with the
3875 Rscript front-end and facilitates turning an R script into an executable
3877 (license license:gpl3+)))
3879 (define-public r-debugme
3886 (uri (cran-uri "debugme" version))
3889 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3890 (build-system r-build-system)
3891 (propagated-inputs `(("r-crayon" ,r-crayon)))
3892 (home-page "https://github.com/r-lib/debugme#readme")
3893 (synopsis "Debug R packages")
3895 "This package allows the user to specify debug messages as special string
3896 constants, and control debugging of packages via environment variables.")
3897 (license license:expat)))
3899 (define-public r-processx
3906 (uri (cran-uri "processx" version))
3909 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
3910 (build-system r-build-system)
3914 (home-page "https://github.com/r-lib/processx3")
3915 (synopsis "Execute and control system processes")
3917 "This package provides portable tools to run system processes in the
3918 background. It can check if a background process is running; wait on a
3919 background process to finish; get the exit status of finished processes; kill
3920 background processes and their children; restart processes. It can read the
3921 standard output and error of the processes, using non-blocking connections.
3922 @code{processx} can poll a process for standard output or error, with a
3923 timeout. It can also poll several processes at once.")
3924 (license license:expat)))
3926 (define-public r-tsp
3933 (uri (cran-uri "TSP" version))
3936 "183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
3937 (properties `((upstream-name . "TSP")))
3938 (build-system r-build-system)
3939 (propagated-inputs `(("r-foreach" ,r-foreach)))
3940 (home-page "https://cran.r-project.org/web/packages/TSP/")
3941 (synopsis "Traveling salesperson problem (TSP)")
3942 (description "This package provides basic infrastructure and some
3943 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3944 traveling salesman problem).")
3945 (license license:gpl3)))
3947 (define-public r-qap
3954 (uri (cran-uri "qap" version))
3957 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3958 (build-system r-build-system)
3959 (native-inputs `(("gfortran" ,gfortran)))
3960 (home-page "https://cran.r-project.org/web/packages/qap/")
3961 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3962 (description "This package implements heuristics for the @dfn{quadratic
3963 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3965 (license license:gpl3)))
3967 (define-public r-gclus
3974 (uri (cran-uri "gclus" version))
3977 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3978 (build-system r-build-system)
3979 (propagated-inputs `(("r-cluster" ,r-cluster)))
3980 (home-page "https://cran.r-project.org/web/packages/gclus/")
3981 (synopsis "Clustering graphics")
3982 (description "This package orders panels in scatterplot matrices and
3983 parallel coordinate displays by some merit index. It contains various indices
3984 of merit, ordering functions, and enhanced versions of @code{pairs} and
3985 @code{parcoord} which color panels according to their merit level.")
3986 (license license:gpl2+)))
3988 (define-public r-webshot
3995 (uri (cran-uri "webshot" version))
3998 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3999 (build-system r-build-system)
4001 `(("r-callr" ,r-callr)
4002 ("r-jsonlite" ,r-jsonlite)
4003 ("r-magrittr" ,r-magrittr)))
4004 (home-page "https://github.com/wch/webshot/")
4005 (synopsis "Take screenshots of web pages")
4007 "Webshot makes it easy to take screenshots of web pages from within R.
4008 It can also run Shiny applications locally and take screenshots of the
4009 application; and it can render and screenshot static as well as interactive R
4010 Markdown documents.")
4011 (license license:gpl2)))
4013 (define-public r-seriation
4015 (name "r-seriation")
4020 (uri (cran-uri "seriation" version))
4023 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4024 (build-system r-build-system)
4026 `(("r-cluster" ,r-cluster)
4027 ("r-colorspace" ,r-colorspace)
4028 ("r-dendextend" ,r-dendextend)
4029 ("r-gclus" ,r-gclus)
4030 ("r-gplots" ,r-gplots)
4033 ("r-registry" ,r-registry)
4035 (native-inputs `(("gfortran" ,gfortran)))
4036 (home-page "https://s2.smu.edu/IDA/seriation/")
4037 (synopsis "Infrastructure for ordering objects using seriation")
4039 "This package provides infrastructure for seriation with an
4040 implementation of several seriation/sequencing techniques to reorder matrices,
4041 dissimilarity matrices, and dendrograms. It also provides (optimally)
4042 reordered heatmaps, color images and clustering visualizations like
4043 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4045 (license license:gpl3)))
4047 (define-public r-xfun
4054 (uri (cran-uri "xfun" version))
4056 (base32 "03iyqgx9mmdbd3qih70qzijjqcdg7k7ps5r1y6q8praanx9qvnm3"))))
4057 (build-system r-build-system)
4058 ;; knitr itself depends on xfun
4061 `(("r-knitr" ,r-knitr)))
4062 (home-page "https://github.com/yihui/xfun")
4063 (synopsis "Miscellaneous functions")
4065 "This package provides miscellaneous functions commonly used in other
4066 packages maintained by Yihui Xie.")
4067 (license license:expat)))
4069 (define-public r-utf8
4076 (uri (cran-uri "utf8" version))
4079 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4080 (build-system r-build-system)
4081 (home-page "https://github.com/patperry/r-utf8")
4082 (synopsis "Unicode text processing")
4084 "This package provides tools to process and print UTF-8 encoded
4085 international text (Unicode). Input, validate, normalize, encode, format, and
4087 (license license:asl2.0)))
4089 (define-public r-zeallot
4096 (uri (cran-uri "zeallot" version))
4099 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4100 (build-system r-build-system)
4101 (home-page "https://github.com/nteetor/zeallot")
4102 (synopsis "Multiple, unpacking, and destructuring assignment")
4104 "This package provides a @code{%<-%} operator to perform multiple,
4105 unpacking, and destructuring assignment in R. The operator unpacks the
4106 right-hand side of an assignment into multiple values and assigns these values
4107 to variables on the left-hand side of the assignment.")
4108 (license license:expat)))
4110 (define-public r-vctrs
4117 (uri (cran-uri "vctrs" version))
4120 "15sgzs6afvmhssk6jcg41rn3bvmzmbm4sgca6f6x8lfrsazvdj6w"))))
4121 (build-system r-build-system)
4123 `(("r-digest" ,r-digest)
4124 ("r-ellipsis" ,r-ellipsis)
4126 ("r-rlang" ,r-rlang)))
4128 `(("r-knitr" ,r-knitr)))
4129 (home-page "https://github.com/r-lib/vctrs")
4130 (synopsis "Vector helpers")
4132 "There are three main goals to the @code{vctrs} package:
4135 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4136 @code{length()} and @code{class()}. These definitions are paired with a
4137 framework for type-coercion and size-recycling.
4138 @item To define type- and size-stability as desirable function properties, use
4139 them to analyse existing base function, and to propose better alternatives.
4140 This work has been particularly motivated by thinking about the ideal
4141 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4142 @item To provide a new @code{vctr} base class that makes it easy to create new
4143 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4144 a few new @code{vctrs} generics, making implementation considerably simpler
4147 (license license:gpl3)))
4149 (define-public r-pillar
4156 (uri (cran-uri "pillar" version))
4159 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4160 (build-system r-build-system)
4163 ("r-crayon" ,r-crayon)
4164 ("r-fansi" ,r-fansi)
4165 ("r-rlang" ,r-rlang)
4167 ("r-vctrs" ,r-vctrs)))
4168 (home-page "https://github.com/r-lib/pillar")
4169 (synopsis "Coloured formatting for columns")
4171 "This package provides a @code{pillar} generic designed for formatting
4172 columns of data using the full range of colours provided by modern
4174 (license license:gpl3)))
4176 (define-public r-uuid
4183 (uri (cran-uri "uuid" version))
4186 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4187 (build-system r-build-system)
4188 (home-page "https://www.rforge.net/uuid")
4189 (synopsis "Tools for generating and handling of UUIDs")
4191 "This package provides tools for generating and handling of
4192 @dfn{Universally Unique Identifiers} (UUIDs).")
4193 (license license:expat)))
4195 (define-public r-tinytex
4202 (uri (cran-uri "tinytex" version))
4205 "088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9"))))
4206 (build-system r-build-system)
4208 `(("r-xfun" ,r-xfun)))
4209 (home-page "https://github.com/yihui/tinytex")
4210 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4212 "This package provides helper functions to install and maintain the LaTeX
4213 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4214 easy-to-maintain version of TeX Live. This package also contains helper
4215 functions to compile LaTeX documents, and install missing LaTeX packages
4217 (license license:expat)))
4219 (define-public r-network
4226 (uri (cran-uri "network" version))
4229 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4230 (build-system r-build-system)
4232 `(("r-magrittr" ,r-magrittr)
4233 ("r-tibble" ,r-tibble)))
4234 (home-page "https://statnet.org/")
4235 (synopsis "Classes for relational data")
4237 "This package provides tools to create and modify network objects. The
4238 @code{network} class can represent a range of relational data types, and
4239 supports arbitrary vertex/edge/graph attributes.")
4240 (license license:gpl2+)))
4242 (define-public r-statnet-common
4244 (name "r-statnet-common")
4249 (uri (cran-uri "statnet.common" version))
4252 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4254 `((upstream-name . "statnet.common")))
4255 (build-system r-build-system)
4257 `(("r-coda" ,r-coda)))
4258 (home-page "https://statnet.org")
4259 (synopsis "R scripts and utilities used by the Statnet software")
4260 (description "This package provides non-statistical utilities used by the
4261 software developed by the Statnet Project.")
4262 (license license:gpl3)))
4264 (define-public r-statcheck
4266 (name "r-statcheck")
4271 (uri (cran-uri "statcheck" version))
4274 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4275 (build-system r-build-system)
4277 `(("r-ggplot2" ,r-ggplot2)
4279 ("r-rmarkdown" ,r-rmarkdown)))
4280 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4281 (synopsis "Extract statistics from articles and recompute p-values")
4282 (description "This package can automatically extract statistical
4283 null-hypothesis significant testing (NHST) results from articles and recompute
4284 the p-values based on the reported test statistic and degrees of freedom to
4285 detect possible inconsistencies.")
4286 (license license:gpl2)))
4288 (define-public r-sna
4295 (uri (cran-uri "sna" version))
4298 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4299 (build-system r-build-system)
4301 `(("r-network" ,r-network)
4302 ("r-statnet-common" ,r-statnet-common)))
4303 (home-page "https://statnet.org")
4304 (synopsis "Tools for social network analysis")
4306 "This package provides a range of tools for social network analysis,
4307 including node and graph-level indices, structural distance and covariance
4308 methods, structural equivalence detection, network regression, random graph
4309 generation, and 2D/3D network visualization.")
4310 (license license:gpl2+)))
4312 (define-public r-tfisher
4319 (uri (cran-uri "TFisher" version))
4322 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4323 (properties `((upstream-name . "TFisher")))
4324 (build-system r-build-system)
4326 `(("r-matrix" ,r-matrix)
4327 ("r-mvtnorm" ,r-mvtnorm)
4329 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4330 (synopsis "Optimal thresholding Fisher's p-value combination method")
4332 "This package provides the @dfn{cumulative distribution function} (CDF),
4333 quantile, and statistical power calculator for a collection of thresholding
4334 Fisher's p-value combination methods, including Fisher's p-value combination
4335 method, truncated product method and, in particular, soft-thresholding
4336 Fisher's p-value combination method which is proven to be optimal in some
4337 context of signal detection. The p-value calculator for the omnibus version
4338 of these tests are also included.")
4339 (license license:gpl2)))
4341 (define-public r-ttr
4348 (uri (cran-uri "TTR" version))
4351 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4352 (properties `((upstream-name . "TTR")))
4353 (build-system r-build-system)
4355 `(("r-curl" ,r-curl)
4358 (home-page "https://github.com/joshuaulrich/TTR")
4359 (synopsis "Technical trading rules")
4361 "This package provides functions and data to construct technical trading
4363 (license license:gpl2)))
4365 (define-public r-leaps
4372 (uri (cran-uri "leaps" version))
4375 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4376 (build-system r-build-system)
4377 (native-inputs `(("gfortran" ,gfortran)))
4378 (home-page "https://cran.r-project.org/web/packages/leaps/")
4379 (synopsis "Regression subset selection")
4381 "This package provides tools for regression subset selection, including
4382 exhaustive search.")
4383 (license license:gpl2+)))
4385 (define-public r-splus2r
4392 (uri (cran-uri "splus2R" version))
4395 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4396 (properties `((upstream-name . "splus2R")))
4397 (build-system r-build-system)
4398 (native-inputs `(("gfortran" ,gfortran)))
4399 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4400 (synopsis "Supplemental S-PLUS functionality in R")
4402 "Currently there are many functions in S-PLUS that are missing in R. To
4403 facilitate the conversion of S-PLUS packages to R packages, this package
4404 provides some missing S-PLUS functionality in R.")
4405 (license license:gpl2)))
4407 (define-public r-ifultools
4409 (name "r-ifultools")
4414 (uri (cran-uri "ifultools" version))
4417 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4418 (build-system r-build-system)
4420 `(("r-mass" ,r-mass)
4421 ("r-splus2r" ,r-splus2r)))
4422 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4423 (synopsis "Insightful research tools")
4424 (description "This package provides C code used by the wmtsa, fractal, and
4426 (license license:gpl2)))
4428 (define-public r-sapa
4435 (uri (cran-uri "sapa" version))
4438 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4439 (build-system r-build-system)
4441 `(("r-ifultools" ,r-ifultools)
4442 ("r-splus2r" ,r-splus2r)))
4443 (home-page "https://cran.r-project.org/web/packages/sapa/")
4444 (synopsis "Spectral analysis for physical applications")
4445 (description "This package provides software for the book Spectral
4446 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4447 Cambridge University Press, 1993.")
4448 (license license:gpl2)))
4450 (define-public r-aggregation
4452 (name "r-aggregation")
4457 (uri (cran-uri "aggregation" version))
4460 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4461 (build-system r-build-system)
4462 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4463 (synopsis "Methods for p-value aggregation")
4465 "This package contains functionality for performing the following methods
4466 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4467 Fisher's method), and Sidak correction.")
4468 (license license:gpl3)))
4470 (define-public r-quantmod
4477 (uri (cran-uri "quantmod" version))
4480 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4481 (build-system r-build-system)
4483 `(("r-curl" ,r-curl)
4487 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4488 (synopsis "Quantitative financial modelling framework")
4489 (description "This package provides a quantitative financial modelling
4490 framework to allow users to specify, build, trade, and analyse quantitative
4491 financial trading strategies.")
4492 (license license:gpl3)))
4494 (define-public r-tseries
4501 (uri (cran-uri "tseries" version))
4504 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4505 (build-system r-build-system)
4507 `(("r-quadprog" ,r-quadprog)
4508 ("r-quantmod" ,r-quantmod)
4511 `(("gfortran" ,gfortran)))
4512 (home-page "https://cran.r-project.org/web/packages/tseries/")
4513 (synopsis "Time series analysis and computational finance")
4515 "This package provides functions relating to time series analysis and
4516 computational finance.")
4517 (license license:gpl2)))
4519 (define-public r-wmtsa
4526 (uri (cran-uri "wmtsa" version))
4529 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4530 (build-system r-build-system)
4532 `(("r-ifultools" ,r-ifultools)
4534 ("r-splus2r" ,r-splus2r)))
4535 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4536 (synopsis "Wavelet methods for time series analysis")
4538 "This package provides software to accompany the book \"Wavelet Methods
4539 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4540 University Press, 2000.")
4541 (license license:gpl2)))
4543 (define-public r-tsa
4550 (uri (cran-uri "TSA" version))
4553 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4554 (properties `((upstream-name . "TSA")))
4555 (build-system r-build-system)
4557 `(("r-leaps" ,r-leaps)
4558 ("r-locfit" ,r-locfit)
4559 ("r-mgcv" ,r-mgcv)))
4560 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4561 (synopsis "Time series analysis")
4563 "This package contains R functions and datasets detailed in the book
4564 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4565 Cryer and Kung-Sik Chan.")
4566 (license license:gpl2+)))
4568 (define-public r-extradistr
4570 (name "r-extradistr")
4575 (uri (cran-uri "extraDistr" version))
4578 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4579 (properties `((upstream-name . "extraDistr")))
4580 (build-system r-build-system)
4582 `(("r-rcpp" ,r-rcpp)))
4583 (home-page "https://github.com/twolodzko/extraDistr")
4584 (synopsis "Additional univariate and multivariate distributions")
4586 "This package implements density, distribution functions, quantile
4587 functions and random generation functions for a large number of univariate and
4588 multivariate distributions.")
4589 (license license:gpl2)))
4591 (define-public r-fractal
4598 (uri (cran-uri "fractal" version))
4601 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4602 (build-system r-build-system)
4604 `(("r-ifultools" ,r-ifultools)
4607 ("r-scatterplot3d" ,r-scatterplot3d)
4608 ("r-splus2r" ,r-splus2r)
4609 ("r-wmtsa" ,r-wmtsa)))
4610 (home-page "https://cran.r-project.org/web/packages/fractal/")
4611 (synopsis "Fractal time series modeling and analysis")
4613 "This package provides tools for stochastic fractal and deterministic
4614 chaotic time series analysis.")
4615 (license license:gpl2)))
4617 (define-public r-urca
4624 (uri (cran-uri "urca" version))
4627 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4628 (build-system r-build-system)
4629 (propagated-inputs `(("r-nlme" ,r-nlme)))
4630 (native-inputs `(("gfortran" ,gfortran)))
4631 (home-page "https://cran.r-project.org/web/packages/urca/")
4632 (synopsis "Unit root and cointegration tests for time series data")
4634 "This package provides unit root and cointegration tests encountered in
4635 applied econometric analysis.")
4636 (license license:gpl2+)))
4638 (define-public r-cubature
4645 (uri (cran-uri "cubature" version))
4648 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4649 (build-system r-build-system)
4651 `(("r-rcpp" ,r-rcpp)))
4652 (home-page "https://github.com/bnaras/cubature")
4653 (synopsis "Adaptive multivariate integration over hypercubes")
4655 "This package is an R wrapper around the cubature C library for adaptive
4656 multivariate integration over hypercubes. This version provides both
4657 @code{hcubature} and @code{pcubature} routines in addition to a vector
4659 ;; The included cubature C library is released under GPLv2+, but the
4660 ;; wrapper declares the license to be GPLv3+.
4661 (license (list license:gpl2+ license:gpl3+))))
4663 (define-public r-trend
4670 (uri (cran-uri "trend" version))
4673 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4674 (build-system r-build-system)
4676 `(("r-extradistr" ,r-extradistr)))
4678 `(("gfortran" ,gfortran)))
4679 (home-page "https://cran.r-project.org/web/packages/trend/")
4680 (synopsis "Non-parametric trend tests and change-point detection")
4682 "The analysis of environmental data often requires the detection of
4683 trends and change-points. This package includes tests for trend
4684 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4685 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4686 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4687 correlation trend test), change-point detection (Lanzante's test procedures,
4688 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4689 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4690 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4691 sample Robust Rank-Order Distributional Test.")
4692 (license license:gpl3)))
4694 (define-public r-expm
4701 (uri (cran-uri "expm" version))
4704 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4705 (build-system r-build-system)
4706 (propagated-inputs `(("r-matrix" ,r-matrix)))
4707 (native-inputs `(("gfortran" ,gfortran)))
4708 (home-page "https://r-forge.r-project.org/projects/expm/")
4709 (synopsis "Tools for matrix exponentials and related quantities")
4711 "This package provides tools for the computation of the matrix
4712 exponential, logarithm, square root, and related quantities.")
4713 (license license:gpl2+)))
4715 (define-public r-complexplus
4717 (name "r-complexplus")
4722 (uri (cran-uri "complexplus" version))
4725 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4726 (build-system r-build-system)
4728 `(("r-expm" ,r-expm)
4729 ("r-matrix" ,r-matrix)))
4730 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4731 (synopsis "Functions of complex or real variables")
4733 "This package extends several functions to the complex domain, including
4734 the matrix exponential and logarithm, and the determinant.")
4735 (license license:gpl2)))
4737 (define-public r-phontools
4739 (name "r-phontools")
4744 (uri (cran-uri "phonTools" version))
4747 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4748 (properties `((upstream-name . "phonTools")))
4749 (build-system r-build-system)
4750 (home-page "http://www.santiagobarreda.com/rscripts.html")
4751 (synopsis "Tools for phonetic and acoustic analyses")
4753 "This package contains tools for the organization, display, and analysis
4754 of the sorts of data frequently encountered in phonetics research and
4755 experimentation, including the easy creation of IPA vowel plots, and the
4756 creation and manipulation of WAVE audio files.")
4757 (license license:bsd-2)))
4766 (uri (cran-uri "np" version))
4769 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
4770 (build-system r-build-system)
4772 `(("r-boot" ,r-boot)
4773 ("r-cubature" ,r-cubature)
4774 ("r-quadprog" ,r-quadprog)
4775 ("r-quantreg" ,r-quantreg)))
4776 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4777 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4778 (description "This package provides non-parametric (and semi-parametric)
4779 kernel methods that seamlessly handle a mix of continuous, unordered, and
4780 ordered factor data types.")
4781 ;; Any version of the GPL.
4782 (license license:gpl3+)))
4784 (define-public r-powerplus
4786 (name "r-powerplus")
4791 (uri (cran-uri "powerplus" version))
4794 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4795 (build-system r-build-system)
4797 `(("r-complexplus" ,r-complexplus)
4800 ("r-matrix" ,r-matrix)
4801 ("r-phontools" ,r-phontools)))
4802 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4803 (synopsis "Exponentiation operations")
4805 "This package provides tools for the computation of matrix and scalar
4807 (license license:gpl2)))
4809 (define-public r-egg
4816 (uri (cran-uri "egg" version))
4819 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4820 (properties `((upstream-name . "egg")))
4821 (build-system r-build-system)
4823 `(("r-ggplot2" ,r-ggplot2)
4824 ("r-gridextra" ,r-gridextra)
4825 ("r-gtable" ,r-gtable)))
4826 (home-page "https://cran.r-project.org/web/packages/egg")
4827 (synopsis "Extensions for ggplot2")
4829 "This package provides miscellaneous functions to help customize ggplot2
4830 objects. High-level functions are provided to post-process ggplot2 layouts
4831 and allow alignment between plot panels, as well as setting panel sizes to
4832 fixed values. Other functions include a custom @code{geom}, and helper
4833 functions to enforce symmetric scales or add tags to facetted plots.")
4834 (license license:gpl3)))
4836 (define-public r-heatmaply
4838 (name "r-heatmaply")
4843 (uri (cran-uri "heatmaply" version))
4846 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
4847 (build-system r-build-system)
4849 `(("r-assertthat" ,r-assertthat)
4850 ("r-colorspace" ,r-colorspace)
4851 ("r-dendextend" ,r-dendextend)
4853 ("r-ggplot2" ,r-ggplot2)
4854 ("r-htmlwidgets" ,r-htmlwidgets)
4855 ("r-magrittr" ,r-magrittr)
4856 ("r-plotly" ,r-plotly)
4857 ("r-rcolorbrewer" ,r-rcolorbrewer)
4858 ("r-reshape2" ,r-reshape2)
4859 ("r-scales" ,r-scales)
4860 ("r-seriation" ,r-seriation)
4861 ("r-viridis" ,r-viridis)
4862 ("r-webshot" ,r-webshot)))
4864 `(("r-knitr" ,r-knitr)))
4865 (home-page "https://cran.r-project.org/package=heatmaply")
4866 (synopsis "Interactive cluster heat maps using plotly")
4868 "This package enables you to create interactive cluster heatmaps that can
4869 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4870 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4871 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4872 a popular graphical method for visualizing high-dimensional data, in which a
4873 table of numbers is encoded as a grid of colored cells. The rows and columns
4874 of the matrix are ordered to highlight patterns and are often accompanied by
4876 ;; Either version of the license.
4877 (license (list license:gpl2 license:gpl3))))
4886 (uri (cran-uri "h5" version))
4889 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4890 (build-system r-build-system)
4895 `(("which" ,which)))
4897 `(("r-rcpp" ,r-rcpp)))
4898 (home-page "https://github.com/mannau/h5")
4899 (synopsis "Interface to the HDF5 Library")
4901 "This package provides an S4 interface to the HDF5 library supporting
4902 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4903 binary files in a language independent format. The HDF5 format can therefore
4904 be used as an alternative to R's save/load mechanism. Since h5 is able to
4905 access only subsets of stored data it can also handle data sets which do not
4907 (license license:bsd-2)))
4909 (define-public r-cgdsr
4916 (uri (cran-uri "cgdsr" version))
4919 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4920 (build-system r-build-system)
4922 `(("r-httr" ,r-httr)
4923 ("r-r-methodss3" ,r-r-methodss3)
4924 ("r-r-oo" ,r-r-oo)))
4925 (home-page "https://github.com/cBioPortal/cgdsr")
4926 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4928 "This package provides a basic set of R functions for querying the Cancer
4929 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4930 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4931 (license license:lgpl3)))
4933 (define-public r-import
4940 (uri (cran-uri "import" version))
4943 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4944 (build-system r-build-system)
4945 (home-page "https://github.com/smbache/import")
4946 (synopsis "Import mechanism for R")
4948 "This is an alternative mechanism for importing objects from packages.
4949 The syntax allows for importing multiple objects from a package with a single
4950 command in an expressive way. The import package bridges some of the gap
4951 between using @code{library} (or @code{require}) and direct (single-object)
4952 imports. Furthermore the imported objects are not placed in the current
4953 environment. It is also possible to import objects from stand-alone @code{.R}
4955 (license license:expat)))
4957 (define-public r-shinyace
4964 (uri (cran-uri "shinyAce" version))
4967 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4968 (properties `((upstream-name . "shinyAce")))
4969 (build-system r-build-system)
4971 `(("r-shiny" ,r-shiny)
4972 ("r-jsonlite" ,r-jsonlite)))
4973 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
4974 (synopsis "Ace editor bindings for Shiny")
4976 "This package provides Ace editor bindings to enable a rich text editing
4977 environment within Shiny.")
4978 (license license:expat)))
4980 (define-public r-randomizr
4982 (name "r-randomizr")
4987 (uri (cran-uri "randomizr" version))
4990 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
4991 (properties `((upstream-name . "randomizr")))
4992 (build-system r-build-system)
4994 `(("r-knitr" ,r-knitr)))
4995 (home-page "https://declaredesign.org/r/randomizr/")
4996 (synopsis "Tools for common forms of random assignment and sampling")
4998 "This package provides tools for generating random assignments for common
4999 experimental designs and random samples for common sampling designs.")
5000 (license license:expat)))
5002 (define-public r-base64url
5004 (name "r-base64url")
5009 (uri (cran-uri "base64url" version))
5012 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5013 (build-system r-build-system)
5015 `(("r-backports" ,r-backports)))
5016 (home-page "https://github.com/mllg/base64url")
5017 (synopsis "Fast and URL-safe base64 encoder and decoder")
5019 "This package provides a URL-safe base64 encoder and decoder. In
5020 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5021 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5022 encoder does not fill the string with trailing @code{=}. The resulting
5023 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5024 and thus are safe to use in URLs or for file names. The package also comes
5025 with a simple base32 encoder/decoder suited for case insensitive file
5027 (license license:gpl3)))
5029 (define-public r-radiant-data
5031 (name "r-radiant-data")
5036 (uri (cran-uri "radiant.data" version))
5039 "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs"))
5040 (modules '((guix build utils)))
5043 ;; Delete files that are under CC-NC-SA.
5044 (delete-file-recursively "inst/app/tools/help")
5046 (properties `((upstream-name . "radiant.data")))
5047 (build-system r-build-system)
5049 `(("r-base64enc" ,r-base64enc)
5050 ("r-broom" ,r-broom)
5053 ("r-dplyr" ,r-dplyr)
5056 ("r-ggplot2" ,r-ggplot2)
5057 ("r-import" ,r-import)
5058 ("r-jsonlite" ,r-jsonlite)
5059 ("r-knitr" ,r-knitr)
5060 ("r-lubridate" ,r-lubridate)
5061 ("r-magrittr" ,r-magrittr)
5062 ("r-markdown" ,r-markdown)
5064 ("r-patchwork" ,r-patchwork)
5065 ("r-plotly" ,r-plotly)
5066 ("r-psych" ,r-psych)
5067 ("r-randomizr" ,r-randomizr)
5068 ("r-readr" ,r-readr)
5069 ("r-readxl" ,r-readxl)
5070 ("r-rlang" ,r-rlang)
5071 ("r-rmarkdown" ,r-rmarkdown)
5072 ("r-rstudioapi" ,r-rstudioapi)
5073 ("r-scales" ,r-scales)
5074 ("r-shiny" ,r-shiny)
5075 ("r-shinyfiles" ,r-shinyfiles)
5076 ("r-shinyace" ,r-shinyace)
5077 ("r-stringi" ,r-stringi)
5078 ("r-tibble" ,r-tibble)
5079 ("r-tidyr" ,r-tidyr)
5080 ("r-writexl" ,r-writexl)))
5081 (home-page "https://github.com/radiant-rstats/radiant.data")
5082 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5084 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5085 visualizing, summarizing, transforming, and combining data. It also contains
5086 functionality to generate reproducible reports of the analyses conducted in
5088 (license license:agpl3)))
5090 (define-public r-algdesign
5092 (name "r-algdesign")
5097 (uri (cran-uri "AlgDesign" version))
5099 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5100 (properties `((upstream-name . "AlgDesign")))
5101 (build-system r-build-system)
5102 (home-page "https://github.com/jvbraun/AlgDesign")
5103 (synopsis "Algorithmic experimental design")
5105 "This package provides tools to calculate exact and approximate theory
5106 experimental designs for D, A, and I criteria. Very large designs may be
5107 created. Experimental designs may be blocked or blocked designs created from
5108 a candidate list, using several criteria. The blocking can be done when whole
5109 and within plot factors interact.")
5110 (license license:gpl2+)))
5112 (define-public r-signal
5119 (uri (cran-uri "signal" version))
5122 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5123 (build-system r-build-system)
5124 (propagated-inputs `(("r-mass" ,r-mass)))
5125 (native-inputs `(("gfortran" ,gfortran)))
5126 (home-page "https://cran.r-project.org/web/packages/signal/")
5127 (synopsis "Signal processing")
5129 "This package provides a set of signal processing functions originally
5130 written for Matlab and GNU Octave. It includes filter generation utilities,
5131 filtering functions, resampling routines, and visualization of filter models.
5132 It also includes interpolation functions.")
5133 (license license:gpl2)))
5135 (define-public r-gsubfn
5142 (uri (cran-uri "gsubfn" version))
5145 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5146 (build-system r-build-system)
5147 (propagated-inputs `(("r-proto" ,r-proto)))
5148 (home-page "https://code.google.com/archive/p/gsubfn/")
5149 (synopsis "Utilities for strings and function arguments.")
5151 "This package provides @code{gsubfn} which is like @code{gsub} but can
5152 take a replacement function or certain other objects instead of the
5153 replacement string. Matches and back references are input to the replacement
5154 function and replaced by the function output. @code{gsubfn} can be used to
5155 split strings based on content rather than delimiters and for quasi-perl-style
5156 string interpolation. The package also has facilities for translating
5157 formulas to functions and allowing such formulas in function calls instead of
5159 (license license:gpl2+)))
5161 (define-public r-sqldf
5168 (uri (cran-uri "sqldf" version))
5171 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5172 (build-system r-build-system)
5174 `(("r-chron" ,r-chron)
5176 ("r-gsubfn" ,r-gsubfn)
5177 ("r-proto" ,r-proto)
5178 ("r-rsqlite" ,r-rsqlite)))
5179 (home-page "https://github.com/ggrothendieck/sqldf")
5180 (synopsis "Manipulate R data frames using SQL")
5182 "The @code{sqldf} function is typically passed a single argument which is
5183 an SQL select statement where the table names are ordinary R data frame names.
5184 @code{sqldf} transparently sets up a database, imports the data frames into
5185 that database, performs the SQL statement and returns the result using a
5186 heuristic to determine which class to assign to each column of the returned
5187 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5188 used to read filtered files into R even if the original files are larger than
5189 R itself can handle.")
5190 (license license:gpl2)))
5192 (define-public r-abind
5199 (uri (cran-uri "abind" version))
5202 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5203 (build-system r-build-system)
5204 (home-page "https://cran.r-project.org/web/packages/abind/")
5205 (synopsis "Combine multidimensional arrays")
5207 "This package provides tools to combine multidimensional arrays into a
5208 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5209 works with vectors, matrices, and higher-dimensional arrays. It also provides
5210 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5211 extracting and replacing data in arrays.")
5212 (license license:lgpl2.0+)))
5214 (define-public r-prroc
5221 (uri (cran-uri "PRROC" version))
5224 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5225 (properties `((upstream-name . "PRROC")))
5226 (build-system r-build-system)
5227 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5228 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5230 "This package computes the areas under the @dfn{precision-recall} (PR)
5231 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5232 contrast to other implementations, the interpolation between points of the PR
5233 curve is done by a non-linear piecewise function. In addition to the areas
5234 under the curves, the curves themselves can also be computed and plotted by a
5235 specific S3-method.")
5236 (license license:gpl3)))
5238 (define-public r-vim
5245 (uri (cran-uri "VIM" version))
5248 "0w22ir0gvym7gqd6nw2j7w5ivlb3az1dkfxv33imimkb7c83056a"))))
5249 (properties `((upstream-name . "VIM")))
5250 (build-system r-build-system)
5253 ("r-colorspace" ,r-colorspace)
5254 ("r-data-table" ,r-data-table)
5255 ("r-e1071" ,r-e1071)
5256 ("r-laeken" ,r-laeken)
5257 ("r-magrittr" ,r-magrittr)
5260 ("r-ranger" ,r-ranger)
5262 ("r-robustbase" ,r-robustbase)
5265 (home-page "https://github.com/alexkowa/VIM")
5266 (synopsis "Visualization and imputation of missing values")
5268 "This package provides tools for the visualization of missing and/or
5269 imputed values are introduced, which can be used for exploring the data and
5270 the structure of the missing and/or imputed values. Depending on this
5271 structure of the missing values, the corresponding methods may help to
5272 identify the mechanism generating the missing values and allows to explore the
5273 data including missing values. In addition, the quality of imputation can be
5274 visually explored using various univariate, bivariate, multiple and
5275 multivariate plot methods.")
5276 (license license:gpl2+)))
5278 (define-public r-fnn
5285 (uri (cran-uri "FNN" version))
5288 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5289 (properties `((upstream-name . "FNN")))
5290 (build-system r-build-system)
5291 (home-page "https://cran.r-project.org/web/packages/FNN")
5292 (synopsis "Fast nearest neighbor search algorithms and applications")
5294 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5295 search algorithms. Related applications including KNN classification,
5296 regression and information measures are implemented.")
5297 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5298 ;; later can be used.
5299 (license license:gpl2+)))
5301 (define-public r-smoother
5308 (uri (cran-uri "smoother" version))
5311 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5312 (build-system r-build-system)
5314 `(("r-ttr" ,r-ttr)))
5315 (home-page "https://cran.r-project.org/web/packages/smoother")
5316 (synopsis "Functions relating to the smoothing of numerical data")
5318 "This package provides a collection of methods for smoothing numerical
5319 data, commencing with a port of the Matlab gaussian window smoothing function.
5320 In addition, several functions typically used in smoothing of financial data
5322 (license license:gpl2)))
5324 (define-public r-riverplot
5326 (name "r-riverplot")
5331 (uri (cran-uri "riverplot" version))
5334 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5335 (build-system r-build-system)
5336 (home-page "https://logfc.wordpress.com")
5337 (synopsis "Sankey or ribbon plots")
5339 "Sankey plots are a type of diagram that is convenient to illustrate how
5340 flow of information, resources etc. separates and joins, much like observing
5341 how rivers split and merge. For example, they can be used to compare
5342 different clusterings. This package provides an implementation of Sankey
5344 (license license:gpl2+)))
5346 (define-public r-dyn
5353 (uri (cran-uri "dyn" version))
5356 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5357 (build-system r-build-system)
5359 `(("r-zoo" ,r-zoo)))
5360 (home-page "https://cran.r-project.org/web/packages/dyn")
5361 (synopsis "Time series regression")
5363 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5364 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5365 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5366 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5367 @code{randomForest::randomForest()} and other regression functions, allowing
5368 those functions to be used with time series including specifications that may
5369 contain lags, diffs and missing values.")
5371 (license license:gpl2+)))
5373 (define-public r-catdap
5380 (uri (cran-uri "catdap" version))
5383 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5384 (build-system r-build-system)
5386 `(("gfortran" ,gfortran)))
5387 (home-page "https://cran.r-project.org/web/packages/catdap/")
5388 (synopsis "Tools for categorical data analysis")
5390 "This package provides functions for analyzing multivariate data.
5391 Dependencies of the distribution of the specified variable (response
5392 variable) to other variables (explanatory variables) are derived and
5393 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5394 (license license:gpl2+)))
5396 (define-public r-arules
5403 (uri (cran-uri "arules" version))
5406 "0bcvfn8lvcv74vv9z3kgg7yq5hm7wjqhmzadi55cbm8zxd76g84v"))))
5407 (build-system r-build-system)
5409 `(("r-matrix" ,r-matrix)))
5410 (home-page "https://github.com/mhahsler/arules")
5411 (synopsis "Mining association rules and frequent itemsets")
5413 "This package provides an infrastructure for representing, manipulating
5414 and analyzing transaction data and patterns (frequent itemsets and association rules).
5415 It also provides C implementations of the association mining algorithms Apriori
5417 (license license:gpl3)))
5419 (define-public r-parsedate
5421 (name "r-parsedate")
5426 (uri (cran-uri "parsedate" version))
5429 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5430 (build-system r-build-system)
5432 `(("r-rematch2" ,r-rematch2)))
5433 (home-page "https://github.com/gaborcsardi/parsedate")
5435 "Recognize and parse dates in various formats")
5437 "This package provides three functions for dealing with dates:
5438 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5439 time formats, @code{parse_date} parses dates in unspecified formats,
5440 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5441 (license license:gpl2)))
5443 (define-public r-abc-data
5450 (uri (cran-uri "abc.data" version))
5453 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5454 (properties `((upstream-name . "abc.data")))
5455 (build-system r-build-system)
5456 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5457 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5459 "This package contains data which are used by functions of the abc
5460 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5461 algorithms for performing parameter estimation, model selection, and
5463 (license license:gpl3+)))
5465 (define-public r-abc
5472 (uri (cran-uri "abc" version))
5475 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5476 (build-system r-build-system)
5478 `(("r-abc-data" ,r-abc-data)
5479 ("r-locfit" ,r-locfit)
5482 ("r-quantreg" ,r-quantreg)))
5483 (home-page "https://cran.r-project.org/web/packages/abc/")
5484 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5486 "This package implements several @dfn{Approximate Bayesian
5487 Computation} (ABC) algorithms for performing parameter estimation, model
5488 selection, and goodness-of-fit. Cross-validation tools are also available for
5489 measuring the accuracy of ABC estimates, and to calculate the
5490 misclassification probabilities of different models.")
5491 (license license:gpl3+)))
5493 (define-public r-zip
5500 (uri (cran-uri "zip" version))
5503 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5504 (build-system r-build-system)
5505 (home-page "https://github.com/gaborcsardi/zip")
5506 (synopsis "Cross-platform Zip compression")
5508 "This package provides a cross-platform Zip compression library for R.
5509 It is a replacement for the @code{zip} function, that does not require any
5510 additional external tools on any platform.")
5511 (license license:cc0)))
5513 (define-public r-openxlsx
5520 (uri (cran-uri "openxlsx" version))
5523 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5524 (build-system r-build-system)
5526 `(("r-rcpp" ,r-rcpp)
5527 ("r-stringi" ,r-stringi)
5529 (home-page "https://github.com/awalker89/openxlsx")
5530 (synopsis "Read, write and edit XLSX files")
5532 "This package simplifies the creation of Excel @code{.xlsx} files by
5533 providing a high level interface to writing, styling and editing worksheets.
5534 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5535 and @code{XLConnect} packages with the added benefit of removing the
5536 dependency on Java.")
5537 (license license:gpl3)))
5539 (define-public r-rio
5546 (uri (cran-uri "rio" version))
5549 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5550 (build-system r-build-system)
5552 `(("r-curl" ,r-curl)
5553 ("r-data-table" ,r-data-table)
5554 ("r-foreign" ,r-foreign)
5555 ("r-haven" ,r-haven)
5556 ("r-openxlsx" ,r-openxlsx)
5557 ("r-readxl" ,r-readxl)
5558 ("r-tibble" ,r-tibble)))
5559 (home-page "https://github.com/leeper/rio")
5560 (synopsis "Swiss-army knife for data I/O")
5562 "This package provides streamlined data import and export infrastructure
5563 by making assumptions that the user is probably willing to make: @code{import}
5564 and @code{export} determine the data structure from the file extension,
5565 reasonable defaults are used for data import and export (e.g.,
5566 @code{stringsAsFactors=FALSE}), web-based import is natively
5567 supported (including from SSL/HTTPS), compressed files can be read directly
5568 without explicit decompression, and fast import packages are used where
5569 appropriate. An additional convenience function, @code{convert}, provides a
5570 simple method for converting between file types.")
5571 (license license:gpl2)))
5573 (define-public r-maptools
5580 (uri (cran-uri "maptools" version))
5583 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5584 (build-system r-build-system)
5586 `(("r-foreign" ,r-foreign)
5587 ("r-lattice" ,r-lattice)
5589 (home-page "https://r-forge.r-project.org/projects/maptools/")
5590 (synopsis "Tools for reading and handling spatial objects")
5592 "This package provides a set of tools for manipulating and reading
5593 geographic data, in particular ESRI Shapefiles. It includes binary access to
5594 GSHHG shoreline files. The package also provides interface wrappers for
5595 exchanging spatial objects with other R packages.")
5596 ;; The C source files from shapelib are released under the Expat license.
5597 ;; The R code is released under GPL version 2 or later.
5598 (license (list license:gpl2+
5601 (define-public r-later
5608 (uri (cran-uri "later" version))
5611 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5612 (build-system r-build-system)
5616 ("r-rlang" ,r-rlang)))
5617 (home-page "https://github.com/r-lib/later")
5618 (synopsis "Utilities for delaying function execution")
5620 "This package provides tools to execute arbitrary R or C functions some
5621 time after the current time, after the R execution stack has emptied.")
5622 (license license:gpl2+)))
5624 (define-public r-promises
5631 (uri (cran-uri "promises" version))
5634 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5635 (build-system r-build-system)
5637 `(("r-later" ,r-later)
5638 ("r-magrittr" ,r-magrittr)
5641 ("r-rlang" ,r-rlang)))
5642 (home-page "https://rstudio.github.io/promises")
5643 (synopsis "Abstractions for promise-based asynchronous programming")
5645 "This package provides fundamental abstractions for doing asynchronous
5646 programming in R using promises. Asynchronous programming is useful for
5647 allowing a single R process to orchestrate multiple tasks in the background
5648 while also attending to something else. Semantics are similar to JavaScript
5649 promises, but with a syntax that is idiomatic R.")
5650 (license license:expat)))
5652 (define-public r-dosnow
5659 (uri (cran-uri "doSNOW" version))
5662 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5663 (properties `((upstream-name . "doSNOW")))
5664 (build-system r-build-system)
5666 `(("r-foreach" ,r-foreach)
5667 ("r-iterators" ,r-iterators)
5668 ("r-snow" ,r-snow)))
5669 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5670 (synopsis "Foreach parallel adaptor for the snow package")
5672 "This package provides a parallel backend for the @code{%dopar%} function
5673 using the @code{snow} package.")
5674 (license license:gpl2)))
5676 (define-public r-snowfall
5679 (version "1.84-6.1")
5682 (uri (cran-uri "snowfall" version))
5684 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5685 (build-system r-build-system)
5687 `(("r-snow" ,r-snow)))
5688 (home-page "https://cran.r-project.org/web/packages/snowfall/")
5689 (synopsis "Easier cluster computing")
5690 (description "This package is a usability wrapper around snow for easier
5691 development of parallel R programs. This package offers e.g. extended error
5692 checks, and additional functions. All functions work in sequential mode, too,
5693 if no cluster is present or wished. The package is also designed as connector
5694 to the cluster management tool @code{sfCluster}, but can also used without
5696 (license license:gpl2+)))
5698 (define-public r-rappdirs
5705 (uri (cran-uri "rappdirs" version))
5708 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5709 (build-system r-build-system)
5710 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5711 (synopsis "Determine where to save data, caches, and logs")
5713 "This package provides an easy way to determine which directories on the
5714 user's computer should be used to save data, caches and logs. It is a port of
5715 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5716 (license license:expat)))
5718 (define-public r-renv
5725 (uri (cran-uri "renv" version))
5728 "02ayfgbpw4b58148dcxz31anaxncwczmxs1zzkskwj0rzhb2x60r"))))
5729 (properties `((upstream-name . "renv")))
5730 (build-system r-build-system)
5731 (home-page "https://rstudio.github.io/renv")
5732 (synopsis "Project environments")
5734 "This package provides a dependency management toolkit for R. Using
5735 renv, you can create and manage project-local R libraries, save the state of
5736 these libraries to a lockfile, and later restore your library as required.
5737 Together, these tools can help make your projects more isolated, portable, and
5739 (license license:expat)))
5741 (define-public r-learnr
5748 (uri (cran-uri "learnr" version))
5751 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
5752 (build-system r-build-system)
5754 `(("r-checkmate" ,r-checkmate)
5755 ("r-ellipsis" ,r-ellipsis)
5756 ("r-evaluate" ,r-evaluate)
5757 ("r-htmltools" ,r-htmltools)
5758 ("r-htmlwidgets" ,r-htmlwidgets)
5759 ("r-jsonlite" ,r-jsonlite)
5760 ("r-knitr" ,r-knitr)
5761 ("r-markdown" ,r-markdown)
5762 ("r-rappdirs" ,r-rappdirs)
5764 ("r-rmarkdown" ,r-rmarkdown)
5765 ("r-rprojroot" ,r-rprojroot)
5766 ("r-shiny" ,r-shiny)
5767 ("r-withr" ,r-withr)))
5768 (home-page "https://rstudio.github.io/learnr/")
5769 (synopsis "Interactive tutorials for R")
5771 "This package provides tools to create interactive tutorials using R
5772 Markdown. Use a combination of narrative, figures, videos, exercises, and
5773 quizzes to create self-paced tutorials for learning about R and R packages.")
5774 (license license:asl2.0)))
5776 (define-public r-analytics
5778 (name "r-analytics")
5783 (uri (cran-uri "analytics" version))
5786 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5787 (build-system r-build-system)
5790 ("r-cluster" ,r-cluster)
5791 ("r-fractal" ,r-fractal)
5792 ("r-lmtest" ,r-lmtest)
5795 ("r-powerplus" ,r-powerplus)
5796 ("r-robust" ,r-robust)
5797 ("r-trend" ,r-trend)
5801 (home-page "https://cran.r-project.org/web/packages/analytics/")
5802 (synopsis "Collection of data analysis tools")
5804 "This package is a collection of data analysis tools. It includes tools
5805 for regression outlier detection in a fitted linear model, stationary
5806 bootstrap using a truncated geometric distribution, a comprehensive test for
5807 weak stationarity, column means by group, weighted biplots, and a heuristic to
5808 obtain a better initial configuration in non-metric MDS.")
5809 (license license:gpl2)))
5811 (define-public r-reticulate
5813 (name "r-reticulate")
5818 (uri (cran-uri "reticulate" version))
5821 "03dmnx9jhxx6vfbv2i5n6sln38kb9zkshz982pg3l9i4jjf3xns7"))))
5822 (build-system r-build-system)
5823 (inputs `(("python" ,python)))
5825 `(("r-rappdirs" ,r-rappdirs)
5826 ("r-jsonlite" ,r-jsonlite)
5827 ("r-matrix" ,r-matrix)
5828 ("r-rcpp" ,r-rcpp)))
5830 `(("r-knitr" ,r-knitr)))
5831 (home-page "https://github.com/rstudio/reticulate")
5832 (synopsis "R interface to Python")
5834 "This package provides an interface from R to Python modules, classes,
5835 and functions. When calling into Python, R data types are automatically
5836 converted to their equivalent Python types. When values are returned from
5837 Python to R they are converted back to R types.")
5838 (license license:asl2.0)))
5840 (define-public r-bibtex
5847 (uri (cran-uri "bibtex" version))
5850 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
5851 (build-system r-build-system)
5852 (propagated-inputs `(("r-stringr" ,r-stringr)))
5853 (home-page "https://github.com/romainfrancois/bibtex")
5854 (synopsis "Bibtex parser")
5855 (description "This package provides a utility for R to parse a bibtex
5857 (license license:gpl2+)))
5859 (define-public r-ggseqlogo
5861 (name "r-ggseqlogo")
5866 (uri (cran-uri "ggseqlogo" version))
5869 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5870 (build-system r-build-system)
5871 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5872 (home-page "https://github.com/omarwagih/ggseqlogo")
5873 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5875 "The range of functions provided by this package makes it possible to
5876 draw highly versatile genomic sequence logos. Features include, but are not
5877 limited to, modifying colour schemes and fonts used to draw the logo,
5878 generating multiple logo plots, and aiding the visualisation with annotations.
5879 Sequence logos can easily be combined with other ggplot2 plots.")
5880 ;; Unspecified version of the LGPL.
5881 (license license:lgpl3+)))
5883 (define-public r-ggsci
5890 (uri (cran-uri "ggsci" version))
5893 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5894 (build-system r-build-system)
5896 `(("r-ggplot2" ,r-ggplot2)
5897 ("r-scales" ,r-scales)))
5898 (home-page "https://nanx.me/ggsci/")
5899 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5901 "This package provides a collection of ggplot2 color palettes inspired by
5902 plots in scientific journals, data visualization libraries, science fiction
5903 movies, and TV shows.")
5904 (license license:gpl3)))
5906 (define-public r-ggsignif
5913 (uri (cran-uri "ggsignif" version))
5916 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5917 (build-system r-build-system)
5919 `(("r-knitr" ,r-knitr)))
5921 `(("r-ggplot2" ,r-ggplot2)))
5922 (home-page "https://github.com/const-ae/ggsignif")
5923 (synopsis "Significance brackets for ggplot2")
5925 "Enrich your ggplots with group-wise comparisons. This package provides
5926 an easy way to indicate if two groups are significantly different. Commonly
5927 this is shown by a bracket on top connecting the groups of interest which
5928 itself is annotated with the level of significance. The package provides a
5929 single layer that takes the groups for comparison and the test as arguments
5930 and adds the annotation to the plot.")
5931 (license license:gpl3)))
5933 (define-public r-ggpubr
5940 (uri (cran-uri "ggpubr" version))
5943 "0kb3hpmnhj4mkbx1kx0kv5y22himr8dijqx7ra0h8hi0pf2l2ha7"))))
5944 (build-system r-build-system)
5946 `(("r-cowplot" ,r-cowplot)
5947 ("r-dplyr" ,r-dplyr)
5948 ("r-ggplot2" ,r-ggplot2)
5949 ("r-ggrepel" ,r-ggrepel)
5950 ("r-ggsci" ,r-ggsci)
5951 ("r-ggsignif" ,r-ggsignif)
5953 ("r-gridextra" ,r-gridextra)
5954 ("r-magrittr" ,r-magrittr)
5955 ("r-polynom" ,r-polynom)
5956 ("r-purrr" ,r-purrr)
5957 ("r-rlang" ,r-rlang)
5958 ("r-scales" ,r-scales)
5959 ("r-tidyr" ,r-tidyr)))
5960 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5961 (synopsis "ggplot2-based publication-ready plots")
5963 "The ggplot2 package is an excellent and flexible package for elegant
5964 data visualization in R. However the default generated plots require some
5965 formatting before we can send them for publication. The ggpubr package
5966 provides some easy-to-use functions for creating and customizing ggplot2-based
5967 publication-ready plots.")
5968 (license license:gpl2)))
5970 (define-public r-ellipse
5977 (uri (cran-uri "ellipse" version))
5980 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5981 (build-system r-build-system)
5982 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5983 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5985 "This package contains various routines for drawing ellipses and
5986 ellipse-like confidence regions, implementing the plots described in Murdoch
5987 and Chow (1996), A graphical display of large correlation matrices, The
5988 American Statistician 50, 178-180. There are also routines implementing the
5989 profile plots described in Bates and Watts (1988), Nonlinear Regression
5990 Analysis and its Applications.")
5991 (license license:gpl2+)))
5993 (define-public r-flashclust
5995 (name "r-flashclust")
6000 (uri (cran-uri "flashClust" version))
6003 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6004 (properties `((upstream-name . "flashClust")))
6005 (build-system r-build-system)
6006 (native-inputs `(("gfortran" ,gfortran)))
6007 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6008 (synopsis "Implementation of optimal hierarchical clustering")
6010 "This package provides a fast implementation of hierarchical
6012 (license license:gpl2+)))
6014 (define-public r-factominer
6016 (name "r-factominer")
6021 (uri (cran-uri "FactoMineR" version))
6024 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6025 (properties `((upstream-name . "FactoMineR")))
6026 (build-system r-build-system)
6029 ("r-cluster" ,r-cluster)
6030 ("r-ellipse" ,r-ellipse)
6031 ("r-flashclust" ,r-flashclust)
6032 ("r-ggplot2" ,r-ggplot2)
6033 ("r-ggrepel" ,r-ggrepel)
6034 ("r-lattice" ,r-lattice)
6035 ("r-leaps" ,r-leaps)
6037 ("r-scatterplot3d" ,r-scatterplot3d)))
6038 (home-page "http://factominer.free.fr")
6039 (synopsis "Multivariate exploratory data analysis and data mining")
6041 "This package provides exploratory data analysis methods to summarize,
6042 visualize and describe datasets. The main principal component methods are
6043 available, those with the largest potential in terms of applications:
6044 principal component analysis (PCA) when variables are quantitative,
6045 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6046 variables are categorical, Multiple Factor Analysis when variables are
6047 structured in groups, etc. and hierarchical cluster analysis.")
6048 (license license:gpl2+)))
6050 (define-public r-factoextra
6052 (name "r-factoextra")
6057 (uri (cran-uri "factoextra" version))
6060 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6061 (build-system r-build-system)
6063 `(("r-abind" ,r-abind)
6064 ("r-cluster" ,r-cluster)
6065 ("r-dendextend" ,r-dendextend)
6066 ("r-factominer" ,r-factominer)
6067 ("r-ggplot2" ,r-ggplot2)
6068 ("r-ggpubr" ,r-ggpubr)
6069 ("r-ggrepel" ,r-ggrepel)
6070 ("r-reshape2" ,r-reshape2)
6071 ("r-tidyr" ,r-tidyr)))
6072 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6073 (synopsis "Extract and visualize the results of multivariate data analyses")
6075 "This package provides some easy-to-use functions to extract and
6076 visualize the output of multivariate data analyses, including
6077 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6078 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6079 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6080 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6081 packages. It contains also functions for simplifying some clustering analysis
6082 steps and provides ggplot2-based elegant data visualization.")
6083 (license license:gpl2)))
6085 (define-public r-fansi
6092 (uri (cran-uri "fansi" version))
6095 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6096 (build-system r-build-system)
6098 `(("r-knitr" ,r-knitr))) ; for vignettes
6099 (home-page "https://github.com/brodieG/fansi")
6100 (synopsis "ANSI control sequence aware string functions")
6102 "This package provides counterparts to R string manipulation functions
6103 that account for the effects of ANSI text formatting control sequences.")
6104 (license license:gpl2+)))
6106 (define-public r-nbclust
6113 (uri (cran-uri "NbClust" version))
6116 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6117 (properties `((upstream-name . "NbClust")))
6118 (build-system r-build-system)
6119 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6120 (synopsis "Determine the best number of clusters in a data set")
6122 "NbClust provides 30 indexes for determining the optimal number of
6123 clusters in a data set and offers the best clustering scheme from different
6124 results to the user.")
6125 (license license:gpl2)))
6127 (define-public r-hdf5r
6134 (uri (cran-uri "hdf5r" version))
6137 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6138 (build-system r-build-system)
6143 `(("r-bit64" ,r-bit64)
6146 `(("r-knitr" ,r-knitr)))
6147 (home-page "https://hhoeflin.github.io/hdf5r")
6148 (synopsis "Interface to the HDF5 binary data format")
6150 "HDF5 is a data model, library and file format for storing and managing
6151 large amounts of data. This package provides a nearly feature complete,
6152 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6153 functionality is added so that HDF5 objects behave very similar to their
6154 corresponding R counterparts.")
6155 (license license:asl2.0)))
6157 (define-public r-itertools
6159 (name "r-itertools")
6164 (uri (cran-uri "itertools" version))
6167 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6168 (build-system r-build-system)
6170 `(("r-iterators" ,r-iterators)))
6171 (home-page "https://cran.r-project.org/web/packages/itertools/")
6172 (synopsis "Iterator tools")
6174 "This package provides various tools for creating iterators, many
6175 patterned after functions in the Python @code{itertools} module, and others
6176 patterned after functions in the snow package.")
6177 (license license:gpl2)))
6179 (define-public r-polynom
6186 (uri (cran-uri "polynom" version))
6189 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6190 (build-system r-build-system)
6191 (home-page "https://cran.r-project.org/web/packages/polynom/")
6192 (synopsis "Functions for univariate polynomial manipulations")
6194 "This package provides a collection of functions to implement a class for
6195 univariate polynomial manipulations.")
6196 (license license:gpl2)))
6198 (define-public r-gbrd
6205 (uri (cran-uri "gbRd" version))
6208 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6209 (properties `((upstream-name . "gbRd")))
6210 (build-system r-build-system)
6211 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6212 (synopsis "Utilities for processing Rd objects and files")
6214 "This package provides utilities for processing Rd objects and files.
6215 Extract argument descriptions and other parts of the help pages of
6217 (license license:gpl2+)))
6219 (define-public r-rjags
6226 (uri (cran-uri "rjags" version))
6229 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6230 (build-system r-build-system)
6232 `(("r-coda" ,r-coda)))
6236 `(("pkg-config" ,pkg-config)))
6237 (home-page "http://mcmc-jags.sourceforge.net")
6238 (synopsis "Bayesian graphical models using MCMC")
6240 "This package provides an R interface to the JAGS MCMC library. JAGS is
6241 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6242 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6243 (license license:gpl2)))
6245 (define-public r-rdpack
6252 (uri (cran-uri "Rdpack" version))
6255 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6256 (properties `((upstream-name . "Rdpack")))
6257 (build-system r-build-system)
6259 `(("r-bibtex" ,r-bibtex)
6260 ("r-gbrd" ,r-gbrd)))
6261 (home-page "https://github.com/GeoBosh/Rdpack")
6262 (synopsis "Update and manipulate Rd documentation objects")
6264 "This package provides functions for manipulation of R documentation
6265 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6266 updating Rd documentation for functions, methods and classes; it also includes
6267 Rd macros for citations and import of references from bibtex files for use in
6268 Rd files and roxygen2 comments, as well as many functions for manipulation of
6269 references and Rd files.")
6270 (license license:gpl2+)))
6272 (define-public r-officer
6279 (uri (cran-uri "officer" version))
6282 "0xhx5n6qksyh2s9hvwhnc8y0hn362asc5y94ld06snad786hz0rw"))))
6283 (build-system r-build-system)
6285 `(("r-magrittr" ,r-magrittr)
6291 `(("r-knitr" ,r-knitr)))
6292 (home-page "https://davidgohel.github.io/officer")
6293 (synopsis "Manipulation of Word and PowerPoint documents")
6295 "This package provides tools to access and manipulate Word and PowerPoint
6296 documents from R. The package focuses on tabular and graphical reporting from
6297 R; it also provides two functions that let users get document content into
6298 data objects. A set of functions lets add and remove images, tables and
6299 paragraphs of text in new or existing documents. When working with PowerPoint
6300 presentations, slides can be added or removed; shapes inside slides can also
6301 be added or removed. When working with Word documents, a cursor can be used
6302 to help insert or delete content at a specific location in the document.")
6303 (license license:gpl3)))
6305 (define-public r-abn
6312 (uri (cran-uri "abn" version))
6315 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6316 (build-system r-build-system)
6320 `(("r-lme4" ,r-lme4)
6324 ("r-rcpparmadillo" ,r-rcpparmadillo)
6325 ("r-rjags" ,r-rjags)))
6326 (home-page "https://r-bayesian-networks.org/")
6327 (synopsis "Modelling multivariate data with additive bayesian networks")
6329 "Bayesian network analysis is a form of probabilistic graphical models
6330 which derives from empirical data a directed acyclic graph, DAG, describing
6331 the dependency structure between random variables. An additive Bayesian
6332 network model consists of a form of a DAG where each node comprises a
6333 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6334 equivalent to Bayesian multivariate regression using graphical modelling, they
6335 generalises the usual multivariable regression, GLM, to multiple dependent
6336 variables. This package provides routines to help determine optimal Bayesian
6337 network models for a given data set, where these models are used to identify
6338 statistical dependencies in messy, complex data.")
6339 (license license:gpl2+)))
6341 (define-public r-acd
6348 (uri (cran-uri "ACD" version))
6351 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6352 (properties `((upstream-name . "ACD")))
6353 (build-system r-build-system)
6354 (home-page "https://cran.r-project.org/web/packages/ACD/")
6355 (synopsis "Categorical data analysis with complete or missing responses")
6357 "This package provides tools for categorical data analysis with complete
6358 or missing responses.")
6359 (license license:gpl2+)))
6361 (define-public r-acdm
6368 (uri (cran-uri "ACDm" version))
6371 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6372 (properties `((upstream-name . "ACDm")))
6373 (build-system r-build-system)
6375 `(("r-dplyr" ,r-dplyr)
6376 ("r-ggplot2" ,r-ggplot2)
6378 ("r-rsolnp" ,r-rsolnp)
6380 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6381 (synopsis "Tools for Autoregressive Conditional Duration Models")
6383 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6384 and Russell, 1998) models. It creates trade, price or volume durations from
6385 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6387 (license license:gpl2+)))
6389 (define-public r-overlap
6396 (uri (cran-uri "overlap" version))
6399 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6400 (build-system r-build-system)
6401 (home-page "https://cran.r-project.org/web/packages/overlap/")
6402 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6404 "This package provides functions to fit kernel density functions to data
6405 on temporal activity patterns of animals; estimate coefficients of overlapping
6406 of densities for two species; and calculate bootstrap estimates of confidence
6408 (license license:gpl3+)))
6410 (define-public r-snakecase
6412 (name "r-snakecase")
6417 (uri (cran-uri "snakecase" version))
6420 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6421 (build-system r-build-system)
6423 `(("r-stringi" ,r-stringi)
6424 ("r-stringr" ,r-stringr)))
6425 (home-page "https://github.com/Tazinho/snakecase")
6426 (synopsis "Convert strings into any case")
6428 "This package provides a consistent, flexible and easy to use tool to
6429 parse and convert strings into cases like snake or camel among others.")
6430 (license license:gpl3)))
6432 (define-public r-prediction
6434 (name "r-prediction")
6439 (uri (cran-uri "prediction" version))
6442 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6443 (build-system r-build-system)
6445 `(("r-data-table" ,r-data-table)))
6446 (home-page "https://github.com/leeper/prediction")
6447 (synopsis "Tidy, type-safe prediction methods")
6449 "This package provides the @code{prediction()} function, a type-safe
6450 alternative to @code{predict()} that always returns a data frame. The package
6451 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6452 from the @code{stats} package, as well as numerous other model classes from
6453 other add-on packages.")
6454 (license license:expat)))
6456 (define-public r-insight
6463 (uri (cran-uri "insight" version))
6466 "0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
6467 (build-system r-build-system)
6469 `(("r-knitr" ,r-knitr)))
6470 (home-page "https://easystats.github.io/insight/")
6471 (synopsis "Easy access to model information for various model objects")
6473 "This package provides a tool to provide an easy, intuitive and
6474 consistent access to information contained in various R models, like model
6475 formulas, model terms, information about random effects, data that was used to
6476 fit the model or data from response variables. The package mainly revolves
6477 around two types of functions: Functions that find (the names of) information,
6478 starting with @code{find_}, and functions that get the underlying data,
6479 starting with @code{get_}. The package has a consistent syntax and works with
6480 many different model objects, where otherwise functions to access these
6481 information are missing.")
6482 (license license:gpl3)))
6484 (define-public r-sjlabelled
6486 (name "r-sjlabelled")
6491 (uri (cran-uri "sjlabelled" version))
6494 "1amq7i9sxf0pkxhskqc53xq5wvc9rdxm7cxyb4b6xh6qsskjnlsj"))))
6495 (build-system r-build-system)
6497 `(("r-haven" ,r-haven)
6498 ("r-insight" ,r-insight)))
6499 (home-page "https://github.com/strengejacke/sjlabelled")
6500 (synopsis "Labelled data utility functions")
6502 "This package provides a collection of functions dealing with labelled
6503 data, like reading and writing data between R and other statistical software
6504 packages. This includes easy ways to get, set or change value and variable
6505 label attributes, to convert labelled vectors into factors or numeric (and
6506 vice versa), or to deal with multiple declared missing values.")
6507 (license license:gpl3)))
6509 (define-public r-sjmisc
6516 (uri (cran-uri "sjmisc" version))
6519 "1ad7ca71w0v9ja4wb47aygczc987zz1lnjljhh2n497nzrpzzv64"))))
6520 (build-system r-build-system)
6522 `(("r-dplyr" ,r-dplyr)
6523 ("r-insight" ,r-insight)
6524 ("r-magrittr" ,r-magrittr)
6525 ("r-purrr" ,r-purrr)
6526 ("r-rlang" ,r-rlang)
6527 ("r-sjlabelled" ,r-sjlabelled)
6528 ("r-tidyselect" ,r-tidyselect)))
6530 `(("r-knitr" ,r-knitr)))
6531 (home-page "https://github.com/strengejacke/sjmisc")
6532 (synopsis "Data and variable transformation functions")
6534 "This package is a collection of miscellaneous utility functions,
6535 supporting data transformation tasks like recoding, dichotomizing or grouping
6536 variables, setting and replacing missing values. The data transformation
6537 functions also support labelled data, and all integrate seamlessly into a
6538 tidyverse workflow.")
6539 (license license:gpl3)))
6541 (define-public r-nortest
6548 (uri (cran-uri "nortest" version))
6551 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6552 (build-system r-build-system)
6553 (home-page "https://cran.r-project.org/web/packages/nortest/")
6554 (synopsis "Tests for normality")
6556 "This package provides five omnibus tests for testing the composite
6557 hypothesis of normality.")
6558 (license license:gpl2+)))
6560 (define-public r-moonbook
6567 (uri (cran-uri "moonBook" version))
6570 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6571 (properties `((upstream-name . "moonBook")))
6572 (build-system r-build-system)
6574 `(("r-magrittr" ,r-magrittr)
6575 ("r-nortest" ,r-nortest)
6576 ("r-purrr" ,r-purrr)
6577 ("r-sjmisc" ,r-sjmisc)
6578 ("r-stringr" ,r-stringr)
6579 ("r-survival" ,r-survival)))
6580 (home-page "https://github.com/cardiomoon/moonBook")
6581 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6583 "This package provides several analysis-related functions for the book
6584 entitled \"R statistics and graph for medical articles\" (written in Korean),
6585 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6587 (license license:gpl2)))
6589 (define-public r-flextable
6591 (name "r-flextable")
6596 (uri (cran-uri "flextable" version))
6599 "1rkz0nhwjy1l8sb0kmna5v492n2ydnk7gydswnmf88r8vfyjczhw"))))
6600 (build-system r-build-system)
6602 `(("r-base64enc" ,r-base64enc)
6603 ("r-data-table" ,r-data-table)
6604 ("r-gdtools" ,r-gdtools)
6605 ("r-htmltools" ,r-htmltools)
6606 ("r-knitr" ,r-knitr)
6607 ("r-officer" ,r-officer)
6608 ("r-rlang" ,r-rlang)
6609 ("r-rmarkdown" ,r-rmarkdown)
6610 ("r-xml2" ,r-xml2)))
6611 (home-page "https://davidgohel.github.io/flextable")
6612 (synopsis "Functions for tabular reporting")
6614 "This package provides tools to create pretty tables for HTML documents
6615 and other formats. Functions are provided to let users create tables, modify
6616 and format their content. It extends the @code{officer} package and can be
6617 used within R markdown documents when rendering to HTML and to Word
6619 (license license:gpl3)))
6621 (define-public r-writexl
6628 (uri (cran-uri "writexl" version))
6631 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6632 (build-system r-build-system)
6633 (inputs `(("zlib" ,zlib)))
6634 (home-page "https://github.com/ropensci/writexl")
6635 (synopsis "Export data frames to xlsx format")
6637 "This package provides a data frame to xlsx exporter based on
6639 (license license:bsd-2)))
6641 (define-public r-biasedurn
6643 (name "r-biasedurn")
6648 (uri (cran-uri "BiasedUrn" version))
6651 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6652 (properties `((upstream-name . "BiasedUrn")))
6653 (build-system r-build-system)
6654 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6655 (synopsis "Biased Urn model distributions")
6657 "This package provides statistical models of biased sampling in the form
6658 of univariate and multivariate noncentral hypergeometric distributions,
6659 including Wallenius' noncentral hypergeometric distribution and Fisher's
6660 noncentral hypergeometric distribution (also called extended hypergeometric
6662 (license license:gpl3)))
6664 (define-public r-goplot
6671 (uri (cran-uri "GOplot" version))
6674 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6675 (properties `((upstream-name . "GOplot")))
6676 (build-system r-build-system)
6678 `(("r-ggdendro" ,r-ggdendro)
6679 ("r-ggplot2" ,r-ggplot2)
6680 ("r-gridextra" ,r-gridextra)
6681 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6682 (home-page "https://github.com/wencke/wencke.github.io")
6683 (synopsis "Visualization of functional analysis data")
6685 "This package provides an implementation of multilayered visualizations
6686 for enhanced graphical representation of functional analysis data. It
6687 combines and integrates omics data derived from expression and functional
6688 annotation enrichment analyses. Its plotting functions have been developed
6689 with an hierarchical structure in mind: starting from a general overview to
6690 identify the most enriched categories (modified bar plot, bubble plot) to a
6691 more detailed one displaying different types of relevant information for the
6692 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6693 Venn diagram, heatmap).")
6694 (license license:gpl2)))
6696 (define-public r-getopt
6703 (uri (cran-uri "getopt" version))
6706 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6707 (build-system r-build-system)
6708 (home-page "https://github.com/trevorld/getopt")
6709 (synopsis "Command-line option processor for R")
6711 "This package is designed to be used with Rscript to write shebang
6712 scripts that accept short and long options. Many users will prefer to
6713 use the packages @code{optparse} or @code{argparse} which add extra
6714 features like automatically generated help options and usage texts,
6715 support for default values, positional argument support, etc.")
6716 (license license:gpl2+)))
6718 (define-public r-findpython
6720 (name "r-findpython")
6725 (uri (cran-uri "findpython" version))
6728 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6729 (build-system r-build-system)
6730 (home-page "https://github.com/trevorld/findpython")
6731 (synopsis "Functions to find an acceptable Python binary")
6733 "This package was designed to find an acceptable Python binary that
6734 matches version and feature constraints.")
6735 (license license:expat)))
6737 ;; This in not the same as "r-argparser"
6738 (define-public r-argparse
6745 (uri (cran-uri "argparse" version))
6748 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6749 (build-system r-build-system)
6750 (inputs `(("python" ,python)))
6752 `(("r-findpython" ,r-findpython)
6753 ("r-jsonlite" ,r-jsonlite)
6755 (home-page "https://github.com/trevorld/argparse")
6756 (synopsis "Command line optional and positional argument parser")
6758 "This package provides a command line parser to be used with Rscript to
6759 write shebang scripts that gracefully accept positional and optional arguments
6760 and automatically generate usage notices.")
6761 (license license:gpl2+)))
6763 (define-public r-hash
6770 (uri (cran-uri "hash" version))
6773 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6774 (build-system r-build-system)
6775 (home-page "https://cran.r-project.org/web/packages/hash/")
6776 (synopsis "Implementation of hash/associated arrays/dictionaries")
6778 "This package implements a data structure similar to hashes in Perl and
6779 dictionaries in Python but with a purposefully R flavor. For objects of
6780 appreciable size, access using hashes outperforms native named lists and
6782 (license license:gpl2+)))
6784 (define-public r-orddom
6791 (uri (cran-uri "orddom" version))
6794 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6795 (build-system r-build-system)
6796 (propagated-inputs `(("r-psych" ,r-psych)))
6797 (home-page "https://cran.r-project.org/web/packages/orddom/")
6798 (synopsis "Ordinal dominance statistics")
6800 "This package provides tools to compute ordinal, statistics and effect
6801 sizes as an alternative to mean comparison: Cliff's delta or success rate
6802 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6803 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6804 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6805 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6806 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6807 Group (Non-)Overlap considerations.")
6808 (license license:gpl2)))
6810 (define-public r-deriv
6817 (uri (cran-uri "Deriv" version))
6820 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6821 (properties `((upstream-name . "Deriv")))
6822 (build-system r-build-system)
6823 (home-page "https://cran.r-project.org/web/packages/Deriv")
6824 (synopsis "Symbolic differentiation")
6826 "This package provides an R-based solution for symbolic differentiation.
6827 It admits user-defined functions as well as function substitution in arguments
6828 of functions to be differentiated. Some symbolic simplification is part of
6830 (license license:gpl3+)))
6832 (define-public r-doby
6839 (uri (cran-uri "doBy" version))
6842 "1ckazh701b4ilg8bj17ji903538jmb49d997gm49ah5j5jc1x0g7"))))
6843 (properties `((upstream-name . "doBy")))
6844 (build-system r-build-system)
6846 `(("r-broom" ,r-broom)
6847 ("r-deriv" ,r-deriv)
6848 ("r-dplyr" ,r-dplyr)
6849 ("r-magrittr" ,r-magrittr)
6851 ("r-matrix" ,r-matrix)
6853 ("r-pbkrtest" ,r-pbkrtest)
6854 ("r-tibble" ,r-tibble)))
6855 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6856 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6858 "This package contains:
6861 @item facilities for working with grouped data: @code{do}
6862 something to data stratified @code{by} some variables.
6863 @item implementations of least-squares means, general linear contrasts, and
6864 @item miscellaneous other utilities.
6866 (license license:gpl2+)))
6868 (define-public r-refgenome
6870 (name "r-refgenome")
6875 (uri (cran-uri "refGenome" version))
6878 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6879 (properties `((upstream-name . "refGenome")))
6880 (build-system r-build-system)
6884 ("r-rsqlite" ,r-rsqlite)))
6885 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6887 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6889 "This package contains functionality for importing and managing of
6890 downloaded genome annotation data from the Ensembl genome browser (European
6891 Bioinformatics Institute) and from the UCSC genome browser (University of
6892 California, Santa Cruz) and annotation routines for genomic positions and
6893 splice site positions.")
6894 (license license:gpl2)))
6896 (define-public r-basix
6903 (uri (cran-uri "BASIX" version))
6906 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6907 (properties `((upstream-name . "BASIX")))
6908 (build-system r-build-system)
6909 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6910 (synopsis "Efficient C/C++ toolset for R")
6912 "BASIX provides some efficient C/C++ implementations of native R
6913 procedures to speed up calculations in R.")
6914 (license license:gpl2)))
6916 (define-public r-blockfest
6918 (name "r-blockfest")
6923 (uri (cran-uri "BlockFeST" version))
6926 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6927 (properties `((upstream-name . "BlockFeST")))
6928 (build-system r-build-system)
6929 (propagated-inputs `(("r-basix" ,r-basix)))
6930 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6931 (synopsis "Bayesian calculation of region-specific fixation index")
6933 "This package provides an R implementation of an extension of the
6934 BayeScan software for codominant markers, adding the option to group
6935 individual SNPs into pre-defined blocks. A typical application of this new
6936 approach is the identification of genomic regions, genes, or gene sets
6937 containing one or more SNPs that evolved under directional selection.")
6938 (license license:gpl2)))
6940 (define-public r-proc
6947 (uri (cran-uri "pROC" version))
6950 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
6951 (properties `((upstream-name . "pROC")))
6952 (build-system r-build-system)
6954 `(("r-plyr" ,r-plyr)
6955 ("r-rcpp" ,r-rcpp)))
6956 (home-page "https://web.expasy.org/pROC/")
6957 (synopsis "Display and analyze ROC curves")
6959 "This package provides tools for visualizing, smoothing and comparing
6960 receiver operating characteristic (ROC curves). The area under the
6961 curve (AUC) can be compared with statistical tests based on U-statistics or
6962 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6963 (license license:gpl3+)))
6965 (define-public r-rootsolve
6967 (name "r-rootsolve")
6972 (uri (cran-uri "rootSolve" version))
6975 "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
6976 (properties `((upstream-name . "rootSolve")))
6977 (build-system r-build-system)
6978 (native-inputs `(("gfortran" ,gfortran)))
6979 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6980 (synopsis "Tools for the analysis of ordinary differential equations")
6982 "This package provides routines to find the root of nonlinear functions,
6983 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6984 differential equations} (ODE). It includes routines that:
6987 @item generate gradient and jacobian matrices (full and banded),
6988 @item find roots of non-linear equations by the Newton-Raphson method,
6989 @item estimate steady-state conditions of a system of (differential) equations
6990 in full, banded or sparse form, using the Newton-Raphson method, or by
6991 dynamically running,
6992 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6993 and 3-D partial differential equations, that have been converted to ordinary
6994 differential equations by numerical differencing (using the method-of-lines
6997 (license license:gpl2+)))
6999 (define-public r-abcanalysis
7001 (name "r-abcanalysis")
7006 (uri (cran-uri "ABCanalysis" version))
7008 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7009 (properties `((upstream-name . "ABCanalysis")))
7010 (build-system r-build-system)
7011 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7012 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7013 (synopsis "Computed ABC Analysis")
7015 "Multivariate data sets often differ in several factors or derived statistical
7016 parameters, which have to be selected for a valid interpretation. Basing this
7017 selection on traditional statistical limits leads occasionally to the perception
7018 of losing information from a data set. This package provides tools to calculate
7019 these limits on the basis of the mathematical properties of the distribution of
7020 the analyzed items.")
7021 (license license:gpl3)))
7023 (define-public r-slam
7030 (uri (cran-uri "slam" version))
7032 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7033 (build-system r-build-system)
7034 (home-page "https://cran.r-project.org/web/packages/slam/")
7035 (synopsis "Sparse lightweight arrays and matrices")
7037 "This package contains data structures and algorithms for sparse arrays and matrices,
7038 based on index arrays and simple triplet representations, respectively.")
7039 (license license:gpl2)))
7041 (define-public r-manipulatewidget
7043 (name "r-manipulatewidget")
7048 (uri (cran-uri "manipulateWidget" version))
7050 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7052 `((upstream-name . "manipulateWidget")))
7053 (build-system r-build-system)
7055 `(("r-base64enc" ,r-base64enc)
7056 ("r-codetools" ,r-codetools)
7057 ("r-htmltools" ,r-htmltools)
7058 ("r-htmlwidgets" ,r-htmlwidgets)
7059 ("r-knitr" ,r-knitr)
7060 ("r-miniui" ,r-miniui)
7061 ("r-shiny" ,r-shiny)
7062 ("r-webshot" ,r-webshot)))
7063 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7064 (synopsis "Add even more interactivity to interactive charts")
7066 "This package lets you create in just a few lines of R code a nice user interface to
7067 modify the data or the graphical parameters of one or multiple interactive
7068 charts. It is useful to quickly explore visually some data or for package
7069 developers to generate user interfaces easy to maintain.")
7070 (license license:gpl2+)))
7079 (uri (cran-uri "A3" version))
7081 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7082 (properties `((upstream-name . "A3")))
7083 (build-system r-build-system)
7085 `(("r-pbapply" ,r-pbapply)
7086 ("r-xtable" ,r-xtable)))
7087 (home-page "https://cran.r-project.org/web/packages/A3/")
7088 (synopsis "Error metrics for predictive models")
7090 "This package supplies tools for tabulating and analyzing the results of predictive
7091 models. The methods employed are applicable to virtually any predictive model
7092 and make comparisons between different methodologies straightforward.")
7093 (license license:gpl2+)))
7095 (define-public r-infotheo
7102 (uri (cran-uri "infotheo" version))
7105 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7106 (build-system r-build-system)
7107 (home-page "http://homepage.meyerp.com/software")
7108 (synopsis "Information-theoretic measures")
7110 "This package implements various measures of information theory based on
7111 several entropy estimators.")
7112 (license license:gpl3+)))
7114 (define-public r-abcoptim
7121 (uri (cran-uri "ABCoptim" version))
7123 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7124 (properties `((upstream-name . "ABCoptim")))
7125 (build-system r-build-system)
7126 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7127 (home-page "https://github.com/gvegayon/ABCoptim/")
7128 (synopsis "Optimization of Artificial Bee Colony algorithm")
7130 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7131 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7132 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7133 algorithms, and uses only common control parameters such as colony size and
7134 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7135 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7136 This version is a work-in-progress and is written in R code.")
7137 (license license:expat)))
7139 (define-public r-abcp2
7146 (uri (cran-uri "ABCp2" version))
7148 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7149 (properties `((upstream-name . "ABCp2")))
7150 (build-system r-build-system)
7151 (propagated-inputs `(("r-mass" ,r-mass)))
7152 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7153 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7155 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7156 Poisson, and Gamma distribution and estimates the proportional paternity of the
7157 second male (P2) based on the best fit distribution.")
7158 (license license:gpl2)))
7160 (define-public r-abcrf
7167 (uri (cran-uri "abcrf" version))
7169 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7170 (build-system r-build-system)
7172 `(("r-doparallel" ,r-doparallel)
7173 ("r-foreach" ,r-foreach)
7175 ("r-matrixstats" ,r-matrixstats)
7176 ("r-ranger" ,r-ranger)
7178 ("r-rcpparmadillo" ,r-rcpparmadillo)
7179 ("r-readr" ,r-readr)
7180 ("r-stringr" ,r-stringr)))
7181 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7182 (synopsis "Approximate bayesian computation via random forests")
7184 "This package performs approximate bayesian computation (ABC) model choice and
7185 parameter inference via random forests. This machine learning tool named random
7186 forests (RF) can conduct selection among the highly complex models covered by
7188 (license license:gpl2+)))
7190 (define-public r-abctools
7197 (uri (cran-uri "abctools" version))
7199 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7200 (build-system r-build-system)
7203 ("r-abind" ,r-abind)
7204 ("r-hmisc" ,r-hmisc)
7205 ("r-plyr" ,r-plyr)))
7206 (home-page "https://github.com/dennisprangle/abctools/")
7207 (synopsis "Tools for ABC analyses")
7209 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7210 including summary statistic selection and assessing coverage. This includes
7211 recent dimension reduction algorithms to tune the choice of summary statistics,
7212 and coverage methods to tune the choice of threshold.")
7213 (license license:gpl2+)))
7215 (define-public r-ggstance
7222 (uri (cran-uri "ggstance" version))
7224 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7225 (build-system r-build-system)
7227 `(("r-ggplot2" ,r-ggplot2)
7229 ("r-rlang" ,r-rlang)
7230 ("r-withr" ,r-withr)))
7231 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7232 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7234 "This package is a @code{r-ggplot2} extension that provides flipped components:
7236 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7237 @item vertical versions of @code{r-ggplot2} positions.
7239 (license license:gpl3)))
7241 (define-public r-mosaiccore
7243 (name "r-mosaiccore")
7248 (uri (cran-uri "mosaicCore" version))
7250 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7251 (properties `((upstream-name . "mosaicCore")))
7252 (build-system r-build-system)
7254 `(("r-dplyr" ,r-dplyr)
7255 ("r-lazyeval" ,r-lazyeval)
7257 ("r-rlang" ,r-rlang)
7258 ("r-tidyr" ,r-tidyr)))
7259 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7260 (synopsis "Common utilities for mosaic family packages")
7262 "Common utilities used in other Mosaic family packages are collected here.")
7263 (license license:gpl2+)))
7265 (define-public r-ggformula
7267 (name "r-ggformula")
7272 (uri (cran-uri "ggformula" version))
7274 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7275 (build-system r-build-system)
7277 `(("r-ggforce" ,r-ggforce)
7278 ("r-ggplot2" ,r-ggplot2)
7279 ("r-ggstance" ,r-ggstance)
7280 ("r-magrittr" ,r-magrittr)
7281 ("r-mosaiccore" ,r-mosaiccore)
7282 ("r-rlang" ,r-rlang)
7283 ("r-stringr" ,r-stringr)
7284 ("r-tibble" ,r-tibble)))
7285 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7286 (synopsis "Formula interface for the @code{r-ggplot2}")
7288 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7289 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7290 and extends the excellent simplicity of the lattice-graphics formula interface,
7291 while providing the intuitive capabilities of @code{r-ggplot2}.")
7292 (license license:expat)))
7294 (define-public r-mosaicdata
7296 (name "r-mosaicdata")
7301 (uri (cran-uri "mosaicData" version))
7303 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7304 (properties `((upstream-name . "mosaicData")))
7305 (build-system r-build-system)
7306 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7307 (synopsis "Data sets for project Mosaic")
7309 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7310 used to teach mathematics, statistics, computation and modeling.")
7311 (license license:gpl2+)))
7313 (define-public r-raster
7320 (uri (cran-uri "raster" version))
7323 "0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
7324 (build-system r-build-system)
7326 `(("r-rcpp" ,r-rcpp)
7328 (home-page "https://www.rspatial.org/")
7329 (synopsis "Geographic data analysis and modeling")
7331 "The package implements basic and high-level functions for reading,
7332 writing, manipulating, analyzing and modeling of gridded spatial data.
7333 Processing of very large files is supported.")
7334 (license license:gpl3+)))
7336 (define-public r-mosaic
7343 (uri (cran-uri "mosaic" version))
7345 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7346 (build-system r-build-system)
7348 `(("r-broom" ,r-broom)
7349 ("r-dplyr" ,r-dplyr)
7350 ("r-ggdendro" ,r-ggdendro)
7351 ("r-ggformula" ,r-ggformula)
7352 ("r-ggplot2" ,r-ggplot2)
7353 ("r-ggrepel" ,r-ggrepel)
7355 ("r-gridextra" ,r-gridextra)
7356 ("r-lattice" ,r-lattice)
7357 ("r-latticeextra" ,r-latticeextra)
7358 ("r-lazyeval" ,r-lazyeval)
7360 ("r-matrix" ,r-matrix)
7361 ("r-mosaiccore" ,r-mosaiccore)
7362 ("r-mosaicdata" ,r-mosaicdata)
7363 ("r-readr" ,r-readr)
7364 ("r-tidyr" ,r-tidyr)))
7366 `(("r-knitr" ,r-knitr)))
7367 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7368 (synopsis "Mathematics, statistics, and computation teaching utilities")
7370 "This package contain data sets and utilities from
7371 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7372 statistics, computation and modeling. Project MOSAIC is a community of
7373 educators working to tie together aspects of quantitative work that students
7374 in science, technology, engineering and mathematics will need in their
7375 professional lives, but which are usually taught in isolation, if at all.")
7376 (license license:gpl2+)))
7378 (define-public r-abd
7385 (uri (cran-uri "abd" version))
7387 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7388 (build-system r-build-system)
7390 `(("r-lattice" ,r-lattice)
7391 ("r-mosaic" ,r-mosaic)
7392 ("r-nlme" ,r-nlme)))
7393 (home-page "https://cran.r-project.org/web/packages/abd/")
7394 (synopsis "Analysis of biological data")
7396 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7397 biological data by Michael Whitlock and Dolph Schluter.")
7398 (license license:gpl2)))
7400 (define-public r-svgui
7407 (uri (cran-uri "svGUI" version))
7409 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7410 (properties `((upstream-name . "svGUI")))
7411 (build-system r-build-system)
7412 (home-page "https://github.com/SciViews/svGUI/")
7413 (synopsis "Functions for managing GUI clients in R")
7415 "The SciViews @code{svGUI} package eases the management of Graphical User
7416 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7417 centralizes info about GUI elements currently used, and it dispatches GUI
7418 calls to the particular toolkits in use in function of the context.")
7419 (license license:gpl2)))
7421 (define-public r-svdialogs
7423 (name "r-svdialogs")
7428 (uri (cran-uri "svDialogs" version))
7430 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7431 (properties `((upstream-name . "svDialogs")))
7432 (build-system r-build-system)
7435 ("zenity" ,zenity)))
7437 `(("r-rstudioapi" ,r-rstudioapi)
7438 ("r-svgui" ,r-svgui)))
7439 (home-page "https://github.com/SciViews/svDialogs/")
7440 (synopsis "Portable dialog boxes")
7442 "This package helps to construct standard dialog boxes for your GUI, including
7443 message boxes, input boxes, list, file or directory selection, and others. In
7444 case R cannot display GUI dialog boxes, a simpler command line version of these
7445 interactive elements is also provided as a fallback solution.")
7446 (license license:gpl2)))
7448 (define-public r-abe
7455 (uri (cran-uri "abe" version))
7458 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7459 (build-system r-build-system)
7460 (home-page "https://cran.r-project.org/web/packages/abe/")
7461 (synopsis "Augmented backward elimination")
7463 "This package performs augmented backward elimination and checks the
7464 stability of the obtained model. Augmented backward elimination combines
7465 significance or information based criteria with the change in estimate to
7466 either select the optimal model for prediction purposes or to serve as a tool
7467 to obtain a practically sound, highly interpretable model.")
7468 (license license:gpl2+)))
7470 (define-public r-abf2
7477 (uri (cran-uri "abf2" version))
7479 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7480 (build-system r-build-system)
7481 (home-page "https://cran.r-project.org/web/packages/abf2/")
7482 (synopsis "Load gap-free axon @code{r-abf2} files")
7484 "This package loads electrophysiology data from ABF2 files, as created by
7485 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7486 mode are currently supported.")
7487 (license license:artistic2.0)))
7489 (define-public r-abhgenotyper
7491 (name "r-abhgenotyper")
7496 (uri (cran-uri "ABHgenotypeR" version))
7498 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7499 (properties `((upstream-name . "ABHgenotypeR")))
7500 (build-system r-build-system)
7502 `(("r-ggplot2" ,r-ggplot2)
7503 ("r-reshape2" ,r-reshape2)))
7504 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7505 (synopsis "Visualize and manipulate ABH genotypes")
7507 "The @code{r-abhgenotyper} package provides simple imputation,
7508 error-correction and plotting capacities for genotype data. The package is
7509 supposed to serve as an intermediate but independent analysis tool between the
7510 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7511 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7512 genotypes as \"graphical genotypes\".")
7513 (license license:gpl3)))
7515 (define-public r-furrr
7522 (uri (cran-uri "furrr" version))
7525 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7526 (build-system r-build-system)
7528 `(("r-future" ,r-future)
7529 ("r-globals" ,r-globals)
7530 ("r-purrr" ,r-purrr)
7531 ("r-rlang" ,r-rlang)))
7532 (home-page "https://github.com/DavisVaughan/furrr")
7533 (synopsis "Apply mapping functions in parallel using futures")
7535 "This package provides implementations of the family of @code{map()}
7536 functions from the @code{purrr} package that can be resolved using any
7537 @code{future}-supported backend, e.g. parallel on the local machine or
7538 distributed on a compute cluster.")
7539 (license license:lgpl2.1+)))
7541 (define-public r-abjutils
7548 (uri (cran-uri "abjutils" version))
7550 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7551 (build-system r-build-system)
7553 `(("r-devtools" ,r-devtools)
7554 ("r-dplyr" ,r-dplyr)
7555 ("r-furrr" ,r-furrr)
7556 ("r-future" ,r-future)
7559 ("r-magrittr" ,r-magrittr)
7560 ("r-progress" ,r-progress)
7561 ("r-purrr" ,r-purrr)
7562 ("r-readr" ,r-readr)
7563 ("r-rlang" ,r-rlang)
7564 ("r-rstudioapi" ,r-rstudioapi)
7565 ("r-scales" ,r-scales)
7566 ("r-stringi" ,r-stringi)
7567 ("r-stringr" ,r-stringr)
7568 ("r-tibble" ,r-tibble)
7569 ("r-tidyr" ,r-tidyr)))
7570 (home-page "https://github.com/abjur/abjutils/")
7571 (synopsis "Collection of tools for jurimetrical analysis")
7573 "This package implements general purpose tools, such as functions for
7574 sampling and basic manipulation of Brazilian lawsuits identification number.
7575 It also implements functions for text cleaning, such as accentuation
7577 (license license:expat)))
7579 (define-public r-abnormality
7581 (name "r-abnormality")
7586 (uri (cran-uri "abnormality" version))
7588 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7589 (build-system r-build-system)
7591 `(("r-mass" ,r-mass)
7592 ("r-matrix" ,r-matrix)))
7593 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7594 (synopsis "Measure a subject's abnormality with respect to a reference population")
7596 "This package contains functions to implement the methodology and
7597 considerations laid out by Marks et al. in the article \"Measuring abnormality
7598 in high dimensional spaces: applications in biomechanical gait analysis\".
7599 Using high-dimensional datasets to measure a subject's overall level of
7600 abnormality as compared to a reference population is often needed in outcomes
7602 (license license:expat)))
7604 (define-public r-abodoutlier
7606 (name "r-abodoutlier")
7611 (uri (cran-uri "abodOutlier" version))
7613 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7614 (properties `((upstream-name . "abodOutlier")))
7615 (build-system r-build-system)
7617 `(("r-cluster" ,r-cluster)))
7618 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7619 (synopsis "Angle-based outlier detection")
7621 "This package performs angle-based outlier detection on a given data
7622 frame. It offers three methods to process data:
7624 @item full but slow implementation using all the data that has cubic
7626 @item a fully randomized method;
7627 @item a method using k-nearest neighbours.
7629 These algorithms are well suited for high dimensional data outlier
7631 (license license:expat)))
7633 (define-public r-abps
7640 (uri (cran-uri "ABPS" version))
7642 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7643 (properties `((upstream-name . "ABPS")))
7644 (build-system r-build-system)
7645 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7646 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7647 (synopsis "Abnormal blood profile score to detect blood doping")
7649 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7650 The ABPS is a part of the Athlete biological passport program of the World
7651 anti-doping agency, which combines several blood parameters into a single
7652 score in order to detect blood doping. The package also contains functions to
7653 calculate other scores used in anti-doping programs, such as the ratio of
7654 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7655 (license license:gpl2+)))
7657 (define-public r-parmigene
7659 (name "r-parmigene")
7664 (uri (cran-uri "parmigene" version))
7667 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7668 (build-system r-build-system)
7669 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7670 (synopsis "Mutual information estimation for gene network reconstruction")
7672 "This package provides a parallel estimation of the mutual information
7673 based on entropy estimates from k-nearest neighbors distances and algorithms
7674 for the reconstruction of gene regulatory networks.")
7675 (license license:agpl3+)))
7677 (define-public r-pscl
7684 (uri (cran-uri "pscl" version))
7686 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
7687 (build-system r-build-system)
7689 `(("r-mass" ,r-mass)))
7690 (home-page "https://github.com/atahk/pscl/")
7691 (synopsis "Political science computational laboratory")
7693 "The @code{pscl} is an R package providing classes and methods for:
7695 @item Bayesian analysis of roll call data (item-response models);
7696 @item elementary Bayesian statistics;
7697 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7699 @item utility functions.
7701 (license license:gpl2)))
7703 (define-public r-accelmissing
7705 (name "r-accelmissing")
7710 (uri (cran-uri "accelmissing" version))
7712 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7713 (build-system r-build-system)
7715 `(("r-mice" ,r-mice)
7716 ("r-pscl" ,r-pscl)))
7717 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7718 (synopsis "Missing value imputation for accelerometer data")
7720 "This package provides a statistical method to impute the missing values in
7721 accelerometer data. The methodology includes both parametric and
7722 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7723 model. It also provides multiple functions to preprocess the accelerometer data
7724 previous to the missing data imputation. These include detecting the wearing
7725 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7726 (license license:gpl2+)))
7728 (define-public r-mhsmm
7735 (uri (cran-uri "mhsmm" version))
7737 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7738 (build-system r-build-system)
7739 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7740 (home-page "https://github.com/jaredo/mhsmm/")
7741 (synopsis "Inference for hidden Markov and semi-Markov models")
7743 "The @code{r-mhsmm} package implements estimation and prediction methods for
7744 hidden Markov and semi-Markov models for multiple observation sequences. Such
7745 techniques are of interest when observed data is thought to be dependent on some
7746 unobserved (or hidden) state. Also, this package is suitable for equidistant
7747 time series data, with multivariate and/or missing data. Allows user defined
7748 emission distributions.")
7749 (license license:gpl2+)))
7751 (define-public r-nleqslv
7758 (uri (cran-uri "nleqslv" version))
7760 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7761 (build-system r-build-system)
7762 (native-inputs `(("gfortran" ,gfortran)))
7763 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7764 (synopsis "Solve systems of nonlinear equations")
7766 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7767 Broyden or a Newton method with a choice of global strategies such as line
7768 search and trust region. There are options for using a numerical or user
7769 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7770 singular or ill-conditioned Jacobian.")
7771 (license license:gpl2+)))
7773 (define-public r-physicalactivity
7775 (name "r-physicalactivity")
7780 (uri (cran-uri "PhysicalActivity" version))
7782 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7784 `((upstream-name . "PhysicalActivity")))
7785 (build-system r-build-system)
7786 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7787 (synopsis "Procesing accelerometer data for physical activity measurement")
7789 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7790 for classification of monitor wear and nonwear time intervals in accelerometer
7791 data collected to assess physical activity. The package also contains functions
7792 for making plots of accelerometer data and obtaining the summary of various
7793 information including daily monitor wear time and the mean monitor wear time
7794 during valid days. The revised package version 0.2-1 improved the functions
7795 regarding speed, robustness and add better support for time zones and daylight
7796 saving. In addition, several functions were added:
7798 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7799 @item the @code{markPAI} can categorize physical activity intensity level based
7800 on user-defined cut-points of accelerometer counts.
7802 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7803 @code{queryActigraph} functions.")
7804 (license license:gpl3+)))
7806 (define-public r-acc
7813 (uri (cran-uri "acc" version))
7815 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7816 (build-system r-build-system)
7818 `(("r-circlize" ,r-circlize)
7820 ("r-ggplot2" ,r-ggplot2)
7821 ("r-iterators" ,r-iterators)
7822 ("r-mhsmm" ,r-mhsmm)
7823 ("r-nleqslv" ,r-nleqslv)
7824 ("r-physicalactivity" ,r-physicalactivity)
7826 ("r-r-utils" ,r-r-utils)
7828 ("r-rcpparmadillo" ,r-rcpparmadillo)
7829 ("r-rsqlite" ,r-rsqlite)
7831 (home-page "https://cran.r-project.org/web/packages/acc/")
7832 (synopsis "Exploring accelerometer data")
7834 "This package processes accelerometer data from uni-axial and tri-axial devices
7835 and generates data summaries. Also, includes functions to plot, analyze, and
7836 simulate accelerometer data.")
7837 (license license:gpl2+)))
7839 (define-public r-rbenchmark
7841 (name "r-rbenchmark")
7846 (uri (cran-uri "rbenchmark" version))
7848 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7849 (build-system r-build-system)
7850 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7851 (synopsis "Benchmarking routine for R")
7853 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7854 and is intended to facilitate benchmarking of arbitrary R code. The library
7855 consists of just one function, benchmark, which is a simple wrapper around
7856 system.time. Given a specification of the benchmarking process (counts of
7857 replications, evaluation environment) and an arbitrary number of expressions,
7858 benchmark evaluates each of the expressions in the specified environment,
7859 replicating the evaluation as many times as specified, and returning the results
7860 conveniently wrapped into a data frame.")
7861 (license license:gpl2+)))
7863 (define-public r-mitools
7870 (uri (cran-uri "mitools" version))
7873 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7874 (build-system r-build-system)
7875 (propagated-inputs `(("r-dbi" ,r-dbi)))
7876 (home-page "https://cran.r-project.org/web/packages/mitools/")
7877 (synopsis "Tools for multiple imputation of missing data")
7879 "This package provides tools to perform analyses and combine results from
7880 multiple-imputation datasets.")
7881 (license license:gpl2)))
7883 (define-public r-magick
7890 (uri (cran-uri "magick" version))
7893 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
7894 (build-system r-build-system)
7896 `(("imagemagick" ,imagemagick)
7899 `(("r-curl" ,r-curl)
7900 ("r-magrittr" ,r-magrittr)
7901 ("r-rcpp" ,r-rcpp)))
7903 `(("pkg-config" ,pkg-config)))
7904 (home-page "https://github.com/ropensci/magick")
7905 (synopsis "Advanced graphics and image-processing in R")
7907 "This package provides bindings to ImageMagick, a comprehensive image
7908 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7909 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7910 operations are vectorized via the Magick++ STL meaning they operate either on
7911 a single frame or a series of frames for working with layers, collages, or
7912 animation. In RStudio, images are automatically previewed when printed to the
7913 console, resulting in an interactive editing environment.")
7914 (license license:expat)))
7916 (define-public r-survey
7923 (uri (cran-uri "survey" version))
7926 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
7927 (build-system r-build-system)
7929 `(("r-lattice" ,r-lattice)
7930 ("r-matrix" ,r-matrix)
7931 ("r-minqa" ,r-minqa)
7932 ("r-mitools" ,r-mitools)
7933 ("r-numderiv" ,r-numderiv)
7934 ("r-survival" ,r-survival)))
7935 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7936 (synopsis "Analysis of complex survey samples")
7938 "This package provides tools for the analysis of complex survey samples.
7939 The provided features include: summary statistics, two-sample tests, rank
7940 tests, generalised linear models, cumulative link models, Cox models,
7941 loglinear models, and general maximum pseudolikelihood estimation for
7942 multistage stratified, cluster-sampled, unequally weighted survey samples;
7943 variances by Taylor series linearisation or replicate weights;
7944 post-stratification, calibration, and raking; two-phase subsampling designs;
7945 graphics; PPS sampling without replacement; principal components, and factor
7947 ;; Either version of the GPL.
7948 (license (list license:gpl2 license:gpl3))))
7950 (define-public r-gee
7957 (uri (cran-uri "gee" version))
7960 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
7961 (properties `((upstream-name . "gee")))
7962 (build-system r-build-system)
7964 `(("gfortran" ,gfortran)))
7965 (home-page "https://cran.r-project.org/web/packages/gee/")
7966 (synopsis "Generalized estimation equation solver")
7968 "This package provides a solver for generalized estimation equations.")
7969 (license license:gpl2)))
7971 (define-public r-tab
7978 (uri (cran-uri "tab" version))
7981 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
7982 (properties `((upstream-name . "tab")))
7983 (build-system r-build-system)
7985 `(("r-dplyr" ,r-dplyr)
7987 ("r-knitr" ,r-knitr)
7989 ("r-survey" ,r-survey)
7990 ("r-survival" ,r-survival)
7991 ("r-xtable" ,r-xtable)))
7992 (home-page "https://cran.r-project.org/web/packages/tab/")
7993 (synopsis "Create summary tables for statistical reports")
7995 "This package contains functions for creating various types of summary
7996 tables, e.g. comparing characteristics across levels of a categorical variable
7997 and summarizing fitted generalized linear models, generalized estimating
7998 equations, and Cox proportional hazards models. Functions are available to
7999 handle data from simple random samples as well as complex surveys.")
8000 (license license:gpl3+)))
8002 (define-public r-dvmisc
8009 (uri (cran-uri "dvmisc" version))
8011 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8012 (build-system r-build-system)
8014 `(("r-cubature" ,r-cubature)
8015 ("r-data-table" ,r-data-table)
8016 ("r-dplyr" ,r-dplyr)
8017 ("r-ggplot2" ,r-ggplot2)
8019 ("r-mvtnorm" ,r-mvtnorm)
8020 ("r-pracma" ,r-pracma)
8021 ("r-rbenchmark" ,r-rbenchmark)
8023 ("r-survey" ,r-survey)
8025 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8026 (synopsis "Faster computation of common statistics and miscellaneous functions")
8028 "This package implements faster versions of base R functions (e.g. mean, standard
8029 deviation, covariance, weighted mean), mostly written in C++, along with
8030 miscellaneous functions for various purposes (e.g. create the histogram with
8031 fitted probability density function or probability mass function curve, create
8032 the body mass index groups, assess the linearity assumption in logistic
8034 (license license:gpl2)))
8036 (define-public r-accelerometry
8038 (name "r-accelerometry")
8043 (uri (cran-uri "accelerometry" version))
8045 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8046 (build-system r-build-system)
8048 `(("r-dvmisc" ,r-dvmisc)
8049 ("r-rcpp" ,r-rcpp)))
8050 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8051 (synopsis "Functions for processing accelerometer data")
8053 "This package provides a collection of functions that perform operations on
8054 time-series accelerometer data, such as identify the non-wear time, flag minutes
8055 that are part of an activity bout, and find the maximum 10-minute average count
8056 value. The functions are generally very flexible, allowing for a variety of
8057 algorithms to be implemented.")
8058 (license license:gpl3)))
8060 (define-public r-absim
8067 (uri (cran-uri "AbSim" version))
8069 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8070 (properties `((upstream-name . "AbSim")))
8071 (build-system r-build-system)
8074 ("r-powerlaw" ,r-powerlaw)))
8075 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8076 (synopsis "Time resolved simulations of antibody repertoires")
8078 "This package provides simulation methods for the evolution of antibody repertoires.
8079 The heavy and light chain variable region of both human and C57BL/6 mice can
8080 be simulated in a time-dependent fashion. Both single lineages using one set of
8081 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8082 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8083 Upon completion, the main loop of the algorithm begins, with each iteration
8084 representing one simulated time step. Various mutation events are possible at
8085 each time step, contributing to a diverse final repertoire.")
8086 (license license:gpl2)))
8088 (define-public r-quic
8095 (uri (cran-uri "QUIC" version))
8097 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8098 (properties `((upstream-name . "QUIC")))
8099 (build-system r-build-system)
8100 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8101 (synopsis "Regularized sparse inverse covariance matrix estimation")
8103 "This package implements the regularized Gaussian maximum likelihood
8104 estimation of the inverse of a covariance matrix. It uses Newton's method and
8105 coordinate descent to solve the regularized inverse covariance matrix
8106 estimation problem.")
8107 ;; The project home page states that the release is under GPLv3 or later.
8108 ;; The CRAN page only says GPL-3.
8109 (license license:gpl3+)))
8111 (define-public r-abundant
8118 (uri (cran-uri "abundant" version))
8120 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8121 (build-system r-build-system)
8123 `(("r-quic" ,r-quic)))
8124 (home-page "https://cran.r-project.org/web/packages/abundant/")
8125 (synopsis "Abundant regression and high-dimensional principal fitted components")
8127 "This package provides tools to fit and predict with the high-dimensional
8128 principal fitted components model. This model is described by Cook, Forzani,
8129 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8130 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8131 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8132 (license license:gpl2+)))
8134 (define-public r-ac3net
8141 (uri (cran-uri "Ac3net" version))
8143 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8144 (properties `((upstream-name . "Ac3net")))
8145 (build-system r-build-system)
8147 `(("r-data-table" ,r-data-table)))
8148 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8149 (synopsis "Inferring directional conservative causal core gene networks")
8150 (description "This package infers directional Conservative causal core
8151 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8152 directional network.")
8153 (license license:gpl3+)))
8155 (define-public r-aca
8162 (uri (cran-uri "ACA" version))
8164 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8165 (properties `((upstream-name . "ACA")))
8166 (build-system r-build-system)
8167 (home-page "https://cran.r-project.org/web/packages/ACA/")
8168 (synopsis "Abrupt change-point or aberration detection in point series")
8170 "This package offers an interactive function for the detection of breakpoints in
8172 ;; Any version of the GPL
8173 (license (list license:gpl2+ license:gpl3+))))
8175 (define-public r-acceptancesampling
8177 (name "r-acceptancesampling")
8182 (uri (cran-uri "AcceptanceSampling" version))
8184 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8186 `((upstream-name . "AcceptanceSampling")))
8187 (build-system r-build-system)
8188 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8189 (synopsis "Creation and evaluation of acceptance sampling plans")
8191 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8192 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8193 in quality control and improvement. International standards of acceptance
8194 sampling provide sampling plans for specific circumstances. The aim of this
8195 package is to provide an easy-to-use interface to visualize single, double or
8196 multiple sampling plans. In addition, methods have been provided to enable the
8197 user to assess sampling plans against pre-specified levels of performance, as
8198 measured by the probability of acceptance for a given level of quality in the
8200 (license license:gpl3+)))
8202 (define-public r-acclma
8209 (uri (cran-uri "ACCLMA" version))
8211 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8212 (properties `((upstream-name . "ACCLMA")))
8213 (build-system r-build-system)
8214 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8215 (synopsis "ACC & LMA graph plotting")
8217 "This package contains a function that imports data from a @acronym{CSV,
8218 Comma-Separated Values} file, or uses manually entered data from the format (x,
8219 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8220 Curve} vs @acronym{LOI, Line of Independence} graph and
8221 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8222 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8223 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8224 string) was passed, a manual data entry window is opened. The header parameter
8225 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8226 a header row or not. The dataset should contain only one independent variable
8227 (x) and one dependent variable (y) and can contain a weight for each
8229 (license license:gpl2)))
8231 (define-public r-aspi
8238 (uri (cran-uri "aspi" version))
8240 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8241 (build-system r-build-system)
8243 "https://cran.r-project.org/web/packages/aspi/")
8245 "Analysis of symmetry of parasitic infections")
8247 "This package provides tools for the analysis and visualization of bilateral
8248 asymmetry in parasitic infections.")
8249 (license license:gpl3+)))
8251 (define-public r-sandwich
8258 (uri (cran-uri "sandwich" version))
8261 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8262 (build-system r-build-system)
8264 `(("r-zoo" ,r-zoo)))
8265 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8266 (synopsis "Robust Covariance Matrix Estimators")
8268 "This package provides model-robust standard error estimators for
8269 cross-sectional, time series, clustered, panel, and longitudinal data.")
8270 ;; Either version of the license.
8271 (license (list license:gpl2 license:gpl3))))
8273 (define-public r-th-data
8280 (uri (cran-uri "TH.data" version))
8283 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8284 (properties `((upstream-name . "TH.data")))
8285 (build-system r-build-system)
8287 `(("r-mass" ,r-mass)
8288 ("r-survival" ,r-survival)))
8289 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8290 (synopsis "Shared data sets")
8292 "This package contains supporting data sets that are used in other
8293 packages maintained by Torsten Hothorn.")
8294 (license license:gpl3)))
8296 (define-public r-multcomp
8303 (uri (cran-uri "multcomp" version))
8306 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8307 (build-system r-build-system)
8309 `(("r-codetools" ,r-codetools)
8310 ("r-mvtnorm" ,r-mvtnorm)
8311 ("r-sandwich" ,r-sandwich)
8312 ("r-survival" ,r-survival)
8313 ("r-th-data" ,r-th-data)))
8314 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8315 (synopsis "Simultaneous inference in general parametric models")
8317 "Simultaneous tests and confidence intervals for general linear
8318 hypotheses in parametric models, including linear, generalized linear, linear
8319 mixed effects, and survival models. The package includes demos reproducing
8320 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8321 Hothorn, Westfall, 2010, CRC Press).")
8322 (license license:gpl2)))
8324 (define-public r-emmeans
8331 (uri (cran-uri "emmeans" version))
8334 "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
8335 (build-system r-build-system)
8337 `(("r-estimability" ,r-estimability)
8338 ("r-mvtnorm" ,r-mvtnorm)
8339 ("r-numderiv" ,r-numderiv)
8341 ("r-xtable" ,r-xtable)))
8342 (home-page "https://github.com/rvlenth/emmeans")
8343 (synopsis "Estimated marginal means, aka least-squares means")
8345 "This package provides tools to obtain @dfn{estimated marginal
8346 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8347 be used to compute contrasts or linear functions of EMMs, trends, and
8348 comparisons of slopes.")
8349 ;; Either version of the license.
8350 (license (list license:gpl2 license:gpl3))))
8352 (define-public r-pwr
8359 (uri (cran-uri "pwr" version))
8362 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8363 (build-system r-build-system)
8365 `(("r-knitr" ,r-knitr)))
8366 (home-page "https://github.com/heliosdrm/pwr")
8367 (synopsis "Basic functions for power analysis")
8369 "This package provides power analysis functions along the lines of
8371 (license license:gpl3+)))
8373 (define-public r-libcoin
8380 (uri (cran-uri "libcoin" version))
8383 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8384 (build-system r-build-system)
8385 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8386 (home-page "https://cran.r-project.org/web/packages/libcoin")
8387 (synopsis "Linear test statistics for permutation inference")
8389 "This package provides basic infrastructure for linear test statistics
8390 and permutation inference in the framework of Strasser and Weber (1999).")
8391 (license license:gpl2)))
8393 (define-public r-coin
8400 (uri (cran-uri "coin" version))
8403 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8404 (build-system r-build-system)
8406 `(("r-libcoin" ,r-libcoin)
8407 ("r-matrixstats" ,r-matrixstats)
8408 ("r-modeltools" ,r-modeltools)
8409 ("r-multcomp" ,r-multcomp)
8410 ("r-mvtnorm" ,r-mvtnorm)
8411 ("r-survival" ,r-survival)))
8412 (home-page "http://coin.r-forge.r-project.org")
8413 (synopsis "Conditional inference procedures in a permutation test framework")
8415 "This package provides conditional inference procedures for the general
8416 independence problem including two-sample, K-sample (non-parametric ANOVA),
8417 correlation, censored, ordered and multivariate problems.")
8418 (license license:gpl2)))
8420 (define-public r-bayesplot
8422 (name "r-bayesplot")
8427 (uri (cran-uri "bayesplot" version))
8430 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8431 (build-system r-build-system)
8433 `(("pandoc" ,ghc-pandoc)
8434 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8436 `(("r-dplyr" ,r-dplyr)
8437 ("r-ggplot2" ,r-ggplot2)
8438 ("r-ggridges" ,r-ggridges)
8440 ("r-reshape2" ,r-reshape2)
8441 ("r-rlang" ,r-rlang)
8442 ("r-tibble" ,r-tibble)
8443 ("r-tidyselect" ,r-tidyselect)))
8444 (home-page "https://mc-stan.org/bayesplot")
8445 (synopsis "Plotting for Bayesian models")
8447 "This package provides plotting functions for posterior analysis, model
8448 checking, and MCMC diagnostics. The package is designed not only to provide
8449 convenient functionality for users, but also a common set of functions that
8450 can be easily used by developers working on a variety of R packages for
8451 Bayesian modeling.")
8452 (license license:gpl3+)))
8454 (define-public r-tmb
8461 (uri (cran-uri "TMB" version))
8464 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8465 (properties `((upstream-name . "TMB")))
8466 (build-system r-build-system)
8468 `(("r-matrix" ,r-matrix)
8469 ("r-rcppeigen" ,r-rcppeigen)))
8470 (home-page "http://tmb-project.org")
8471 (synopsis "Template model builder: a general random effect tool")
8473 "With this tool, a user should be able to quickly implement complex
8474 random effect models through simple C++ templates. The package combines
8475 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8476 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8477 from R) to obtain an efficient implementation of the applied Laplace
8478 approximation with exact derivatives. Key features are: Automatic sparseness
8479 detection, parallelism through BLAS and parallel user templates.")
8480 (license license:gpl2)))
8482 (define-public r-sjstats
8489 (uri (cran-uri "sjstats" version))
8491 (base32 "0938ac6ixvkif07azd2msa8g3qnn9rabj6jg17almbysl83kg4nm"))))
8492 (build-system r-build-system)
8494 `(("r-bayestestr" ,r-bayestestr)
8495 ("r-broom" ,r-broom)
8496 ("r-dplyr" ,r-dplyr)
8497 ("r-effectsize" ,r-effectsize)
8498 ("r-emmeans" ,r-emmeans)
8499 ("r-insight" ,r-insight)
8501 ("r-magrittr" ,r-magrittr)
8503 ("r-modelr" ,r-modelr)
8504 ("r-parameters" ,r-parameters)
8505 ("r-performance" ,r-performance)
8506 ("r-purrr" ,r-purrr)
8507 ("r-rlang" ,r-rlang)
8508 ("r-sjlabelled" ,r-sjlabelled)
8509 ("r-sjmisc" ,r-sjmisc)
8510 ("r-tidyr" ,r-tidyr)))
8511 (home-page "https://github.com/strengejacke/sjstats")
8512 (synopsis "Functions for common statistical computations")
8514 "This package provides a collection of convenient functions for common
8515 statistical computations, which are not directly provided by R's @code{base}
8516 or @code{stats} packages. This package aims at providing, first, shortcuts
8517 for statistical measures, which otherwise could only be calculated with
8518 additional effort. Second, these shortcut functions are generic, and can be
8519 applied not only to vectors, but also to other objects as well. The focus of
8520 most functions lies on summary statistics or fit measures for regression
8521 models, including generalized linear models, mixed effects models and Bayesian
8523 (license license:gpl3)))
8525 (define-public r-glmmtmb
8532 (uri (cran-uri "glmmTMB" version))
8535 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8536 (properties `((upstream-name . "glmmTMB")))
8537 (build-system r-build-system)
8539 `(("r-lme4" ,r-lme4)
8540 ("r-matrix" ,r-matrix)
8542 ("r-rcppeigen" ,r-rcppeigen)
8545 `(("r-knitr" ,r-knitr))) ; for vignettes
8546 (home-page "https://github.com/glmmTMB")
8547 (synopsis "Generalized linear mixed models")
8549 "Fit linear and generalized linear mixed models with various extensions,
8550 including zero-inflation. The models are fitted using maximum likelihood
8551 estimation via the Template Model Builder. Random effects are assumed to be
8552 Gaussian on the scale of the linear predictor and are integrated out using the
8553 Laplace approximation. Gradients are calculated using automatic
8555 (license license:agpl3+)))
8557 (define-public r-bayestestr
8559 (name "r-bayestestr")
8564 (uri (cran-uri "bayestestR" version))
8567 "1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz"))))
8568 (properties `((upstream-name . "bayestestR")))
8569 (build-system r-build-system)
8571 `(("r-insight" ,r-insight)))
8573 `(("r-knitr" ,r-knitr)))
8574 (home-page "https://github.com/easystats/bayestestR")
8575 (synopsis "Describe Bayesian models and posterior distributions")
8577 "This package provides utilities to understand and describe posterior
8578 distributions and Bayesian models. It includes point-estimates such as
8579 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8580 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8581 ROPE percentage and pd).")
8582 (license license:gpl3)))
8584 (define-public r-performance
8586 (name "r-performance")
8591 (uri (cran-uri "performance" version))
8594 "0j6wmnwhfdd3v1a17qmg491q50579knjzscmyr4yk3xr0jbsbg8x"))))
8595 (build-system r-build-system)
8597 `(("r-bayestestr" ,r-bayestestr)
8598 ("r-insight" ,r-insight)))
8599 (home-page "https://easystats.github.io/performance/")
8600 (synopsis "Assessment of regression models performance")
8602 "This package provides utilities for computing measures to assess model
8603 quality, which are not directly provided by R's @code{base} or @code{stats}
8604 packages. These include e.g. measures like r-squared, intraclass correlation
8605 coefficient, root mean squared error or functions to check models for
8606 overdispersion, singularity or zero-inflation and more. Functions apply to a
8607 large variety of regression models, including generalized linear models, mixed
8608 effects models and Bayesian models.")
8609 (license license:gpl3)))
8611 (define-public r-ggeffects
8613 (name "r-ggeffects")
8618 (uri (cran-uri "ggeffects" version))
8621 "1y3yfb07jrr6vkc8hk6rp52l70dj7042jvqgjzllslzy7hx2jhyw"))))
8622 (build-system r-build-system)
8624 `(("r-insight" ,r-insight)
8626 ("r-sjlabelled" ,r-sjlabelled)))
8628 `(("r-knitr" ,r-knitr)))
8629 (home-page "https://github.com/strengejacke/ggeffects")
8630 (synopsis "Create tidy data frames of marginal effects for ggplot")
8632 "This package provides tools to compute marginal effects from statistical
8633 models and return the result as tidy data frames. These data frames are ready
8634 to use with the @code{ggplot2} package. Marginal effects can be calculated
8635 for many different models. Interaction terms, splines and polynomial terms
8636 are also supported. The two main functions are @code{ggpredict()} and
8637 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8638 results using @code{ggplot2}.")
8639 (license license:gpl3)))
8641 (define-public r-effectsize
8643 (name "r-effectsize")
8648 (uri (cran-uri "effectsize" version))
8651 "0kijp4wamkidaxysc11dd4vhvnm4wnbi87871wcbwn27k5b6i5dg"))))
8652 (properties `((upstream-name . "effectsize")))
8653 (build-system r-build-system)
8655 `(("r-bayestestr" ,r-bayestestr)
8656 ("r-insight" ,r-insight)
8657 ("r-parameters" ,r-parameters)))
8659 `(("r-knitr" ,r-knitr)))
8660 (home-page "https://github.com/easystats/effectsize")
8661 (synopsis "Indices of effect size and standardized parameters")
8663 "This package provides utilities to work with indices of effect size and
8664 standardized parameters for a wide variety of models, allowing computation and
8665 conversion of indices such as Cohen's d, r, odds, etc.")
8666 (license license:gpl3)))
8668 (define-public r-sjplot
8675 (uri (cran-uri "sjPlot" version))
8677 (base32 "0ip1rkjlhyf3axlc8qqss1qq1f0xrda890c1jmcbhm98wwjw264f"))))
8678 (properties `((upstream-name . "sjPlot")))
8679 (build-system r-build-system)
8681 `(("r-bayestestr" ,r-bayestestr)
8682 ("r-dplyr" ,r-dplyr)
8683 ("r-effectsize" ,r-effectsize)
8684 ("r-ggeffects" ,r-ggeffects)
8685 ("r-ggplot2" ,r-ggplot2)
8686 ("r-insight" ,r-insight)
8687 ("r-knitr" ,r-knitr)
8689 ("r-parameters" ,r-parameters)
8690 ("r-performance" ,r-performance)
8691 ("r-purrr" ,r-purrr)
8692 ("r-rlang" ,r-rlang)
8693 ("r-scales" ,r-scales)
8694 ("r-sjlabelled" ,r-sjlabelled)
8695 ("r-sjmisc" ,r-sjmisc)
8696 ("r-sjstats" ,r-sjstats)
8697 ("r-tidyr" ,r-tidyr)))
8699 `(("r-knitr" ,r-knitr)))
8700 (home-page "https://strengejacke.github.io/sjPlot/")
8701 (synopsis "Data visualization for statistics in social science")
8703 "This package represents a collection of plotting and table output
8704 functions for data visualization. Results of various statistical
8705 analyses (that are commonly used in social sciences) can be visualized using
8706 this package, including simple and cross tabulated frequencies, histograms,
8707 box plots, (generalized) linear models, mixed effects models, principal
8708 component analysis and correlation matrices, cluster analyses, scatter plots,
8709 stacked scales, effects plots of regression models (including interaction
8710 terms) and much more. This package supports labelled data.")
8711 (license license:gpl3)))
8713 (define-public r-ini
8720 (uri (cran-uri "ini" version))
8723 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8724 (build-system r-build-system)
8725 (home-page "https://github.com/dvdscripter/ini")
8726 (synopsis "Read and write configuration files")
8728 "This package provides tools to parse simple @code{.ini} configuration
8729 files to an structured list. Users can manipulate this resulting list with
8730 @code{lapply()} functions. This same structured list can be used to write
8731 back to file after modifications.")
8732 (license license:gpl3)))
8741 (uri (cran-uri "gh" version))
8744 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
8745 (build-system r-build-system)
8750 ("r-jsonlite" ,r-jsonlite)))
8751 (home-page "https://github.com/r-lib/gh#readme")
8752 (synopsis "Access the GitHub API via R")
8754 "This package provides a minimal R client to access the GitHub API.")
8755 (license license:expat)))
8764 (uri (cran-uri "fs" version))
8767 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
8768 (build-system r-build-system)
8770 `(("pkg-config" ,pkg-config)
8771 ("r-knitr" ,r-knitr)))
8772 (home-page "https://fs.r-lib.org")
8773 (synopsis "Cross-platform file system operations based on libuv")
8775 "This package provides a cross-platform interface to file system
8776 operations, built on top of the libuv C library.")
8777 (license license:gpl3)))
8779 (define-public r-clisymbols
8781 (name "r-clisymbols")
8786 (uri (cran-uri "clisymbols" version))
8789 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8790 (build-system r-build-system)
8791 (home-page "https://github.com/gaborcsardi/clisymbols")
8792 (synopsis "Unicode symbols at the R prompt")
8794 "This package provides a small subset of Unicode symbols, that are useful
8795 when building command line applications. They fall back to alternatives on
8796 terminals that do not support Unicode.")
8797 (license license:expat)))
8799 (define-public r-usethis
8806 (uri (cran-uri "usethis" version))
8809 "12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
8810 (build-system r-build-system)
8813 ("r-clipr" ,r-clipr)
8814 ("r-crayon" ,r-crayon)
8819 ("r-git2r" ,r-git2r)
8821 ("r-purrr" ,r-purrr)
8822 ("r-rematch2" ,r-rematch2)
8823 ("r-rlang" ,r-rlang)
8824 ("r-rprojroot" ,r-rprojroot)
8825 ("r-rstudioapi" ,r-rstudioapi)
8826 ("r-whisker" ,r-whisker)
8827 ("r-withr" ,r-withr)
8828 ("r-yaml" ,r-yaml)))
8829 (home-page "https://github.com/r-lib/usethis")
8830 (synopsis "Automate R package and project setup")
8832 "This package helps you to automate R package and project setup tasks
8833 that are otherwise performed manually. This includes setting up unit testing,
8834 test coverage, continuous integration, Git, GitHub integration, licenses,
8835 Rcpp, RStudio projects, and more.")
8836 (license license:gpl3)))
8838 (define-public r-sessioninfo
8840 (name "r-sessioninfo")
8845 (uri (cran-uri "sessioninfo" version))
8848 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8849 (build-system r-build-system)
8852 ("r-withr" ,r-withr)))
8853 (home-page "https://github.com/r-lib/sessioninfo#readme")
8854 (synopsis "R session information")
8856 "This package provides tools to query and print information about the
8857 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8858 more information about packages, and where they were installed from.")
8859 (license license:gpl2)))
8861 (define-public r-remotes
8868 (uri (cran-uri "remotes" version))
8871 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
8872 (build-system r-build-system)
8873 (home-page "https://github.com/r-lib/remotes#readme")
8874 (synopsis "R package installation from remote repositories")
8876 "Download and install R packages stored in GitHub, BitBucket, or plain
8877 subversion or git repositories. This package is a lightweight replacement of
8878 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8879 the code was copied over from @code{devtools}.")
8880 (license license:gpl2+)))
8882 (define-public r-xopen
8889 (uri (cran-uri "xopen" version))
8892 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8893 (build-system r-build-system)
8895 `(("r-processx" ,r-processx)))
8896 (home-page "https://github.com/r-lib/xopen#readme")
8897 (synopsis "Open system files, URLs, anything")
8899 "This package provides a cross-platform solution to open files,
8900 directories or URLs with their associated programs.")
8901 (license license:expat)))
8903 (define-public r-rcmdcheck
8905 (name "r-rcmdcheck")
8910 (uri (cran-uri "rcmdcheck" version))
8913 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8914 (build-system r-build-system)
8916 `(("r-callr" ,r-callr)
8918 ("r-crayon" ,r-crayon)
8920 ("r-digest" ,r-digest)
8921 ("r-pkgbuild" ,r-pkgbuild)
8922 ("r-prettyunits" ,r-prettyunits)
8924 ("r-rprojroot" ,r-rprojroot)
8925 ("r-sessioninfo" ,r-sessioninfo)
8926 ("r-withr" ,r-withr)
8927 ("r-xopen" ,r-xopen)))
8928 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8929 (synopsis "Run R CMD check from R and capture results")
8931 "Run @code{R CMD check} from R programmatically, and capture the results
8932 of the individual checks.")
8933 (license license:expat)))
8935 (define-public r-rapportools
8937 (name "r-rapportools")
8942 (uri (cran-uri "rapportools" version))
8945 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8946 (build-system r-build-system)
8948 `(("r-pander" ,r-pander)
8950 ("r-reshape" ,r-reshape)))
8951 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8952 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8954 "This package provides helper functions that act as wrappers to more
8955 advanced statistical methods with the advantage of having sane defaults for
8957 (license license:agpl3+)))
8959 (define-public r-pander
8966 (uri (cran-uri "pander" version))
8969 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8970 (build-system r-build-system)
8972 `(("r-digest" ,r-digest)
8973 ("r-rcpp" ,r-rcpp)))
8974 (home-page "https://rapporter.github.io/pander")
8975 (synopsis "Render R objects into Pandoc's markdown")
8977 "The main aim of the pander R package is to provide a minimal and easy
8978 tool for rendering R objects into Pandoc's markdown. The package is also
8979 capable of exporting/converting complex Pandoc documents (reports) in various
8981 ;; This package is licensed under either the AGPLv3+ or the very rarely
8983 (license license:agpl3+)))
8985 (define-public r-summarytools
8987 (name "r-summarytools")
8992 (uri (cran-uri "summarytools" version))
8995 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
8996 (build-system r-build-system)
8998 `(("r-base64enc" ,r-base64enc)
8999 ("r-checkmate" ,r-checkmate)
9000 ("r-dplyr" ,r-dplyr)
9001 ("r-htmltools" ,r-htmltools)
9002 ("r-lubridate" ,r-lubridate)
9003 ("r-magick" ,r-magick)
9004 ("r-matrixstats" ,r-matrixstats)
9005 ("r-pander" ,r-pander)
9007 ("r-rapportools" ,r-rapportools)
9008 ("r-tibble" ,r-tibble)
9009 ("r-tidyr" ,r-tidyr)))
9010 (home-page "https://github.com/dcomtois/summarytools")
9011 (synopsis "Tools to quickly and neatly summarize data")
9013 "This package provides tools for data frame summaries, cross-tabulations,
9014 weight-enabled frequency tables and common univariate statistics in concise
9015 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9016 good point-of-entry for exploring data, both for experienced and new R
9018 (license license:gpl2)))
9020 (define-public r-lsei
9027 (uri (cran-uri "lsei" version))
9030 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
9031 (build-system r-build-system)
9033 `(("gfortran" ,gfortran)))
9034 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9035 (synopsis "Solve regression problems under equality/inequality constraints")
9037 "It contains functions that solve least squares linear regression
9038 problems under linear equality/inequality constraints. Functions for solving
9039 quadratic programming problems are also available, which transform such
9040 problems into least squares ones first.")
9041 (license license:gpl2+)))
9043 (define-public r-npsurv
9050 (uri (cran-uri "npsurv" version))
9053 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
9054 (build-system r-build-system)
9056 `(("r-lsei" ,r-lsei)))
9057 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9058 (synopsis "Nonparametric survival analysis")
9060 "This package contains functions for non-parametric survival analysis of
9061 exact and interval-censored observations.")
9062 (license license:gpl2+)))
9064 (define-public r-clusteval
9066 (name "r-clusteval")
9071 (uri (cran-uri "clusteval" version))
9074 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9075 (build-system r-build-system)
9077 `(("r-mvtnorm" ,r-mvtnorm)
9078 ("r-rcpp" ,r-rcpp)))
9079 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9080 (synopsis "Evaluation of clustering algorithms")
9082 "This R package provides a suite of tools to evaluate clustering
9083 algorithms, clusterings, and individual clusters.")
9084 (license license:expat)))
9086 (define-public r-tweedie
9093 (uri (cran-uri "tweedie" version))
9096 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9097 (build-system r-build-system)
9098 (native-inputs `(("gfortran" ,gfortran)))
9099 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9100 (synopsis "Evaluation of Tweedie exponential family models")
9102 "Maximum likelihood computations for Tweedie families, including the
9103 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9104 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9105 and related methods.")
9106 (license license:gpl2+)))
9108 (define-public r-rcppgsl
9115 (uri (cran-uri "RcppGSL" version))
9117 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9118 (properties `((upstream-name . "RcppGSL")))
9119 (build-system r-build-system)
9121 `(("r-rcpp" ,r-rcpp)
9124 `(("r-knitr" ,r-knitr))) ; for vignettes
9125 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9126 (synopsis "Rcpp integration for GSL vectors and matrices")
9128 "The GNU Scientific Library (or GSL) is a collection of numerical
9129 routines for scientific computing. It is particularly useful for C and C++
9130 programs as it provides a standard C interface to a wide range of mathematical
9131 routines. There are over 1000 functions in total with an extensive test
9132 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9133 structures and R using concepts from Rcpp which is itself a package that eases
9134 the interfaces between R and C++.")
9135 (license license:gpl2+)))
9137 (define-public r-mvabund
9144 (uri (cran-uri "mvabund" version))
9147 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9148 (build-system r-build-system)
9150 `(("r-mass" ,r-mass)
9152 ("r-rcppgsl" ,r-rcppgsl)
9153 ("r-statmod" ,r-statmod)
9154 ("r-tweedie" ,r-tweedie)))
9155 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9156 (synopsis "Statistical methods for analysing multivariate abundance data")
9158 "This package provides a set of tools for displaying, modeling and
9159 analysing multivariate abundance data in community ecology.")
9160 (license license:lgpl2.1+)))
9162 (define-public r-afex
9169 (uri (cran-uri "afex" version))
9172 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9173 (build-system r-build-system)
9177 ("r-lmertest" ,r-lmertest)
9178 ("r-pbkrtest" ,r-pbkrtest)
9179 ("r-reshape2" ,r-reshape2)))
9181 `(("r-knitr" ,r-knitr)))
9182 (home-page "https://afex.singmann.science/")
9183 (synopsis "Analysis of factorial experiments")
9185 "This package provides convenience functions for analyzing factorial
9186 experiments using ANOVA or mixed models.")
9187 (license license:gpl2+)))
9189 (define-public r-lmertest
9196 (uri (cran-uri "lmerTest" version))
9199 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9200 (properties `((upstream-name . "lmerTest")))
9201 (build-system r-build-system)
9203 `(("r-ggplot2" ,r-ggplot2)
9206 ("r-numderiv" ,r-numderiv)))
9207 (home-page "https://github.com/runehaubo/lmerTestR")
9208 (synopsis "Tests in linear mixed effects models")
9210 "This package provides p-values in type I, II or III anova and summary
9211 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9212 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9213 package. Model selection methods include step, drop1 and anova-like tables
9214 for random effects (ranova). Methods for Least-Square means (LS-means) and
9215 tests of linear contrasts of fixed effects are also available.")
9216 (license license:gpl2+)))
9218 (define-public r-r2glmm
9225 (uri (cran-uri "r2glmm" version))
9228 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9229 (build-system r-build-system)
9231 `(("r-afex" ,r-afex)
9232 ("r-data-table" ,r-data-table)
9233 ("r-dplyr" ,r-dplyr)
9234 ("r-ggplot2" ,r-ggplot2)
9235 ("r-gridextra" ,r-gridextra)
9236 ("r-lmertest" ,r-lmertest)
9238 ("r-matrix" ,r-matrix)
9240 ("r-pbkrtest" ,r-pbkrtest)))
9241 (home-page "https://github.com/bcjaeger/r2glmm")
9242 (synopsis "Compute R squared for mixed (multilevel) models")
9244 "This package computes model and semi partial R squared with confidence
9245 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9246 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9247 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9249 (license license:gpl2)))
9251 (define-public r-weights
9258 (uri (cran-uri "weights" version))
9261 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9262 (build-system r-build-system)
9264 `(("r-gdata" ,r-gdata)
9265 ("r-hmisc" ,r-hmisc)
9266 ("r-mice" ,r-mice)))
9268 "https://cran.r-project.org/web/packages/weights/")
9269 (synopsis "Weighting and weighted statistics")
9270 (description "This package Provides a variety of functions for producing
9271 simple weighted statistics, such as weighted Pearson's correlations, partial
9272 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9273 includes some software for quickly recoding survey data and plotting point
9274 estimates from interaction terms in regressions (and multiply imputed
9275 regressions). NOTE: Weighted partial correlation calculations pulled to
9277 (license license:gpl2+)))
9279 (define-public r-rcppannoy
9281 (name "r-rcppannoy")
9286 (uri (cran-uri "RcppAnnoy" version))
9289 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9290 (properties `((upstream-name . "RcppAnnoy")))
9291 (build-system r-build-system)
9293 `(("r-rcpp" ,r-rcpp)))
9294 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9295 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9297 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9298 for efficient memory usage as well an ability to load from and save to disk.
9299 This package provides an R interface.")
9300 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9302 (license (list license:gpl2+ license:asl2.0))))
9304 (define-public r-rcpphnsw
9311 (uri (cran-uri "RcppHNSW" version))
9314 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9315 (properties `((upstream-name . "RcppHNSW")))
9316 (build-system r-build-system)
9317 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9318 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9319 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9321 "Hnswlib is a C++ library for approximate nearest neighbors. This
9322 package provides a minimal R interface by relying on the Rcpp package.")
9323 ;; hnswlib is released under Version 2.0 of the Apache License.
9324 (license (list license:gpl3 license:asl2.0))))
9326 (define-public r-rcppparallel
9328 (name "r-rcppparallel")
9333 (uri (cran-uri "RcppParallel" version))
9336 "1mhd6vp47xmfw533h0pkvydv96m57fspvd85g8m7iqb5rcxvhhdb"))))
9337 (properties `((upstream-name . "RcppParallel")))
9338 (build-system r-build-system)
9339 (home-page "https://rcppcore.github.io/RcppParallel/")
9340 (synopsis "Parallel programming tools for Rcpp")
9342 "This package provides high level functions for parallel programming with
9343 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9344 the work of a standard serial @code{for} loop into a parallel one and the
9345 @code{parallelReduce()} function can be used for accumulating aggregates or
9347 (license license:gpl2)))
9349 (define-public r-ncdf4
9356 (uri (cran-uri "ncdf4" version))
9359 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9360 (build-system r-build-system)
9362 `(("netcdf" ,netcdf)
9364 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9365 (synopsis "R interface to Unidata netCDF format data files")
9367 "This package provides a high-level R interface to data files written
9368 using Unidata's netCDF library (version 4 or earlier), which are binary data
9369 files that are portable across platforms and include metadata information in
9370 addition to the data sets. Using this package, netCDF files can be opened and
9371 data sets read in easily. It is also easy to create new netCDF dimensions,
9372 variables, and files, in either version 3 or 4 format, and manipulate existing
9374 (license license:gpl3+)))
9376 (define-public r-biocmanager
9378 (name "r-biocmanager")
9383 (uri (cran-uri "BiocManager" version))
9385 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9386 (properties `((upstream-name . "BiocManager")))
9387 (build-system r-build-system)
9388 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9389 (synopsis "Access the Bioconductor project package repository")
9391 "This package provides a convenient tool to install and update
9392 Bioconductor packages.")
9393 (license license:artistic2.0)))
9395 (define-public r-rgl
9398 (version "0.100.50")
9402 (uri (cran-uri "rgl" version))
9405 "165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay"))))
9406 (build-system r-build-system)
9408 `(("pkg-config" ,pkg-config)))
9410 `(("freetype" ,freetype)
9414 ("ghc-pandoc" ,ghc-pandoc)
9417 `(("r-crosstalk" ,r-crosstalk)
9418 ("r-htmltools" ,r-htmltools)
9419 ("r-htmlwidgets" ,r-htmlwidgets)
9420 ("r-jsonlite" ,r-jsonlite)
9421 ("r-knitr" ,r-knitr)
9422 ("r-magrittr" ,r-magrittr)
9423 ("r-manipulatewidget" ,r-manipulatewidget)
9424 ("r-shiny" ,r-shiny)))
9425 (home-page "https://r-forge.r-project.org/projects/rgl/")
9426 (synopsis "3D visualization using OpenGL")
9428 "This package provides medium to high level functions for 3D interactive graphics,
9429 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9430 as functions for constructing representations of geometric
9431 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9432 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9433 image formats, including PNG, Postscript, SVG, PGF.")
9434 ;; Any version of the GPL.
9435 (license (list license:gpl2+ license:gpl3+))))
9437 (define-public r-multicool
9439 (name "r-multicool")
9444 (uri (cran-uri "multicool" version))
9447 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9448 (build-system r-build-system)
9449 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9450 (home-page "https://cran.r-project.org/web/packages/multicool/")
9451 (synopsis "Permutations of multisets in cool-lex order")
9453 "This package provides a set of tools to permute multisets without loops
9454 or hash tables and to generate integer partitions. Cool-lex order is similar
9455 to colexicographical order.")
9456 (license license:gpl2)))
9458 (define-public r-misc3d
9465 (uri (cran-uri "misc3d" version))
9468 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9469 (build-system r-build-system)
9470 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9471 (synopsis "Miscellaneous 3D Plots")
9473 "This package provides a collection of miscellaneous 3d plots, including
9475 ;; Any version of the GPL.
9476 (license (list license:gpl2+ license:gpl3+))))
9485 (uri (cran-uri "ks" version))
9487 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9488 (build-system r-build-system)
9491 ("r-kernlab" ,r-kernlab)
9492 ("r-kernsmooth" ,r-kernsmooth)
9493 ("r-matrix" ,r-matrix)
9494 ("r-mclust" ,r-mclust)
9496 ("r-multicool" ,r-multicool)
9497 ("r-mvtnorm" ,r-mvtnorm)))
9498 (home-page "http://www.mvstat.net/tduong/")
9499 (synopsis "Kernel smoothing")
9501 "This package provides kernel smoothers for univariate and multivariate
9502 data, including density functions, density derivatives, cumulative
9503 distributions, modal clustering, discriminant analysis, and two-sample
9504 hypothesis testing.")
9505 ;; Either version of the GPL.
9506 (license (list license:gpl2 license:gpl3))))
9508 (define-public r-feature
9515 (uri (cran-uri "feature" version))
9518 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9519 (build-system r-build-system)
9522 ("r-misc3d" ,r-misc3d)
9524 (home-page "http://www.mvstat.net/tduong/")
9525 (synopsis "Inferential feature significance for kernel density estimation")
9527 "The feature package contains functions to display and compute kernel
9528 density estimates, significant gradient and significant curvature regions.
9529 Significant gradient and/or curvature regions often correspond to significant
9530 features (e.g. local modes).")
9531 ;; Either version of the GPL.
9532 (license (list license:gpl2 license:gpl3))))
9534 (define-public r-arm
9541 (uri (cran-uri "arm" version))
9544 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9545 (build-system r-build-system)
9547 `(("r-abind" ,r-abind)
9551 ("r-matrix" ,r-matrix)
9552 ("r-nlme" ,r-nlme)))
9553 (home-page "https://cran.r-project.org/web/packages/arm/")
9554 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9556 "This package provides functions to accompany A. Gelman and J. Hill,
9557 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9558 University Press, 2007.")
9559 (license license:gpl3+)))
9561 (define-public r-circular
9568 (uri (cran-uri "circular" version))
9571 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9572 (build-system r-build-system)
9574 `(("r-boot" ,r-boot)
9575 ("r-mvtnorm" ,r-mvtnorm)))
9577 `(("gfortran" ,gfortran)))
9578 (home-page "https://cran.r-project.org/web/packages/circular/")
9579 (synopsis "Circular statistics")
9581 "This package provides tools for circular statistics, from \"Topics in
9582 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9584 (license license:gpl2+)))
9586 (define-public r-activity
9593 (uri (cran-uri "activity" version))
9596 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9597 (build-system r-build-system)
9599 `(("r-circular" ,r-circular)
9600 ("r-insol" ,r-insol)
9601 ("r-pbapply" ,r-pbapply)))
9602 (home-page "https://cran.r-project.org/web/packages/activity/")
9603 (synopsis "Animal activity statistics")
9605 "This package provides functions to fit kernel density functions to
9606 animal activity time data; plot activity distributions; quantify overall
9607 levels of activity; statistically compare activity metrics through
9608 bootstrapping; and evaluate variation in linear variables with time (or other
9609 circular variables).")
9610 (license license:gpl3)))
9612 (define-public r-ouch
9619 (uri (cran-uri "ouch" version))
9622 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9623 (build-system r-build-system)
9624 (propagated-inputs `(("r-subplex" ,r-subplex)))
9625 (home-page "https://kingaa.github.io/ouch/")
9626 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9628 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9629 for evolution along a phylogenetic tree.")
9630 (license license:gpl2+)))
9632 (define-public r-fmsb
9639 (uri (cran-uri "fmsb" version))
9642 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9643 (build-system r-build-system)
9644 (home-page "http://minato.sip21c.org/msb/")
9645 (synopsis "Functions for medical statistics book with demographic data")
9647 "This package provides several utility functions for the book entitled
9648 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9649 Japan, 2007) with Japanese demographic data and some demographic analysis
9650 related functions.")
9651 (license license:gpl2+)))
9653 (define-public r-stabledist
9655 (name "r-stabledist")
9660 (uri (cran-uri "stabledist" version))
9663 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9664 (build-system r-build-system)
9665 (home-page "https://www.rmetrics.org")
9666 (synopsis "Stable distribution functions")
9668 "This package provides density, probability and quantile functions, and
9669 random number generation for (skew) stable distributions, using the
9670 parametrizations of Nolan.")
9671 (license license:gpl2+)))
9673 (define-public r-gsl
9680 (uri (cran-uri "gsl" version))
9683 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9684 (build-system r-build-system)
9687 (home-page "https://cran.r-project.org/web/packages/gsl")
9688 (synopsis "Wrapper for the GNU Scientific Library")
9690 "This package provides an R wrapper for the special functions and quasi
9691 random number generators of the GNU Scientific Library.")
9692 (license license:gpl2+)))
9694 (define-public r-adgoftest
9696 (name "r-adgoftest")
9701 (uri (cran-uri "ADGofTest" version))
9704 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9705 (properties `((upstream-name . "ADGofTest")))
9706 (build-system r-build-system)
9707 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9708 (synopsis "Anderson-Darling GoF test")
9710 "This package provides an implementation of the Anderson-Darling GoF test
9711 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9712 Anderson-Darling Distribution\".")
9713 ;; Any version of the GPL.
9714 (license license:gpl3+)))
9716 (define-public r-softimpute
9718 (name "r-softimpute")
9723 (uri (cran-uri "softImpute" version))
9726 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9727 (properties `((upstream-name . "softImpute")))
9728 (build-system r-build-system)
9730 `(("r-matrix" ,r-matrix)))
9732 `(("gfortran" ,gfortran)))
9733 (home-page "https://cran.r-project.org/web/packages/softImpute")
9734 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9736 "This package provides iterative methods for matrix completion that use
9737 nuclear-norm regularization. The package includes procedures for centering
9738 and scaling rows, columns or both, and for computing low-rank @dfn{single
9739 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9741 (license license:gpl2)))
9743 (define-public r-fftwtools
9745 (name "r-fftwtools")
9750 (uri (cran-uri "fftwtools" version))
9753 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9754 (build-system r-build-system)
9755 (inputs `(("fftw" ,fftw)))
9756 (home-page "https://github.com/krahim/fftwtools")
9757 (synopsis "Wrapper for FFTW3")
9759 "This package provides a wrapper for several FFTW functions. It provides
9760 access to the two-dimensional FFT, the multivariate FFT, and the
9761 one-dimensional real to complex FFT using the FFTW3 library. The package
9762 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9763 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9764 The FFT functions have a parameter that allows them to not return the
9765 redundant complex conjugate when the input is real data.")
9766 (license license:gpl2+)))
9768 (define-public r-tiff
9775 (uri (cran-uri "tiff" version))
9778 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9779 (build-system r-build-system)
9781 `(("libtiff" ,libtiff)
9782 ("libjpeg" ,libjpeg-turbo)
9784 (home-page "https://www.rforge.net/tiff/")
9785 (synopsis "Read and write TIFF images")
9787 "This package provides an easy and simple way to read, write and display
9788 bitmap images stored in the TIFF format. It can read and write both files and
9789 in-memory raw vectors.")
9790 ;; Either of these two license versions.
9791 (license (list license:gpl2 license:gpl3))))
9793 (define-public r-nlp
9800 (uri (cran-uri "NLP" version))
9803 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9804 (properties `((upstream-name . "NLP")))
9805 (build-system r-build-system)
9806 (home-page "https://cran.r-project.org/web/packages/NLP/")
9807 (synopsis "Natural language processing infrastructure")
9809 "This package provides basic classes and methods for Natural Language
9811 (license license:gpl3)))
9820 (uri (cran-uri "tm" version))
9823 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9824 (properties `((upstream-name . "tm")))
9825 (build-system r-build-system)
9831 ("r-xml2" ,r-xml2)))
9832 (home-page "http://tm.r-forge.r-project.org/")
9833 (synopsis "Text mining package")
9835 "This package provides a framework for text mining applications within R.")
9836 (license license:gpl3)))
9838 (define-public r-waveslim
9845 (uri (cran-uri "waveslim" version))
9848 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
9849 (build-system r-build-system)
9851 `(("gfortran" ,gfortran)))
9852 (home-page "http://waveslim.blogspot.com")
9853 (synopsis "Basic wavelet routines for signal processing")
9855 "This package provides basic wavelet routines for time series (1D),
9856 image (2D) and array (3D) analysis. The code provided here is based on
9857 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9858 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9859 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9860 pairs (Selesnick 2001, 2002).")
9861 (license license:bsd-3)))
9863 (define-public r-wordcloud
9865 (name "r-wordcloud")
9870 (uri (cran-uri "wordcloud" version))
9873 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9874 (build-system r-build-system)
9876 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9878 ;; The "tm" package is only "suggested" according to CRAN, but the
9879 ;; wordcloud package cannot be loaded without it.
9881 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9882 (synopsis "Word clouds")
9884 "This package provides functionality to create pretty word clouds,
9885 visualize differences and similarity between documents, and avoid
9886 over-plotting in scatter plots with text.")
9887 (license license:lgpl2.1)))
9889 (define-public r-colorramps
9891 (name "r-colorramps")
9896 (uri (cran-uri "colorRamps" version))
9899 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9900 (properties `((upstream-name . "colorRamps")))
9901 (build-system r-build-system)
9902 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9903 (synopsis "Build color tables")
9904 (description "This package provides features to build gradient color
9906 ;; Any version of the GPL
9907 (license license:gpl3+)))
9909 (define-public r-tidytree
9916 (uri (cran-uri "tidytree" version))
9918 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
9919 (build-system r-build-system)
9922 ("r-dplyr" ,r-dplyr)
9923 ("r-lazyeval" ,r-lazyeval)
9924 ("r-magrittr" ,r-magrittr)
9925 ("r-rlang" ,r-rlang)
9926 ("r-tibble" ,r-tibble)))
9928 `(("r-knitr" ,r-knitr)))
9929 (home-page "https://github.com/GuangchuangYu/tidytree")
9930 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9932 "Phylogenetic trees generally contain multiple components including nodes,
9933 edges, branches and associated data. This package provides an approach to
9934 convert tree objects to tidy data frames. It also provides tidy interfaces to
9935 manipulate tree data.")
9936 (license license:artistic2.0)))
9938 (define-public r-rvcheck
9945 (uri (cran-uri "rvcheck" version))
9947 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
9948 (build-system r-build-system)
9950 `(("r-biocmanager" ,r-biocmanager)
9951 ("r-rlang" ,r-rlang)))
9952 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9953 (synopsis "R package version check")
9955 "This package provides tools to check the latest release version of R and
9956 R packages (on CRAN, Bioconductor or Github).")
9957 (license license:artistic2.0)))
9959 (define-public r-docopt
9966 (uri (cran-uri "docopt" version))
9969 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9970 (build-system r-build-system)
9971 (home-page "https://github.com/docopt/docopt.R")
9972 (synopsis "Command-line interface specification language")
9974 "This package enables you to define a command-line interface by just
9975 giving it a description in the specific format.")
9976 (license license:expat)))
9978 (define-public r-sparsesvd
9980 (name "r-sparsesvd")
9985 (uri (cran-uri "sparsesvd" version))
9988 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9989 (build-system r-build-system)
9990 (propagated-inputs `(("r-matrix" ,r-matrix)))
9991 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9992 (synopsis "Sparse truncated singular value decomposition")
9994 "This package provides a Wrapper around the SVDLIBC library
9995 for (truncated) singular value decomposition of a sparse matrix. Currently,
9996 only sparse real matrices in Matrix package format are supported.")
9997 ;; SVDLIBC is released under BSD-2. The R interface is released under
9999 (license (list license:bsd-3 license:bsd-2))))
10001 (define-public r-speedglm
10003 (name "r-speedglm")
10008 (uri (cran-uri "speedglm" version))
10011 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10012 (build-system r-build-system)
10014 `(("r-mass" ,r-mass)
10015 ("r-matrix" ,r-matrix)))
10016 (home-page "https://cran.r-project.org/web/packages/speedglm")
10017 (synopsis "Fit linear and generalized linear models to large data sets")
10019 "This package provides tools for fitting linear models and generalized
10020 linear models to large data sets by updating algorithms.")
10021 ;; Any version of the GPL
10022 (license license:gpl2+)))
10024 (define-public r-densityclust
10026 (name "r-densityclust")
10031 (uri (cran-uri "densityClust" version))
10034 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10035 (properties `((upstream-name . "densityClust")))
10036 (build-system r-build-system)
10039 ("r-ggplot2" ,r-ggplot2)
10040 ("r-ggrepel" ,r-ggrepel)
10041 ("r-gridextra" ,r-gridextra)
10042 ("r-rcolorbrewer" ,r-rcolorbrewer)
10044 ("r-rtsne" ,r-rtsne)))
10045 (home-page "https://cran.r-project.org/web/packages/densityClust")
10046 (synopsis "Clustering by fast search and find of density peaks")
10048 "This package provides an improved implementation (based on k-nearest
10049 neighbors) of the density peak clustering algorithm, originally described by
10050 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10051 large datasets (> 100,000 samples) very efficiently.")
10052 (license license:gpl2+)))
10054 (define-public r-combinat
10056 (name "r-combinat")
10061 (uri (cran-uri "combinat" version))
10064 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10065 (build-system r-build-system)
10066 (home-page "https://cran.r-project.org/web/packages/combinat")
10067 (synopsis "Combinatorics utilities")
10068 (description "This package provides assorted routines for combinatorics.")
10069 (license license:gpl2)))
10071 (define-public r-qlcmatrix
10073 (name "r-qlcmatrix")
10078 (uri (cran-uri "qlcMatrix" version))
10081 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10082 (properties `((upstream-name . "qlcMatrix")))
10083 (build-system r-build-system)
10085 `(("r-docopt" ,r-docopt)
10086 ("r-matrix" ,r-matrix)
10088 ("r-sparsesvd" ,r-sparsesvd)))
10089 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10090 (synopsis "Sparse matrix functions for quantitative language comparison")
10092 "This package provides an extension of the functionality of the Matrix
10093 package for using sparse matrices. Some of the functions are very general,
10094 while other are highly specific for the special data format used for
10095 @dfn{quantitative language comparison} (QLC).")
10096 (license license:gpl3)))
10098 (define-public r-ddrtree
10105 (uri (cran-uri "DDRTree" version))
10108 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10109 (properties `((upstream-name . "DDRTree")))
10110 (build-system r-build-system)
10113 ("r-irlba" ,r-irlba)
10115 ("r-rcppeigen" ,r-rcppeigen)))
10116 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10117 (synopsis "Learning principal graphs with DDRTree")
10119 "This package provides an implementation of the framework of
10120 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10121 dimensional space while constructs a principal tree which passes through the
10122 middle of the data simultaneously. DDRTree shows superiority to
10123 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10124 intrinsic structure of single cell genomics data. In general, it could be
10125 used to reconstruct the temporal progression as well as the bifurcation
10126 structure of any data type.")
10127 (license license:asl2.0)))
10129 (define-public r-corpcor
10136 (uri (cran-uri "corpcor" version))
10139 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10140 (build-system r-build-system)
10141 (home-page "http://strimmerlab.org/software/corpcor/")
10142 (synopsis "Efficient estimation of covariance and (partial) correlation")
10144 "This package implements a James-Stein-type shrinkage estimator for the
10145 covariance matrix, with separate shrinkage for variances and correlations.
10146 Furthermore, functions are available for fast singular value decomposition,
10147 for computing the pseudoinverse, and for checking the rank and positive
10148 definiteness of a matrix.")
10149 (license license:gpl3+)))
10151 (define-public r-rspectra
10153 (name "r-rspectra")
10158 (uri (cran-uri "RSpectra" version))
10161 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10162 (properties `((upstream-name . "RSpectra")))
10163 (build-system r-build-system)
10165 `(("r-matrix" ,r-matrix)
10167 ("r-rcppeigen" ,r-rcppeigen)))
10168 (home-page "https://github.com/yixuan/RSpectra")
10169 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10171 "This package provides an R interface to the Spectra library for
10172 large-scale eigenvalue and SVD problems. It is typically used to compute a
10173 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10174 which is usually more efficient than @code{eigen()} if k << n.")
10176 (license license:mpl2.0)))
10178 (define-public r-vbsr
10185 (uri (cran-uri "vbsr" version))
10188 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10189 (build-system r-build-system)
10190 (home-page "https://cran.r-project.org/web/packages/vbsr")
10191 (synopsis "Variational Bayes spike regression regularized linear models")
10193 "This package provides an efficient algorithm for solving ultra-sparse
10194 regularized regression models using a variational Bayes algorithm with a spike
10195 prior. The algorithm is solved on a path, with coordinate updates, and is
10196 capable of generating very sparse models. Very general model
10197 diagnostics for controlling type-1 errors are also provided.")
10198 (license license:gpl2)))
10200 (define-public r-flare
10203 (version "1.6.0.2")
10207 (uri (cran-uri "flare" version))
10210 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10211 (build-system r-build-system)
10213 `(("r-igraph" ,r-igraph)
10214 ("r-lattice" ,r-lattice)
10216 ("r-matrix" ,r-matrix)))
10217 (home-page "https://cran.r-project.org/web/packages/flare")
10218 (synopsis "Family of Lasso regression implementations")
10220 "This package provides implementations of a family of Lasso variants
10221 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10222 high dimensional sparse linear models.")
10223 (license license:gpl2)))
10225 (define-public r-lassopv
10232 (uri (cran-uri "lassopv" version))
10235 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10236 (build-system r-build-system)
10237 (propagated-inputs `(("r-lars" ,r-lars)))
10238 (home-page "https://github.com/lingfeiwang/lassopv")
10239 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10241 "This package enables you to estimate the p-values for predictors x
10242 against target variable y in Lasso regression, using the regularization
10243 strength when each predictor enters the active set of regularization path for
10244 the first time as the statistic.")
10245 (license license:gpl3)))
10247 (define-public r-splitstackshape
10249 (name "r-splitstackshape")
10254 (uri (cran-uri "splitstackshape" version))
10257 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10258 (build-system r-build-system)
10260 `(("r-data-table" ,r-data-table)))
10261 (home-page "https://github.com/mrdwab/splitstackshape")
10262 (synopsis "Stack and reshape datasets after splitting concatenated values")
10264 "Online data collection tools like Google Forms often export
10265 multiple-response questions with data concatenated in cells. The
10266 @code{concat.split} (cSplit) family of functions provided by this package
10267 splits such data into separate cells. This package also includes functions to
10268 stack groups of columns and to reshape wide data, even when the data are
10269 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10270 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10272 (license license:gpl3)))
10274 (define-public r-tfmpvalue
10276 (name "r-tfmpvalue")
10281 (uri (cran-uri "TFMPvalue" version))
10284 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10285 (properties `((upstream-name . "TFMPvalue")))
10286 (build-system r-build-system)
10287 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10288 (home-page "https://github.com/ge11232002/TFMPvalue")
10289 (synopsis "P-value computation for position weight matrices")
10291 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10292 identification from sequence/alignments, we are interested in the significance
10293 of certain match scores. TFMPvalue provides the accurate calculation of a
10294 p-value with a score threshold for position weight matrices, or the score with
10295 a given p-value. It is an interface to code originally made available by
10296 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10297 Touzet and Varre (2007).")
10298 (license license:gpl2)))
10300 (define-public r-rnifti
10307 (uri (cran-uri "RNifti" version))
10310 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10311 (properties `((upstream-name . "RNifti")))
10312 (build-system r-build-system)
10313 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10314 (home-page "https://github.com/jonclayden/RNifti")
10315 (synopsis "Fast R and C++ access to NIfTI images")
10317 "This package provides very fast read and write access to images stored
10318 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10319 compiled C and interpreted R code. It also provides a C/C++ API that can be
10320 used by other packages.")
10321 (license license:gpl2)))
10323 (define-public r-shades
10330 (uri (cran-uri "shades" version))
10333 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10334 (build-system r-build-system)
10335 (home-page "https://github.com/jonclayden/shades")
10336 (synopsis "Simple color manipulation")
10338 "This package provides functions for easily manipulating colors,
10339 creating color scales and calculating color distances.")
10340 (license license:bsd-3)))
10342 (define-public r-ore
10349 (uri (cran-uri "ore" version))
10351 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10352 (build-system r-build-system)
10353 (home-page "https://github.com/jonclayden/ore")
10354 (synopsis "R interface to the Onigmo regular expression library")
10356 "This package provides an alternative to R's built-in functionality for
10357 handling regular expressions, based on the Onigmo library. It offers
10358 first-class compiled regex objects, partial matching and function-based
10359 substitutions, amongst other features.")
10360 (license license:bsd-3)))
10362 (define-public r-reportr
10369 (uri (cran-uri "reportr" version))
10372 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10373 (build-system r-build-system)
10374 (propagated-inputs `(("r-ore" ,r-ore)))
10375 (home-page "https://github.com/jonclayden/reportr")
10376 (synopsis "General message and error reporting system")
10378 "This package provides a system for reporting messages, which offers
10379 certain useful features over the standard R system, such as the incorporation
10380 of output consolidation, message filtering, assertions, expression
10381 substitution, automatic generation of stack traces for debugging, and
10382 conditional reporting based on the current \"output level\".")
10383 (license license:gpl2)))
10385 (define-public r-tractor-base
10387 (name "r-tractor-base")
10392 (uri (cran-uri "tractor.base" version))
10395 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10396 (properties `((upstream-name . "tractor.base")))
10397 (build-system r-build-system)
10400 ("r-reportr" ,r-reportr)
10401 ("r-rnifti" ,r-rnifti)
10402 ("r-shades" ,r-shades)))
10403 (home-page "https://www.tractor-mri.org.uk")
10404 (synopsis "Read, manipulate and visualize magnetic resonance images")
10406 "This package provides functions for working with magnetic resonance
10407 images. It supports reading and writing of popular file formats (DICOM,
10408 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10409 visualization; flexible image manipulation; metadata and sparse image
10411 (license license:gpl2)))
10413 (define-public r-grimport
10415 (name "r-grimport")
10420 (uri (cran-uri "grImport" version))
10423 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10424 (properties `((upstream-name . "grImport")))
10425 (build-system r-build-system)
10427 `(("ghostscript" ,ghostscript)))
10429 `(("r-xml" ,r-xml)))
10430 (home-page "https://cran.r-project.org/web/packages/grImport")
10431 (synopsis "Convert, import, and draw PostScript pictures")
10433 "This package provides functions for converting, importing, and drawing
10434 PostScript pictures in R plots.")
10435 (license license:gpl2+)))
10437 (define-public r-grimport2
10439 (name "r-grimport2")
10444 (uri (cran-uri "grImport2" version))
10447 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10448 (properties `((upstream-name . "grImport2")))
10449 (build-system r-build-system)
10451 `(("r-base64enc" ,r-base64enc)
10455 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10456 (synopsis "Import SVG graphics")
10458 "This package provides functions for importing external vector images and
10459 drawing them as part of R plots. This package is different from the
10460 @code{grImport} package because, where that package imports PostScript format
10461 images, this package imports SVG format images. Furthermore, this package
10462 imports a specific subset of SVG, so external images must be preprocessed
10463 using a package like @code{rsvg} to produce SVG that this package can import.
10464 SVG features that are not supported by R graphics, such as gradient fills, can
10465 be imported and then exported via the @code{gridSVG} package.")
10466 (license license:gpl2+)))
10468 (define-public r-kohonen
10475 (uri (cran-uri "kohonen" version))
10478 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10479 (build-system r-build-system)
10481 `(("r-rcpp" ,r-rcpp)))
10482 (home-page "https://cran.r-project.org/web/packages/kohonen")
10483 (synopsis "Supervised and unsupervised self-organising maps")
10485 "This package provides functions to train @dfn{self-organising
10486 maps} (SOMs). Also interrogation of the maps and prediction using trained
10487 maps are supported. The name of the package refers to Teuvo Kohonen, the
10488 inventor of the SOM.")
10489 (license license:gpl2+)))
10491 (define-public r-nnls
10498 (uri (cran-uri "nnls" version))
10501 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10502 (build-system r-build-system)
10503 (native-inputs `(("gfortran" ,gfortran)))
10504 (home-page "https://cran.r-project.org/web/packages/nnls")
10505 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10507 "This package provides an R interface to the Lawson-Hanson implementation
10508 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10509 the combination of non-negative and non-positive constraints.")
10510 (license license:gpl2+)))
10512 (define-public r-iso
10519 (uri (cran-uri "Iso" version))
10522 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10523 (properties `((upstream-name . "Iso")))
10524 (build-system r-build-system)
10525 (native-inputs `(("gfortran" ,gfortran)))
10526 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10527 (synopsis "Functions to perform isotonic regression")
10529 "This package provides support for linear order and unimodal
10530 order (univariate) isotonic regression and bivariate isotonic regression with
10531 linear order on both variables.")
10532 (license license:gpl2+)))
10534 (define-public r-chemometricswithr
10536 (name "r-chemometricswithr")
10541 (uri (cran-uri "ChemometricsWithR" version))
10544 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10546 `((upstream-name . "ChemometricsWithR")))
10547 (build-system r-build-system)
10549 `(("r-devtools" ,r-devtools)
10550 ("r-kohonen" ,r-kohonen)
10553 (home-page "https://github.com/rwehrens/CWR")
10554 (synopsis "Chemometrics with R")
10556 "This package provides functions and scripts used in the book
10557 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10558 Life Sciences\" by Ron Wehrens, Springer (2011).")
10559 (license license:gpl2+)))
10561 (define-public r-als
10568 (uri (cran-uri "ALS" version))
10571 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10572 (properties `((upstream-name . "ALS")))
10573 (build-system r-build-system)
10576 ("r-nnls" ,r-nnls)))
10577 (home-page "https://cran.r-project.org/web/packages/ALS")
10578 (synopsis "Multivariate curve resolution alternating least squares")
10580 "Alternating least squares is often used to resolve components
10581 contributing to data with a bilinear structure; the basic technique may be
10582 extended to alternating constrained least squares. This package provides an
10583 implementation of @dfn{multivariate curve resolution alternating least
10584 squares} (MCR-ALS).
10586 Commonly applied constraints include unimodality, non-negativity, and
10587 normalization of components. Several data matrices may be decomposed
10588 simultaneously by assuming that one of the two matrices in the bilinear
10589 decomposition is shared between datasets.")
10590 (license license:gpl2+)))
10592 (define-public r-strucchange
10594 (name "r-strucchange")
10599 (uri (cran-uri "strucchange" version))
10602 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10603 (build-system r-build-system)
10605 `(("r-sandwich" ,r-sandwich)
10607 (home-page "https://cran.r-project.org/web/packages/strucchange")
10608 (synopsis "Testing, monitoring, and dating structural changes")
10610 "This package provides tools for testing, monitoring and dating
10611 structural changes in (linear) regression models. It features tests/methods
10612 from the generalized fluctuation test framework as well as from the F
10613 test (Chow test) framework. This includes methods to fit, plot and test
10614 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10615 statistics, respectively. It is possible to monitor incoming data online
10616 using fluctuation processes. Finally, the breakpoints in regression models
10617 with structural changes can be estimated together with confidence intervals.
10618 Emphasis is always given to methods for visualizing the data.")
10619 ;; Either of these two GPL versions
10620 (license (list license:gpl2 license:gpl3))))
10622 (define-public r-pixmap
10629 (uri (cran-uri "pixmap" version))
10632 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10633 (build-system r-build-system)
10634 (home-page "https://cran.r-project.org/web/packages/pixmap")
10635 (synopsis "Tools for bitmap images")
10637 "This package provides functions for importing, exporting, plotting and
10638 other manipulations of bitmapped images.")
10639 (license license:gpl2)))
10641 (define-public r-rapidjsonr
10643 (name "r-rapidjsonr")
10648 (uri (cran-uri "rapidjsonr" version))
10651 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
10652 (build-system r-build-system)
10653 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10654 (synopsis "JSON parser")
10656 "This package provides JSON parsing capability through the Rapidjson
10658 (license license:expat)))
10660 (define-public r-ontologyindex
10662 (name "r-ontologyindex")
10667 (uri (cran-uri "ontologyIndex" version))
10670 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10671 (properties `((upstream-name . "ontologyIndex")))
10672 (build-system r-build-system)
10673 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10674 (synopsis "Functions for processing ontologies in R")
10676 "This package provides functions for reading ontologies into R as lists
10677 and manipulating sets of ontological terms.")
10678 (license license:gpl2+)))
10680 (define-public r-gargle
10687 (uri (cran-uri "gargle" version))
10690 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10691 (build-system r-build-system)
10696 ("r-jsonlite" ,r-jsonlite)
10697 ("r-rlang" ,r-rlang)
10698 ("r-withr" ,r-withr)))
10699 (home-page "https://gargle.r-lib.org")
10700 (synopsis "Utilities for working with Google APIs")
10702 "This package provides utilities for working with Google APIs. This
10703 includes functions and classes for handling common credential types and for
10704 preparing, executing, and processing HTTP requests.")
10705 (license license:expat)))
10707 (define-public r-bigrquery
10709 (name "r-bigrquery")
10714 (uri (cran-uri "bigrquery" version))
10717 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10718 (build-system r-build-system)
10720 `(("r-assertthat" ,r-assertthat)
10721 ("r-bit64" ,r-bit64)
10724 ("r-gargle" ,r-gargle)
10727 ("r-jsonlite" ,r-jsonlite)
10728 ("r-prettyunits" ,r-prettyunits)
10729 ("r-progress" ,r-progress)
10730 ("r-rapidjsonr" ,r-rapidjsonr)
10732 ("r-rlang" ,r-rlang)
10733 ("r-tibble" ,r-tibble)))
10734 (home-page "https://github.com/rstats-db/bigrquery")
10735 (synopsis "R interface to Google's BigQuery API")
10737 "This package provides an R interface to Google's BigQuery database.")
10738 (license license:gpl3)))
10740 (define-public r-gmp
10743 (version "0.5-13.6")
10747 (uri (cran-uri "gmp" version))
10750 "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
10751 (build-system r-build-system)
10754 (modify-phases %standard-phases
10755 (add-after 'unpack 'set-CC
10756 (lambda _ (setenv "CC" "gcc") #t)))))
10757 (inputs `(("gmp" ,gmp)))
10758 (home-page "https://cran.r-project.org/web/packages/gmp")
10759 (synopsis "Multiple precision arithmetic")
10761 "This package supports multiple precision arithmetic (big integers and
10762 rationals, prime number tests, matrix computation), \"arithmetic without
10763 limitations\" using the GNU Multiple Precision library.")
10764 ;; Any version of the GPL.
10765 (license license:gpl3+)))
10767 (define-public r-rmpfr
10774 (uri (cran-uri "Rmpfr" version))
10777 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
10778 (properties `((upstream-name . "Rmpfr")))
10779 (build-system r-build-system)
10784 `(("r-gmp" ,r-gmp)))
10786 `(("pkg-config" ,pkg-config)))
10787 (home-page "http://rmpfr.r-forge.r-project.org/")
10788 (synopsis "R bindings to the MPFR library")
10790 "This package supports arithmetic (via S4 classes and methods) for
10791 arbitrary precision floating point numbers, including transcendental
10792 functions. To this end, the package interfaces with the @dfn{Multiple
10793 Precision Floating-Point Reliable} (MPFR) library.")
10794 (license license:gpl2+)))
10796 (define-public r-assertive-base
10798 (name "r-assertive-base")
10803 (uri (cran-uri "assertive.base" version))
10806 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10808 `((upstream-name . "assertive.base")))
10809 (build-system r-build-system)
10810 (home-page "https://bitbucket.org/richierocks/assertive.base")
10811 (synopsis "Core of the assertive package")
10813 "This package provides a minimal set of predicates and assertions used by
10814 the assertive package. This is mainly for use by other package developers who
10815 want to include run-time testing features in their own packages.")
10816 (license license:gpl3+)))
10818 (define-public r-assertive-properties
10820 (name "r-assertive-properties")
10825 (uri (cran-uri "assertive.properties" version))
10828 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10830 `((upstream-name . "assertive.properties")))
10831 (build-system r-build-system)
10833 `(("r-assertive-base" ,r-assertive-base)))
10834 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10835 (synopsis "Assertions to check properties of variables")
10837 "This package provides a set of predicates and assertions for checking
10838 the properties of variables, such as length, names and attributes. This is
10839 mainly for use by other package developers who want to include run-time
10840 testing features in their own packages.")
10841 (license license:gpl3+)))
10843 (define-public r-assertive-numbers
10845 (name "r-assertive-numbers")
10850 (uri (cran-uri "assertive.numbers" version))
10853 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10855 `((upstream-name . "assertive.numbers")))
10856 (build-system r-build-system)
10858 `(("r-assertive-base" ,r-assertive-base)))
10859 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10860 (synopsis "Assertions to check properties of numbers")
10862 "This package provides a set of predicates and assertions for checking
10863 the properties of numbers. This is mainly for use by other package developers
10864 who want to include run-time testing features in their own packages.")
10865 (license license:gpl3+)))
10867 (define-public r-assertive-sets
10869 (name "r-assertive-sets")
10874 (uri (cran-uri "assertive.sets" version))
10877 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10879 `((upstream-name . "assertive.sets")))
10880 (build-system r-build-system)
10882 `(("r-assertive-base" ,r-assertive-base)))
10883 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10884 (synopsis "Assertions to check properties of sets")
10886 "This package provides a set of predicates and assertions for checking
10887 the properties of sets. This is mainly for use by other package developers
10888 who want to include run-time testing features in their own packages.")
10889 (license license:gpl3+)))
10891 (define-public r-assertive-matrices
10893 (name "r-assertive-matrices")
10898 (uri (cran-uri "assertive.matrices" version))
10901 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10903 `((upstream-name . "assertive.matrices")))
10904 (build-system r-build-system)
10906 `(("r-assertive-base" ,r-assertive-base)))
10907 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10908 (synopsis "Assertions to check properties of matrices")
10910 "This package provides a set of predicates and assertions for checking
10911 the properties of matrices. This is mainly for use by other package
10912 developers who want to include run-time testing features in their own
10914 (license license:gpl3+)))
10916 (define-public r-assertive-models
10918 (name "r-assertive-models")
10923 (uri (cran-uri "assertive.models" version))
10926 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10928 `((upstream-name . "assertive.models")))
10929 (build-system r-build-system)
10931 `(("r-assertive-base" ,r-assertive-base)))
10932 (home-page "https://bitbucket.org/richierocks/assertive.models")
10933 (synopsis "Assertions to check properties of models")
10935 "This package provides a set of predicates and assertions for checking
10936 the properties of models. This is mainly for use by other package developers
10937 who want to include run-time testing features in their own packages.")
10938 (license license:gpl3+)))
10940 (define-public r-assertive-reflection
10942 (name "r-assertive-reflection")
10947 (uri (cran-uri "assertive.reflection" version))
10950 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10952 `((upstream-name . "assertive.reflection")))
10953 (build-system r-build-system)
10955 `(("r-assertive-base" ,r-assertive-base)))
10956 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10957 (synopsis "Assertions for checking the state of R")
10959 "This package provides a set of predicates and assertions for checking
10960 the state and capabilities of R, the operating system it is running on, and
10961 the IDE being used. This is mainly for use by other package developers who
10962 want to include run-time testing features in their own packages.")
10963 (license license:gpl3+)))
10965 (define-public r-assertive-types
10967 (name "r-assertive-types")
10972 (uri (cran-uri "assertive.types" version))
10975 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10977 `((upstream-name . "assertive.types")))
10978 (build-system r-build-system)
10980 `(("r-assertive-base" ,r-assertive-base)
10981 ("r-assertive-properties" ,r-assertive-properties)
10982 ("r-codetools" ,r-codetools)))
10983 (home-page "https://bitbucket.org/richierocks/assertive.types")
10984 (synopsis "Assertions to check types of variables")
10986 "This package provides a set of predicates and assertions for checking
10987 the types of variables. This is mainly for use by other package developers
10988 who want to include run-time testing features in their own packages.")
10989 (license license:gpl3+)))
10991 (define-public r-assertive-files
10993 (name "r-assertive-files")
10998 (uri (cran-uri "assertive.files" version))
11001 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11003 `((upstream-name . "assertive.files")))
11004 (build-system r-build-system)
11006 `(("r-assertive-base" ,r-assertive-base)
11007 ("r-assertive-numbers" ,r-assertive-numbers)))
11008 (home-page "https://bitbucket.org/richierocks/assertive.files")
11009 (synopsis "Assertions to check properties of files")
11011 "This package provides a set of predicates and assertions for checking
11012 the properties of files and connections. This is mainly for use by other
11013 package developers who want to include run-time testing features in their own
11015 (license license:gpl3+)))
11017 (define-public r-assertive-code
11019 (name "r-assertive-code")
11024 (uri (cran-uri "assertive.code" version))
11027 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11029 `((upstream-name . "assertive.code")))
11030 (build-system r-build-system)
11032 `(("r-assertive-base" ,r-assertive-base)
11033 ("r-assertive-properties" ,r-assertive-properties)
11034 ("r-assertive-types" ,r-assertive-types)))
11035 (home-page "https://bitbucket.org/richierocks/assertive.code")
11036 (synopsis "Assertions to check properties of code")
11038 "This package provides a set of predicates and assertions for checking
11039 the properties of code. This is mainly for use by other package developers
11040 who want to include run-time testing features in their own packages.")
11041 (license license:gpl3+)))
11043 (define-public r-assertive-datetimes
11045 (name "r-assertive-datetimes")
11050 (uri (cran-uri "assertive.datetimes" version))
11053 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11055 `((upstream-name . "assertive.datetimes")))
11056 (build-system r-build-system)
11058 `(("r-assertive-base" ,r-assertive-base)
11059 ("r-assertive-types" ,r-assertive-types)))
11060 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11061 (synopsis "Assertions to check properties of dates and times")
11063 "This package provides a set of predicates and assertions for checking
11064 the properties of dates and times. This is mainly for use by other package
11065 developers who want to include run-time testing features in their own
11067 (license license:gpl3+)))
11069 (define-public r-assertive-strings
11071 (name "r-assertive-strings")
11076 (uri (cran-uri "assertive.strings" version))
11079 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11081 `((upstream-name . "assertive.strings")))
11082 (build-system r-build-system)
11084 `(("r-assertive-base" ,r-assertive-base)
11085 ("r-assertive-types" ,r-assertive-types)
11086 ("r-stringi" ,r-stringi)))
11087 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11088 (synopsis "Assertions to check properties of strings")
11090 "This package provides a set of predicates and assertions for checking
11091 the properties of strings. This is mainly for use by other package developers
11092 who want to include run-time testing features in their own packages.")
11093 (license license:gpl3+)))
11095 (define-public r-assertive-data-us
11097 (name "r-assertive-data-us")
11102 (uri (cran-uri "assertive.data.us" version))
11105 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11107 `((upstream-name . "assertive.data.us")))
11108 (build-system r-build-system)
11110 `(("r-assertive-base" ,r-assertive-base)
11111 ("r-assertive-strings" ,r-assertive-strings)))
11112 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11113 (synopsis "Assertions to check properties of strings")
11115 "This package provides a set of predicates and assertions for checking
11116 the properties of US-specific complex data types. This is mainly for use by
11117 other package developers who want to include run-time testing features in
11118 their own packages.")
11119 (license license:gpl3+)))
11121 (define-public r-assertive-data-uk
11123 (name "r-assertive-data-uk")
11128 (uri (cran-uri "assertive.data.uk" version))
11131 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11133 `((upstream-name . "assertive.data.uk")))
11134 (build-system r-build-system)
11136 `(("r-assertive-base" ,r-assertive-base)
11137 ("r-assertive-strings" ,r-assertive-strings)))
11138 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11139 (synopsis "Assertions to check properties of strings")
11141 "This package provides a set of predicates and assertions for checking
11142 the properties of UK-specific complex data types. This is mainly for use by
11143 other package developers who want to include run-time testing features in
11144 their own packages.")
11145 (license license:gpl3+)))
11147 (define-public r-assertive-data
11149 (name "r-assertive-data")
11154 (uri (cran-uri "assertive.data" version))
11157 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11159 `((upstream-name . "assertive.data")))
11160 (build-system r-build-system)
11162 `(("r-assertive-base" ,r-assertive-base)
11163 ("r-assertive-strings" ,r-assertive-strings)))
11164 (home-page "https://bitbucket.org/richierocks/assertive.data")
11165 (synopsis "Assertions to check properties of data")
11167 "This package provides a set of predicates and assertions for checking
11168 the properties of (country independent) complex data types. This is mainly
11169 for use by other package developers who want to include run-time testing
11170 features in their own packages.")
11171 (license license:gpl3+)))
11173 (define-public r-assertive
11175 (name "r-assertive")
11180 (uri (cran-uri "assertive" version))
11183 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11184 (build-system r-build-system)
11186 `(("r-assertive-base" ,r-assertive-base)
11187 ("r-assertive-code" ,r-assertive-code)
11188 ("r-assertive-data" ,r-assertive-data)
11189 ("r-assertive-data-uk" ,r-assertive-data-uk)
11190 ("r-assertive-data-us" ,r-assertive-data-us)
11191 ("r-assertive-datetimes" ,r-assertive-datetimes)
11192 ("r-assertive-files" ,r-assertive-files)
11193 ("r-assertive-matrices" ,r-assertive-matrices)
11194 ("r-assertive-models" ,r-assertive-models)
11195 ("r-assertive-numbers" ,r-assertive-numbers)
11196 ("r-assertive-properties" ,r-assertive-properties)
11197 ("r-assertive-reflection" ,r-assertive-reflection)
11198 ("r-assertive-sets" ,r-assertive-sets)
11199 ("r-assertive-strings" ,r-assertive-strings)
11200 ("r-assertive-types" ,r-assertive-types)
11201 ("r-knitr" ,r-knitr)))
11202 (home-page "https://bitbucket.org/richierocks/assertive")
11203 (synopsis "Readable check functions to ensure code integrity")
11205 "This package provides lots of predicates (@code{is_*} functions) to
11206 check the state of your variables, and assertions (@code{assert_*} functions)
11207 to throw errors if they aren't in the right form.")
11208 (license license:gpl3+)))
11210 (define-public r-dotcall64
11212 (name "r-dotcall64")
11217 (uri (cran-uri "dotCall64" version))
11220 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11221 (properties `((upstream-name . "dotCall64")))
11222 (build-system r-build-system)
11223 (native-inputs `(("gfortran" ,gfortran)))
11224 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11225 (synopsis "Enhanced foreign function interface supporting long vectors")
11227 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11228 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11229 supports long vectors, arguments of type 64-bit integer, and provides a
11230 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11231 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11232 (license license:gpl2+)))
11234 (define-public r-spam
11241 (uri (cran-uri "spam" version))
11243 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11244 (build-system r-build-system)
11246 `(("r-dotcall64" ,r-dotcall64)))
11247 (native-inputs `(("gfortran" ,gfortran)))
11248 (home-page "https://www.math.uzh.ch/pages/spam/")
11249 (synopsis "Sparse matrix algebra")
11251 "This package provides a set of functions for sparse matrix algebra.
11252 Differences with other sparse matrix packages are:
11255 @item it only supports (essentially) one sparse matrix format;
11256 @item it is based on transparent and simple structure(s);
11257 @item it is tailored for MCMC calculations within G(M)RF;
11258 @item and it is fast and scalable (with the extension package @code{spam64}).
11260 ;; Either of these licenses
11261 (license (list license:bsd-3 license:lgpl2.0))))
11263 (define-public r-fields
11270 (uri (cran-uri "fields" version))
11272 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11273 (build-system r-build-system)
11275 `(("r-maps" ,r-maps)
11276 ("r-spam" ,r-spam)))
11278 `(("gfortran" ,gfortran)))
11279 (home-page "https://www.image.ucar.edu/fields")
11280 (synopsis "Tools for spatial data")
11282 "This is a package for curve, surface and function fitting with an
11283 emphasis on splines, spatial data and spatial statistics. The major methods
11284 include cubic, and thin plate splines, Kriging, and compactly supported
11285 covariance functions for large data sets.")
11286 (license license:gpl2+)))
11288 (define-public r-spatialextremes
11290 (name "r-spatialextremes")
11295 (uri (cran-uri "SpatialExtremes" version))
11298 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11300 `((upstream-name . "SpatialExtremes")))
11301 (build-system r-build-system)
11303 `(("r-fields" ,r-fields)
11304 ("r-maps" ,r-maps)))
11305 (home-page "http://spatialextremes.r-forge.r-project.org/")
11306 (synopsis "Modelling spatial extremes")
11308 "This package provides tools for the statistical modelling of spatial
11309 extremes using max-stable processes, copula or Bayesian hierarchical models.
11310 More precisely, this package allows (conditional) simulations from various
11311 parametric max-stable models, analysis of the extremal spatial dependence, the
11312 fitting of such processes using composite likelihoods or least square (simple
11313 max-stable processes only), model checking and selection and prediction.")
11314 (license license:gpl2+)))
11316 (define-public r-drc
11323 (uri (cran-uri "drc" version))
11326 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11327 (build-system r-build-system)
11330 ("r-gtools" ,r-gtools)
11332 ("r-multcomp" ,r-multcomp)
11333 ("r-plotrix" ,r-plotrix)
11334 ("r-scales" ,r-scales)))
11335 (home-page "https://cran.r-project.org/web/packages/drc")
11336 (synopsis "Analysis of dose-response curves")
11338 "This package provides a suite of flexible and versatile model fitting
11339 and after-fitting functions for the analysis of dose-response data.")
11340 (license license:gpl2+)))
11342 (define-public r-rmeta
11349 (uri (cran-uri "rmeta" version))
11352 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11353 (build-system r-build-system)
11354 (home-page "https://cran.r-project.org/web/packages/rmeta")
11355 (synopsis "Tools for meta-analysis")
11357 "This package provides functions for simple fixed and random effects
11358 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11359 draws standard summary plots, funnel plots, and computes summaries and tests
11360 for association and heterogeneity.")
11361 (license license:gpl2)))
11363 (define-public r-bootstrap
11365 (name "r-bootstrap")
11370 (uri (cran-uri "bootstrap" version))
11373 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11374 (build-system r-build-system)
11375 (native-inputs `(("gfortran" ,gfortran)))
11376 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11377 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11379 "This package provides software and data for the book \"An Introduction
11380 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11381 This package is primarily provided for projects already based on it, and for
11382 support of the book. New projects should preferentially use the recommended
11383 package \"boot\".")
11384 (license license:bsd-3)))
11386 (define-public r-survivalroc
11388 (name "r-survivalroc")
11393 (uri (cran-uri "survivalROC" version))
11396 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11397 (properties `((upstream-name . "survivalROC")))
11398 (build-system r-build-system)
11399 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11400 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11402 "Compute time-dependent ROC curve from censored survival data using
11403 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11404 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11405 (license license:gpl2+)))
11407 (define-public r-longitudinal
11409 (name "r-longitudinal")
11414 (uri (cran-uri "longitudinal" version))
11417 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11418 (build-system r-build-system)
11419 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11420 (home-page "http://strimmerlab.org/software/longitudinal/")
11421 (synopsis "Analysis of multiple time course data")
11423 "This package contains general data structures and functions for
11424 longitudinal data with multiple variables, repeated measurements, and
11425 irregularly spaced time points. It also implements a shrinkage estimator of
11426 dynamical correlation and dynamical covariance.")
11427 (license license:gpl3+)))
11429 (define-public r-genenet
11436 (uri (cran-uri "GeneNet" version))
11439 "0cdhrj15rz0w0pyw3r8mikrzsdh95y5i1c0pa3cn0c2bjnjx3x3n"))))
11440 (properties `((upstream-name . "GeneNet")))
11441 (build-system r-build-system)
11443 `(("r-corpcor" ,r-corpcor)
11444 ("r-fdrtool" ,r-fdrtool)
11445 ("r-longitudinal" ,r-longitudinal)))
11446 (home-page "http://strimmerlab.org/software/genenet/")
11447 (synopsis "Modeling and inferring gene networks")
11449 "This package analyzes gene expression (time series) data with focus on
11450 the inference of gene networks. In particular, GeneNet implements the methods
11451 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11452 for learning large-scale gene association networks (including assignment of
11453 putative directions).")
11454 (license license:gpl3+)))
11456 (define-public r-rbamtools
11458 (name "r-rbamtools")
11459 (version "2.16.17")
11463 (uri (cran-uri "rbamtools" version))
11466 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11467 (build-system r-build-system)
11468 (inputs `(("zlib" ,zlib)))
11470 `(("r-refgenome" ,r-refgenome)))
11471 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11472 (synopsis "Read and write BAM (binary alignment) files")
11474 "This package provides an R interface to functions of the SAMtools
11476 (license license:artistic2.0)))
11478 (define-public r-protviz
11485 (uri (cran-uri "protViz" version))
11488 "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7"))))
11489 (properties `((upstream-name . "protViz")))
11490 (build-system r-build-system)
11491 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11492 (home-page "https://github.com/protViz/protViz/")
11493 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11495 "This package helps with quality checks, visualizations and analysis of
11496 mass spectrometry data, coming from proteomics experiments. The package is
11497 developed, tested and used at the Functional Genomics Center Zurich, where it
11498 is used mainly for prototyping, teaching, and having fun with proteomics data.
11499 But it can also be used to do data analysis for small scale data sets.")
11500 (license license:gpl3)))
11502 (define-public r-cmprsk
11509 (uri (cran-uri "cmprsk" version))
11511 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11512 (build-system r-build-system)
11514 `(("r-survival" ,r-survival)))
11516 `(("gfortran" ,gfortran)))
11517 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11518 (synopsis "Subdistribution analysis of competing risks")
11520 "This package provides tool for estimation, testing and regression
11521 modeling of subdistribution functions in competing risks, as described in
11522 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11523 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11524 A proportional hazards model for the subdistribution of a competing risk,
11525 JASA, 94:496-509.")
11526 (license license:gpl2+)))
11528 (define-public r-etm
11531 (version "1.0.5.1")
11535 (uri (cran-uri "etm" version))
11538 "0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7"))))
11539 (build-system r-build-system)
11541 `(("r-data-table" ,r-data-table)
11542 ("r-lattice" ,r-lattice)
11544 ("r-rcpparmadillo" ,r-rcpparmadillo)
11545 ("r-survival" ,r-survival)))
11546 (home-page "https://cran.r-project.org/web/packages/etm")
11547 (synopsis "Empirical transition matrix")
11549 "The @dfn{empirical transition matrix} (etm) package estimates
11550 the matrix of transition probabilities for any time-inhomogeneous multistate
11551 model with finite state space using the Aalen-Johansen estimator.")
11552 (license license:expat)))
11554 (define-public r-epi
11561 (uri (cran-uri "Epi" version))
11564 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11565 (properties `((upstream-name . "Epi")))
11566 (build-system r-build-system)
11568 `(("r-cmprsk" ,r-cmprsk)
11569 ("r-data-table" ,r-data-table)
11572 ("r-matrix" ,r-matrix)
11574 ("r-numderiv" ,r-numderiv)
11576 ("r-survival" ,r-survival)
11578 (home-page "https://BendixCarstensen.com/Epi/")
11579 (synopsis "Statistical analysis in epidemiology")
11581 "This package provides functions for demographic and epidemiological
11582 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11583 particular representation, manipulation and simulation of multistate data -
11584 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11585 @code{etm} and @code{cmprsk} packages. It also contains functions for
11586 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11587 data and some useful functions for tabulation and plotting, as well as a
11588 number of epidemiological data sets.")
11589 (license license:gpl2)))
11591 (define-public r-ppls
11594 (version "1.6-1.1")
11598 (uri (cran-uri "ppls" version))
11601 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11602 (build-system r-build-system)
11603 (propagated-inputs `(("r-mass" ,r-mass)))
11604 (home-page "https://cran.r-project.org/web/packages/ppls")
11605 (synopsis "Penalized partial least squares")
11607 "This package contains linear and nonlinear regression methods based on
11608 partial least squares and penalization techniques. Model parameters are
11609 selected via cross-validation, and confidence intervals ans tests for the
11610 regression coefficients can be conducted via jackknifing.")
11611 (license license:gpl2+)))
11613 (define-public r-huge
11616 (version "1.3.4.1")
11620 (uri (cran-uri "huge" version))
11622 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
11623 (build-system r-build-system)
11625 `(("r-igraph" ,r-igraph)
11627 ("r-matrix" ,r-matrix)
11629 ("r-rcppeigen" ,r-rcppeigen)))
11630 (home-page "https://cran.r-project.org/web/packages/huge")
11631 (synopsis "High-dimensional undirected graph estimation")
11633 "This package provides a general framework for high-dimensional
11634 undirected graph estimation. It integrates data preprocessing, neighborhood
11635 screening, graph estimation, and model selection techniques into a pipeline.")
11636 (license license:gpl2)))
11638 (define-public r-parcor
11645 (uri (cran-uri "parcor" version))
11648 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11649 (build-system r-build-system)
11652 ("r-genenet" ,r-genenet)
11653 ("r-glmnet" ,r-glmnet)
11655 ("r-ppls" ,r-ppls)))
11656 (home-page "https://cran.r-project.org/web/packages/parcor")
11657 (synopsis "Regularized estimation of partial correlation matrices")
11659 "This package estimates the matrix of partial correlations based on
11660 different regularized regression methods: lasso, adaptive lasso, PLS, and
11661 Ridge Regression. In addition, the package provides model selection for
11662 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11663 (license license:gpl2+)))
11665 (define-public r-mcmc
11672 (uri (cran-uri "mcmc" version))
11675 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
11676 (build-system r-build-system)
11677 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
11678 (synopsis "Markov chain Monte Carlo")
11680 "This package simulates continuous distributions of random vectors using
11681 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11682 function that evaluates the log unnormalized density. Algorithms are random
11683 walk Metropolis algorithm (function @code{metrop}), simulated
11684 tempering (function @code{temper}), and morphometric random walk
11685 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11686 by change of variable.")
11687 (license license:expat)))
11689 (define-public r-listenv
11696 (uri (cran-uri "listenv" version))
11699 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11700 (build-system r-build-system)
11702 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11703 (home-page "https://github.com/HenrikBengtsson/listenv")
11704 (synopsis "Environments behaving (almost) as lists")
11706 "This package implements list environments. List environments are
11707 environments that have list-like properties. For instance, the elements of a
11708 list environment are ordered and can be accessed and iterated over using index
11710 (license license:lgpl2.1+)))
11712 (define-public r-globals
11719 (uri (cran-uri "globals" version))
11722 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11723 (build-system r-build-system)
11725 `(("r-codetools" ,r-codetools)))
11726 (home-page "https://github.com/HenrikBengtsson/globals")
11727 (synopsis "Identify global objects in R expressions")
11729 "This package provides tools to identify global (\"unknown\" or \"free\")
11730 objects in R expressions by code inspection using various strategies, e.g.
11731 conservative or liberal. The objective of this package is to make it as
11732 simple as possible to identify global objects for the purpose of exporting
11733 them in distributed compute environments.")
11734 (license license:lgpl2.1+)))
11736 (define-public r-future
11743 (uri (cran-uri "future" version))
11746 "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
11747 (build-system r-build-system)
11749 `(("r-digest" ,r-digest)
11750 ("r-globals" ,r-globals)
11751 ("r-listenv" ,r-listenv)))
11753 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11754 (home-page "https://github.com/HenrikBengtsson/future")
11755 (synopsis "Unified parallel and distributed processing in R")
11757 "The purpose of this package is to provide a lightweight and unified
11758 Future API for sequential and parallel processing of R expression via futures.
11759 This package implements sequential, multicore, multisession, and cluster
11760 futures. With these, R expressions can be evaluated on the local machine, in
11761 parallel a set of local machines, or distributed on a mix of local and remote
11762 machines. Extensions to this package implement additional backends for
11763 processing futures via compute cluster schedulers etc. Because of its unified
11764 API, there is no need to modify any code in order to switch from sequential on
11765 the local machine to, say, distributed processing on a remote compute cluster.")
11766 (license license:lgpl2.1+)))
11768 (define-public r-future-apply
11770 (name "r-future-apply")
11775 (uri (cran-uri "future.apply" version))
11778 "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
11779 (properties `((upstream-name . "future.apply")))
11780 (build-system r-build-system)
11782 `(("r-future" ,r-future)
11783 ("r-globals" ,r-globals)))
11785 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11786 (home-page "https://github.com/HenrikBengtsson/future.apply")
11787 (synopsis "Apply function to elements in parallel using futures")
11789 "This package provides implementations of @code{apply()},
11790 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11791 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11792 can be resolved using any future-supported backend, e.g. parallel on the local
11793 machine or distributed on a compute cluster.")
11794 (license license:gpl2+)))
11796 (define-public r-rsvd
11803 (uri (cran-uri "rsvd" version))
11806 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
11807 (build-system r-build-system)
11809 `(("r-matrix" ,r-matrix)))
11810 (home-page "https://github.com/erichson/rSVD")
11811 (synopsis "Randomized singular value decomposition")
11813 "Low-rank matrix decompositions are fundamental tools and widely used for
11814 data analysis, dimension reduction, and data compression. Classically, highly
11815 accurate deterministic matrix algorithms are used for this task. However, the
11816 emergence of large-scale data has severely challenged our computational
11817 ability to analyze big data. The concept of randomness has been demonstrated
11818 as an effective strategy to quickly produce approximate answers to familiar
11819 problems such as the @dfn{singular value decomposition} (SVD). This package
11820 provides several randomized matrix algorithms such as the randomized singular
11821 value decomposition (@code{rsvd}), randomized principal component
11822 analysis (@code{rpca}), randomized robust principal component
11823 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11824 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11825 functions are provided.")
11826 (license license:gpl3+)))
11828 (define-public r-sloop
11835 (uri (cran-uri "sloop" version))
11838 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11839 (build-system r-build-system)
11841 `(("r-codetools" ,r-codetools)
11842 ("r-crayon" ,r-crayon)
11843 ("r-purrr" ,r-purrr)
11844 ("r-rlang" ,r-rlang)
11845 ("r-tibble" ,r-tibble)))
11846 (home-page "https://github.com/r-lib/sloop")
11847 (synopsis "Helpers for object-oriented programming in R")
11849 "This package provides a collection of helper functions designed to
11850 help you to better understand object oriented programming in R, particularly
11852 (license license:gpl3)))
11854 (define-public r-capushe
11861 (uri (cran-uri "capushe" version))
11864 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11865 (build-system r-build-system)
11866 (propagated-inputs `(("r-mass" ,r-mass)))
11867 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11868 (synopsis "Calibrating penalties using slope heuristics")
11870 "This package provides tools for the calibration of penalized criteria
11871 for model selection. The calibration methods available are based on the slope
11873 (license license:gpl2+)))
11875 (define-public r-dorng
11882 (uri (cran-uri "doRNG" version))
11885 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
11886 (properties `((upstream-name . "doRNG")))
11887 (build-system r-build-system)
11889 `(("r-foreach" ,r-foreach)
11890 ("r-iterators" ,r-iterators)
11891 ("r-rngtools" ,r-rngtools)))
11892 (home-page "https://renozao.github.io/doRNG/")
11893 (synopsis "Generic reproducible parallel backend for foreach loops")
11895 "This package provides functions to perform reproducible parallel
11896 @code{foreach} loops, using independent random streams as generated by
11897 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11898 convert standard @code{%dopar%} loops into fully reproducible loops,
11899 independently of the number of workers, the task scheduling strategy, or the
11900 chosen parallel environment and associated foreach backend.")
11901 (license license:gpl2+)))
11903 (define-public r-blockmodeling
11905 (name "r-blockmodeling")
11910 (uri (cran-uri "blockmodeling" version))
11913 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
11914 (build-system r-build-system)
11916 `(("r-matrix" ,r-matrix)))
11917 (native-inputs `(("gfortran" ,gfortran)))
11918 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11919 (synopsis "Generalized and classical blockmodeling of valued networks")
11921 "This package is primarily meant as an implementation of generalized
11922 blockmodeling for valued networks. In addition, measures of similarity or
11923 dissimilarity based on structural equivalence and regular equivalence (REGE
11924 algorithms) can be computed and partitioned matrices can be plotted.")
11925 (license license:gpl2+)))
11927 (define-public r-upsetr
11934 (uri (cran-uri "UpSetR" version))
11937 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11938 (properties `((upstream-name . "UpSetR")))
11939 (build-system r-build-system)
11941 `(("r-ggplot2" ,r-ggplot2)
11942 ("r-gridextra" ,r-gridextra)
11944 ("r-scales" ,r-scales)))
11945 (home-page "https://github.com/hms-dbmi/UpSetR")
11946 (synopsis "Visualize intersecting sets")
11948 "This package provides a more scalable alternative to Venn and Euler
11949 diagrams for visualizing intersecting sets. Create visualizations of
11950 intersecting sets using a novel matrix design, along with visualizations of
11951 several common set, element and attribute related tasks.")
11952 (license license:expat)))
11954 ;; This package includes a JavaScript file, which is not minified. When
11955 ;; upgrading please check that there are no new minified JavaScript files.
11956 (define-public r-shinybs
11963 (uri (cran-uri "shinyBS" version))
11966 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11967 (properties `((upstream-name . "shinyBS")))
11968 (build-system r-build-system)
11969 ;; The tests spawn Shiny browser apps. They cannot be run
11970 ;; non-interactively.
11971 (arguments '(#:tests? #f))
11973 `(("r-htmltools" ,r-htmltools)
11974 ("r-shiny" ,r-shiny)))
11975 (home-page "https://ebailey78.github.io/shinyBS/")
11976 (synopsis "Twitter Bootstrap components for Shiny")
11978 "This package adds additional Twitter Bootstrap components to Shiny.")
11979 (license license:gpl3)))
11981 (define-public r-outliers
11983 (name "r-outliers")
11988 (uri (cran-uri "outliers" version))
11991 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11992 (build-system r-build-system)
11993 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11994 (synopsis "Tests for outliers")
11996 "This package provides a collection of some tests commonly used for
11997 identifying outliers.")
11998 (license license:gpl2+)))
12000 (define-public r-bayesm
12007 (uri (cran-uri "bayesm" version))
12009 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12010 (build-system r-build-system)
12012 `(("r-rcpp" ,r-rcpp)
12013 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12014 (home-page "http://www.perossi.org/home/bsm-1")
12015 (synopsis "Bayesian inference for marketing/micro-econometrics")
12017 "This package covers many important models used in marketing and
12018 micro-econometrics applications, including Bayes Regression (univariate or
12019 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12020 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12021 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12022 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12023 Estimation with normal base, Hierarchical Linear Models with normal prior and
12024 covariates, Hierarchical Linear Models with a mixture of normals prior and
12025 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12026 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12027 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12028 analysis of choice-based conjoint data, Bayesian treatment of linear
12029 instrumental variables models, Analysis of Multivariate Ordinal survey data
12030 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12031 Coefficient Logit Models.")
12032 (license license:gpl2+)))
12034 (define-public r-tensora
12041 (uri (cran-uri "tensorA" version))
12044 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12045 (properties `((upstream-name . "tensorA")))
12046 (build-system r-build-system)
12047 (home-page "http://www.stat.boogaart.de/tensorA")
12048 (synopsis "Advanced tensor arithmetic with named indices")
12050 "This package provides convenience functions for advanced linear algebra
12051 with tensors and computation with datasets of tensors on a higher level
12052 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12053 co- and contravariate indices, and parallel computations on sequences of
12055 (license license:gpl2+)))
12057 (define-public r-rarpack
12064 (uri (cran-uri "rARPACK" version))
12067 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12068 (properties `((upstream-name . "rARPACK")))
12069 (build-system r-build-system)
12070 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12071 (home-page "https://github.com/yixuan/rARPACK")
12072 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12074 "This package was previously an R wrapper of the ARPACK library, and now
12075 a shell of the R package RSpectra, an R interface to the Spectra library for
12076 solving large scale eigenvalue/vector problems. The current version of
12077 rARPACK simply imports and exports the functions provided by RSpectra. New
12078 users of rARPACK are advised to switch to the RSpectra package.")
12079 (license license:bsd-3)))
12081 (define-public r-compositions
12083 (name "r-compositions")
12088 (uri (cran-uri "compositions" version))
12091 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12092 (build-system r-build-system)
12094 `(("r-bayesm" ,r-bayesm)
12095 ("r-robustbase" ,r-robustbase)
12096 ("r-tensora" ,r-tensora)))
12097 (home-page "http://www.stat.boogaart.de/compositions")
12098 (synopsis "Compositional data analysis")
12100 "This package provides functions for the consistent analysis of
12101 compositional data (e.g. portions of substances) and positive
12102 numbers (e.g. concentrations).")
12103 (license license:gpl2+)))
12105 (define-public r-cobs
12112 (uri (cran-uri "cobs" version))
12115 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12116 (build-system r-build-system)
12118 `(("r-quantreg" ,r-quantreg)
12119 ("r-sparsem" ,r-sparsem)))
12120 (home-page "https://cran.r-project.org/web/packages/cobs")
12121 (synopsis "Constrained B-Splines (sparse matrix based)")
12123 "This package provides qualitatively constrained (regression) smoothing
12124 splines via linear programming and sparse matrices.")
12125 (license license:gpl2+)))
12127 (define-public r-drimpute
12129 (name "r-drimpute")
12134 (uri (cran-uri "DrImpute" version))
12137 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12138 (properties `((upstream-name . "DrImpute")))
12139 (build-system r-build-system)
12141 `(("r-rcpp" ,r-rcpp)
12142 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12143 (home-page "https://github.com/ikwak2/DrImpute")
12144 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12146 "This is an R package for imputing dropout events. Many statistical
12147 methods in cell type identification, visualization and lineage reconstruction
12148 do not account for dropout events. DrImpute can improve the performance of
12149 such software by imputing dropout events.")
12150 (license license:gpl3)))
12152 (define-public r-gamlss-dist
12154 (name "r-gamlss-dist")
12159 (uri (cran-uri "gamlss.dist" version))
12161 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12162 (properties `((upstream-name . "gamlss.dist")))
12163 (build-system r-build-system)
12164 (propagated-inputs `(("r-mass" ,r-mass)))
12165 (home-page "http://www.gamlss.org/")
12166 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12168 "This package provides a set of distributions which can be used for
12169 modelling the response variables in Generalized Additive Models for Location
12170 Scale and Shape. The distributions can be continuous, discrete or mixed
12171 distributions. Extra distributions can be created, by transforming, any
12172 continuous distribution defined on the real line, to a distribution defined on
12173 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12174 transformation, respectively.")
12175 ;; Either version of the GPL.
12176 (license (list license:gpl2 license:gpl3))))
12178 ;; This package includes JavaScript files, which are not minified. When
12179 ;; upgrading please check that there are no new minified JavaScript files.
12180 (define-public r-shinyjs
12187 (uri (cran-uri "shinyjs" version))
12190 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12191 (build-system r-build-system)
12193 `(("r-digest" ,r-digest)
12194 ("r-htmltools" ,r-htmltools)
12195 ("r-jsonlite" ,r-jsonlite)
12196 ("r-shiny" ,r-shiny)))
12197 (home-page "https://deanattali.com/shinyjs")
12198 (synopsis "Improve the user experience of your Shiny apps")
12200 "Perform common useful JavaScript operations in Shiny apps that will
12201 greatly improve your apps without having to know any JavaScript. Examples
12202 include: hiding an element, disabling an input, resetting an input back to its
12203 original value, delaying code execution by a few seconds, and many more useful
12204 functions for both the end user and the developer. Shinyjs can also be used
12205 to easily call your own custom JavaScript functions from R.")
12206 (license license:agpl3+)))
12208 ;; This package includes minified JavaScript files. When upgrading please
12209 ;; check that there are no new minified JavaScript files.
12210 (define-public r-colourpicker
12212 (name "r-colourpicker")
12217 (uri (cran-uri "colourpicker" version))
12220 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12221 (build-system r-build-system)
12223 `(#:modules ((guix build utils)
12224 (guix build r-build-system)
12228 (modify-phases %standard-phases
12229 (add-after 'unpack 'process-javascript
12230 (lambda* (#:key inputs #:allow-other-keys)
12231 (with-directory-excursion "inst"
12235 `((,(assoc-ref inputs "js-salvattore")
12236 "examples/colourInput/www/salvattore.min.js")
12237 (,(assoc-ref inputs "js-jquery")
12238 "htmlwidgets/lib/jquery/jquery.min.js")
12239 ("www/shared/colourpicker/js/colourpicker.js"
12240 "www/shared/colourpicker/js/colourpicker.min.js"))))
12241 (lambda (sources targets)
12242 (for-each (lambda (source target)
12243 (format #t "Processing ~a --> ~a~%"
12245 (delete-file target)
12246 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12247 (call-with-output-file target
12249 (dump-port minified port)))))
12250 sources targets))))
12253 `(("r-ggplot2" ,r-ggplot2)
12254 ("r-htmltools" ,r-htmltools)
12255 ("r-htmlwidgets" ,r-htmlwidgets)
12256 ("r-jsonlite" ,r-jsonlite)
12257 ("r-miniui" ,r-miniui)
12258 ("r-shiny" ,r-shiny)
12259 ("r-shinyjs" ,r-shinyjs)))
12261 `(("uglify-js" ,uglify-js)
12265 (uri "https://code.jquery.com/jquery-3.3.1.js")
12268 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12272 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12275 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12276 (home-page "https://github.com/daattali/colourpicker")
12277 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12279 "This package provides a color picker that can be used as an input in
12280 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12281 custom color palettes, and many more options. A plot color helper tool is
12282 available as an RStudio Addin, which helps you pick colors to use in your
12283 plots. A more generic color picker RStudio Addin is also provided to let you
12284 select colors to use in your R code.")
12285 (license license:expat)))
12287 (define-public r-ggextra
12294 (uri (cran-uri "ggExtra" version))
12297 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12298 (properties `((upstream-name . "ggExtra")))
12299 (build-system r-build-system)
12301 `(("r-colourpicker" ,r-colourpicker)
12302 ("r-ggplot2" ,r-ggplot2)
12303 ("r-gtable" ,r-gtable)
12304 ("r-miniui" ,r-miniui)
12306 ("r-scales" ,r-scales)
12307 ("r-shiny" ,r-shiny)
12308 ("r-shinyjs" ,r-shinyjs)))
12309 (home-page "https://github.com/daattali/ggExtra")
12310 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12312 "This package is a collection of functions and layers to enhance ggplot2.
12313 The flagship function is @code{ggMarginal()}, which can be used to add
12314 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12315 (license license:expat)))
12317 (define-public r-minpack-lm
12319 (name "r-minpack-lm")
12324 (uri (cran-uri "minpack.lm" version))
12327 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12328 (properties `((upstream-name . "minpack.lm")))
12329 (build-system r-build-system)
12330 (native-inputs `(("gfortran" ,gfortran)))
12331 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12332 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12334 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12335 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12336 problems by a modification of the Levenberg-Marquardt algorithm, with support
12337 for lower and upper parameter bounds. The implementation can be used via
12338 @code{nls}-like calls using the @code{nlsLM} function.")
12339 (license license:gpl3)))
12341 (define-public r-moments
12348 (uri (cran-uri "moments" version))
12351 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12352 (build-system r-build-system)
12353 (home-page "https://cran.r-project.org/web/packages/moments")
12354 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12356 "This package provides functions to calculate: moments, Pearson's
12357 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12358 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12359 (license license:gpl2+)))
12361 (define-public r-msir
12368 (uri (cran-uri "msir" version))
12371 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12372 (build-system r-build-system)
12374 `(("r-mclust" ,r-mclust)))
12375 (home-page "https://cran.r-project.org/web/packages/msir")
12376 (synopsis "Model-based sliced inverse regression")
12378 "This is an R package for dimension reduction based on finite Gaussian
12379 mixture modeling of inverse regression.")
12380 (license license:gpl2+)))
12382 (define-public r-pbivnorm
12384 (name "r-pbivnorm")
12389 (uri (cran-uri "pbivnorm" version))
12392 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12393 (build-system r-build-system)
12394 (native-inputs `(("gfortran" ,gfortran)))
12395 (home-page "https://github.com/brentonk/pbivnorm")
12396 (synopsis "Vectorized bivariate normal CDF")
12398 "This package provides a vectorized R function for calculating
12399 probabilities from a standard bivariate normal CDF.")
12400 (license license:gpl2+)))
12402 (define-public r-lavaan
12409 (uri (cran-uri "lavaan" version))
12412 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12413 (build-system r-build-system)
12415 `(("r-mass" ,r-mass)
12416 ("r-mnormt" ,r-mnormt)
12417 ("r-numderiv" ,r-numderiv)
12418 ("r-pbivnorm" ,r-pbivnorm)))
12419 (home-page "http://lavaan.ugent.be")
12420 (synopsis "Latent variable analysis")
12422 "This package provides tools to fit a variety of latent variable models,
12423 including confirmatory factor analysis, structural equation modeling and
12424 latent growth curve models.")
12425 (license license:gpl2+)))
12427 (define-public r-nonnest2
12429 (name "r-nonnest2")
12434 (uri (cran-uri "nonnest2" version))
12437 "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
12438 (build-system r-build-system)
12440 `(("r-compquadform" ,r-compquadform)
12441 ("r-lavaan" ,r-lavaan)
12442 ("r-mvtnorm" ,r-mvtnorm)
12443 ("r-sandwich" ,r-sandwich)))
12445 `(("r-knitr" ,r-knitr)))
12446 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12447 (synopsis "Tests of non-nested models")
12449 "This package allows for testing of non-nested models. It includes tests
12450 of model distinguishability and of model fit that can be applied to both
12451 nested and non-nested models. The package also includes functionality to
12452 obtain confidence intervals associated with AIC and BIC.")
12453 ;; Either version of the GPL.
12454 (license (list license:gpl2 license:gpl3))))
12456 (define-public r-penalized
12458 (name "r-penalized")
12463 (uri (cran-uri "penalized" version))
12466 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12467 (build-system r-build-system)
12469 `(("r-rcpp" ,r-rcpp)
12470 ("r-rcpparmadillo" ,r-rcpparmadillo)
12471 ("r-survival" ,r-survival)))
12472 (home-page "https://cran.r-project.org/web/packages/penalized/")
12473 (synopsis "Penalized estimation in GLMs and in the Cox model")
12475 "This package provides tools for fitting possibly high dimensional
12476 penalized regression models. The penalty structure can be any combination of
12477 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12478 constraint on the regression coefficients. The supported regression models
12479 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12480 model. Cross-validation routines allow optimization of the tuning
12482 (license license:gpl2+)))
12484 (define-public r-zim
12491 (uri (cran-uri "ZIM" version))
12494 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12495 (properties `((upstream-name . "ZIM")))
12496 (build-system r-build-system)
12497 (propagated-inputs `(("r-mass" ,r-mass)))
12498 (home-page "https://github.com/biostatstudio/ZIM")
12499 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12501 "Analyze count time series with excess zeros. Two types of statistical
12502 models are supported: Markov regression and state-space models. They are also
12503 known as observation-driven and parameter-driven models respectively in the
12504 time series literature. The functions used for Markov regression or
12505 observation-driven models can also be used to fit ordinary regression models
12506 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12507 negative binomial (ZINB) assumption. The package also contains miscellaneous
12508 functions to compute density, distribution, quantile, and generate random
12509 numbers from ZIP and ZINB distributions.")
12510 (license license:gpl3)))
12512 (define-public r-nor1mix
12519 (uri (cran-uri "nor1mix" version))
12522 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12523 (build-system r-build-system)
12524 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12525 (synopsis "Normal (1-d) mixture models")
12527 "This package provides S3 classes and methods for one-dimensional normal
12528 mixture models, for, e.g., density estimation or clustering algorithms
12529 research and teaching; it provides the widely used Marron-Wand densities. It
12530 also provides tools for efficient random number generation and graphics.")
12531 (license license:gpl2+)))
12533 (define-public r-beanplot
12535 (name "r-beanplot")
12540 (uri (cran-uri "beanplot" version))
12543 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12544 (build-system r-build-system)
12545 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12546 (synopsis "Visualization via beanplots")
12548 "This package provides beanplots, an alternative to
12549 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12551 (license license:gpl2)))
12553 (define-public r-pbdzmq
12560 (uri (cran-uri "pbdZMQ" version))
12563 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12564 (properties `((upstream-name . "pbdZMQ")))
12565 (build-system r-build-system)
12567 `(("zeromq" ,zeromq)
12570 `(("pkg-config" ,pkg-config)))
12571 (home-page "https://pbdr.org/")
12572 (synopsis "R interface to ZeroMQ")
12574 "ZeroMQ is a well-known library for high-performance asynchronous
12575 messaging in scalable, distributed applications. This package provides high
12576 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12577 interactive client/server programming frameworks. A few wrapper functions
12578 compatible with @code{rzmq} are also provided.")
12579 (license license:gpl3)))
12581 (define-public r-repr
12588 (uri (cran-uri "repr" version))
12591 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
12592 (build-system r-build-system)
12594 `(("r-base64enc" ,r-base64enc)
12595 ("r-htmltools" ,r-htmltools)
12596 ("r-jsonlite" ,r-jsonlite)
12597 ("r-pillar" ,r-pillar)))
12598 (home-page "https://cran.r-project.org/web/packages/repr/")
12599 (synopsis "Serializable representations")
12601 "This package provides string and binary representations of objects for
12602 several formats and MIME types.")
12603 (license license:gpl3)))
12605 (define-public r-irdisplay
12607 (name "r-irdisplay")
12612 (uri (cran-uri "IRdisplay" version))
12615 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12616 (properties `((upstream-name . "IRdisplay")))
12617 (build-system r-build-system)
12619 `(("r-repr" ,r-repr)))
12620 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12621 (synopsis "Jupyter display machinery")
12623 "This package provides an interface to the rich display capabilities of
12624 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12625 running IRkernel session.")
12626 (license license:expat)))
12628 (define-public r-irkernel
12630 (name "r-irkernel")
12635 (uri (cran-uri "IRkernel" version))
12638 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12639 (properties `((upstream-name . "IRkernel")))
12640 (build-system r-build-system)
12643 (modify-phases %standard-phases
12644 (add-after 'install 'install-kernelspec
12645 (lambda* (#:key outputs #:allow-other-keys)
12646 (let ((out (assoc-ref outputs "out")))
12647 (setenv "HOME" "/tmp")
12648 (invoke "jupyter" "kernelspec" "install"
12651 (string-append out "/site-library/IRkernel/kernelspec"))
12652 ;; Record the absolute file name of the 'R' executable in
12654 (substitute* (string-append out "/share/jupyter"
12655 "/kernels/ir/kernel.json")
12657 (string-append "[\"" (which "R") "\",")))
12660 `(("jupyter" ,jupyter)))
12662 `(("r-crayon" ,r-crayon)
12663 ("r-digest" ,r-digest)
12664 ("r-evaluate" ,r-evaluate)
12665 ("r-irdisplay" ,r-irdisplay)
12666 ("r-jsonlite" ,r-jsonlite)
12667 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12668 ("r-minimal" ,r-minimal)
12669 ("r-pbdzmq" ,r-pbdzmq)
12671 ("r-uuid" ,r-uuid)))
12672 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12673 (synopsis "Native R kernel for Jupyter")
12675 "The R kernel for the Jupyter environment executes R code which the
12676 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12678 (license license:expat)))
12680 (define-public r-gmodels
12687 (uri (cran-uri "gmodels" version))
12690 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12691 (build-system r-build-system)
12693 `(("r-gdata" ,r-gdata)
12694 ("r-mass" ,r-mass)))
12695 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12696 (synopsis "Various R programming tools for model fitting")
12698 "This package provides various R programming tools for model fitting.")
12699 (license license:gpl2)))
12701 (define-public r-apcluster
12703 (name "r-apcluster")
12708 (uri (cran-uri "apcluster" version))
12711 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12712 (build-system r-build-system)
12714 `(("r-matrix" ,r-matrix)
12715 ("r-rcpp" ,r-rcpp)))
12716 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12717 (synopsis "Affinity propagation clustering")
12719 "This package implements affinity propagation clustering introduced by
12720 Frey and Dueck (2007). The package further provides leveraged affinity
12721 propagation and an algorithm for exemplar-based agglomerative clustering that
12722 can also be used to join clusters obtained from affinity propagation. Various
12723 plotting functions are available for analyzing clustering results.")
12724 (license license:gpl2+)))
12726 (define-public r-valr
12733 (uri (cran-uri "valr" version))
12736 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12737 (build-system r-build-system)
12739 `(("r-broom" ,r-broom)
12740 ("r-dplyr" ,r-dplyr)
12741 ("r-ggplot2" ,r-ggplot2)
12743 ("r-readr" ,r-readr)
12744 ("r-rlang" ,r-rlang)
12745 ("r-stringr" ,r-stringr)
12746 ("r-tibble" ,r-tibble)))
12747 (home-page "http://github.com/rnabioco/valr")
12748 (synopsis "Genome interval arithmetic in R")
12750 "This package enables you to read and manipulate genome intervals and
12751 signals. It provides functionality similar to command-line tool suites within
12752 R, enabling interactive analysis and visualization of genome-scale data.")
12753 (license license:expat)))
12755 (define-public r-rematch2
12757 (name "r-rematch2")
12762 (uri (cran-uri "rematch2" version))
12765 "13siaa8s2ji9q6hykhb2r34ag76335ypmbqr90xaqilbir0klhnh"))))
12766 (build-system r-build-system)
12768 `(("r-tibble" ,r-tibble)))
12769 (home-page "https://github.com/r-lib/rematch2")
12770 (synopsis "Tidy output from regular expression matching")
12772 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12773 return the match results in tidy data frames.")
12774 (license license:expat)))
12776 (define-public r-picante
12783 (uri (cran-uri "picante" version))
12786 "1b16zm8zjjsl181b8krkdcrbcw347kf772c4w7y5332qmfi7jhz0"))))
12787 (build-system r-build-system)
12791 ("r-vegan" ,r-vegan)))
12792 (home-page "https://cran.r-project.org/web/packages/picante/")
12793 (synopsis "Integrating phylogenies and ecology")
12795 "This package provides functions for phylocom integration, community
12796 analyses, null-models, traits and evolution. It implements numerous
12797 ecophylogenetic approaches including measures of community phylogenetic and
12798 trait diversity, phylogenetic signal, estimation of trait values for
12799 unobserved taxa, null models for community and phylogeny randomizations, and
12800 utility functions for data input/output and phylogeny plotting. A full
12801 description of package functionality and methods are provided by Kembel et
12803 (license license:gpl2)))
12805 (define-public r-reinforcelearn
12807 (name "r-reinforcelearn")
12812 (uri (cran-uri "reinforcelearn" version))
12815 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12816 (build-system r-build-system)
12818 `(("r-checkmate" ,r-checkmate)
12820 ("r-purrr" ,r-purrr)
12822 (home-page "https://markusdumke.github.io/reinforcelearn")
12823 (synopsis "Reinforcement learning")
12825 "This package implements reinforcement learning environments and
12826 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12827 can be used with function approximation, eligibility traces (Singh & Sutton,
12828 1996) and experience replay (Mnih et al., 2013).")
12829 (license license:expat)))
12831 (define-public r-lemon
12838 (uri (cran-uri "lemon" version))
12841 "0m9hqwi709j9iwsxn8jh63741jiyr7ppwgqaw2zkv285p3m5wvd5"))))
12842 (build-system r-build-system)
12844 `(("r-ggplot2" ,r-ggplot2)
12845 ("r-gridextra" ,r-gridextra)
12846 ("r-gtable" ,r-gtable)
12847 ("r-knitr" ,r-knitr)
12848 ("r-lattice" ,r-lattice)
12850 ("r-rlang" ,r-rlang)
12851 ("r-scales" ,r-scales)))
12852 (home-page "https://github.com/stefanedwards/lemon")
12853 (synopsis "Freshen up your ggplot2 plots")
12855 "This package provides functions for working with legends and axis lines
12856 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12858 (license license:gpl3)))
12860 (define-public r-wgaim
12867 (uri (cran-uri "wgaim" version))
12869 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12870 (build-system r-build-system)
12872 `(("r-ggplot2" ,r-ggplot2)
12874 (home-page "https://cran.r-project.org/web/packages/wgaim")
12875 (synopsis "Whole genome average interval mapping for QTL detection")
12877 "This package integrates sophisticated mixed modelling methods with a
12878 whole genome approach to detecting significant QTL in linkage maps.")
12879 (license license:gpl2+)))
12881 (define-public r-bedr
12888 (uri (cran-uri "bedr" version))
12891 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12892 (build-system r-build-system)
12894 `(("r-data-table" ,r-data-table)
12895 ("r-r-utils" ,r-r-utils)
12896 ("r-testthat" ,r-testthat)
12897 ("r-venndiagram" ,r-venndiagram)
12900 ("bedtools" ,bedtools)
12901 ("htslib" ,htslib))) ; for tabix
12903 `(("r-knitr" ,r-knitr))) ; for vignettes
12904 (home-page "https://cran.r-project.org/web/packages/bedr")
12905 (synopsis "Genomic region processing")
12907 "This package is for genomic regions processing using command line tools
12908 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12909 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12910 The bedr package's API enhances access to these tools as well as offers
12911 additional utilities for genomic regions processing.")
12912 (license license:gpl2)))
12914 (define-public r-sets
12921 (uri (cran-uri "sets" version))
12924 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12925 (properties `((upstream-name . "sets")))
12926 (build-system r-build-system)
12927 (home-page "https://cran.r-project.org/web/packages/sets")
12928 (synopsis "Sets, generalized sets, customizable sets and intervals")
12930 "This package provides data structures and basic operations for ordinary
12931 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12932 customizable sets, and intervals.")
12933 (license license:gpl2)))
12935 (define-public r-partitions
12937 (name "r-partitions")
12942 (uri (cran-uri "partitions" version))
12945 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12946 (build-system r-build-system)
12949 ("r-polynom" ,r-polynom)
12950 ("r-sets" ,r-sets)))
12951 (home-page "https://cran.r-project.org/web/packages/partitions")
12952 (synopsis "Additive partitions of integers")
12954 "This package provides tools to enumerates the partitions, unequal
12955 partitions, and restricted partitions of an integer; the three corresponding
12956 partition functions are also given.")
12957 ;; Any version of the GPL
12958 (license license:gpl2+)))
12960 (define-public r-brobdingnag
12962 (name "r-brobdingnag")
12967 (uri (cran-uri "Brobdingnag" version))
12970 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12971 (properties `((upstream-name . "Brobdingnag")))
12972 (build-system r-build-system)
12973 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12974 (synopsis "Very large numbers in R")
12976 "This package handles very large numbers in R. Real numbers are held
12977 using their natural logarithms, plus a logical flag indicating sign. The
12978 package includes a vignette that gives a step-by-step introduction to using S4
12980 ;; Any version of the GPL
12981 (license license:gpl2+)))
12983 (define-public r-untb
12990 (uri (cran-uri "untb" version))
12993 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12994 (build-system r-build-system)
12996 `(("r-brobdingnag" ,r-brobdingnag)
12997 ("r-partitions" ,r-partitions)
12998 ("r-polynom" ,r-polynom)))
12999 (home-page "https://github.com/RobinHankin/untb.git")
13000 (synopsis "Ecological drift under the UNTB")
13002 "This package provides numerical simulations, and visualizations, of
13003 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13004 (license license:gpl2+)))
13006 (define-public r-stepwise
13008 (name "r-stepwise")
13013 (uri (cran-uri "stepwise" version))
13016 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13017 (build-system r-build-system)
13018 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13019 (synopsis "Stepwise detection of recombination breakpoints")
13021 "This package provides a stepwise approach to identifying recombination
13022 breakpoints in a genomic sequence alignment.")
13023 (license license:gpl2+)))
13025 (define-public r-snpmaxsel
13027 (name "r-snpmaxsel")
13032 (uri (cran-uri "SNPmaxsel" version))
13035 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13036 (properties `((upstream-name . "SNPmaxsel")))
13037 (build-system r-build-system)
13039 `(("r-combinat" ,r-combinat)
13040 ("r-mvtnorm" ,r-mvtnorm)))
13041 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13042 (synopsis "Maximally selected statistics for SNP data")
13044 "This package implements asymptotic methods related to maximally selected
13045 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13047 (license license:gpl2+)))
13049 (define-public r-acsnminer
13051 (name "r-acsnminer")
13052 (version "0.16.8.25")
13055 (uri (cran-uri "ACSNMineR" version))
13058 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13059 (properties `((upstream-name . "ACSNMineR")))
13060 (build-system r-build-system)
13062 `(("r-ggplot2" ,r-ggplot2)
13063 ("r-gridextra" ,r-gridextra)))
13064 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13065 (synopsis "Gene enrichment analysis")
13067 "This package provides tools to compute and represent gene set enrichment
13068 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13069 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13070 enrichment can be run with hypergeometric test or Fisher exact test, and can
13071 use multiple corrections. Visualization of data can be done either by
13072 barplots or heatmaps.")
13073 (license license:gpl2+)))
13075 (define-public r-seqinr
13082 (uri (cran-uri "seqinr" version))
13085 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13086 (build-system r-build-system)
13088 `(("r-ade4" ,r-ade4)
13089 ("r-segmented" ,r-segmented)))
13092 (home-page "http://seqinr.r-forge.r-project.org/")
13093 (synopsis "Biological sequences retrieval and analysis")
13095 "This package provides tools for exploratory data analysis and data
13096 visualization of biological sequence (DNA and protein) data. It also includes
13097 utilities for sequence data management under the ACNUC system.")
13098 (license license:gpl2+)))
13100 (define-public r-units
13107 (uri (cran-uri "units" version))
13110 "11x6xz1fbml28xmrhgn4sii9vfyj3gyfc1dfxahdg9cszdmcgdnh"))))
13111 (build-system r-build-system)
13113 `(("udunits" ,udunits)))
13115 `(("r-rcpp" ,r-rcpp)))
13117 `(("r-knitr" ,r-knitr)))
13118 (home-page "https://github.com/r-quantities/units/")
13119 (synopsis "Measurement Units for R Vectors")
13121 "This package provides support for measurement units in R vectors,
13122 matrices and arrays: automatic propagation, conversion, derivation and
13123 simplification of units; raising errors in case of unit incompatibility. It
13124 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13126 (license license:gpl2)))
13128 (define-public r-classint
13130 (name "r-classint")
13135 (uri (cran-uri "classInt" version))
13138 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13139 (properties `((upstream-name . "classInt")))
13140 (build-system r-build-system)
13142 `(("r-class" ,r-class)
13143 ("r-e1071" ,r-e1071)
13144 ("r-kernsmooth" ,r-kernsmooth)))
13146 `(("gfortran" ,gfortran)
13147 ("r-knitr" ,r-knitr)))
13148 (home-page "https://github.com/r-spatial/classInt/")
13149 (synopsis "Choose univariate class intervals")
13151 "This package provides selected commonly used methods for choosing
13152 univariate class intervals for mapping or other graphics purposes.")
13153 (license license:gpl2+)))
13155 (define-public r-spdata
13162 (uri (cran-uri "spData" version))
13165 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13166 (properties `((upstream-name . "spData")))
13167 (build-system r-build-system)
13169 `(("r-raster" ,r-raster)
13171 (home-page "https://github.com/Nowosad/spData")
13172 (synopsis "Datasets for spatial analysis")
13174 "This a package containing diverse spatial datasets for demonstrating,
13175 benchmarking and teaching spatial data analysis. It includes R data of class
13176 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13177 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13178 of the datasets are designed to illustrate specific analysis techniques.
13179 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13180 illustrate point pattern analysis techniques.")
13181 (license license:cc0)))
13183 (define-public r-learnbayes
13185 (name "r-learnbayes")
13190 (uri (cran-uri "LearnBayes" version))
13193 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13194 (properties `((upstream-name . "LearnBayes")))
13195 (build-system r-build-system)
13196 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13197 (synopsis "Functions for learning Bayesian inference")
13199 "This package provides a collection of functions helpful in learning the
13200 basic tenets of Bayesian statistical inference. It contains functions for
13201 summarizing basic one and two parameter posterior distributions and predictive
13202 distributions. It contains MCMC algorithms for summarizing posterior
13203 distributions defined by the user. It also contains functions for regression
13204 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13206 (license license:gpl2+)))
13208 (define-public r-deldir
13215 (uri (cran-uri "deldir" version))
13218 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13219 (build-system r-build-system)
13220 (native-inputs `(("gfortran" ,gfortran)))
13221 (home-page "https://cran.r-project.org/web/packages/deldir")
13222 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13224 "This package provides tools for calculating the Delaunay triangulation
13225 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13226 of a planar point set. It plots triangulations and tessellations in various
13227 ways, clips tessellations to sub-windows, calculates perimeters of
13228 tessellations, and summarizes information about the tiles of the
13230 (license license:gpl2+)))
13232 (define-public r-sf
13239 (uri (cran-uri "sf" version))
13242 "1qghrskqwwlwxmmvkv7knhlr1a32ngyimycasy5gfazgviljsfn4"))))
13243 (build-system r-build-system)
13250 `(("r-classint" ,r-classint)
13252 ("r-magrittr" ,r-magrittr)
13254 ("r-units" ,r-units)))
13256 `(("pkg-config" ,pkg-config)
13257 ("r-knitr" ,r-knitr)))
13258 (home-page "https://github.com/r-spatial/sf/")
13259 (synopsis "Simple features for R")
13261 "This package provides support for simple features, a standardized way to
13262 encode spatial vector data. It binds to GDAL for reading and writing data, to
13263 GEOS for geometrical operations, and to PROJ for projection conversions and
13264 datum transformations.")
13265 ;; Either of these licenses
13266 (license (list license:gpl2 license:expat))))
13268 (define-public r-spdep
13275 (uri (cran-uri "spdep" version))
13278 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13279 (build-system r-build-system)
13281 `(("r-boot" ,r-boot)
13283 ("r-deldir" ,r-deldir)
13285 ("r-gmodels" ,r-gmodels)
13286 ("r-learnbayes" ,r-learnbayes)
13288 ("r-matrix" ,r-matrix)
13292 ("r-spdata" ,r-spdata)))
13293 (home-page "https://github.com/r-spatial/spdep/")
13294 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13296 "This package provides a collection of functions to create spatial
13297 weights matrix objects from polygon contiguities, from point patterns by
13298 distance and tessellations, for summarizing these objects, and for permitting
13299 their use in spatial data analysis, including regional aggregation by minimum
13301 (license license:gpl2+)))
13303 (define-public r-adegenet
13305 (name "r-adegenet")
13310 (uri (cran-uri "adegenet" version))
13313 "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
13314 (build-system r-build-system)
13316 `(("r-ade4" ,r-ade4)
13319 ("r-dplyr" ,r-dplyr)
13320 ("r-ggplot2" ,r-ggplot2)
13321 ("r-igraph" ,r-igraph)
13323 ("r-reshape2" ,r-reshape2)
13324 ("r-seqinr" ,r-seqinr)
13325 ("r-shiny" ,r-shiny)
13326 ("r-spdep" ,r-spdep)
13327 ("r-vegan" ,r-vegan)))
13328 (home-page "https://github.com/thibautjombart/adegenet")
13329 (synopsis "Exploratory analysis of genetic and genomic data")
13331 "This package provides a toolset for the exploration of genetic and
13332 genomic data. Adegenet provides formal (S4) classes for storing and handling
13333 various genetic data, including genetic markers with varying ploidy and
13334 hierarchical population structure (@code{genind} class), alleles counts by
13335 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13336 also implements original multivariate methods (DAPC, sPCA), graphics,
13337 statistical tests, simulation tools, distance and similarity measures, and
13338 several spatial methods. A range of both empirical and simulated datasets is
13339 also provided to illustrate various methods.")
13340 (license license:gpl2+)))
13342 (define-public r-pegas
13349 (uri (cran-uri "pegas" version))
13351 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13352 (build-system r-build-system)
13354 `(("r-adegenet" ,r-adegenet)
13356 (home-page "http://ape-package.ird.fr/pegas.html")
13357 (synopsis "Population and evolutionary genetics analysis system")
13359 "This package provides functions for reading, writing, plotting,
13360 analysing, and manipulating allelic and haplotypic data, including from VCF
13361 files, and for the analysis of population nucleotide sequences and
13362 micro-satellites including coalescent analyses, linkage disequilibrium,
13363 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13364 minimum spanning tree and network, and median-joining networks.")
13365 (license license:gpl2+)))
13367 (define-public r-rmetasim
13369 (name "r-rmetasim")
13374 (uri (cran-uri "rmetasim" version))
13377 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13378 (build-system r-build-system)
13380 `(("r-ade4" ,r-ade4)
13381 ("r-adegenet" ,r-adegenet)
13382 ("r-gtools" ,r-gtools)
13383 ("r-pegas" ,r-pegas)))
13384 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13385 (synopsis "Individual-based population genetic simulation environment")
13387 "This package provides an interface between R and the metasim simulation
13388 engine. The simulation environment is documented in: Strand, A.(2002),
13389 Metasim 1.0: an individual-based environment for simulating population
13390 genetics of complex population dynamics.")
13392 (license license:gpl2+)))
13394 (define-public r-genetics
13396 (name "r-genetics")
13397 (version "1.3.8.1.2")
13401 (uri (cran-uri "genetics" version))
13404 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13405 (build-system r-build-system)
13407 `(("r-combinat" ,r-combinat)
13408 ("r-gdata" ,r-gdata)
13409 ("r-gtools" ,r-gtools)
13411 ("r-mvtnorm" ,r-mvtnorm)))
13412 (home-page "https://cran.r-project.org/web/packages/genetics/")
13413 (synopsis "Population genetics")
13415 "This package provides classes and methods for handling genetic data.
13416 It includes classes to represent genotypes and haplotypes at single markers up
13417 to multiple markers on multiple chromosomes. Function include allele
13418 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13419 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13420 and testing for linkage disequilibrium, ...")
13421 ;; Any GPL version.
13422 (license license:gpl2+)))
13424 (define-public r-snp-plotter
13426 (name "r-snp-plotter")
13431 (uri (cran-uri "snp.plotter" version))
13434 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13435 (properties `((upstream-name . "snp.plotter")))
13436 (build-system r-build-system)
13437 (propagated-inputs `(("r-genetics" ,r-genetics)))
13438 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13439 (synopsis "Plot p-values using single SNP and/or haplotype data")
13441 "This package helps you create plots of p-values using single SNP and/or
13442 haplotype data. Main features of the package include options to display a
13443 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13444 datasets simultaneously. Plots can be created using global and/or individual
13445 haplotype p-values along with single SNP p-values. Images are created as
13446 either PDF/EPS files.")
13447 (license license:gpl2+)))
13449 (define-public r-polspline
13451 (name "r-polspline")
13456 (uri (cran-uri "polspline" version))
13458 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13459 (build-system r-build-system)
13460 (native-inputs `(("gfortran" ,gfortran)))
13461 (home-page "https://cran.r-project.org/web/packages/polspline/")
13462 (synopsis "Polynomial spline routines")
13464 "This package provides routines for the polynomial spline fitting
13465 routines hazard regression, hazard estimation with flexible tails, logspline,
13466 lspec, polyclass, and polymars.")
13467 (license license:gpl2+)))
13469 (define-public r-rms
13476 (uri (cran-uri "rms" version))
13478 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13479 (build-system r-build-system)
13481 `(("r-ggplot2" ,r-ggplot2)
13482 ("r-hmisc" ,r-hmisc)
13483 ("r-htmltable" ,r-htmltable)
13484 ("r-htmltools" ,r-htmltools)
13485 ("r-lattice" ,r-lattice)
13486 ("r-multcomp" ,r-multcomp)
13488 ("r-polspline" ,r-polspline)
13489 ("r-quantreg" ,r-quantreg)
13490 ("r-rpart" ,r-rpart)
13491 ("r-sparsem" ,r-sparsem)
13492 ("r-survival" ,r-survival)))
13493 (native-inputs `(("gfortran" ,gfortran)))
13494 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13495 (synopsis "Regression modeling strategies")
13497 "This is a package for regression modeling, testing, estimation,
13498 validation, graphics, prediction, and typesetting by storing enhanced model
13499 design attributes in the fit. The rms package is a collection of functions
13500 that assist with and streamline modeling. It also contains functions for
13501 binary and ordinal logistic regression models, ordinal models for continuous Y
13502 with a variety of distribution families, and the Buckley-James multiple
13503 regression model for right-censored responses, and implements penalized
13504 maximum likelihood estimation for logistic and ordinary linear models. The
13505 package works with almost any regression model, but it was especially written
13506 to work with binary or ordinal regression models, Cox regression, accelerated
13507 failure time models, ordinary linear models, the Buckley-James model,
13508 generalized least squares for serially or spatially correlated observations,
13509 generalized linear models, and quantile regression.")
13510 (license license:gpl2+)))
13512 (define-public r-haplo-stats
13514 (name "r-haplo-stats")
13519 (uri (cran-uri "haplo.stats" version))
13522 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13523 (properties `((upstream-name . "haplo.stats")))
13524 (build-system r-build-system)
13526 `(("r-rms" ,r-rms)))
13528 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13529 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13530 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13532 "This package provides routines for the analysis of indirectly measured
13533 haplotypes. The statistical methods assume that all subjects are unrelated
13534 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13535 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13536 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13537 examples in the vignette.")
13538 (license license:gpl2+)))
13540 (define-public r-bqtl
13547 (uri (cran-uri "bqtl" version))
13550 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13551 (build-system r-build-system)
13552 (native-inputs `(("gfortran" ,gfortran)))
13553 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13554 (synopsis "Bayesian QTL mapping toolkit")
13556 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13557 lines. It includes maximum likelihood and Bayesian tools.")
13558 (license license:gpl2+)))
13560 (define-public r-ibdreg
13567 (uri (cran-uri "ibdreg" version))
13570 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13571 (build-system r-build-system)
13572 (home-page "https://www.mayo.edu/research/labs/\
13573 statistical-genetics-genetic-epidemiology/software")
13574 (synopsis "Regression methods for IBD linkage with covariates")
13576 "This package provides a method to test genetic linkage with covariates
13577 by regression methods with response IBD sharing for relative pairs. Account
13578 for correlations of IBD statistics and covariates for relative pairs within
13579 the same pedigree.")
13580 (license license:gpl2+)))
13582 (define-public r-dlmap
13589 (uri (cran-uri "dlmap" version))
13592 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13593 (build-system r-build-system)
13595 `(("r-ibdreg" ,r-ibdreg)
13599 ("r-wgaim" ,r-wgaim)))
13600 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13601 (synopsis "Detection localization mapping for QTL")
13603 "This is package for QTL mapping in a mixed model framework with separate
13604 detection and localization stages. The first stage detects the number of QTL
13605 on each chromosome based on the genetic variation due to grouped markers on
13606 the chromosome; the second stage uses this information to determine the most
13607 likely QTL positions. The mixed model can accommodate general fixed and
13608 random effects, including spatial effects in field trials and pedigree
13609 effects. It is applicable to backcrosses, doubled haploids, recombinant
13610 inbred lines, F2 intercrosses, and association mapping populations.")
13611 (license license:gpl2)))
13613 (define-public r-ldheatmap
13615 (name "r-ldheatmap")
13620 (uri (cran-uri "LDheatmap" version))
13623 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13624 (properties `((upstream-name . "LDheatmap")))
13625 (build-system r-build-system)
13627 `(("r-genetics" ,r-genetics)
13629 ("r-snpstats" ,r-snpstats)))
13630 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
13631 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13633 "This package provides tools to produce a graphical display, as a heat
13634 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13635 optionally include the physical locations or genetic map distances of each SNP
13637 (license license:gpl3)))
13639 (define-public r-hwde
13646 (uri (cran-uri "hwde" version))
13649 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13650 (build-system r-build-system)
13651 (home-page "https://cran.r-project.org/web/packages/hwde/")
13652 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13654 "This package fits models for genotypic disequilibria, as described in
13655 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13656 terms are available that account for first order interactions between loci.
13657 It also implements, for a single locus in a single population, a conditional
13658 exact test for Hardy-Weinberg equilibrium.")
13659 (license license:gpl2+)))
13661 (define-public r-tdthap
13668 (uri (cran-uri "tdthap" version))
13671 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13672 (build-system r-build-system)
13673 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13674 (synopsis "TDT tests for extended haplotypes")
13676 "Functions and examples are provided for transmission/disequilibrium
13677 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13678 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13679 (license license:artistic2.0)))
13681 (define-public r-sparql
13687 (uri (cran-uri "SPARQL" version))
13690 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13691 (properties `((upstream-name . "SPARQL")))
13692 (build-system r-build-system)
13694 `(("r-rcurl" ,r-rcurl)
13696 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13697 (synopsis "SPARQL client for R")
13698 (description "This package provides an interface to use SPARQL to pose
13699 SELECT or UPDATE queries to an end-point.")
13700 ;; The only license indication is found in the DESCRIPTION file,
13701 ;; which states GPL-3. So we cannot assume GPLv3+.
13702 (license license:gpl3)))
13704 (define-public r-bookdown
13706 (name "r-bookdown")
13710 (uri (cran-uri "bookdown" version))
13713 "1my6g16phx21v5cvfqcnjibh3zcv02xkix347aafd6a7r3hnxpq5"))))
13714 (build-system r-build-system)
13716 `(("r-htmltools" ,r-htmltools)
13717 ("r-knitr" ,r-knitr)
13718 ("r-rmarkdown" ,r-rmarkdown)
13719 ("r-tinytex" ,r-tinytex)
13721 ("pandoc" ,ghc-pandoc)))
13722 (home-page "https://github.com/rstudio/bookdown")
13723 (synopsis "Authoring books and technical documents with R markdown")
13724 (description "This package provides output formats and utilities for
13725 authoring books and technical documents with R Markdown.")
13726 (license license:gpl3)))
13728 (define-public r-optparse
13730 (name "r-optparse")
13735 (uri (cran-uri "optparse" version))
13738 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13739 (build-system r-build-system)
13741 `(("r-getopt" ,r-getopt)))
13742 (home-page "https://github.com/trevorld/optparse")
13743 (synopsis "Command line option parser")
13745 "This package provides a command line parser inspired by Python's
13746 @code{optparse} library to be used with Rscript to write shebang scripts
13747 that accept short and long options.")
13748 (license license:gpl2+)))
13750 (define-public r-wgcna
13757 (uri (cran-uri "WGCNA" version))
13760 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
13761 (properties `((upstream-name . "WGCNA")))
13762 (build-system r-build-system)
13764 `(("r-annotationdbi" ,r-annotationdbi)
13765 ("r-doparallel" ,r-doparallel)
13766 ("r-dynamictreecut" ,r-dynamictreecut)
13767 ("r-fastcluster" ,r-fastcluster)
13768 ("r-foreach" ,r-foreach)
13769 ("r-go-db" ,r-go-db)
13770 ("r-hmisc" ,r-hmisc)
13771 ("r-impute" ,r-impute)
13773 ("r-survival" ,r-survival)
13774 ("r-matrixstats" ,r-matrixstats)
13775 ("r-preprocesscore" ,r-preprocesscore)))
13777 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13778 (synopsis "Weighted correlation network analysis")
13780 "This package provides functions necessary to perform Weighted
13781 Correlation Network Analysis on high-dimensional data. It includes functions
13782 for rudimentary data cleaning, construction and summarization of correlation
13783 networks, module identification and functions for relating both variables and
13784 modules to sample traits. It also includes a number of utility functions for
13785 data manipulation and visualization.")
13786 (license license:gpl2+)))
13788 (define-public r-kernlab
13795 (uri (cran-uri "kernlab" version))
13797 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13798 (build-system r-build-system)
13799 (home-page "https://cran.r-project.org/web/packages/kernlab")
13800 (synopsis "Kernel-based machine learning tools")
13802 "This package provides kernel-based machine learning methods for
13803 classification, regression, clustering, novelty detection, quantile regression
13804 and dimensionality reduction. Among other methods @code{kernlab} includes
13805 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13807 (license license:gpl2)))
13809 (define-public r-hierfstat
13811 (name "r-hierfstat")
13812 (version "0.04-22")
13816 (uri (cran-uri "hierfstat" version))
13819 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13820 (build-system r-build-system)
13822 `(("r-ade4" ,r-ade4)
13823 ("r-adegenet" ,r-adegenet)
13824 ("r-gtools" ,r-gtools)))
13825 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13826 (synopsis "Estimation and tests of hierarchical F-statistics")
13828 "This package allows the estimation of hierarchical F-statistics from
13829 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13830 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13831 are also given to test via randomisations the significance of each F and
13832 variance components, using the likelihood-ratio statistics G.")
13833 (license license:gpl2+)))
13835 (define-public r-hapassoc
13837 (name "r-hapassoc")
13842 (uri (cran-uri "hapassoc" version))
13845 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13846 (build-system r-build-system)
13847 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
13848 (synopsis "Inference of trait associations with SNP haplotypes")
13850 "Hapassoc performs likelihood inference of trait associations with
13851 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13852 functions are developed primarily for data collected in cohort or
13853 cross-sectional studies. They can accommodate uncertain haplotype phase and
13854 handle missing genotypes at some SNPs.")
13855 (license license:gpl2)))
13857 (define-public r-sampling
13859 (name "r-sampling")
13864 (uri (cran-uri "sampling" version))
13867 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13868 (build-system r-build-system)
13870 `(("r-lpsolve" ,r-lpsolve)
13871 ("r-mass" ,r-mass)))
13872 (home-page "https://cran.r-project.org/web/packages/sampling/")
13873 (synopsis "Survey sampling")
13875 "This package provides functions for drawing and calibrating samples.")
13876 (license license:gpl2+)))
13878 (define-public r-r2html
13885 (uri (cran-uri "R2HTML" version))
13888 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13889 (properties `((upstream-name . "R2HTML")))
13890 (build-system r-build-system)
13891 (home-page "https://github.com/nalimilan/R2HTML")
13892 (synopsis "HTML export for R objects")
13894 "This package includes HTML functions and methods to write in an HTML
13895 file. Thus, making HTML reports is easy. It includes a function that allows
13896 redirection on the fly, which appears to be very useful for teaching purposes,
13897 as the student can keep a copy of the produced output to keep all that they
13898 did during the course. The package comes with a vignette describing how to
13899 write HTML reports for statistical analysis. Finally, a driver for Sweave
13900 parses HTML flat files containing R code and to automatically write
13901 the corresponding outputs (tables and graphs).")
13902 (license license:gpl2+)))
13904 (define-public r-rjava
13911 (uri (cran-uri "rJava" version))
13914 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
13915 (properties `((upstream-name . "rJava")))
13916 (build-system r-build-system)
13918 `(#:modules ((guix build utils)
13919 (guix build r-build-system)
13922 (modify-phases %standard-phases
13923 (add-after 'unpack 'set-JAVA_HOME
13924 (lambda* (#:key inputs #:allow-other-keys)
13925 (let ((jdk (assoc-ref inputs "jdk")))
13926 (setenv "JAVA_HOME" jdk)
13927 (setenv "JAVA" (which "java"))
13928 (setenv "JAR" (which "jar"))
13929 (setenv "JAVAC" (which "javac"))
13930 (setenv "JAVAH" (which "javah"))
13931 (setenv "JAVA_CPPFLAGS"
13932 (string-append "-I" jdk "/include "
13933 "-I" jdk "/include/linux"))
13934 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13935 ((lib) (setenv "JAVA_LIBS" lib))
13936 (_ (error "Could not find libjvm.so"))))
13940 ("jdk" ,icedtea-8 "jdk")
13943 (home-page "https://www.rforge.net/rJava/")
13944 (synopsis "Low-Level R to Java interface")
13946 "This package provides a low-level interface to the Java VM very much
13947 like .C/.Call and friends. It allows the creation of objects, calling methods
13948 and accessing fields.")
13949 (license license:gpl2)))
13951 (define-public r-svmisc
13958 (uri (cran-uri "svMisc" version))
13961 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13962 (properties `((upstream-name . "svMisc")))
13963 (build-system r-build-system)
13964 (home-page "https://github.com/SciViews/svMisc")
13965 (synopsis "Miscellaneous functions for SciViews")
13967 "This package provides miscellaneous functions for SciViews or general
13968 use, including tools to manage a temporary environment attached to the search
13969 path for temporary variables you do not want to @code{save()} or
13970 @code{load()}; test the current platform; showing progress bars, etc.")
13971 (license license:gpl2)))
13973 (define-public r-xyz
13980 (uri (cran-uri "xyz" version))
13983 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13984 (build-system r-build-system)
13986 `(("r-rcpp" ,r-rcpp)))
13987 (home-page "https://cran.r-project.org/web/packages/xyz/")
13988 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13990 "High dimensional interaction search by brute force requires a quadratic
13991 computational cost in the number of variables. The xyz algorithm provably
13992 finds strong interactions in almost linear time. For details of the algorithm
13993 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13994 interaction search in high-dimensional data.")
13995 ;; Any version of the GPL.
13996 (license license:gpl2+)))
13998 (define-public r-rttf2pt1
14000 (name "r-rttf2pt1")
14005 (uri (cran-uri "Rttf2pt1" version))
14008 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14009 (properties `((upstream-name . "Rttf2pt1")))
14010 (build-system r-build-system)
14011 (home-page "https://github.com/wch/Rttf2pt1")
14012 (synopsis "Font conversion utility")
14014 "This package contains the program @code{ttf2pt1}, for use with the
14015 @code{extrafont} package.")
14016 ;; Most of the files are covered under the Expat license. Some files are
14017 ;; covered under BSD-3. Deviations for individual files are recorded in
14018 ;; the LICENSE file.
14019 (license (list license:bsd-3 license:expat
14020 (license:non-copyleft "file://LICENSE")))))
14022 (define-public r-extrafontdb
14024 (name "r-extrafontdb")
14029 (uri (cran-uri "extrafontdb" version))
14032 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14033 (build-system r-build-system)
14034 (home-page "https://github.com/wch/extrafontdb")
14035 (synopsis "Database for the extrafont package")
14037 "This package holds the database for the @code{extrafont} package.")
14038 (license license:gpl2)))
14040 (define-public r-extrafont
14042 (name "r-extrafont")
14047 (uri (cran-uri "extrafont" version))
14050 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14051 (build-system r-build-system)
14053 `(("r-extrafontdb" ,r-extrafontdb)
14054 ("r-rttf2pt1" ,r-rttf2pt1)))
14055 (home-page "https://github.com/wch/extrafont")
14056 (synopsis "Tools for using fonts in R")
14058 "The extrafont package makes it easier to use fonts other than the basic
14059 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14060 used with PDF or PostScript output files. There are two hurdles for using
14061 fonts in PDF (or Postscript) output files:
14064 @item Making R aware of the font and the dimensions of the characters.
14065 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14066 properly on a device that doesn't have the font. This is usually needed if
14067 you want to print the PDF file or share it with others.
14070 The extrafont package makes both of these things easier.")
14071 (license license:gpl2)))
14073 (define-public r-xkcd
14080 (uri (cran-uri "xkcd" version))
14083 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14084 (build-system r-build-system)
14086 `(("r-extrafont" ,r-extrafont)
14087 ("r-ggplot2" ,r-ggplot2)
14088 ("r-hmisc" ,r-hmisc)))
14089 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14090 (synopsis "Plot ggplot2 graphics in the XKCD style")
14092 "This package provides the means to plot ggplot2 graphs in the style of
14093 the XKCD web comic.")
14094 (license license:gpl3)))
14096 (define-public r-msigdbr
14103 (uri (cran-uri "msigdbr" version))
14106 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14107 (build-system r-build-system)
14109 `(("r-dplyr" ,r-dplyr)
14110 ("r-magrittr" ,r-magrittr)
14111 ("r-rlang" ,r-rlang)
14112 ("r-tibble" ,r-tibble)))
14113 (home-page "https://github.com/igordot/msigdbr")
14114 (synopsis "MSigDB gene sets for multiple organisms")
14116 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14117 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14118 software in a standard R data frame with key-value pairs. Included are the
14119 original human gene symbols and Entrez IDs as well as the equivalents for
14120 various frequently studied model organisms such as mouse, rat, pig, fly, and
14122 ;; The package is covered under the Expat license, but the upstream MSigDB
14123 ;; files are made available under the Creative Commons Attribution 4.0
14124 ;; International license.
14125 (license (list license:expat license:cc-by4.0))))
14127 (define-public r-gridgraphics
14129 (name "r-gridgraphics")
14134 (uri (cran-uri "gridGraphics" version))
14137 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14138 (properties `((upstream-name . "gridGraphics")))
14139 (build-system r-build-system)
14140 (home-page "https://github.com/pmur002/gridgraphics")
14141 (synopsis "Redraw base graphics using @code{grid} graphics")
14143 "This package provides functions to convert a page of plots drawn with
14144 the @code{graphics} package into identical output drawn with the @code{grid}
14145 package. The result looks like the original @code{graphics}-based plot, but
14146 consists of @code{grid} grobs and viewports that can then be manipulated with
14147 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14148 (license license:gpl2+)))
14150 (define-public r-farver
14157 (uri (cran-uri "farver" version))
14160 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14161 (build-system r-build-system)
14162 (home-page "https://github.com/thomasp85/farver")
14163 (synopsis "Vectorized color conversion and comparison")
14165 "The encoding of color can be handled in many different ways, using
14166 different color spaces. As different color spaces have different uses,
14167 efficient conversion between these representations are important. This
14168 package provides a set of functions that gives access to very fast color space
14169 conversion and comparisons implemented in C++, and offers 100-fold speed
14170 improvements over the @code{convertColor} function in the @code{grDevices}
14172 (license license:expat)))
14174 (define-public r-ggplotify
14176 (name "r-ggplotify")
14181 (uri (cran-uri "ggplotify" version))
14184 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14185 (build-system r-build-system)
14187 `(("r-ggplot2" ,r-ggplot2)
14188 ("r-gridgraphics" ,r-gridgraphics)
14189 ("r-rvcheck" ,r-rvcheck)))
14191 `(("r-knitr" ,r-knitr)))
14192 (home-page "https://github.com/GuangchuangYu/ggplotify")
14193 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14195 "This package provides tools to convert plot function calls (using
14196 expression or formula) to @code{grob} or @code{ggplot} objects that are
14197 compatible with the @code{grid} and @code{ggplot2} environment. With this
14198 package, we are able to e.g. use @code{cowplot} to align plots produced by
14199 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14200 converting them to @code{ggplot} objects.")
14201 (license license:artistic2.0)))
14203 (define-public r-triebeard
14205 (name "r-triebeard")
14210 (uri (cran-uri "triebeard" version))
14213 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14214 (build-system r-build-system)
14215 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14216 (home-page "https://github.com/Ironholds/triebeard/")
14217 (synopsis "Radix trees in Rcpp")
14219 "Radix trees, or tries, are key-value data structures optimized for
14220 efficient lookups, similar in purpose to hash tables. This package provides
14221 an implementation of radix trees for use in R programming and in developing
14222 packages with Rcpp.")
14223 (license license:expat)))
14225 (define-public r-tweenr
14232 (uri (cran-uri "tweenr" version))
14235 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14236 (build-system r-build-system)
14238 `(("r-farver" ,r-farver)
14239 ("r-magrittr" ,r-magrittr)
14241 ("r-rlang" ,r-rlang)))
14242 (home-page "https://github.com/thomasp85/tweenr")
14243 (synopsis "Interpolate data for smooth animations")
14245 "In order to create smooth animation between states of data, tweening is
14246 necessary. This package provides a range of functions for creating tweened
14247 data that can be used as basis for animation. Furthermore it adds a number of
14248 vectorized interpolaters for common R data types such as numeric, date and
14250 (license license:expat)))
14252 (define-public r-polyclip
14254 (name "r-polyclip")
14259 (uri (cran-uri "polyclip" version))
14262 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14263 (build-system r-build-system)
14264 (native-inputs `(("pkg-config" ,pkg-config)))
14265 (home-page "http://www.angusj.com/delphi/clipper.php")
14266 (synopsis "Polygon clipping")
14268 "This package provides an R port of the library Clipper. It performs
14269 polygon clipping operations (intersection, union, set minus, set difference)
14270 for polygonal regions of arbitrary complexity, including holes. It computes
14271 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14272 dilations) for polygonal regions and polygonal lines. It computes the
14273 Minkowski Sum of general polygons. There is a function for removing
14274 self-intersections from polygon data.")
14275 (license license:boost1.0)))
14277 (define-public r-urltools
14279 (name "r-urltools")
14284 (uri (cran-uri "urltools" version))
14287 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14288 (build-system r-build-system)
14290 `(("r-rcpp" ,r-rcpp)
14291 ("r-triebeard" ,r-triebeard)))
14292 (home-page "https://github.com/Ironholds/urltools/")
14293 (synopsis "Vectorized tools for URL handling and parsing")
14295 "This package provides a toolkit for all URL-handling needs, including
14296 encoding and decoding, parsing, parameter extraction and modification. All
14297 functions are designed to be both fast and entirely vectorized. It is
14298 intended to be useful for people dealing with web-related datasets, such as
14299 server-side logs, although may be useful for other situations involving large
14301 (license license:expat)))
14303 (define-public r-ggforce
14310 (uri (cran-uri "ggforce" version))
14313 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14314 (build-system r-build-system)
14316 `(("r-ggplot2" ,r-ggplot2)
14317 ("r-gtable" ,r-gtable)
14319 ("r-polyclip" ,r-polyclip)
14321 ("r-rcppeigen" ,r-rcppeigen)
14322 ("r-rlang" ,r-rlang)
14323 ("r-scales" ,r-scales)
14324 ("r-tidyselect" ,r-tidyselect)
14325 ("r-tweenr" ,r-tweenr)
14326 ("r-withr" ,r-withr)))
14327 (home-page "https://ggforce.data-imaginist.com")
14328 (synopsis "Accelerating ggplot2")
14330 "The aim of the ggplot2 package is to aid in visual data investigations.
14331 This focus has led to a lack of facilities for composing specialized plots.
14332 Thi package aims to be a collection of mainly new statistics and geometries
14333 that fills this gap.")
14334 (license license:expat)))
14336 (define-public r-europepmc
14338 (name "r-europepmc")
14343 (uri (cran-uri "europepmc" version))
14346 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14347 (build-system r-build-system)
14349 `(("r-dplyr" ,r-dplyr)
14351 ("r-jsonlite" ,r-jsonlite)
14353 ("r-progress" ,r-progress)
14354 ("r-purrr" ,r-purrr)
14355 ("r-urltools" ,r-urltools)
14356 ("r-xml2" ,r-xml2)))
14357 (home-page "https://github.com/ropensci/europepmc/")
14358 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14360 "This package provides an R Client for the
14361 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14362 Service}. It gives access to both metadata on life science literature and
14363 open access full texts. Europe PMC indexes all PubMed content and other
14364 literature sources including Agricola, a bibliographic database of citations
14365 to the agricultural literature, or Biological Patents. In addition to
14366 bibliographic metadata, the client allows users to fetch citations and
14367 reference lists. Links between life-science literature and other EBI
14368 databases, including ENA, PDB or ChEMBL are also accessible.")
14369 (license license:gpl3)))
14371 (define-public r-ggraph
14378 (uri (cran-uri "ggraph" version))
14381 "1ckq82hg52vr2wydkqv2wrppgjyvddd6bwqzrngqlm7j71xapjl0"))))
14382 (build-system r-build-system)
14384 `(("r-digest" ,r-digest)
14385 ("r-dplyr" ,r-dplyr)
14386 ("r-ggforce" ,r-ggforce)
14387 ("r-ggplot2" ,r-ggplot2)
14388 ("r-ggrepel" ,r-ggrepel)
14389 ("r-graphlayouts" ,r-graphlayouts)
14390 ("r-gtable" ,r-gtable)
14391 ("r-igraph" ,r-igraph)
14394 ("r-rlang" ,r-rlang)
14395 ("r-scales" ,r-scales)
14396 ("r-tidygraph" ,r-tidygraph)
14397 ("r-viridis" ,r-viridis)))
14399 `(("r-knitr" ,r-knitr)))
14400 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14401 (synopsis "Implementation of grammar of graphics for graphs and networks")
14403 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14404 graph and network visualizations due to its reliance on tabular data input.
14405 The ggraph package is an extension of the ggplot2 API tailored to graph
14406 visualizations and provides the same flexible approach to building up plots
14408 (license license:gpl3)))
14410 (define-public r-varselrf
14412 (name "r-varselrf")
14417 (uri (cran-uri "varSelRF" version))
14420 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14421 (properties `((upstream-name . "varSelRF")))
14422 (build-system r-build-system)
14424 `(("r-randomforest" ,r-randomforest)))
14425 (home-page "https://www.ligarto.org/rdiaz/software/software")
14426 (synopsis "Variable selection using random forests")
14428 "This package provides tools for the variable selection from random
14429 forests using both backwards variable elimination (for the selection of small
14430 sets of non-redundant variables) and selection based on the importance
14431 spectrum (somewhat similar to scree plots; for the selection of large,
14432 potentially highly-correlated variables). The main applications are in
14433 high-dimensional data (e.g., microarray data, and other genomics and
14434 proteomics applications).")
14435 (license license:gpl2+)))
14437 (define-public r-pamr
14444 (uri (cran-uri "pamr" version))
14447 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14448 (build-system r-build-system)
14450 `(("r-cluster" ,r-cluster)
14451 ("r-survival" ,r-survival)))
14452 (native-inputs `(("gfortran" ,gfortran)))
14453 (home-page "https://cran.r-project.org/web/packages/pamr/")
14454 (synopsis "Prediction Analysis for Microarrays")
14456 "This package provides some functions for sample classification in
14458 (license license:gpl2)))
14460 (define-public r-rda
14463 (version "1.0.2-2.1")
14467 (uri (cran-uri "rda" version))
14470 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14471 (build-system r-build-system)
14472 (home-page "https://cran.r-project.org/web/packages/rda/")
14473 (synopsis "Shrunken centroids regularized discriminant analysis")
14475 "This package provides tools for shrunken centroids regularized
14476 discriminant analysis for the purpose of classifying high dimensional data.")
14477 (license license:gpl2+)))
14479 (define-public r-ggvis
14486 (uri (cran-uri "ggvis" version))
14489 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14490 (build-system r-build-system)
14492 `(("r-assertthat" ,r-assertthat)
14493 ("r-dplyr" ,r-dplyr)
14494 ("r-htmltools" ,r-htmltools)
14495 ("r-jsonlite" ,r-jsonlite)
14496 ("r-lazyeval" ,r-lazyeval)
14497 ("r-magrittr" ,r-magrittr)
14498 ("r-shiny" ,r-shiny)))
14499 (home-page "https://ggvis.rstudio.com/")
14500 (synopsis "Interactive grammar of graphics")
14502 "This package is a data visualization package for R providing an
14503 implementation of an interactive grammar of graphics, taking the best parts of
14504 ggplot2, combining them with the reactive framework of Shiny and drawing web
14505 graphics using Vega.")
14506 (license license:gpl2)))
14508 (define-public r-gbm
14515 (uri (cran-uri "gbm" version))
14518 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14519 (build-system r-build-system)
14521 `(("r-gridextra" ,r-gridextra)
14522 ("r-lattice" ,r-lattice)
14523 ("r-survival" ,r-survival)))
14524 (home-page "https://github.com/gbm-developers/gbm")
14525 (synopsis "Generalized boosted regression models")
14527 "This package is an implementation of extensions to Freund and Schapire's
14528 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14529 regression methods for least squares, absolute loss, t-distribution loss,
14530 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14531 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14532 and Learning to Rank measures (LambdaMart).")
14533 (license license:gpl2+)))
14535 (define-public r-threejs
14542 (uri (cran-uri "threejs" version))
14545 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14546 (build-system r-build-system)
14548 `(#:modules ((guix build utils)
14549 (guix build r-build-system)
14553 (modify-phases %standard-phases
14554 (add-after 'unpack 'process-javascript
14555 (lambda* (#:key inputs #:allow-other-keys)
14556 (with-directory-excursion "inst"
14560 `((,(assoc-ref inputs "js-jquery")
14561 "htmlwidgets/lib/jquery/jquery.min.js")
14562 (,(assoc-ref inputs "js-threejs-111")
14563 "htmlwidgets/lib/threejs-111/three.min.js"))))
14564 (lambda (sources targets)
14565 (for-each (lambda (source target)
14566 (format #t "Processing ~a --> ~a~%"
14568 (delete-file target)
14569 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14570 (call-with-output-file target
14572 (dump-port minified port)))))
14573 sources targets))))
14576 `(("r-base64enc" ,r-base64enc)
14577 ("r-crosstalk" ,r-crosstalk)
14578 ("r-htmlwidgets" ,r-htmlwidgets)
14579 ("r-igraph" ,r-igraph)))
14581 `(("uglify-js" ,uglify-js)
14585 (uri "https://code.jquery.com/jquery-1.12.4.js")
14588 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
14592 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
14595 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
14596 (home-page "https://bwlewis.github.io/rthreejs")
14597 (synopsis "Interactive 3D scatter plots, networks and globes")
14599 "Create interactive 3D scatter plots, network plots, and globes in R
14600 using the three.js visualization library.")
14601 (license license:expat)))
14603 (define-public r-mlbench
14610 (uri (cran-uri "mlbench" version))
14613 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14614 (build-system r-build-system)
14615 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14616 (synopsis "Machine learning benchmark problems")
14618 "This package provides a collection of artificial and real-world machine
14619 learning benchmark problems, including, e.g., several data sets from the UCI
14621 (license license:gpl2)))
14623 (define-public r-mpm
14630 (uri (cran-uri "mpm" version))
14633 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14634 (build-system r-build-system)
14636 `(("r-kernsmooth" ,r-kernsmooth)
14637 ("r-mass" ,r-mass)))
14638 (home-page "http://mpm.r-forge.r-project.org")
14639 (synopsis "Multivariate projection methods")
14641 "This is a package for exploratory graphical analysis of multivariate
14642 data, specifically gene expression data with different projection methods:
14643 principal component analysis, correspondence analysis, spectral map
14645 (license license:gpl2+)))
14647 (define-public r-png
14653 (uri (cran-uri "png" version))
14656 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14657 (build-system r-build-system)
14659 `(("libpng" ,libpng)
14661 (home-page "https://www.rforge.net/png/")
14662 (synopsis "Read and write PNG images")
14664 "This package provides an easy and simple way to read, write and display
14665 bitmap images stored in the PNG format. It can read and write both files and
14666 in-memory raw vectors.")
14667 ;; Any of these GPL versions.
14668 (license (list license:gpl2 license:gpl3))))
14670 (define-public r-ggcorrplot
14672 (name "r-ggcorrplot")
14677 (uri (cran-uri "ggcorrplot" version))
14680 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14681 (build-system r-build-system)
14683 `(("r-ggplot2" ,r-ggplot2)
14684 ("r-reshape2" ,r-reshape2)))
14685 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14686 (synopsis "Visualization of a correlation matrix using ggplot2")
14688 "The ggcorrplot package can be used to visualize easily a correlation
14689 matrix using ggplot2. It provides a solution for reordering the correlation
14690 matrix and displays the significance level on the plot. It also includes a
14691 function for computing a matrix of correlation p-values.")
14692 (license license:gpl2)))
14694 (define-public r-flexdashboard
14696 (name "r-flexdashboard")
14697 (version "0.5.1.1")
14701 (uri (cran-uri "flexdashboard" version))
14704 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14705 (build-system r-build-system)
14707 `(#:modules ((guix build utils)
14708 (guix build r-build-system)
14712 (ice-9 textual-ports))
14714 (modify-phases %standard-phases
14715 (add-after 'unpack 'process-javascript
14716 (lambda* (#:key inputs #:allow-other-keys)
14717 (with-directory-excursion "inst"
14718 ;; Concatenate all components of prism.js
14719 (let ((contents (string-join
14720 (map (lambda (name)
14721 (call-with-input-file
14722 (assoc-ref inputs name)
14726 "js-prism-line-numbers"))
14728 (call-with-output-file "prism-src.js"
14729 (cut display contents <>)))
14733 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14734 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14736 "www/sly/sly.min.js")
14738 "www/prism/prism.js")
14739 (,(assoc-ref inputs "js-raphael")
14740 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14741 (,(assoc-ref inputs "js-featherlight")
14742 "www/featherlight/featherlight.min.js"))))
14743 (lambda (sources targets)
14744 (for-each (lambda (source target)
14745 (format #t "Processing ~a --> ~a~%"
14747 (delete-file target)
14748 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14749 (call-with-output-file target
14751 (dump-port minified port)))))
14752 sources targets))))
14755 `(("r-htmltools" ,r-htmltools)
14756 ("r-htmlwidgets" ,r-htmlwidgets)
14757 ("r-jsonlite" ,r-jsonlite)
14758 ("r-knitr" ,r-knitr)
14759 ("r-rmarkdown" ,r-rmarkdown)
14760 ("r-shiny" ,r-shiny)))
14762 `(("uglify-js" ,uglify-js)
14766 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14769 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14773 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14776 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14780 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14783 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14784 ("js-prism-line-numbers"
14787 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14790 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14794 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14797 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14798 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14799 (synopsis "R Markdown format for flexible dashboards")
14801 "This package provides an R Markdown format for converting an R Markdown
14802 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14803 of its components to the containing web page.")
14804 (license license:expat)))
14806 (define-public r-preseqr
14813 (uri (cran-uri "preseqR" version))
14816 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14817 (properties `((upstream-name . "preseqR")))
14818 (build-system r-build-system)
14820 `(("r-polynom" ,r-polynom)))
14821 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14822 (synopsis "Predicting species accumulation curves")
14824 "This package can be used to predict the r-species accumulation
14825 curve (r-SAC), which is the number of species represented at least r times as
14826 a function of the sampling effort. When r = 1, the curve is known as the
14827 species accumulation curve, or the library complexity curve in high-throughput
14828 genomic sequencing. The package includes both parametric and nonparametric
14829 methods, as described by Deng C, et al. (2018).")
14830 (license license:gpl3)))
14832 (define-public r-mapplots
14834 (name "r-mapplots")
14839 (uri (cran-uri "mapplots" version))
14842 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14843 (build-system r-build-system)
14844 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14845 (synopsis "Data visualization on maps")
14847 "This package helps you create simple maps; add sub-plots like pie plots
14848 to a map or any other plot; format, plot and export gridded data. The package
14849 was developed for displaying fisheries data but most functions can be used for
14850 more generic data visualisation.")
14851 (license license:gpl2+)))
14853 (define-public r-pmcmr
14860 (uri (cran-uri "PMCMR" version))
14863 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14864 (properties `((upstream-name . "PMCMR")))
14865 (build-system r-build-system)
14866 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14867 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14869 "This is a deprecated package for calculating pairwise multiple
14870 comparisons of mean rank sums. This package is superseded by the novel
14871 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14872 compatibility of dependent packages for some time.")
14873 (license license:gpl3+)))
14875 (define-public r-downloader
14877 (name "r-downloader")
14882 (uri (cran-uri "downloader" version))
14885 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14886 (build-system r-build-system)
14888 `(("r-digest" ,r-digest)))
14889 (home-page "https://github.com/wch/downloader")
14890 (synopsis "Download files over HTTP and HTTPS")
14892 "This package provides a wrapper for the @code{download.file} function,
14893 making it possible to download files over HTTPS across platforms. The
14894 @code{RCurl} package provides this functionality (and much more) but has
14895 external dependencies. This package has is implemented purely in R.")
14896 (license license:gpl2)))
14898 (define-public r-rex
14905 (uri (cran-uri "rex" version))
14908 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14909 (build-system r-build-system)
14911 `(("r-lazyeval" ,r-lazyeval)
14912 ("r-magrittr" ,r-magrittr)))
14913 (home-page "https://github.com/kevinushey/rex")
14914 (synopsis "Friendly regular expressions")
14916 "This package provides a friendly interface for the construction of
14917 regular expressions. Regular expressions are a very powerful feature, however
14918 they are often difficult to interpret. Rex allows you to build complex
14919 regular expressions from human readable expressions")
14920 (license license:expat)))
14922 (define-public r-xmlparsedata
14924 (name "r-xmlparsedata")
14929 (uri (cran-uri "xmlparsedata" version))
14932 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14933 (properties `((upstream-name . "xmlparsedata")))
14934 (build-system r-build-system)
14935 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14936 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14938 "This package provides tools to convert the output of
14939 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14940 @code{XPath}, and is easier to manipulate in general.")
14941 (license license:expat)))
14943 (define-public r-cyclocomp
14945 (name "r-cyclocomp")
14950 (uri (cran-uri "cyclocomp" version))
14953 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14954 (properties `((upstream-name . "cyclocomp")))
14955 (build-system r-build-system)
14957 `(("r-callr" ,r-callr)
14958 ("r-crayon" ,r-crayon)
14960 ("r-remotes" ,r-remotes)
14961 ("r-withr" ,r-withr)))
14962 (home-page "https://github.com/MangoTheCat/cyclocomp")
14963 (synopsis "Cyclomatic complexity of R code")
14965 "Cyclomatic complexity is a software metric, used to indicate the
14966 complexity of a program. It is a quantitative measure of the number of
14967 linearly independent paths through a program's source code. This package
14968 provides tools to compute this metric.")
14969 (license license:expat)))
14971 (define-public r-lintr
14978 (uri (cran-uri "lintr" version))
14981 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
14982 (properties `((upstream-name . "lintr")))
14983 (build-system r-build-system)
14985 `(("r-codetools" ,r-codetools)
14986 ("r-crayon" ,r-crayon)
14987 ("r-cyclocomp" ,r-cyclocomp)
14988 ("r-digest" ,r-digest)
14990 ("r-jsonlite" ,r-jsonlite)
14991 ("r-knitr" ,r-knitr)
14993 ("r-rstudioapi" ,r-rstudioapi)
14994 ("r-testthat" ,r-testthat)
14996 ("r-xmlparsedata" ,r-xmlparsedata)))
14997 (home-page "https://github.com/jimhester/lintr")
14998 (synopsis "Linter for R code")
14999 (description "This package checks adherence to a given style, syntax
15000 errors and possible semantic issues. It supports on the fly checking of R
15001 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15002 (license license:expat)))
15004 (define-public r-sctransform
15006 (name "r-sctransform")
15011 (uri (cran-uri "sctransform" version))
15014 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15015 (build-system r-build-system)
15017 `(("r-future-apply" ,r-future-apply)
15018 ("r-ggplot2" ,r-ggplot2)
15019 ("r-gridextra" ,r-gridextra)
15021 ("r-matrix" ,r-matrix)
15023 ("r-rcppeigen" ,r-rcppeigen)
15024 ("r-reshape2" ,r-reshape2)))
15025 (home-page "https://github.com/ChristophH/sctransform")
15026 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15028 "This package provides a normalization method for single-cell UMI count
15029 data using a variance stabilizing transformation. The transformation is based
15030 on a negative binomial regression model with regularized parameters. As part
15031 of the same regression framework, this package also provides functions for
15032 batch correction, and data correction.")
15033 (license license:gpl3)))
15035 (define-public r-styler
15042 (uri (cran-uri "styler" version))
15045 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15046 (build-system r-build-system)
15048 `(("r-backports" ,r-backports)
15050 ("r-magrittr" ,r-magrittr)
15051 ("r-purrr" ,r-purrr)
15052 ("r-r-cache" ,r-r-cache)
15053 ("r-rematch2" ,r-rematch2)
15054 ("r-rlang" ,r-rlang)
15055 ("r-rprojroot" ,r-rprojroot)
15056 ("r-tibble" ,r-tibble)
15057 ("r-withr" ,r-withr)
15058 ("r-xfun" ,r-xfun)))
15059 (home-page "https://github.com/r-lib/styler")
15060 (synopsis "Non-invasive pretty printing of R code")
15062 "This is a package for pretty-printing R code without changing the user's
15063 formatting intent.")
15064 (license license:gpl3)))
15066 (define-public r-scrime
15073 (uri (cran-uri "scrime" version))
15076 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15077 (build-system r-build-system)
15078 (home-page "https://cran.r-project.org/web/packages/scrime/")
15079 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15081 "This package provides tools for the analysis of high-dimensional data
15082 developed/implemented at the group \"Statistical Complexity Reduction In
15083 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15084 the functions can also be applied to other types of categorical data.")
15085 (license license:gpl2)))
15087 (define-public r-pbmcapply
15089 (name "r-pbmcapply")
15094 (uri (cran-uri "pbmcapply" version))
15097 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15098 (build-system r-build-system)
15099 (home-page "https://github.com/kvnkuang/pbmcapply")
15100 (synopsis "Track the progress of apply procedures with a progress bar")
15102 "This light-weight package helps you track and visualize the progress of
15103 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15104 (license license:expat)))
15106 (define-public r-blme
15113 (uri (cran-uri "blme" version))
15116 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15117 (build-system r-build-system)
15118 (propagated-inputs `(("r-lme4" ,r-lme4)))
15119 (home-page "https://github.com/vdorie/blme")
15120 (synopsis "Bayesian linear mixed-effects models")
15122 "This package provides tools for maximum a posteriori estimation for
15123 linear and generalized linear mixed-effects models in a Bayesian setting. It
15124 extends the lme4 package.")
15125 (license license:gpl2+)))
15127 (define-public r-batchtools
15129 (name "r-batchtools")
15134 (uri (cran-uri "batchtools" version))
15137 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15138 (build-system r-build-system)
15140 `(("r-backports" ,r-backports)
15141 ("r-base64url" ,r-base64url)
15143 ("r-checkmate" ,r-checkmate)
15144 ("r-data-table" ,r-data-table)
15145 ("r-digest" ,r-digest)
15147 ("r-progress" ,r-progress)
15149 ("r-rappdirs" ,r-rappdirs)
15150 ("r-stringi" ,r-stringi)
15151 ("r-withr" ,r-withr)))
15153 `(("r-knitr" ,r-knitr)))
15154 (home-page "https://github.com/mllg/batchtools")
15155 (synopsis "Tools for computation on batch systems")
15157 "As a successor of the packages BatchJobs and BatchExperiments, this
15158 package provides a parallel implementation of the Map function for high
15159 performance computing systems managed by various schedulers. A multicore and
15160 socket mode allow the parallelization on a local machines, and multiple
15161 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15162 the package provides an abstraction mechanism to define large-scale computer
15163 experiments in a well-organized and reproducible way.")
15164 (license license:lgpl3)))
15166 (define-public r-clue
15173 (uri (cran-uri "clue" version))
15176 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15177 (build-system r-build-system)
15178 (propagated-inputs `(("r-cluster" ,r-cluster)))
15179 (home-page "https://cran.r-project.org/web/packages/clue/")
15180 (synopsis "Tools for analyzing cluster ensembles")
15181 (description "Cluster ensembles are collections of individual solutions to
15182 a given clustering problem which are useful or necessary to consider in a wide
15183 range of applications. This R package provides an extensible computational
15184 environment for creating and analyzing cluster ensembles, with basic data
15185 structures for representing partitions and hierarchies, and facilities for
15186 computing on them, including methods for measuring proximity and obtaining
15187 consensus and secondary clusterings.")
15188 (license license:gpl2)))
15190 (define-public r-sitmo
15197 (uri (cran-uri "sitmo" version))
15200 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15201 (build-system r-build-system)
15202 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15203 (home-page "https://github.com/coatless/sitmo/")
15204 (synopsis "Parallel pseudo random number generator header files")
15206 "This package provides two high quality and fast PPRNGs that may be used
15207 in an OpenMP parallel environment. In addition, there is a generator for one
15208 dimensional low-discrepancy sequence.")
15209 (license license:expat)))
15211 (define-public r-dqrng
15218 (uri (cran-uri "dqrng" version))
15221 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15222 (build-system r-build-system)
15226 ("r-sitmo" ,r-sitmo)))
15227 (home-page "https://www.daqana.org/dqrng")
15228 (synopsis "Fast pseudo random number generators")
15230 "Several fast random number generators are provided as C++ header-only
15231 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15232 Additionally, fast functions for generating random numbers according to a
15233 uniform, normal and exponential distribution are included. The latter two use
15234 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15235 functions are exported to R and as a C++ interface and are enabled for use
15236 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15237 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15238 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15239 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15240 ;; whole is distributed under the terms of the AGPL 3.
15241 (license license:agpl3)))
15243 (define-public r-dalex
15250 (uri (cran-uri "DALEX" version))
15253 "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0"))))
15254 (properties `((upstream-name . "DALEX")))
15255 (build-system r-build-system)
15256 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15257 (home-page "https://pbiecek.github.io/DALEX/")
15258 (synopsis "Descriptive machine learning explanations")
15260 "Machine Learning models are widely used and have various applications in
15261 classification or regression. Models created with boosting, bagging, stacking
15262 or similar techniques are often used due to their high performance, but such
15263 black-box models usually lack interpretability. The DALEX package contains
15264 various explainers that help to understand the link between input variables
15265 and model output.")
15266 ;; Any version of the GPL
15267 (license license:gpl3+)))
15269 (define-public r-enrichr
15276 (uri (cran-uri "enrichR" version))
15279 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15280 (properties `((upstream-name . "enrichR")))
15281 (build-system r-build-system)
15283 `(("r-httr" ,r-httr)
15284 ("r-rjson" ,r-rjson)))
15285 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15286 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15288 "This package provides an R interface to all Enrichr databases, a
15289 web-based tool for analyzing gene sets and returns any enrichment of common
15290 annotated biological functions.")
15291 (license license:gpl2+)))
15293 (define-public r-plot3d
15300 (uri (cran-uri "plot3D" version))
15303 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15304 (properties `((upstream-name . "plot3D")))
15305 (build-system r-build-system)
15306 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15307 (home-page "https://cran.r-project.org/web/packages/plot3D")
15308 (synopsis "Plot multi-dimensional data")
15310 "This package provides functions for viewing 2D and 3D data, including
15311 perspective plots, slice plots, surface plots, scatter plots, etc. It
15312 includes data sets from oceanography.")
15313 (license license:gpl3+)))
15315 (define-public r-ggfortify
15317 (name "r-ggfortify")
15322 (uri (cran-uri "ggfortify" version))
15325 "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5"))))
15326 (build-system r-build-system)
15328 `(("r-dplyr" ,r-dplyr)
15329 ("r-ggplot2" ,r-ggplot2)
15330 ("r-gridextra" ,r-gridextra)
15331 ("r-scales" ,r-scales)
15332 ("r-stringr" ,r-stringr)
15333 ("r-tibble" ,r-tibble)
15334 ("r-tidyr" ,r-tidyr)))
15336 `(("r-knitr" ,r-knitr)))
15337 (home-page "https://github.com/sinhrks/ggfortify")
15338 (synopsis "Data visualization tools for statistical analysis results")
15340 "This package provides unified plotting tools for statistics commonly
15341 used, such as GLM, time series, PCA families, clustering and survival
15342 analysis. The package offers a single plotting interface for these analysis
15343 results and plots in a unified style using the @code{ggplot2} package.")
15344 (license license:gpl2)))
15346 (define-public r-refmanager
15348 (name "r-refmanager")
15353 (uri (cran-uri "RefManageR" version))
15356 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15357 (properties `((upstream-name . "RefManageR")))
15358 (build-system r-build-system)
15360 `(("r-bibtex" ,r-bibtex)
15362 ("r-jsonlite" ,r-jsonlite)
15363 ("r-lubridate" ,r-lubridate)
15365 ("r-stringr" ,r-stringr)
15366 ("r-xml2" ,r-xml2)))
15367 (home-page "https://github.com/ropensci/RefManageR/")
15368 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15370 "This package provides tools for importing and working with bibliographic
15371 references. It greatly enhances the @code{bibentry} class by providing a
15372 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15373 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15374 by various formats for name lists (author by last names, translator by full
15375 names, etc.). Entries can be updated, combined, sorted, printed in a number
15376 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15377 into R and converted to @code{BibEntry} objects.")
15378 ;; Any of these licenses may be picked.
15379 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15381 (define-public r-citr
15388 (uri (cran-uri "citr" version))
15391 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15392 (build-system r-build-system)
15394 `(("r-assertthat" ,r-assertthat)
15397 ("r-miniui" ,r-miniui)
15398 ("r-refmanager" ,r-refmanager)
15399 ("r-rstudioapi" ,r-rstudioapi)
15400 ("r-shiny" ,r-shiny)
15401 ("r-shinyjs" ,r-shinyjs)
15402 ("r-yaml" ,r-yaml)))
15403 (home-page "https://github.com/crsh/citr")
15404 (synopsis "RStudio add-in to insert Markdown citations")
15406 "This package provides functions and an RStudio add-in that search a
15407 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15408 the current document.")
15409 (license license:expat)))
15411 (define-public r-xgboost
15414 (version "1.0.0.2")
15418 (uri (cran-uri "xgboost" version))
15421 "1ld2w51c5fy3bl0kvjn1iplffc4lmin9s9zz5xx7xsm44d6j6kzd"))))
15422 (build-system r-build-system)
15424 `(("r-data-table" ,r-data-table)
15425 ("r-magrittr" ,r-magrittr)
15426 ("r-matrix" ,r-matrix)
15427 ("r-stringi" ,r-stringi)))
15429 `(("r-knitr" ,r-knitr)))
15430 (home-page "https://github.com/dmlc/xgboost")
15431 (synopsis "Extreme gradient boosting")
15433 "This package provides an R interface to Extreme Gradient Boosting, which
15434 is an efficient implementation of the gradient boosting framework from Chen
15435 and Guestrin (2016). The package includes efficient linear model solver and
15436 tree learning algorithms. The package can automatically do parallel
15437 computation on a single machine. It supports various objective functions,
15438 including regression, classification and ranking. The package is made to be
15439 extensible, so that users are also allowed to define their own objectives
15441 (license license:asl2.0)))
15443 (define-public r-umap
15446 (version "0.2.5.0")
15450 (uri (cran-uri "umap" version))
15453 "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
15454 (build-system r-build-system)
15456 `(("r-openssl" ,r-openssl)
15458 ("r-reticulate" ,r-reticulate)
15459 ("r-rspectra" ,r-rspectra)))
15461 `(("r-knitr" ,r-knitr)))
15462 (home-page "https://github.com/tkonopka/umap")
15463 (synopsis "Uniform manifold approximation and projection")
15465 "Uniform manifold approximation and projection is a technique for
15466 dimension reduction. This package provides an interface to the UMAP algorithm
15467 in R, including a translation of the original algorithm into R.")
15468 (license license:expat)))
15470 (define-public r-uwot
15477 (uri (cran-uri "uwot" version))
15480 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
15481 (build-system r-build-system)
15483 `(("r-dqrng" ,r-dqrng)
15485 ("r-irlba" ,r-irlba)
15486 ("r-matrix" ,r-matrix)
15488 ("r-rcppannoy" ,r-rcppannoy)
15489 ("r-rcppprogress" ,r-rcppprogress)
15490 ("r-rspectra" ,r-rspectra)))
15491 (home-page "https://github.com/jlmelville/uwot")
15492 (synopsis "Uniform manifold approximation and projection")
15494 "This package provides an implementation of the Uniform Manifold
15495 Approximation and Projection dimensionality reduction by McInnes et
15496 al. (2018). It also provides means to transform new data and to carry out
15497 supervised dimensionality reduction. An implementation of the related
15498 LargeVis method of Tang et al. (2016) is also provided.")
15499 (license license:gpl3)))
15501 (define-public r-kableextra
15503 (name "r-kableextra")
15508 (uri (cran-uri "kableExtra" version))
15511 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15512 (properties `((upstream-name . "kableExtra")))
15513 (build-system r-build-system)
15515 `(("r-digest" ,r-digest)
15517 ("r-htmltools" ,r-htmltools)
15518 ("r-knitr" ,r-knitr)
15519 ("r-magrittr" ,r-magrittr)
15520 ("r-readr" ,r-readr)
15521 ("r-rmarkdown" ,r-rmarkdown)
15522 ("r-rstudioapi" ,r-rstudioapi)
15523 ("r-rvest" ,r-rvest)
15524 ("r-scales" ,r-scales)
15525 ("r-stringr" ,r-stringr)
15526 ("r-viridislite" ,r-viridislite)
15527 ("r-webshot" ,r-webshot)
15528 ("r-xml2" ,r-xml2)))
15529 (home-page "https://haozhu233.github.io/kableExtra/")
15530 (synopsis "Construct complex tables with pipe syntax")
15532 "Build complex HTML or LaTeX tables using @code{kable()} from
15533 @code{knitr} and the piping syntax from @code{magrittr}. The function
15534 @code{kable()} is a light weight table generator coming from @code{knitr}.
15535 This package simplifies the way to manipulate the HTML or LaTeX codes
15536 generated by @code{kable()} and allows users to construct complex tables and
15537 customize styles using a readable syntax.")
15538 (license license:expat)))
15540 (define-public r-glasso
15547 (uri (cran-uri "glasso" version))
15549 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15550 (build-system r-build-system)
15551 (native-inputs `(("gfortran" ,gfortran)))
15552 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
15553 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15555 "This is a package for estimation of a sparse inverse covariance matrix
15556 using a lasso (L1) penalty. Facilities are provided for estimates along a
15557 path of values for the regularization parameter.")
15558 (license license:gpl2)))
15560 (define-public r-rhpcblasctl
15562 (name "r-rhpcblasctl")
15563 (version "0.20-17")
15567 (uri (cran-uri "RhpcBLASctl" version))
15570 "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
15571 (properties `((upstream-name . "RhpcBLASctl")))
15572 (build-system r-build-system)
15573 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
15574 (synopsis "Control the number of threads on BLAS")
15576 "This package allows you to control the number of threads the BLAS
15577 library uses. It is also possible to control the number of threads in
15579 (license license:agpl3+)))
15581 (define-public r-lda
15588 (uri (cran-uri "lda" version))
15591 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15592 (build-system r-build-system)
15593 (home-page "https://cran.r-project.org/web/packages/lda/")
15594 (synopsis "Collapsed Gibbs sampling methods for topic models")
15596 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15597 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15598 mixed-membership stochastic blockmodel. Inference for all of these models is
15599 implemented via a fast collapsed Gibbs sampler written in C. Utility
15600 functions for reading/writing data typically used in topic models, as well as
15601 tools for examining posterior distributions are also included.")
15602 ;; Any version of the LGPL
15603 (license license:lgpl3+)))
15605 (define-public r-rann-l1
15612 (uri (cran-uri "RANN.L1" version))
15615 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15616 (properties `((upstream-name . "RANN.L1")))
15617 (build-system r-build-system)
15618 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15619 (synopsis "Fast nearest neighbour search using L1 metric")
15621 "This package provides tools to find the k nearest neighbours for every
15622 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15623 library. There is support for approximate as well as exact searches, fixed
15624 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15625 computed using the L1 (Manhattan, taxicab) metric.")
15626 (license license:gpl3+)))
15628 (define-public r-leiden
15635 (uri (cran-uri "leiden" version))
15638 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
15639 (properties `((upstream-name . "leiden")))
15640 (build-system r-build-system)
15642 `(("r-igraph" ,r-igraph)
15643 ("r-matrix" ,r-matrix)
15644 ("r-reticulate" ,r-reticulate)))
15645 (home-page "https://github.com/TomKellyGenetics/leiden")
15646 (synopsis "R implementation of Leiden clustering algorithm")
15648 "This package implements the Python @code{leidenalg} module to be called
15649 in R. It enables clustering using the Leiden algorithm for partitioning a
15650 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15651 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15652 (license license:gpl3)))
15654 (define-public r-patchwork
15656 (name "r-patchwork")
15661 (uri (cran-uri "patchwork" version))
15664 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
15665 (build-system r-build-system)
15667 `(("r-ggplot2" ,r-ggplot2)
15668 ("r-gtable" ,r-gtable)))
15670 `(("r-knitr" ,r-knitr)))
15671 (home-page "https://github.com/thomasp85/patchwork")
15672 (synopsis "Compose ggplot2 plots")
15674 "The @code{ggplot2} package provides a strong API for sequentially
15675 building up a plot, but does not concern itself with composition of multiple
15676 plots. Patchwork is a package that expands the API to allow for arbitrarily
15677 complex composition of plots by providing mathmatical operators for combining
15679 (license license:expat)))
15681 (define-public r-liger
15688 (uri (git-reference
15689 (url "https://github.com/MacoskoLab/liger.git")
15690 (commit (string-append "v" version))))
15691 (file-name (git-file-name name version))
15694 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15695 (modules '((guix build utils)))
15698 (delete-file "inst/java/ModularityOptimizer.jar")
15700 (build-system r-build-system)
15703 (modify-phases %standard-phases
15704 (add-after 'unpack 'build-java-part
15705 (lambda* (#:key inputs #:allow-other-keys)
15706 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15707 (for-each (lambda (file) (invoke "javac" file))
15708 (find-files "." "\\.java$"))
15709 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15710 (find-files "." "\\.class$"))
15713 `(("r-cowplot" ,r-cowplot)
15714 ("r-dosnow" ,r-dosnow)
15715 ("r-dplyr" ,r-dplyr)
15717 ("r-foreach" ,r-foreach)
15718 ("r-ggplot2" ,r-ggplot2)
15719 ("r-ggrepel" ,r-ggrepel)
15720 ("r-hmisc" ,r-hmisc)
15722 ("r-irlba" ,r-irlba)
15723 ("r-matrix" ,r-matrix)
15724 ("r-mclust" ,r-mclust)
15725 ("r-patchwork" ,r-patchwork)
15727 ("r-rann-l1" ,r-rann-l1)
15729 ("r-rcpparmadillo" ,r-rcpparmadillo)
15730 ("r-riverplot" ,r-riverplot)
15731 ("r-rtsne" ,r-rtsne)
15732 ("r-snow" ,r-snow)))
15734 `(("jdk" ,icedtea "jdk")
15735 ;; See https://github.com/MacoskoLab/liger/issues/96
15736 ;; The optimizer is released under the Expat license.
15740 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15743 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15745 ("r-knitr" ,r-knitr))) ; for vignettes
15746 (home-page "https://github.com/MacoskoLab/liger")
15747 (synopsis "Integrate and analyze multiple single-cell datasets")
15749 "LIGER is a package for integrating and analyzing multiple single-cell
15750 datasets, developed and maintained by the Macosko lab. It relies on
15751 integrative non-negative matrix factorization to identify shared and
15752 dataset-specific factors.")
15753 (license license:gpl3)))
15755 (define-public r-harmony
15762 (uri (git-reference
15763 (url "https://github.com/immunogenomics/harmony")
15765 (file-name (git-file-name name version))
15768 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
15769 (modules '((guix build utils)))
15772 (for-each delete-file '("config.status" "configure"))
15774 (build-system r-build-system)
15776 `(("r-cowplot" ,r-cowplot)
15777 ("r-dplyr" ,r-dplyr)
15778 ("r-ggplot2" ,r-ggplot2)
15779 ("r-irlba" ,r-irlba)
15780 ("r-matrix" ,r-matrix)
15782 ("r-rcpparmadillo" ,r-rcpparmadillo)
15783 ("r-rcppprogress" ,r-rcppprogress)
15784 ("r-rlang" ,r-rlang)
15785 ("r-tibble" ,r-tibble)
15786 ("r-tidyr" ,r-tidyr)))
15788 `(("autoconf" ,autoconf)))
15789 (home-page "https://github.com/immunogenomics/harmony")
15790 (synopsis "Integration of single cell sequencing data")
15792 "This package provides an implementation of the Harmony algorithm for
15793 single cell integration, described in Korsunsky et al
15794 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15795 function and interfaces to external frameworks.")
15796 (license license:gpl3)))
15798 (define-public r-covr
15805 (uri (cran-uri "covr" version))
15807 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
15808 (properties `((upstream-name . "covr")))
15809 (build-system r-build-system)
15811 `(("r-crayon" ,r-crayon)
15812 ("r-digest" ,r-digest)
15814 ("r-jsonlite" ,r-jsonlite)
15816 ("r-withr" ,r-withr)
15817 ("r-yaml" ,r-yaml)))
15819 `(("r-knitr" ,r-knitr))) ; for vignettes
15820 (home-page "https://github.com/r-lib/covr")
15821 (synopsis "Test coverage for R packages")
15823 "Thisp package enables you to track and report code coverage for your
15824 package and (optionally) upload the results to a coverage service. Code
15825 coverage is a measure of the amount of code being exercised by a set of tests.
15826 It is an indirect measure of test quality and completeness. This package is
15827 compatible with any testing methodology or framework and tracks coverage of
15828 both R code and compiled C/C++/FORTRAN code.")
15829 (license license:gpl3)))
15831 (define-public r-systemfonts
15833 (name "r-systemfonts")
15838 (uri (cran-uri "systemfonts" version))
15841 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15842 (properties `((upstream-name . "systemfonts")))
15843 (build-system r-build-system)
15845 `(("fontconfig" ,fontconfig)
15846 ("freetype" ,freetype)
15849 `(("pkg-config" ,pkg-config)))
15850 (home-page "https://github.com/r-lib/systemfonts")
15851 (synopsis "System native font finding")
15853 "This package provides system native access to the font catalogue. As
15854 font handling varies between systems it is difficult to correctly locate
15855 installed fonts across different operating systems. The 'systemfonts' package
15856 provides bindings to the native libraries for finding font files that can then
15857 be used further by e.g. graphic devices.")
15858 (license license:expat)))
15860 (define-public r-graphlayouts
15862 (name "r-graphlayouts")
15867 (uri (cran-uri "graphlayouts" version))
15870 "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0"))))
15871 (properties `((upstream-name . "graphlayouts")))
15872 (build-system r-build-system)
15874 `(("r-igraph" ,r-igraph)
15876 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15877 (home-page "https://github.com/schochastics/graphlayouts")
15878 (synopsis "Additional layout algorithms for network visualizations")
15880 "This package provides several layout algorithms to visualize networks
15881 which are not part of the igraph library. Most are based on the concept of
15882 stress majorization by Gansner et al. (2004)
15883 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
15884 emphasize hidden group structures in networks or focus on specific nodes.")
15885 (license license:expat)))
15887 (define-public r-tidygraph
15889 (name "r-tidygraph")
15894 (uri (cran-uri "tidygraph" version))
15897 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15898 (properties `((upstream-name . "tidygraph")))
15899 (build-system r-build-system)
15901 `(("r-dplyr" ,r-dplyr)
15902 ("r-igraph" ,r-igraph)
15903 ("r-magrittr" ,r-magrittr)
15904 ("r-pillar" ,r-pillar)
15907 ("r-rlang" ,r-rlang)
15908 ("r-tibble" ,r-tibble)
15909 ("r-tidyr" ,r-tidyr)))
15910 (home-page "https://github.com/thomasp85/tidygraph")
15911 (synopsis "Tidy API for graph manipulation")
15913 "This package provides a graph implementation that can be thought of as
15914 two tidy data frames describing node and edge data respectively. It provides
15915 an approach to manipulate these two virtual data frames using the API defined
15916 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15917 common graph algorithms.")
15918 (license license:expat)))
15920 (define-public r-soupx
15921 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15925 (version (git-version "0.3.1" revision commit))
15929 (uri (git-reference
15930 (url "https://github.com/constantAmateur/SoupX")
15932 (file-name (git-file-name name version))
15935 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15936 (properties `((upstream-name . "SoupX")))
15937 (build-system r-build-system)
15939 `(("r-ggplot2" ,r-ggplot2)
15940 ("r-matrix" ,r-matrix)
15941 ("r-seurat" ,r-seurat)))
15942 (home-page "https://github.com/constantAmateur/SoupX")
15943 (synopsis "Single cell mRNA Soup eXterminator")
15945 "This package provides a package for quantifying, profiling and
15946 removing cell free mRNA contamination (the \"soup\") from droplet based single
15947 cell RNA-seq experiments.")
15948 (license license:gpl2))))
15950 (define-public r-assertr
15957 (uri (cran-uri "assertr" version))
15960 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
15961 (build-system r-build-system)
15963 `(("r-dplyr" ,r-dplyr)
15965 ("r-rlang" ,r-rlang)))
15967 `(("r-knitr" ,r-knitr))) ; needed for vignette
15968 (home-page "https://github.com/ropensci/assertr")
15969 (synopsis "Assertive programming for R analysis pipelines")
15971 "This package provides functionality to assert conditions that have to be
15972 met so that errors in data used in analysis pipelines can fail quickly. It is
15973 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15975 (license license:expat)))
15977 (define-public r-parameters
15979 (name "r-parameters")
15984 (uri (cran-uri "parameters" version))
15987 "0mylxkf1y6mk4kf6c57x102sf4c800pfasjcfbf1hnsh6ya0m6dy"))))
15988 (properties `((upstream-name . "parameters")))
15989 (build-system r-build-system)
15991 `(("r-bayestestr" ,r-bayestestr)
15992 ("r-insight" ,r-insight)))
15994 `(("r-knitr" ,r-knitr)))
15995 (home-page "https://cran.r-project.org/web/packages/parameters")
15996 (synopsis "Processing of model parameters")
15998 "This package provides utilities for processing the parameters of various
15999 statistical models. Beyond computing p values, CIs, and other indices for a
16000 wide variety of models, this package implements features like standardization
16001 or bootstrapping of parameters and models, feature reduction (feature
16002 extraction and variable selection) as well as conversion between indices of
16004 (license license:gpl3)))
16006 (define-public r-rgdal
16013 (uri (cran-uri "rgdal" version))
16015 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
16016 (properties `((upstream-name . "rgdal")))
16017 (build-system r-build-system)
16025 `(("pkg-config" ,pkg-config)))
16026 (home-page "http://rgdal.r-forge.r-project.org")
16027 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16029 "This package provides bindings to the Geospatial Data Abstraction
16030 Library (GDAL) and access to projection/transformation operations from the
16032 (license license:gpl2+)))
16034 (define-public r-insol
16041 (uri (cran-uri "insol" version))
16044 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16045 (properties `((upstream-name . "insol")))
16046 (build-system r-build-system)
16048 `(("r-raster" ,r-raster)))
16050 `(("gfortran" ,gfortran)))
16051 (home-page "https://meteoexploration.com/R/insol/index.html")
16052 (synopsis "Tools for calculating solar radiation")
16054 "This package provides functions to compute insolation on tilted
16055 surfaces, computes atmospheric transmittance and related parameters such as:
16056 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16057 time, vector in the direction of the sun, vector normal to surface, and some
16058 atmospheric physics.")
16059 (license license:gpl2+)))
16061 (define-public r-lifecycle
16063 (name "r-lifecycle")
16068 (uri (cran-uri "lifecycle" version))
16071 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16072 (properties `((upstream-name . "lifecycle")))
16073 (build-system r-build-system)
16075 `(("r-glue" ,r-glue)
16076 ("r-rlang" ,r-rlang)))
16078 `(("r-knitr" ,r-knitr))) ; for vignettes
16079 (home-page "https://github.com/r-lib/lifecycle")
16080 (synopsis "Manage the life cycle of your package functions")
16082 "Manage the life cycle of your exported functions with shared
16083 conventions, documentation badges, and non-invasive deprecation warnings. The
16084 lifecycle package defines four development stages (experimental, maturing,
16085 stable, and questioning) and three deprecation stages (soft-deprecated,
16086 deprecated, and defunct). It makes it easy to insert badges corresponding to
16087 these stages in your documentation. Usage of deprecated functions are
16088 signalled with increasing levels of non-invasive verbosity.")
16089 (license license:gpl3)))
16091 (define-public r-assertable
16093 (name "r-assertable")
16098 (uri (cran-uri "assertable" version))
16101 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16102 (build-system r-build-system)
16104 `(("r-data-table" ,r-data-table)))
16105 (home-page "https://cran.r-project.org/web/packages/assertable/")
16106 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16107 (description "This package provides simple, flexible assertions on
16108 data.frame or data.table objects with verbose output for vetting. While other
16109 assertion packages apply towards more general use-cases, @code{assertable} is
16110 tailored towards tabular data. It includes functions to check variable names
16111 and values, whether the dataset contains all combinations of a given set of
16112 unique identifiers, and whether it is a certain length. In addition,
16113 @code{assertable} includes utility functions to check the existence of target
16114 files and to efficiently import multiple tabular data files into one
16116 (license license:gpl3)))
16118 (define-public r-quadprog
16120 (name "r-quadprog")
16125 (uri (cran-uri "quadprog" version))
16127 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16128 (build-system r-build-system)
16130 `(("gfortran" ,gfortran)))
16131 (home-page "https://cran.r-project.org/web/packages/quadprog")
16132 (synopsis "Functions to solve quadratic programming problems")
16134 "This package contains routines and documentation for solving quadratic
16135 programming problems.")
16136 (license license:gpl3+)))
16138 (define-public r-desolve
16145 (uri (cran-uri "deSolve" version))
16147 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16148 (properties `((upstream-name . "deSolve")))
16149 (build-system r-build-system)
16151 `(("gfortran" ,gfortran)))
16152 (home-page "https://desolve.r-forge.r-project.org/")
16153 (synopsis "Solvers for initial value problems of differential equations")
16154 (description "This package provides functions that solve initial value
16155 problems of a system of first-order @dfn{ordinary differential
16156 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16157 @dfn{differential algebraic equations} (DAE), and of delay differential
16158 equations. The functions provide an interface to the FORTRAN functions
16159 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16160 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16161 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16162 time steps. The package contains routines designed for solving ODEs resulting
16163 from 1-D, 2-D and 3-D partial differential equations that have been converted
16164 to ODEs by numerical differencing.")
16165 (license license:gpl2+)))
16167 (define-public r-pracma
16173 (uri (cran-uri "pracma" version))
16175 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16176 (build-system r-build-system)
16177 (home-page "https://cran.r-project.org/web/packages/pracma/")
16178 (synopsis "Practical numerical math functions")
16179 (description "This package provides functions for numerical analysis and
16180 linear algebra, numerical optimization, differential equations, plus some
16181 special functions. It uses Matlab function names where appropriate to simplify
16183 (license license:gpl3+)))
16185 (define-public r-subplex
16192 (uri (cran-uri "subplex" version))
16195 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16196 (build-system r-build-system)
16198 `(("gfortran" ,gfortran)))
16199 (home-page "https://cran.r-project.org/web/packages/subplex")
16200 (synopsis "Unconstrained optimization using the subplex algorithm")
16202 "This package implements the Subplex optimization algorithm.
16203 It solves unconstrained optimization problems using a simplex method on
16204 subspaces. The method is well suited for optimizing objective functions that
16205 are noisy or are discontinuous at the solution.")
16206 (license license:gpl3+)))
16208 (define-public r-txtplot
16215 (uri (cran-uri "txtplot" version))
16218 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16219 (build-system r-build-system)
16220 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16221 (synopsis "Text-based plotting")
16222 (description "This package provides functions to produce rudimentary ASCII
16223 graphics directly in the terminal window. This package provides a basic
16224 plotting function (and equivalents of curve, density, acf and barplot) as well
16225 as a boxplot function.")
16226 (license license:lgpl3+)))
16228 (define-public r-bio3d
16235 (uri (cran-uri "bio3d" version))
16238 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16239 (properties `((upstream-name . "bio3d")))
16240 (build-system r-build-system)
16241 (inputs `(("zlib" ,zlib)))
16242 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16243 (home-page "http://thegrantlab.org/bio3d/")
16244 (synopsis "Biological structure analysis")
16246 "This package provides utilities to process, organize and explore protein
16247 structure, sequence and dynamics data. Features include the ability to read
16248 and write structure, sequence and dynamic trajectory data, perform sequence
16249 and structure database searches, data summaries, atom selection, alignment,
16250 superposition, rigid core identification, clustering, torsion analysis,
16251 distance matrix analysis, structure and sequence conservation analysis, normal
16252 mode analysis, principal component analysis of heterogeneous structure data,
16253 and correlation network analysis from normal mode and molecular dynamics data.
16254 In addition, various utility functions are provided to enable the statistical
16255 and graphical power of the R environment to work with biological sequence and
16257 (license license:gpl2+)))
16259 (define-public r-bios2cor
16261 (name "r-bios2cor")
16266 (uri (cran-uri "Bios2cor" version))
16269 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16270 (properties `((upstream-name . "Bios2cor")))
16271 (build-system r-build-system)
16273 `(("r-bigmemory" ,r-bigmemory)
16274 ("r-bio3d" ,r-bio3d)
16275 ("r-circular" ,r-circular)
16276 ("r-igraph" ,r-igraph)))
16277 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16278 (synopsis "From biological sequences and simulations to correlation analysis")
16280 "This package provides utilities for computation and analysis of
16281 correlation/covariation in multiple sequence alignments and in side chain
16282 motions during molecular dynamics simulations. Features include the
16283 computation of correlation/covariation scores using a variety of scoring
16284 functions between either sequence positions in alignments or side chain
16285 dihedral angles in molecular dynamics simulations and utilities to analyze the
16286 correlation/covariation matrix through a variety of tools including network
16287 representation and principal components analysis. In addition, several
16288 utility functions are based on the R graphical environment to provide friendly
16289 tools for help in data interpretation.")
16290 (license license:gpl2+)))
16292 ;; This package includes minified JavaScript files. When upgrading please
16293 ;; check that there are no new minified JavaScript files.
16294 (define-public r-networkd3
16296 (name "r-networkd3")
16301 (uri (cran-uri "networkD3" version))
16304 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16307 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16309 (properties `((upstream-name . "networkD3")))
16310 (build-system r-build-system)
16312 `(#:modules ((guix build utils)
16313 (guix build r-build-system)
16317 (modify-phases %standard-phases
16318 (add-after 'unpack 'process-javascript
16319 (lambda* (#:key inputs #:allow-other-keys)
16320 (with-directory-excursion "inst/htmlwidgets/lib/"
16324 `((,(assoc-ref inputs "d3.v4.js")
16325 "d3-4.5.0/d3.min.js"))))
16326 (lambda (sources targets)
16327 (for-each (lambda (source target)
16328 (format #t "Processing ~a --> ~a~%"
16330 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16331 (call-with-output-file target
16333 (dump-port minified port)))))
16334 sources targets))))
16337 `(("uglify-js" ,uglify-js)
16338 ;; NOTE: Make sure that this version of d3 is still valid when
16339 ;; upgrading the package.
16343 (uri "https://d3js.org/d3.v4.js")
16346 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16348 `(("r-htmlwidgets" ,r-htmlwidgets)
16349 ("r-igraph" ,r-igraph)
16350 ("r-magrittr" ,r-magrittr)))
16351 (home-page "https://cran.r-project.org/package=networkD3")
16352 (synopsis "D3 JavaScript network graphs from R")
16354 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16356 (license license:gpl3+)))
16358 (define-public r-aasea
16365 (uri (cran-uri "aaSEA" version))
16368 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16369 (properties `((upstream-name . "aaSEA")))
16370 (build-system r-build-system)
16372 `(("r-bios2cor" ,r-bios2cor)
16374 ("r-hmisc" ,r-hmisc)
16375 ("r-magrittr" ,r-magrittr)
16376 ("r-networkd3" ,r-networkd3)
16377 ("r-plotly" ,r-plotly)
16378 ("r-seqinr" ,r-seqinr)
16379 ("r-shiny" ,r-shiny)
16380 ("r-shinydashboard" ,r-shinydashboard)))
16381 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16382 (synopsis "Amino acid substitution effect analyzer")
16384 "Given a protein multiple sequence alignment, it is a daunting task to
16385 assess the effects of substitutions along sequence length. The aaSEA package
16386 is intended to help researchers to rapidly analyze property changes caused by
16387 single, multiple and correlated amino acid substitutions in proteins.")
16388 (license license:gpl3)))
16390 (define-public r-abacus
16397 (uri (cran-uri "ABACUS" version))
16400 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16401 (properties `((upstream-name . "ABACUS")))
16402 (build-system r-build-system)
16404 `(("r-ggplot2" ,r-ggplot2)
16405 ("r-shiny" ,r-shiny)))
16406 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16407 (synopsis "Apps-based activities for communicating and understanding statistics")
16409 "This package provides a set of Shiny apps for effective communication
16410 and understanding in statistics. The current version includes properties of
16411 normal distribution, properties of sampling distribution, one-sample z and t
16412 tests, two samples independent (unpaired) t test and analysis of variance.")
16413 (license license:gpl3)))
16415 (define-public r-abc-rap
16422 (uri (cran-uri "ABC.RAP" version))
16425 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16426 (properties `((upstream-name . "ABC.RAP")))
16427 (build-system r-build-system)
16428 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16429 (synopsis "Array-based CpG region analysis pipeline")
16431 "This package aims to identify candidate genes that are differentially
16432 methylated between cases and controls. It applies Student's t-test and delta
16433 beta analysis to identify candidate genes containing multiple CpG sites.")
16434 (license license:gpl3)))
16436 (define-public r-abcadm
16443 (uri (cran-uri "abcADM" version))
16446 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16447 (properties `((upstream-name . "abcADM")))
16448 (build-system r-build-system)
16451 ("r-rcpp" ,r-rcpp)))
16452 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16453 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16455 "This package provides tools to estimate parameters of accumulated
16456 damage (load duration) models based on failure time data under a Bayesian
16457 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16458 long-term reliability under stochastic load profiles.")
16459 (license license:gpl3)))
16461 (define-public r-rglpk
16468 (uri (cran-uri "Rglpk" version))
16471 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16472 (properties `((upstream-name . "Rglpk")))
16473 (build-system r-build-system)
16475 `(("r-slam" ,r-slam)))
16478 (home-page "https://r-forge.r-project.org/projects/rglp/")
16479 (synopsis "R interface to the GNU Linear Programming Kit")
16481 "This package provides an R interface to the GNU Linear Programming Kit,
16482 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16483 integer linear programming} (MILP) and other related problems.")
16485 (license (list license:gpl2 license:gpl3))))
16487 (define-public r-abcdefba
16489 (name "r-abcdefba")
16494 (uri (cran-uri "abcdeFBA" version))
16497 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16498 (properties `((upstream-name . "abcdeFBA")))
16499 (build-system r-build-system)
16501 `(("r-corrplot" ,r-corrplot)
16502 ("r-lattice" ,r-lattice)
16504 ("r-rglpk" ,r-rglpk)))
16505 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16506 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16508 "This package provides functions for Constraint Based Simulation using
16509 Flux Balance Analysis and informative analysis of the data generated during
16511 (license license:gpl2)))
16513 (define-public r-abcrlda
16520 (uri (cran-uri "abcrlda" version))
16523 "0zjdrbg3zx0znqnh0dvmifs9c12b8vjhbaf3nbwab9xh25nsmg75"))))
16524 (properties `((upstream-name . "abcrlda")))
16525 (build-system r-build-system)
16526 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16527 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16529 "This package offers methods to perform @dfn{asymptotically
16530 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16531 cost-sensitive binary classification. The bias-correction is an estimate of
16532 the bias term added to regularized discriminant analysis that minimizes the
16534 (license license:gpl3)))
16536 (define-public r-abemus
16543 (uri (cran-uri "abemus" version))
16546 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16547 (properties `((upstream-name . "abemus")))
16548 (build-system r-build-system)
16550 `(("r-data-table" ,r-data-table)))
16551 (home-page "https://cran.r-project.org/web/packages/abemus/")
16552 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16554 "This package provides an implementation of @dfn{Adaptive Base Error
16555 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16556 platform-specific genetic knowledge and empirical signal to readily detect and
16557 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16558 cell free DNA} (cfDNA).")
16559 (license license:gpl3)))
16561 ;; This package includes minified JavaScript files. When upgrading please
16562 ;; check that there are no new minified JavaScript files.
16563 (define-public r-rintrojs
16565 (name "r-rintrojs")
16570 (uri (cran-uri "rintrojs" version))
16573 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16574 (properties `((upstream-name . "rintrojs")))
16575 (build-system r-build-system)
16577 `(#:modules ((guix build utils)
16578 (guix build r-build-system)
16582 (modify-phases %standard-phases
16583 (add-after 'unpack 'process-javascript
16584 (lambda* (#:key inputs #:allow-other-keys)
16585 (with-directory-excursion "inst/javascript/introjs/"
16589 `((,(assoc-ref inputs "intro.js")
16591 (lambda (sources targets)
16592 (for-each (lambda (source target)
16593 (format #t "Processing ~a --> ~a~%"
16595 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16596 (call-with-output-file target
16598 (dump-port minified port)))))
16599 sources targets))))
16602 `(("uglify-js" ,uglify-js)
16606 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16609 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16611 `(("r-jsonlite" ,r-jsonlite)
16612 ("r-shiny" ,r-shiny)))
16613 (home-page "https://github.com/carlganz/rintrojs")
16614 (synopsis "Wrapper for the Intro.js library")
16616 "This package provides a wrapper for the @url{http://www.introjs.com,
16617 Intro.js} library. This package makes it easy to include step-by-step
16618 introductions, and clickable hints in a Shiny application. It supports both
16619 static introductions in the UI, and programmatic introductions from the
16621 (license license:agpl3+)))
16623 (define-public r-sysfonts
16625 (name "r-sysfonts")
16630 (uri (cran-uri "sysfonts" version))
16633 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16634 (properties `((upstream-name . "sysfonts")))
16635 (build-system r-build-system)
16637 `(("freetype" ,freetype)
16641 `(("pkg-config" ,pkg-config)))
16642 (home-page "https://github.com/yixuan/sysfonts")
16643 (synopsis "Loading fonts into R")
16645 "This is a package to simplify loading of system fonts and Google Fonts
16646 into R, in order to support other packages.")
16647 (license license:gpl2)))
16649 (define-public r-showtextdb
16651 (name "r-showtextdb")
16656 (uri (cran-uri "showtextdb" version))
16659 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16660 (properties `((upstream-name . "showtextdb")))
16661 (build-system r-build-system)
16663 `(("r-sysfonts" ,r-sysfonts)))
16664 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16665 (synopsis "Font files for the 'showtext' package")
16667 "This package provides font files that can be used by the @code{showtext}
16669 (license license:asl2.0)))
16671 (define-public r-showtext
16673 (name "r-showtext")
16678 (uri (cran-uri "showtext" version))
16681 "0a5gg72bfrc7wm0phj1aflj1wc08kfi81ac32na6ya9s2ivyimw5"))))
16682 (properties `((upstream-name . "showtext")))
16683 (build-system r-build-system)
16685 `(("freetype" ,freetype)
16689 `(("r-showtextdb" ,r-showtextdb)
16690 ("r-sysfonts" ,r-sysfonts)))
16691 (native-inputs `(("pkg-config" ,pkg-config)))
16692 (home-page "https://github.com/yixuan/showtext")
16693 (synopsis "Using fonts more easily in R graphs")
16695 "This package aims to make it easy to use various types of
16696 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16697 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16698 will be converted into polygons or raster images, hence after the plot has
16699 been created, it no longer relies on the font files. No external software
16700 such as Ghostscript is needed to use this package.")
16701 (license license:asl2.0)))
16703 (define-public r-emojifont
16705 (name "r-emojifont")
16710 (uri (cran-uri "emojifont" version))
16713 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16714 (properties `((upstream-name . "emojifont")))
16715 (build-system r-build-system)
16717 `(("r-ggplot2" ,r-ggplot2)
16718 ("r-proto" ,r-proto)
16719 ("r-showtext" ,r-showtext)
16720 ("r-sysfonts" ,r-sysfonts)))
16721 (home-page "https://guangchuangyu.github.io/emojifont")
16722 (synopsis "Emoji and Font Awesome in R graphics")
16724 "This package enables the use of emoji and the Font Awesome glyphs in
16725 both base and ggplot2 graphics.")
16726 (license license:artistic2.0)))
16728 (define-public r-abstractr
16730 (name "r-abstractr")
16735 (uri (cran-uri "abstractr" version))
16738 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16739 (properties `((upstream-name . "abstractr")))
16740 (build-system r-build-system)
16742 `(("r-colourpicker" ,r-colourpicker)
16743 ("r-emojifont" ,r-emojifont)
16744 ("r-ggplot2" ,r-ggplot2)
16745 ("r-gridextra" ,r-gridextra)
16746 ("r-rintrojs" ,r-rintrojs)
16747 ("r-shiny" ,r-shiny)
16748 ("r-shinythemes" ,r-shinythemes)))
16749 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16750 (synopsis "R-Shiny application for creating visual abstracts")
16752 "This package provides an R Shiny application to create visual abstracts
16753 for original research. A variety of user defined options and formatting are
16755 (license license:gpl3)))
16757 (define-public r-abtest
16764 (uri (cran-uri "abtest" version))
16767 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16768 (properties `((upstream-name . "abtest")))
16769 (build-system r-build-system)
16771 `(("r-matrix" ,r-matrix)
16772 ("r-mvtnorm" ,r-mvtnorm)
16773 ("r-plotrix" ,r-plotrix)
16774 ("r-rcolorbrewer" ,r-rcolorbrewer)
16777 ("r-truncnorm" ,r-truncnorm)
16778 ("r-vgam" ,r-vgam)))
16779 (home-page "https://cran.r-project.org/web/packages/abtest/")
16780 (synopsis "Bayesian A/B testing")
16782 "This package provides functions for Bayesian A/B testing including prior
16783 elicitation options based on Kass and Vaidyanathan (1992)
16784 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16785 (license license:gpl2+)))
16787 (define-public r-accept
16794 (uri (cran-uri "accept" version))
16797 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
16798 (properties `((upstream-name . "accept")))
16799 (build-system r-build-system)
16801 `(("r-dplyr" ,r-dplyr)
16802 ("r-extrafont" ,r-extrafont)
16804 ("r-plotly" ,r-plotly)
16805 ("r-stringr" ,r-stringr)
16806 ("r-viridis" ,r-viridis)))
16807 (home-page "https://cran.r-project.org/web/packages/accept/")
16808 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16810 "This package allows clinicians to predict the rate and severity of
16811 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16812 Disease} (COPD) patients, based on the clinical prediction model published in
16813 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16814 (license license:gpl3)))
16816 (define-public r-smpracticals
16818 (name "r-smpracticals")
16823 (uri (cran-uri "SMPracticals" version))
16826 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16827 (properties `((upstream-name . "SMPracticals")))
16828 (build-system r-build-system)
16830 `(("r-ellipse" ,r-ellipse)
16833 ("r-survival" ,r-survival)))
16834 (home-page "http://statwww.epfl.ch/davison/SM/")
16835 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16837 "This package contains the datasets and a few functions for use with the
16838 practicals outlined in Appendix A of the book Statistical Models (Davison,
16839 2003, Cambridge University Press). The practicals themselves can be found at
16840 @url{http://statwww.epfl.ch/davison/SM/}.")
16841 (license license:gpl2+)))
16843 (define-public r-fgui
16850 (uri (cran-uri "fgui" version))
16853 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16854 (properties `((upstream-name . "fgui")))
16855 (build-system r-build-system)
16857 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16858 (synopsis "Create GUI for R functions")
16860 "Rapidly create a GUI for a function you created by automatically
16861 creating widgets for arguments of the function. This package automatically
16862 parses help routines for context-sensitive help to these arguments. The
16863 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16864 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16865 incorporated into the interface for greater customization for the more
16867 ;; Any version of the GPL.
16868 (license (list license:gpl2+ license:gpl3+))))
16870 (define-public r-tcltk2
16877 (uri (cran-uri "tcltk2" version))
16880 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16881 (properties `((upstream-name . "tcltk2")))
16882 (build-system r-build-system)
16886 (home-page "https://www.sciviews.org/SciViews-R")
16887 (synopsis "Tcl/Tk additions")
16889 "This package provides a series of additional Tcl commands and Tk widgets
16890 with style and various functions to supplement the tcltk package")
16891 (license license:lgpl3)))
16893 (define-public r-accrual
16900 (uri (cran-uri "accrual" version))
16903 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16904 (properties `((upstream-name . "accrual")))
16905 (build-system r-build-system)
16907 `(("r-fgui" ,r-fgui)
16908 ("r-smpracticals" ,r-smpracticals)
16909 ("r-tcltk2" ,r-tcltk2)))
16910 (home-page "https://cran.r-project.org/web/packages/accrual/")
16911 (synopsis "Bayesian accrual prediction")
16913 "Subject recruitment for medical research is challenging. Slow patient
16914 accrual leads to delay in research. Accrual monitoring during the process of
16915 recruitment is critical. Researchers need reliable tools to manage the
16916 accrual rate. This package provides an implementation of a Bayesian method
16917 that integrates researcher's experience on previous trials and data from the
16918 current study, providing reliable prediction on accrual rate for clinical
16919 studies. It provides functions for Bayesian accrual prediction which can be
16920 easily used by statisticians and clinical researchers.")
16921 (license license:gpl2)))
16923 (define-public r-accrued
16930 (uri (cran-uri "accrued" version))
16933 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16934 (properties `((upstream-name . "accrued")))
16935 (build-system r-build-system)
16936 (home-page "https://cran.r-project.org/web/packages/accrued/")
16937 (synopsis "Data quality visualization tools for partially accruing data")
16939 "This is a package for visualizing data quality of partially accruing
16941 (license license:gpl3)))
16943 (define-public r-mda
16950 (uri (cran-uri "mda" version))
16953 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16954 (properties `((upstream-name . "mda")))
16955 (build-system r-build-system)
16956 (propagated-inputs `(("r-class" ,r-class)))
16957 (native-inputs `(("gfortran" ,gfortran)))
16958 (home-page "https://cran.r-project.org/web/packages/mda/")
16959 (synopsis "Mixture and flexible discriminant analysis")
16961 "This is a package for mixture and flexible discriminant analysis,
16962 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16963 (license license:gpl2)))
16965 (define-public r-elasticnet
16967 (name "r-elasticnet")
16972 (uri (cran-uri "elasticnet" version))
16975 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16976 (properties `((upstream-name . "elasticnet")))
16977 (build-system r-build-system)
16979 `(("r-lars" ,r-lars)))
16980 (home-page "http://users.stat.umn.edu/~zouxx019/")
16981 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16983 "This package provides functions for fitting the entire solution path of
16984 the Elastic-Net and also provides functions for estimating sparse Principal
16985 Components. The Lasso solution paths can be computed by the same function.")
16986 (license license:gpl2+)))
16988 (define-public r-sparselda
16990 (name "r-sparselda")
16995 (uri (cran-uri "sparseLDA" version))
16998 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16999 (properties `((upstream-name . "sparseLDA")))
17000 (build-system r-build-system)
17002 `(("r-elasticnet" ,r-elasticnet)
17005 (home-page "https://www.imm.dtu.dk/~lkhc/")
17006 (synopsis "Sparse discriminant analysis")
17008 "This package performs sparse linear discriminant analysis for Gaussians
17009 and mixture of Gaussian models.")
17010 (license license:gpl2+)))
17012 (define-public r-accsda
17019 (uri (cran-uri "accSDA" version))
17022 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17023 (properties `((upstream-name . "accSDA")))
17024 (build-system r-build-system)
17026 `(("r-ggplot2" ,r-ggplot2)
17027 ("r-ggthemes" ,r-ggthemes)
17028 ("r-gridextra" ,r-gridextra)
17030 ("r-rarpack" ,r-rarpack)
17031 ("r-sparselda" ,r-sparselda)))
17032 (home-page "https://github.com/gumeo/accSDA/wiki")
17033 (synopsis "Accelerated sparse discriminant analysis")
17035 "This package provides an implementation of sparse linear discriminant
17036 analysis, which is a supervised classification method for multiple classes.
17037 Various novel optimization approaches to this problem are implemented
17038 including @dfn{alternating direction method of multipliers} (ADMM),
17039 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17040 Functions for performing cross validation are also supplied along with basic
17041 prediction and plotting functions. @dfn{Sparse zero variance
17042 discriminant} (SZVD) analysis is also included in the package.")
17043 (license license:gpl2+)))
17045 (define-public r-ace2fastq
17047 (name "r-ace2fastq")
17052 (uri (cran-uri "ace2fastq" version))
17055 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17056 (properties `((upstream-name . "ace2fastq")))
17057 (build-system r-build-system)
17059 `(("r-stringr" ,r-stringr)))
17060 (home-page "https://github.com/c5sire/ace2fastq")
17061 (synopsis "ACE file to FASTQ converter")
17063 "The ACE file format is used in genomics to store contigs from sequencing
17064 machines. This tools converts it into FASTQ format. Both formats contain the
17065 sequence characters and their corresponding quality information. Unlike the
17066 FASTQ file, the ACE file stores the quality values numerically. The
17067 conversion algorithm uses the standard Sanger formula. The package
17068 facilitates insertion into pipelines, and content inspection.")
17069 (license license:gpl3)))
17071 (define-public r-rngwell
17078 (uri (cran-uri "rngWELL" version))
17081 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17082 (properties `((upstream-name . "rngWELL")))
17083 (build-system r-build-system)
17084 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17085 (synopsis "Toolbox for WELL random number generators")
17087 "This is a dedicated package to WELL pseudo random generators, which were
17088 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17089 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17090 (license license:bsd-3)))
17092 (define-public r-randtoolbox
17094 (name "r-randtoolbox")
17099 (uri (cran-uri "randtoolbox" version))
17102 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17103 (properties `((upstream-name . "randtoolbox")))
17104 (build-system r-build-system)
17106 `(("r-rngwell" ,r-rngwell)))
17108 `(("gfortran" ,gfortran)))
17109 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17110 (synopsis "Toolbox for pseudo and quasi random number generation")
17112 "This package provides
17115 @item pseudo random generators, such as general linear
17116 congruential generators, multiple recursive generators and generalized
17117 feedback shift register (SF-Mersenne Twister algorithm and WELL
17120 @item quasi random generators, such as the Torus algorithm, the Sobol
17121 sequence, the Halton sequence (including the Van der Corput sequence), and
17123 @item some generator tests: the gap test, the serial test, the poker test.
17126 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17127 (license license:bsd-3)))
17129 (define-public r-lhs
17136 (uri (cran-uri "lhs" version))
17139 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17140 (properties `((upstream-name . "lhs")))
17141 (build-system r-build-system)
17142 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17144 `(("r-knitr" ,r-knitr)))
17145 (home-page "https://github.com/bertcarnell/lhs")
17146 (synopsis "Latin Hypercube Samples")
17148 "This package provides a number of methods for creating and augmenting
17149 Latin Hypercube Samples.")
17150 (license license:gpl3)))
17152 (define-public r-acebayes
17154 (name "r-acebayes")
17159 (uri (cran-uri "acebayes" version))
17162 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17163 (properties `((upstream-name . "acebayes")))
17164 (build-system r-build-system)
17166 `(("r-compare" ,r-compare)
17168 ("r-randtoolbox" ,r-randtoolbox)
17170 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17171 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17172 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17174 "Finding an optimal Bayesian experimental design involves maximizing an
17175 objective function given by the expectation of some appropriately chosen
17176 utility function with respect to the joint distribution of unknown
17177 quantities (including responses). This objective function is usually not
17178 available in closed form and the design space can be continuous and of high
17179 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17180 to maximise an approximation to the expectation of the utility function.")
17181 (license license:gpl2)))
17183 (define-public r-acet
17190 (uri (cran-uri "ACEt" version))
17193 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17194 (properties `((upstream-name . "ACEt")))
17195 (build-system r-build-system)
17200 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17201 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17202 (synopsis "Estimating dynamic heritability and twin model comparison")
17204 "This package supports twin models that are able to estimate the dynamic
17205 behaviour of the variance components in the classical twin models with respect
17206 to age using B-splines and P-splines.")
17207 (license license:gpl2+)))
17209 (define-public r-acfmperiod
17211 (name "r-acfmperiod")
17216 (uri (cran-uri "acfMPeriod" version))
17219 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17220 (properties `((upstream-name . "acfMPeriod")))
17221 (build-system r-build-system)
17223 `(("r-mass" ,r-mass)))
17224 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17225 (synopsis "Estimation of the ACF from the M-periodogram")
17227 "This package support non-robust and robust computations of the sample
17228 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17229 univariate and multivariate processes. The methodology consists in reversing
17230 the diagonalization procedure involving the periodogram or the
17231 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17232 ACOVF or the ACF as discussed in Fuller (1995)
17233 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17234 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17235 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17236 (license license:gpl2+)))
17238 (define-public r-gamlss-data
17240 (name "r-gamlss-data")
17245 (uri (cran-uri "gamlss.data" version))
17248 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17249 (properties `((upstream-name . "gamlss.data")))
17250 (build-system r-build-system)
17251 (home-page "http://www.gamlss.org/")
17252 (synopsis "GAMLSS data")
17254 "This package provides data used as examples to demonstrate GAMLSS
17256 ;; Either version of the license
17257 (license (list license:gpl2 license:gpl3))))
17259 (define-public r-gamlss
17266 (uri (cran-uri "gamlss" version))
17269 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17270 (properties `((upstream-name . "gamlss")))
17271 (build-system r-build-system)
17273 `(("r-gamlss-data" ,r-gamlss-data)
17274 ("r-gamlss-dist" ,r-gamlss-dist)
17277 ("r-survival" ,r-survival)))
17278 (home-page "http://www.gamlss.org/")
17279 (synopsis "Generalized additive models for location scale and shape")
17281 "This package provides functions for fitting the generalized additive
17282 models for location scale and shape introduced by Rigby and
17283 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17284 use a distributional regression approach where all the parameters of the
17285 conditional distribution of the response variable are modelled using
17286 explanatory variables.")
17287 ;; Either version of the license
17288 (license (list license:gpl2 license:gpl3))))
17290 (define-public r-acid
17297 (uri (cran-uri "acid" version))
17300 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17301 (properties `((upstream-name . "acid")))
17302 (build-system r-build-system)
17304 `(("r-gamlss" ,r-gamlss)
17305 ("r-gamlss-dist" ,r-gamlss-dist)
17306 ("r-hmisc" ,r-hmisc)))
17307 (home-page "https://cran.r-project.org/web/packages/acid/")
17308 (synopsis "Analysing conditional income distributions")
17310 "This package provides functions for the analysis of income distributions
17311 for subgroups of the population as defined by a set of variables like age,
17312 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17313 distribution as well as functions for moments, inequality measures, entropy
17314 measures and polarisation measures of income distributions. This package thus
17315 aides the analysis of income inequality by offering tools for the exploratory
17316 analysis of income distributions at the disaggregated level.")
17317 (license license:gpl3)))
17319 (define-public r-acm4r
17326 (uri (cran-uri "acm4r" version))
17329 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17330 (properties `((upstream-name . "acm4r")))
17331 (build-system r-build-system)
17332 (propagated-inputs `(("r-mass" ,r-mass)))
17333 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17334 (synopsis "Align-and-count method comparisons of RFLP data")
17336 "This is a package to compare sequence fragment lengths or molecular
17337 weights from pairs of lanes. The number of matching bands in the
17338 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17339 the align-and-count method.")
17340 ;; Any version of the GPL
17341 (license (list license:gpl2+ license:gpl3+))))
17343 (define-public r-filematrix
17345 (name "r-filematrix")
17350 (uri (cran-uri "filematrix" version))
17353 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17354 (properties `((upstream-name . "filematrix")))
17355 (build-system r-build-system)
17356 ;; These inputs are needed for vignettes
17358 `(("r-knitr" ,r-knitr)
17359 ("r-rmarkdown" ,r-rmarkdown)
17360 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17361 (home-page "https://github.com/andreyshabalin/filematrix")
17362 (synopsis "File-backed matrix class with convenient read and write access")
17364 "This package provides an interface for working with large matrices
17365 stored in files, not in computer memory. It supports multiple non-character
17366 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17367 byte real values). Access to parts of the matrix is done by indexing, exactly
17368 as with usual R matrices. It supports very large matrices; the package has
17369 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17370 columns, ad allows for quick addition of extra columns to a filematrix.")
17371 (license license:lgpl3)))
17373 (define-public r-acmeeqtl
17375 (name "r-acmeeqtl")
17380 (uri (cran-uri "ACMEeqtl" version))
17383 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17384 (properties `((upstream-name . "ACMEeqtl")))
17385 (build-system r-build-system)
17387 `(("r-filematrix" ,r-filematrix)))
17388 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17389 (synopsis "Estimation of interpretable eQTL effect sizes")
17391 "This package provides a non-linear model, termed ACME, that reflects a
17392 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17393 With non-linear least-squares algorithm the maximum likelihood parameters can
17394 be estimated. The ACME model provides interpretable effect size estimates and
17395 p-values with well controlled Type-I error.")
17396 (license license:lgpl3)))
17398 (define-public r-acmer
17405 (uri (cran-uri "acmeR" version))
17408 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17409 (properties `((upstream-name . "acmeR")))
17410 (build-system r-build-system)
17411 (propagated-inputs `(("r-foreign" ,r-foreign)))
17412 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17413 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17415 "This package provides an implementation of the ACME estimator, described
17416 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17417 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17418 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17419 as carcasses age; variable bleed-through at successive searches; and interval
17420 mortality estimates. The package provides, based on search data, functions
17421 for estimating the mortality inflation factor in Frequentist and Bayesian
17423 (license license:expat)))
17425 (define-public r-r-huge
17432 (uri (cran-uri "R.huge" version))
17435 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17436 (properties `((upstream-name . "R.huge")))
17437 (build-system r-build-system)
17439 `(("r-r-methodss3" ,r-r-methodss3)
17441 ("r-r-utils" ,r-r-utils)))
17442 (home-page "https://github.com/HenrikBengtsson/R.huge")
17443 (synopsis "Methods for accessing huge amounts of data")
17445 "This is a deprecated package for accessing huge amounts of data.
17446 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17447 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17448 the @code{aroma.affymetrix} package.")
17449 (license license:lgpl2.1+)))
17451 (define-public r-r-filesets
17453 (name "r-r-filesets")
17458 (uri (cran-uri "R.filesets" version))
17461 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17462 (properties `((upstream-name . "R.filesets")))
17463 (build-system r-build-system)
17465 `(("r-digest" ,r-digest)
17466 ("r-r-cache" ,r-r-cache)
17467 ("r-r-methodss3" ,r-r-methodss3)
17469 ("r-r-utils" ,r-r-utils)))
17470 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17471 (synopsis "Easy handling of and access to files")
17473 "This package provides classes and methods to locate, setup, subset,
17474 navigate and iterate file sets, i.e. sets of files located in one or more
17475 directories on the file system. The API is designed such that these classes
17476 can be extended via inheritance to provide a richer API for special file
17477 formats. Moreover, a specific name format is defined such that filenames and
17478 directories can be considered to have full names which consists of a name
17479 followed by comma-separated tags. This adds additional flexibility to
17480 identify file sets and individual files.")
17481 (license license:lgpl2.1+)))
17483 (define-public r-r-devices
17485 (name "r-r-devices")
17490 (uri (cran-uri "R.devices" version))
17493 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17494 (properties `((upstream-name . "R.devices")))
17495 (build-system r-build-system)
17497 `(("r-base64enc" ,r-base64enc)
17498 ("r-r-methodss3" ,r-r-methodss3)
17500 ("r-r-utils" ,r-r-utils)))
17501 (home-page "https://github.com/HenrikBengtsson/R.devices")
17502 (synopsis "Unified handling of graphics devices")
17504 "This package provides functions for creating plots and image files in a
17505 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17506 Default device options as well as scales and aspect ratios are controlled in a
17507 uniform way across all device types. Switching output format requires minimal
17508 changes in code. This package is ideal for large-scale batch processing,
17509 because it will never leave open graphics devices or incomplete image files
17510 behind, even on errors or user interrupts.")
17511 (license license:lgpl2.1+)))
17513 (define-public r-acnr
17520 (uri (cran-uri "acnr" version))
17523 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17524 (properties `((upstream-name . "acnr")))
17525 (build-system r-build-system)
17526 (home-page "https://github.com/mpierrejean/acnr")
17527 (synopsis "Annotated copy-number regions")
17529 "This package provides SNP array data from different types of copy-number
17530 regions. These regions were identified manually by the authors of the package
17531 and may be used to generate realistic data sets with known truth.")
17532 (license license:lgpl2.1+)))
17534 (define-public r-acopula
17541 (uri (cran-uri "acopula" version))
17544 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17545 (properties `((upstream-name . "acopula")))
17546 (build-system r-build-system)
17547 (home-page "https://cran.r-project.org/web/packages/acopula/")
17548 (synopsis "Modelling dependence with multivariate Archimax copulas")
17550 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17551 package provides definitions of several parametric families of generator and
17552 dependence function, computes CDF and PDF, estimates parameters, tests for
17553 goodness of fit, generates random sample and checks copula properties for
17554 custom constructs. In the 2-dimensional case explicit formulas for density
17555 are used, contrary to higher dimensions when all derivatives are linearly
17556 approximated. Several non-archimax families (normal, FGM, Plackett) are
17557 provided as well.")
17558 (license license:gpl2)))
17560 (define-public r-tuner
17567 (uri (cran-uri "tuneR" version))
17570 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17571 (properties `((upstream-name . "tuneR")))
17572 (build-system r-build-system)
17573 (propagated-inputs `(("r-signal" ,r-signal)))
17574 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17575 (synopsis "Analysis of music and speech")
17577 "This is a package for the analysis of music and speech. Analyze music
17578 and speech, extract features like MFCCs, handle wave files and their
17579 representation in various ways, read MP3, read MIDI, perform steps of a
17580 transcription, ...")
17581 ;; Either of these versions.
17582 (license (list license:gpl2 license:gpl3))))
17584 (define-public r-seewave
17591 (uri (cran-uri "seewave" version))
17594 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17595 (properties `((upstream-name . "seewave")))
17596 (build-system r-build-system)
17598 `(("r-tuner" ,r-tuner)))
17599 (home-page "http://rug.mnhn.fr/seewave")
17600 (synopsis "Sound analysis and synthesis")
17602 "This package provides functions for analysing, manipulating, displaying,
17603 editing and synthesizing time waves (particularly sound). This package
17604 processes time analysis (oscillograms and envelopes), spectral content,
17605 resonance quality factor, entropy, cross correlation and autocorrelation,
17606 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17607 and 3D spectrograms and many other analyses.")
17608 (license license:gpl2+)))
17610 (define-public r-acousticndlcoder
17612 (name "r-acousticndlcoder")
17617 (uri (cran-uri "AcousticNDLCodeR" version))
17620 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17622 `((upstream-name . "AcousticNDLCodeR")))
17623 (build-system r-build-system)
17625 `(("r-seewave" ,r-seewave)
17626 ("r-tuner" ,r-tuner)
17628 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17629 (synopsis "Coding sound files for use with NDL")
17631 "Make acoustic cues to use with the R package @code{ndl}.
17632 The package implements functions used in the PLoS ONE paper \"Words from
17633 spontaneous conversational speech can be recognized with human-like accuracy
17634 by an error-driven learning algorithm that discriminates between meanings
17635 straight from smart acoustic features, bypassing the phoneme as recognition
17636 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17637 (license license:gpl2+)))
17639 (define-public r-acp
17646 (uri (cran-uri "acp" version))
17649 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17650 (properties `((upstream-name . "acp")))
17651 (build-system r-build-system)
17653 `(("r-quantmod" ,r-quantmod)
17654 ("r-tseries" ,r-tseries)))
17655 (home-page "https://cran.r-project.org/web/packages/acp/")
17656 (synopsis "Autoregressive conditional Poisson")
17658 "This package supports the analysis of count data exhibiting
17659 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17660 model (ACP(p,q)) proposed by Heinen (2003).")
17661 (license license:gpl2)))
17663 (define-public r-ada
17670 (uri (cran-uri "ada" version))
17673 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17674 (properties `((upstream-name . "ada")))
17675 (build-system r-build-system)
17676 (propagated-inputs `(("r-rpart" ,r-rpart)))
17677 (home-page "https://cran.r-project.org/web/packages/ada/")
17678 (synopsis "Stochastic boosting")
17680 "This package provides a straightforward, well-documented, and broad
17681 boosting routine for classification, ideally suited for small to
17682 moderate-sized data sets. It performs discrete, real, and gentle boost under
17683 both exponential and logistic loss on a given data set.")
17684 ;; Any version of the GPL.
17685 (license (list license:gpl2+ license:gpl3+))))
17687 (define-public r-genalg
17694 (uri (cran-uri "genalg" version))
17697 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17698 (properties `((upstream-name . "genalg")))
17699 (build-system r-build-system)
17700 (home-page "https://github.com/egonw/genalg")
17701 (synopsis "R based genetic algorithm")
17703 "This package provides an R based genetic algorithm for binary and
17704 floating point chromosomes.")
17705 (license license:gpl2)))
17707 (define-public r-kernelfactory
17709 (name "r-kernelfactory")
17714 (uri (cran-uri "kernelFactory" version))
17717 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17718 (properties `((upstream-name . "kernelFactory")))
17719 (build-system r-build-system)
17722 ("r-genalg" ,r-genalg)
17723 ("r-kernlab" ,r-kernlab)
17724 ("r-randomforest" ,r-randomforest)))
17725 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17726 (synopsis "Ensemble of kernel machines")
17728 "Kernel factory is an ensemble method where each base classifier (random
17729 forest) is fit on the kernel matrix of a subset of the training data.")
17730 (license license:gpl2+)))
17732 (define-public r-dummies
17739 (uri (cran-uri "dummies" version))
17742 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17743 (properties `((upstream-name . "dummies")))
17744 (build-system r-build-system)
17745 (home-page "https://decisionpatterns.com")
17746 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17748 "This package lets you expand factors, characters and other eligible
17749 classes into dummy/indicator variables.")
17750 (license license:gpl2+)))
17752 (define-public r-acrm
17759 (uri (cran-uri "aCRM" version))
17762 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17763 (properties `((upstream-name . "aCRM")))
17764 (build-system r-build-system)
17767 ("r-dummies" ,r-dummies)
17768 ("r-kernelfactory" ,r-kernelfactory)
17769 ("r-randomforest" ,r-randomforest)))
17770 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17771 (synopsis "Convenience functions for analytical customer relationship management")
17773 "This package provides convenience functions for data preparation and
17774 modeling often used in @dfn{analytical customer relationship
17775 management} (aCRM).")
17776 (license license:gpl2+)))
17778 (define-public r-treeclust
17780 (name "r-treeclust")
17785 (uri (cran-uri "treeClust" version))
17788 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
17789 (properties `((upstream-name . "treeClust")))
17790 (build-system r-build-system)
17792 `(("r-cluster" ,r-cluster)
17793 ("r-rpart" ,r-rpart)))
17794 (home-page "https://cran.r-project.org/web/packages/treeClust/")
17795 (synopsis "Cluster distances through trees")
17797 "This package provides tools to create a measure of inter-point
17798 dissimilarity useful for clustering mixed data, and, optionally, perform the
17800 (license license:gpl2+)))
17802 (define-public r-acrosstic
17804 (name "r-acrosstic")
17809 (uri (cran-uri "AcrossTic" version))
17812 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
17813 (properties `((upstream-name . "AcrossTic")))
17814 (build-system r-build-system)
17816 `(("r-lpsolve" ,r-lpsolve)
17817 ("r-treeclust" ,r-treeclust)))
17818 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
17819 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
17821 "This is a package for constructing minimum-cost regular spanning
17822 subgraph as part of a non-parametric two-sample test for equality of
17824 (license license:gpl2+)))
17826 (define-public r-acrt
17833 (uri (cran-uri "acrt" version))
17836 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
17837 (properties `((upstream-name . "acrt")))
17838 (build-system r-build-system)
17840 `(("r-rcpp" ,r-rcpp)
17841 ("r-rcppeigen" ,r-rcppeigen)
17842 ("r-sandwich" ,r-sandwich)))
17843 (home-page "https://cran.r-project.org/web/packages/acrt/")
17844 (synopsis "Autocorrelation robust testing")
17846 "This package provides functions for testing affine hypotheses on the
17847 regression coefficient vector in regression models with autocorrelated
17849 (license license:gpl2)))
17851 (define-public r-acs
17858 (uri (cran-uri "acs" version))
17861 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
17862 (properties `((upstream-name . "acs")))
17863 (build-system r-build-system)
17865 `(("r-httr" ,r-httr)
17868 ("r-stringr" ,r-stringr)
17870 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
17871 (synopsis "Work with data from the US Census")
17873 "This package provides a general toolkit for downloading, managing,
17874 analyzing, and presenting data from the
17875 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
17876 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
17877 American Community Survey (ACS). Confidence intervals provided with ACS data
17878 are converted to standard errors to be bundled with estimates in complex
17879 @code{acs} objects. The package provides new methods to conduct standard
17880 operations on @code{acs} objects and present/plot data in statistically
17881 appropriate ways.")
17882 (license license:gpl3)))
17884 (define-public r-acss-data
17886 (name "r-acss-data")
17891 (uri (cran-uri "acss.data" version))
17894 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
17895 (properties `((upstream-name . "acss.data")))
17896 (build-system r-build-system)
17897 (home-page "http://complexitycalculator.com/methodology.html")
17898 (synopsis "Data for algorithmic complexity of short strings")
17900 "This is a data only package providing the algorithmic complexity of
17901 short strings, computed using the coding theorem method. For a given set of
17902 symbols in a string, all possible or a large number of random samples of
17903 Turing machines with a given number of states (e.g., 5) and number of symbols
17904 corresponding to the number of symbols in the strings were simulated until
17905 they reached a halting state or failed to end. This package contains data on
17906 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
17907 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
17908 distribution of the halting states.")
17909 (license license:gpl2+)))
17911 (define-public r-acss
17918 (uri (cran-uri "acss" version))
17921 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
17922 (properties `((upstream-name . "acss")))
17923 (build-system r-build-system)
17925 `(("r-acss-data" ,r-acss-data)
17927 (home-page "http://complexitycalculator.com/methodology.html")
17928 (synopsis "Algorithmic complexity for short strings")
17930 "The main purpose of this package is to provide the algorithmic
17931 complexity for short strings, an approximation of the Kolmogorov Complexity of
17932 a short string using the coding theorem method. While the database containing
17933 the complexity is provided in the data only package @code{acss.data}, this
17934 package provides functions accessing the data such as @code{prob_random}
17935 returning the posterior probability that a given string was produced by a
17936 random process. In addition, two traditional (but problematic) measures of
17937 complexity are also provided: entropy and change complexity.")
17938 (license license:gpl2+)))
17940 (define-public r-acswr
17947 (uri (cran-uri "ACSWR" version))
17950 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
17951 (properties `((upstream-name . "ACSWR")))
17952 (build-system r-build-system)
17954 `(("r-mass" ,r-mass)))
17955 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
17956 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
17958 "This is a companion package for the book \"A Course in Statistics with
17959 R\" (ISBN 978-1-119-15272-9.)")
17960 (license license:gpl2)))
17962 (define-public r-alabama
17965 (version "2015.3-1")
17969 (uri (cran-uri "alabama" version))
17972 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
17973 (properties `((upstream-name . "alabama")))
17974 (build-system r-build-system)
17975 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
17976 (home-page "https://cran.r-project.org/web/packages/alabama/")
17977 (synopsis "Constrained nonlinear optimization")
17979 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
17980 Algorithm; it is used for optimizing smooth nonlinear objective functions with
17981 constraints. Linear or nonlinear equality and inequality constraints are
17983 (license license:gpl2+)))
17985 (define-public r-gdina
17992 (uri (cran-uri "GDINA" version))
17995 "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx"))))
17996 (properties `((upstream-name . "GDINA")))
17997 (build-system r-build-system)
17999 `(("r-alabama" ,r-alabama)
18000 ("r-ggplot2" ,r-ggplot2)
18002 ("r-nloptr" ,r-nloptr)
18003 ("r-numderiv" ,r-numderiv)
18005 ("r-rcpparmadillo" ,r-rcpparmadillo)
18006 ("r-rsolnp" ,r-rsolnp)
18007 ("r-shiny" ,r-shiny)
18008 ("r-shinydashboard" ,r-shinydashboard)))
18009 (home-page "https://github.com/Wenchao-Ma/GDINA")
18010 (synopsis "Generalized DINA model framework")
18012 "This package provides a set of psychometric tools for cognitive
18013 diagnosis modeling based on the generalized deterministic inputs, noisy and
18014 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18015 and its extensions, including the sequential G-DINA model by Ma and de la
18016 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18017 polytomous G-DINA model by Chen and de la Torre
18018 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18019 distribution can be independent, saturated, higher-order, loglinear smoothed
18020 or structured. Q-matrix validation, item and model fit statistics, model
18021 comparison at test and item level and differential item functioning can also
18022 be conducted. A graphical user interface is also provided.")
18023 (license license:gpl3)))
18025 (define-public r-actcd
18032 (uri (cran-uri "ACTCD" version))
18035 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18036 (properties `((upstream-name . "ACTCD")))
18037 (build-system r-build-system)
18039 `(("r-gdina" ,r-gdina)
18040 ("r-r-methodss3" ,r-r-methodss3)))
18042 `(("gfortran" ,gfortran)))
18043 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18044 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18046 "This is a package supporting cluster analysis for cognitive diagnosis
18047 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18048 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18049 sum-scores, cluster analysis techniques can be used to classify examinees into
18050 latent classes based on their attribute patterns. In addition to the
18051 algorithms used to classify data, three labeling approaches are proposed to
18052 label clusters so that examinees' attribute profiles can be obtained.")
18053 (license license:gpl2+)))
18055 (define-public r-ineq
18062 (uri (cran-uri "ineq" version))
18065 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18066 (properties `((upstream-name . "ineq")))
18067 (build-system r-build-system)
18068 (home-page "https://cran.r-project.org/web/packages/ineq/")
18069 (synopsis "Measuring inequality, concentration, and poverty")
18071 "This package provides tools for measuring inequality, concentration, and
18072 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18073 ;; Either of these two versions.
18074 (license (list license:gpl2 license:gpl3))))
18076 (define-public r-actfrag
18083 (uri (cran-uri "ActFrag" version))
18086 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18087 (properties `((upstream-name . "ActFrag")))
18088 (build-system r-build-system)
18090 `(("r-accelerometry" ,r-accelerometry)
18091 ("r-dplyr" ,r-dplyr)
18093 ("r-survival" ,r-survival)
18094 ("r-tidyr" ,r-tidyr)))
18095 (home-page "https://github.com/junruidi/ActFrag")
18096 (synopsis "Activity fragmentation metrics extraction")
18098 "This package provides functions to extract commonly used fragmentation
18099 metrics to quantify time accumulation strategies based on minute level
18100 actigraphy-measured activity counts data.")
18101 (license license:gpl3)))
18103 (define-public r-fda
18106 (version "2.4.8.1")
18110 (uri (cran-uri "fda" version))
18113 "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
18114 (properties `((upstream-name . "fda")))
18115 (build-system r-build-system)
18117 `(("r-matrix" ,r-matrix)))
18118 (home-page "https://www.functionaldata.org")
18119 (synopsis "Functional data analysis")
18121 "These functions were developed to support functional data analysis as
18122 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18123 Analysis. The package includes data sets and script files working many
18125 (license license:gpl2+)))
18127 (define-public r-actigraphy
18129 (name "r-actigraphy")
18134 (uri (cran-uri "Actigraphy" version))
18137 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18138 (properties `((upstream-name . "Actigraphy")))
18139 (build-system r-build-system)
18141 `(("r-fda" ,r-fda)))
18142 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18143 (synopsis "Actigraphy data analysis")
18145 "This package provides tools for functional linear modeling and analysis
18146 of actigraphy data.")
18147 (license license:asl2.0)))
18149 (define-public r-activedriver
18151 (name "r-activedriver")
18156 (uri (cran-uri "ActiveDriver" version))
18159 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18160 (properties `((upstream-name . "ActiveDriver")))
18161 (build-system r-build-system)
18163 `(("r-mass" ,r-mass)))
18164 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18165 (synopsis "Tools for finding cancer driver proteins")
18167 "This package provides a mutation analysis tool that discovers cancer
18168 driver genes with frequent mutations in protein signalling sites such as
18169 post-translational modifications (phosphorylation, ubiquitination, etc). The
18170 Poisson generalized linear regression model identifies genes where cancer
18171 mutations in signalling sites are more frequent than expected from the
18172 sequence of the entire gene. Integration of mutations with signalling
18173 information helps find new driver genes and propose candidate mechanisms to
18175 (license license:gpl2+)))
18177 (define-public r-activitycounts
18179 (name "r-activitycounts")
18184 (uri (cran-uri "activityCounts" version))
18187 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18189 `((upstream-name . "activityCounts")))
18190 (build-system r-build-system)
18192 `(("r-lubridate" ,r-lubridate)
18193 ("r-magrittr" ,r-magrittr)
18194 ("r-seewave" ,r-seewave)
18195 ("r-signal" ,r-signal)
18196 ("r-tibble" ,r-tibble)))
18197 (home-page "https://github.com/walkabillylab/activityCounts")
18198 (synopsis "Generate ActiLife counts")
18200 "ActiLife generates activity counts from data collected by Actigraph
18201 accelerometers. Actigraph is one of the most common research-grade
18202 accelerometers. There is considerable research validating and developing
18203 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18204 counts are proprietary and difficult to implement if researchers use different
18205 accelerometer brands. The code creates ActiLife counts from raw acceleration
18206 data for different accelerometer brands.")
18207 (license license:gpl3)))
18209 (define-public r-activityindex
18211 (name "r-activityindex")
18216 (uri (cran-uri "ActivityIndex" version))
18219 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18220 (properties `((upstream-name . "ActivityIndex")))
18221 (build-system r-build-system)
18223 `(("r-data-table" ,r-data-table)
18224 ("r-matrixstats" ,r-matrixstats)
18225 ("r-r-utils" ,r-r-utils)))
18226 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18227 (synopsis "Activity Index calculation using raw accelerometry data")
18229 "This is a package to read raw accelerometry from GT3X+ accelerometry
18230 data and plain table data to calculate the Activity Index from Bai et
18231 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18232 (license license:gpl3)))
18234 (define-public r-activpal
18236 (name "r-activpal")
18241 (uri (cran-uri "activPAL" version))
18244 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18245 (properties `((upstream-name . "activPAL")))
18246 (build-system r-build-system)
18248 `(("r-devtools" ,r-devtools)
18249 ("r-dplyr" ,r-dplyr)
18250 ("r-ggplot2" ,r-ggplot2)
18251 ("r-lubridate" ,r-lubridate)
18252 ("r-magrittr" ,r-magrittr)
18253 ("r-tidyr" ,r-tidyr)))
18254 (home-page "https://cran.r-project.org/web/packages/activPAL")
18255 (synopsis "Processing and chart generation from activPAL events files")
18257 "This package contains functions to generate pre-defined summary
18258 statistics from activPAL events files. The package also contains functions to
18259 produce informative graphics that visualize physical activity behaviour and
18260 trends. This includes generating graphs that align physical activity
18261 behaviour with additional time based observations described by other data
18262 sets, such as sleep diaries and continuous glucose monitoring data.")
18263 (license license:gpl3)))
18265 (define-public r-activpalprocessing
18267 (name "r-activpalprocessing")
18272 (uri (cran-uri "activpalProcessing" version))
18275 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18277 `((upstream-name . "activpalProcessing")))
18278 (build-system r-build-system)
18280 `(("r-chron" ,r-chron)))
18281 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18282 (synopsis "Process activPAL events files")
18284 "This package performs estimation of physical activity and sedentary
18285 behavior variables from activPAL events files.")
18286 ;; Either version of the GPL.
18287 (license (list license:gpl2 license:gpl3))))
18289 (define-public r-actogrammr
18291 (name "r-actogrammr")
18296 (uri (cran-uri "actogrammr" version))
18299 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18300 (properties `((upstream-name . "actogrammr")))
18301 (build-system r-build-system)
18303 `(("r-dplyr" ,r-dplyr)
18304 ("r-ggplot2" ,r-ggplot2)
18305 ("r-lubridate" ,r-lubridate)
18306 ("r-readr" ,r-readr)
18307 ("r-tidyr" ,r-tidyr)))
18308 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18309 (synopsis "Read in activity data and plot actograms")
18311 "Read in activity measurements from standard file formats used by
18312 circadian rhythm researchers, currently only ClockLab format, and process and
18313 plot the data. The central type of plot is the actogram, as first described
18314 in \"Activity and distribution of certain wild mice in relation to biotic
18315 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18316 (license license:gpl3)))
18318 (define-public r-expint
18325 (uri (cran-uri "expint" version))
18328 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18329 (properties `((upstream-name . "expint")))
18330 (build-system r-build-system)
18331 (home-page "https://gitlab.com/vigou3/expint")
18332 (synopsis "Exponential integral and incomplete Gamma function")
18334 "This package provides the exponential integrals @code{E_1(x)},
18335 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18336 function @code{G(a, x)} defined for negative values of its first argument.
18337 The package also gives easy access to the underlying C routines through an
18338 API; see the package vignette for details.")
18339 (license license:gpl2+)))
18341 (define-public r-actuar
18348 (uri (cran-uri "actuar" version))
18351 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18352 (properties `((upstream-name . "actuar")))
18353 (build-system r-build-system)
18354 (propagated-inputs `(("r-expint" ,r-expint)))
18355 (home-page "https://gitlab.com/vigou3/actuar")
18356 (synopsis "Actuarial functions and heavy tailed distributions")
18358 "This package provides functions and data sets for actuarial science:
18359 modeling of loss distributions; risk theory and ruin theory; simulation of
18360 compound models, discrete mixtures and compound hierarchical models;
18361 credibility theory. It boasts support for many additional probability
18362 distributions to model insurance loss amounts and loss frequency: 19
18363 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18364 distribution; zero-truncated and zero-modified extensions of the standard
18365 discrete distributions. It also supports phase-type distributions commonly
18366 used to compute ruin probabilities.")
18367 (license license:gpl2+)))
18369 (define-public r-bmp
18376 (uri (cran-uri "bmp" version))
18379 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18380 (properties `((upstream-name . "bmp")))
18381 (build-system r-build-system)
18382 (home-page "https://cran.r-project.org/web/packages/bmp/")
18383 (synopsis "Read Bitmap (BMP) images")
18385 "This package provides pure R tools to read BMP format images. It is
18386 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18387 (license license:gpl2+)))
18389 (define-public r-readbitmap
18391 (name "r-readbitmap")
18396 (uri (cran-uri "readbitmap" version))
18399 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18400 (properties `((upstream-name . "readbitmap")))
18401 (build-system r-build-system)
18403 `(("libjpeg" ,libjpeg-turbo)
18404 ("libpng" ,libpng)))
18409 ("r-tiff" ,r-tiff)))
18410 (home-page "https://github.com/jefferis/readbitmap")
18411 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18413 "This package provides tools to identify and read BMP, JPEG, PNG, and
18414 TIFF format bitmap images. Identification defaults to the use of the magic
18415 number embedded in the file rather than the file extension.")
18416 (license license:gpl2+)))
18418 (define-public r-imager
18425 (uri (cran-uri "imager" version))
18428 "1d7a49lcna77wyfjf5q1b89jck3p3vnysnkgz4drb0qkpy6hz76b"))))
18429 (properties `((upstream-name . "imager")))
18430 (build-system r-build-system)
18433 ("libtiff" ,libtiff)
18437 `(("r-downloader" ,r-downloader)
18438 ("r-igraph" ,r-igraph)
18440 ("r-magrittr" ,r-magrittr)
18442 ("r-purrr" ,r-purrr)
18444 ("r-readbitmap" ,r-readbitmap)
18445 ("r-stringr" ,r-stringr)))
18446 (native-inputs `(("pkg-config" ,pkg-config)))
18447 (home-page "https://dahtah.github.io/imager/")
18448 (synopsis "Image processing library")
18450 "This is a package for fast image processing for images in up to 4
18451 dimensions (two spatial dimensions, one time/depth dimension, one color
18452 dimension). It provides most traditional image processing tools (filtering,
18453 morphology, transformations, etc.) as well as various functions for easily
18454 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18455 simple, modern C++ library for image processing.")
18456 (license license:lgpl3)))
18458 (define-public r-acuityview
18460 (name "r-acuityview")
18465 (uri (cran-uri "AcuityView" version))
18468 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18469 (properties `((upstream-name . "AcuityView")))
18470 (build-system r-build-system)
18472 `(("r-fftwtools" ,r-fftwtools)
18473 ("r-imager" ,r-imager)
18474 ("r-plotrix" ,r-plotrix)))
18475 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18476 (synopsis "Display scenes as seen by an animal with less acute vision")
18478 "This package provides a simple method for representing a visual scene as
18479 it may be seen by an animal with less acute vision.")
18480 (license license:gpl2+)))
18482 (define-public r-caret
18489 (uri (cran-uri "caret" version))
18492 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
18493 (build-system r-build-system)
18495 `(("r-foreach" ,r-foreach)
18496 ("r-ggplot2" ,r-ggplot2)
18497 ("r-lattice" ,r-lattice)
18498 ("r-modelmetrics" ,r-modelmetrics)
18502 ("r-recipes" ,r-recipes)
18503 ("r-reshape2" ,r-reshape2)
18504 ("r-withr" ,r-withr)))
18506 `(("r-knitr" ,r-knitr)))
18507 (home-page "https://github.com/topepo/caret")
18508 (synopsis "Classification and regression training")
18510 "This package provides miscellaneous functions for training and plotting
18511 classification and regression models.")
18512 (license license:gpl2+)))
18514 (define-public r-adabag
18521 (uri (cran-uri "adabag" version))
18524 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18525 (properties `((upstream-name . "adabag")))
18526 (build-system r-build-system)
18528 `(("r-caret" ,r-caret)
18529 ("r-doparallel" ,r-doparallel)
18530 ("r-foreach" ,r-foreach)
18531 ("r-rpart" ,r-rpart)))
18532 (home-page "https://cran.r-project.org/web/packages/adabag/")
18533 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18535 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18536 Breiman's Bagging algorithm using classification trees as individual
18537 classifiers. Once these classifiers have been trained, they can be used to
18538 predict on new data. Also, cross validation estimation of the error can be
18540 (license license:gpl2+)))
18542 (define-public r-adagio
18549 (uri (cran-uri "adagio" version))
18552 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18553 (properties `((upstream-name . "adagio")))
18554 (build-system r-build-system)
18555 (native-inputs `(("gfortran" ,gfortran)))
18556 (home-page "https://cran.r-project.org/web/packages/adagio/")
18557 (synopsis "Discrete and global optimization routines")
18559 "This package provides methods and algorithms for discrete optimization,
18560 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18561 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18563 (license license:gpl3+)))
18565 (define-public r-univoutl
18567 (name "r-univoutl")
18572 (uri (cran-uri "univOutl" version))
18575 "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
18576 (properties `((upstream-name . "univOutl")))
18577 (build-system r-build-system)
18579 `(("r-hmisc" ,r-hmisc)
18580 ("r-robustbase" ,r-robustbase)))
18581 (home-page "https://github.com/marcellodo/univOutl")
18582 (synopsis "Detection of univariate outliers")
18584 "This package provides well-known outlier detection techniques in the
18585 univariate case. Methods to deal with skewed distribution are included too.
18586 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18587 historical data is implemented as well. When available, survey weights can be
18588 used in outliers detection.")
18589 (license license:gpl2+)))
18591 (define-public r-tolerance
18593 (name "r-tolerance")
18598 (uri (cran-uri "tolerance" version))
18601 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
18602 (properties `((upstream-name . "tolerance")))
18603 (build-system r-build-system)
18605 `(("r-mass" ,r-mass)
18607 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18608 (synopsis "Statistical tolerance intervals and regions")
18610 "This package provides functions for estimating tolerance
18611 limits (intervals) for various univariate distributions (binomial, Cauchy,
18612 discrete Pareto, exponential, two-parameter exponential, extreme value,
18613 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18614 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18615 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18616 nonparametric tolerance intervals, tolerance bands for regression
18617 settings (linear regression, nonlinear regression, nonparametric regression,
18618 and multivariate regression), and analysis of variance tolerance intervals.
18619 Visualizations are also available for most of these settings.")
18620 (license license:gpl2+)))
18622 (define-public r-additivitytests
18624 (name "r-additivitytests")
18629 (uri (cran-uri "additivityTests" version))
18632 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18634 `((upstream-name . "additivityTests")))
18635 (build-system r-build-system)
18636 (home-page "https://github.com/simecek/additivityTests")
18637 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18639 "This package provides an implementation of the Tukey, Mandel,
18640 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18641 (license license:gpl3)))
18643 (define-public r-flexclust
18645 (name "r-flexclust")
18650 (uri (cran-uri "flexclust" version))
18653 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18654 (properties `((upstream-name . "flexclust")))
18655 (build-system r-build-system)
18657 `(("r-class" ,r-class)
18658 ("r-lattice" ,r-lattice)
18659 ("r-modeltools" ,r-modeltools)))
18660 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18661 (synopsis "Flexible cluster algorithms")
18663 "The main function @code{kcca} implements a general framework for
18664 k-centroids cluster analysis supporting arbitrary distance measures and
18665 centroid computation. Further cluster methods include hard competitive
18666 learning, neural gas, and QT clustering. There are numerous visualization
18667 methods for cluster results (neighborhood graphs, convex cluster hulls,
18668 barcharts of centroids, ...), and bootstrap methods for the analysis of
18669 cluster stability.")
18670 (license license:gpl2)))
18672 (define-public r-biclust
18679 (uri (cran-uri "biclust" version))
18682 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
18683 (properties `((upstream-name . "biclust")))
18684 (build-system r-build-system)
18686 `(("r-additivitytests" ,r-additivitytests)
18687 ("r-colorspace" ,r-colorspace)
18688 ("r-flexclust" ,r-flexclust)
18689 ("r-ggplot2" ,r-ggplot2)
18690 ("r-lattice" ,r-lattice)
18692 ("r-tidyr" ,r-tidyr)))
18693 (home-page "https://cran.r-project.org/web/packages/biclust/")
18694 (synopsis "BiCluster algorithms")
18696 "The main function @code{biclust()} provides several algorithms to find
18697 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18698 In addition, the package provides methods for data
18699 preprocessing (normalization and discretization), visualization, and
18700 validation of bicluster solutions.")
18701 (license license:gpl3)))
18703 (define-public r-icge
18710 (uri (cran-uri "ICGE" version))
18713 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18714 (properties `((upstream-name . "ICGE")))
18715 (build-system r-build-system)
18717 `(("r-cluster" ,r-cluster)
18718 ("r-mass" ,r-mass)))
18719 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18720 (synopsis "Cluster estimation and identification of atypical units")
18722 "ICGE is a package that helps to estimate the number of real clusters in
18723 data as well as to identify atypical units. The underlying methods are based
18724 on distances rather than on unit x variables.")
18725 (license license:gpl2+)))
18727 (define-public r-depth
18730 (version "2.1-1.1")
18734 (uri (cran-uri "depth" version))
18737 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18738 (properties `((upstream-name . "depth")))
18739 (build-system r-build-system)
18741 `(("r-abind" ,r-abind)
18742 ("r-circular" ,r-circular)
18745 `(("gfortran" ,gfortran)))
18746 (home-page "https://cran.r-project.org/web/packages/depth/")
18747 (synopsis "Nonparametric depth functions for multivariate analysis")
18749 "This package provides tools for depth functions methodology applied to
18750 multivariate analysis. Besides allowing calculation of depth values and
18751 depth-based location estimators, the package includes functions or drawing
18752 contour plots and perspective plots of depth functions. Euclidian and
18753 spherical depths are supported.")
18754 (license license:gpl2)))
18756 (define-public r-archetypes
18758 (name "r-archetypes")
18759 (version "2.2-0.1")
18763 (uri (cran-uri "archetypes" version))
18766 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18767 (properties `((upstream-name . "archetypes")))
18768 (build-system r-build-system)
18770 `(("r-modeltools" ,r-modeltools)
18771 ("r-nnls" ,r-nnls)))
18772 (home-page "https://cran.r-project.org/web/packages/archetypes")
18773 (synopsis "Archetypal analysis")
18775 "The main function @code{archetypes} implements a framework for
18776 archetypal analysis supporting arbitrary problem solving mechanisms for the
18777 different conceptual parts of the algorithm.")
18778 (license license:gpl2+)))
18780 (define-public r-shapes
18787 (uri (cran-uri "shapes" version))
18790 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
18791 (properties `((upstream-name . "shapes")))
18792 (build-system r-build-system)
18794 `(("r-mass" ,r-mass)
18795 ("r-minpack-lm" ,r-minpack-lm)
18797 ("r-scatterplot3d" ,r-scatterplot3d)))
18798 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
18799 (synopsis "Statistical shape analysis")
18801 "This package provides routines for the statistical analysis of landmark
18802 shapes, including Procrustes analysis, graphical displays, principal
18803 components analysis, permutation and bootstrap tests, thin-plate spline
18804 transformation grids and comparing covariance matrices. See Dryden, I.L. and
18805 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
18806 Edition), John Wiley and Sons.")
18807 (license license:gpl2)))
18809 (define-public r-anthropometry
18811 (name "r-anthropometry")
18816 (uri (cran-uri "Anthropometry" version))
18819 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
18820 (properties `((upstream-name . "Anthropometry")))
18821 (build-system r-build-system)
18823 `(("r-archetypes" ,r-archetypes)
18824 ("r-biclust" ,r-biclust)
18825 ("r-cluster" ,r-cluster)
18826 ("r-depth" ,r-depth)
18831 ("r-shapes" ,r-shapes)))
18833 `(("r-knitr" ,r-knitr)))
18834 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
18835 (synopsis "Statistical methods for anthropometric data")
18837 "This package provides statistical methods especially developed to
18838 analyze anthropometric data. These methods are aimed at providing effective
18839 solutions to some commons problems related to Ergonomics and Anthropometry.
18840 They are based on clustering, the statistical concept of data depth,
18841 statistical shape analysis and archetypal analysis.")
18842 (license license:gpl2+)))
18844 (define-public r-adamethods
18846 (name "r-adamethods")
18851 (uri (cran-uri "adamethods" version))
18854 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
18855 (properties `((upstream-name . "adamethods")))
18856 (build-system r-build-system)
18858 `(("r-anthropometry" ,r-anthropometry)
18859 ("r-archetypes" ,r-archetypes)
18861 ("r-foreach" ,r-foreach)
18863 ("r-tolerance" ,r-tolerance)
18864 ("r-univoutl" ,r-univoutl)))
18865 (home-page "https://cran.r-project.org/web/packages/adamethods/")
18866 (synopsis "Archetypoid algorithms and anomaly detection")
18868 "This package is a collection of several algorithms to obtain
18869 archetypoids with small and large databases and with both classical
18870 multivariate data and functional data (univariate and multivariate). Some of
18871 these algorithms also allow to detect anomalies (outliers).")
18872 (license license:gpl2+)))
18874 (define-public r-idpmisc
18881 (uri (cran-uri "IDPmisc" version))
18884 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
18885 (properties `((upstream-name . "IDPmisc")))
18886 (build-system r-build-system)
18888 `(("r-lattice" ,r-lattice)))
18889 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
18890 (synopsis "Functions for data analyses and visualization")
18892 "This package provides different high-level graphics functions for
18893 displaying large datasets, displaying circular data in a very flexible way,
18894 finding local maxima, brewing color ramps, drawing nice arrows, zooming
18895 2D-plots, creating figures with differently colored margin and plot region.
18896 In addition, the package contains auxiliary functions for data manipulation
18897 like omitting observations with irregular values or selecting data by logical
18898 vectors, which include NAs. Other functions are especially useful in
18899 spectroscopy and analyses of environmental data: robust baseline fitting,
18900 finding peaks in spectra, converting humidity measures.")
18901 (license license:gpl3+)))
18903 (define-public r-qqman
18910 (uri (cran-uri "qqman" version))
18913 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
18914 (properties `((upstream-name . "qqman")))
18915 (build-system r-build-system)
18917 `(("r-calibrate" ,r-calibrate)))
18918 (home-page "https://cran.r-project.org/web/packages/qqman/")
18919 (synopsis "Q-Q and Manhattan plots for GWAS data")
18921 "This package allows you to create Q-Q and Manhattan plots for GWAS data
18922 from PLINK results.")
18923 (license license:gpl3)))
18925 (define-public r-ggplot-multistats
18927 (name "r-ggplot-multistats")
18932 (uri (cran-uri "ggplot.multistats" version))
18935 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
18937 `((upstream-name . "ggplot.multistats")))
18938 (build-system r-build-system)
18940 `(("r-ggplot2" ,r-ggplot2)
18941 ("r-hexbin" ,r-hexbin)
18942 ("r-rlang" ,r-rlang)
18943 ("r-scales" ,r-scales)))
18944 (home-page "https://github.com/flying-sheep/ggplot.multistats")
18945 (synopsis "Multiple summary statistics for binned stats/geometries")
18947 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
18948 which functions similar to its singular form, but allows the use of multiple
18949 statistics per bin. Those statistics can be mapped to multiple bin
18951 (license license:gpl3)))
18953 (define-public r-knn-covertree
18955 (name "r-knn-covertree")
18960 (uri (cran-uri "knn.covertree" version))
18963 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
18964 (properties `((upstream-name . "knn.covertree")))
18965 (build-system r-build-system)
18967 `(("r-matrix" ,r-matrix)
18969 ("r-rcppeigen" ,r-rcppeigen)))
18970 (home-page "https://github.com/flying-sheep/knn.covertree")
18971 (synopsis "Accurate kNN Implementation with multiple distance measures")
18973 "Similarly to the FNN package, this package allows calculation of the k
18974 nearest neighbors (kNN) of a data matrix. The implementation is based on
18975 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
18976 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
18977 (license license:agpl3+)))
18979 (define-public r-poibin
18986 (uri (cran-uri "poibin" version))
18989 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
18990 (properties `((upstream-name . "poibin")))
18991 (build-system r-build-system)
18992 (home-page "https://cran.r-project.org/web/packages/poibin/")
18993 (synopsis "Poisson binomial distribution")
18995 "This package provides an implementation of both the exact and
18996 approximation methods for computing the @dfn{cumulative distribution
18997 function} (CDF) of the Poisson binomial distribution. It also provides the
18998 @dfn{probability mass function} (PMF), quantile function, and random number
18999 generation for the Poisson binomial distribution.")
19000 (license license:gpl2)))
19002 (define-public r-diagram
19009 (uri (cran-uri "diagram" version))
19012 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19013 (properties `((upstream-name . "diagram")))
19014 (build-system r-build-system)
19016 `(("r-shape" ,r-shape)))
19017 (home-page "https://cran.r-project.org/web/packages/diagram/")
19018 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19020 "This package provides tools to visualize simple graphs (networks) based
19021 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19022 electrical networks, etc. It also includes supporting material for the book
19023 \"A practical guide to ecological modelling - using R as a simulation
19024 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19025 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19026 Francesca Mazzia (2012).")
19027 (license license:gpl2+)))
19029 (define-public r-lim
19036 (uri (cran-uri "LIM" version))
19039 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19040 (properties `((upstream-name . "LIM")))
19041 (build-system r-build-system)
19043 `(("r-diagram" ,r-diagram)
19044 ("r-limsolve" ,r-limsolve)))
19045 (home-page "https://cran.r-project.org/web/packages/LIM/")
19046 (synopsis "Linear inverse model examples and solution methods")
19048 "This package provides functions that read and solve linear inverse
19049 problems (food web problems, linear programming problems).")
19050 (license license:gpl2+)))
19052 (define-public r-shinycssloaders
19054 (name "r-shinycssloaders")
19059 (uri (cran-uri "shinycssloaders" version))
19062 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19064 `((upstream-name . "shinycssloaders")))
19065 (build-system r-build-system)
19067 `(("r-digest" ,r-digest)
19069 ("r-shiny" ,r-shiny)))
19070 (home-page "https://github.com/andrewsali/shinycssloaders")
19071 (synopsis "Add CSS loading animations to Shiny outputs")
19073 "This package provides tools to create a lightweight Shiny wrapper for
19074 the css-loaders created by Luke Hass
19075 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19076 automatically show a loader when the output is (re)calculating.")
19077 (license license:gpl3)))
19079 (define-public r-rsvg
19086 (uri (cran-uri "rsvg" version))
19089 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
19090 (properties `((upstream-name . "rsvg")))
19091 (build-system r-build-system)
19093 `(("librsvg" ,librsvg)
19096 `(("pkg-config" ,pkg-config)))
19097 (home-page "https://github.com/jeroen/rsvg#readme")
19098 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19100 "This package allows you to render vector-based SVG images into
19101 high-quality custom-size bitmap arrays using the librsvg2 library. The
19102 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19103 addition, the package can convert images directly to various formats such as
19104 PDF or PostScript.")
19105 (license license:expat)))
19107 (define-public r-influencer
19109 (name "r-influencer")
19114 (uri (cran-uri "influenceR" version))
19117 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19118 (properties `((upstream-name . "influenceR")))
19119 (build-system r-build-system)
19121 `(("r-igraph" ,r-igraph)
19122 ("r-matrix" ,r-matrix)))
19123 (home-page "https://github.com/rcc-uchicago/influenceR")
19124 (synopsis "Tools to quantify structural importance of nodes in a network")
19126 "This package provides functionality to compute various node centrality
19127 measures on networks. Included are functions to compute betweenness
19128 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19129 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19130 algorithm to identify key players, and Valente's bridging metric. The
19131 betweenness, Key Players, and bridging implementations are parallelized with
19133 (license license:gpl2)))
19135 (define-public r-emplik
19138 (version "1.0-4.3")
19142 (uri (cran-uri "emplik" version))
19145 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19146 (properties `((upstream-name . "emplik")))
19147 (build-system r-build-system)
19149 `(("r-quantreg" ,r-quantreg)))
19150 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19151 (synopsis "Empirical likelihood ratio for censored/truncated data")
19153 "This package provides empirical likelihood ratio tests for
19154 means/quantiles/hazards from possibly censored and/or truncated data. It also
19156 (license license:gpl2+)))
19158 (define-public r-imputeyn
19160 (name "r-imputeyn")
19165 (uri (cran-uri "imputeYn" version))
19168 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19169 (properties `((upstream-name . "imputeYn")))
19170 (build-system r-build-system)
19172 `(("r-boot" ,r-boot)
19173 ("r-emplik" ,r-emplik)
19174 ("r-mvtnorm" ,r-mvtnorm)
19175 ("r-quadprog" ,r-quadprog)
19176 ("r-survival" ,r-survival)))
19177 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19178 (synopsis "Impute last largest censored observation under weighted least squares")
19180 "This package allows for the imputation of the last largest censored
19181 observantions. This method brings less bias and more efficient estimates for
19183 (license license:gpl2)))
19185 (define-public r-adapenetclass
19187 (name "r-adapenetclass")
19192 (uri (cran-uri "AdapEnetClass" version))
19195 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19196 (properties `((upstream-name . "AdapEnetClass")))
19197 (build-system r-build-system)
19199 `(("r-glmnet" ,r-glmnet)
19200 ("r-imputeyn" ,r-imputeyn)
19202 ("r-quadprog" ,r-quadprog)))
19203 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19204 (synopsis "Class of adaptive elastic net methods for censored data")
19206 "This package provides methods for variable selection for AFT models.")
19207 (license license:gpl2)))
19209 (define-public r-flock
19216 (uri (cran-uri "flock" version))
19219 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19220 (properties `((upstream-name . "flock")))
19221 (build-system r-build-system)
19222 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19223 (home-page "https://cran.r-project.org/web/packages/flock/")
19224 (synopsis "Process synchronization using file locks")
19226 "This package implements synchronization between R processes (spawned by
19227 using the @code{parallel} package for instance) using file locks. It supports
19228 both exclusive and shared locking.")
19229 (license license:asl2.0)))
19231 (define-public r-archivist
19233 (name "r-archivist")
19238 (uri (cran-uri "archivist" version))
19241 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19242 (properties `((upstream-name . "archivist")))
19243 (build-system r-build-system)
19246 ("r-digest" ,r-digest)
19247 ("r-flock" ,r-flock)
19249 ("r-lubridate" ,r-lubridate)
19250 ("r-magrittr" ,r-magrittr)
19251 ("r-rcurl" ,r-rcurl)
19252 ("r-rsqlite" ,r-rsqlite)))
19253 (home-page "https://pbiecek.github.io/archivist/")
19254 (synopsis "Tools for storing, restoring and searching for R objects")
19256 "Data exploration and modelling is a process in which a lot of data
19257 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19258 statistical models, different versions of data sets and different versions of
19259 results. Archivist helps to store and manage artifacts created in R. It
19260 allows you to store selected artifacts as binary files together with their
19261 metadata and relations. Archivist allows sharing artifacts with others. It
19262 can look for already created artifacts by using its class, name, date of the
19263 creation or other properties. It also makes it easy to restore such
19265 (license license:gpl2)))
19267 (define-public r-versions
19269 (name "r-versions")
19274 (uri (cran-uri "versions" version))
19277 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19278 (properties `((upstream-name . "versions")))
19279 (build-system r-build-system)
19280 (home-page "https://cran.r-project.org/web/packages/versions/")
19281 (synopsis "Query and install specific versions of CRAN packages")
19283 "This package allows you to install specified versions of R packages
19284 hosted on CRAN and provides functions to list available versions and the
19285 versions of currently installed packages.")
19286 (license license:bsd-3)))
19288 (define-public r-adapr
19295 (uri (cran-uri "adapr" version))
19298 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19299 (properties `((upstream-name . "adapr")))
19300 (build-system r-build-system)
19302 `(("r-archivist" ,r-archivist)
19303 ("r-devtools" ,r-devtools)
19304 ("r-digest" ,r-digest)
19305 ("r-doparallel" ,r-doparallel)
19306 ("r-gdata" ,r-gdata)
19307 ("r-ggplot2" ,r-ggplot2)
19308 ("r-git2r" ,r-git2r)
19309 ("r-igraph" ,r-igraph)
19310 ("r-knitr" ,r-knitr)
19311 ("r-plotly" ,r-plotly)
19313 ("r-rmarkdown" ,r-rmarkdown)
19314 ("r-shiny" ,r-shiny)
19315 ("r-shinydashboard" ,r-shinydashboard)
19316 ("r-versions" ,r-versions)))
19317 (home-page "https://cran.r-project.org/web/packages/adapr/")
19318 (synopsis "Implementation of an accountable data analysis process")
19320 "This package tracks reading and writing within R scripts that are
19321 organized into a directed acyclic graph. It contains an interactive Shiny
19322 application @code{adaprApp()}. It uses Git and file hashes to track version
19323 histories of inputs and outputs.")
19324 (license license:lgpl2.0)))
19326 (define-public r-adapsamp
19328 (name "r-adapsamp")
19333 (uri (cran-uri "AdapSamp" version))
19336 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19337 (properties `((upstream-name . "AdapSamp")))
19338 (build-system r-build-system)
19339 (propagated-inputs `(("r-pracma" ,r-pracma)))
19340 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19341 (synopsis "Adaptive sampling algorithms")
19343 "For distributions whose probability density functions are log-concave,
19344 the adaptive rejection sampling algorithm can be used to build envelope
19345 functions for sampling. For others, the modified adaptive rejection sampling
19346 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19347 adaptive slice sampling algorithm can be used. This R package mainly includes
19348 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19349 @code{rASS()}. These functions can realize sampling based on the algorithms
19351 (license license:gpl2)))
19353 (define-public r-adaptalint
19355 (name "r-adaptalint")
19360 (uri (cran-uri "adaptalint" version))
19363 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19364 (properties `((upstream-name . "adaptalint")))
19365 (build-system r-build-system)
19367 `(("r-dplyr" ,r-dplyr)
19368 ("r-lintr" ,r-lintr)
19369 ("r-purrr" ,r-purrr)))
19370 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19371 (synopsis "Check R code style")
19373 "This package provides tools to infer the code style (which style rules
19374 are followed and which ones are not) from one package and use it to check
19375 another. This makes it easier to find and correct the most important problems
19377 (license license:gpl3)))
19379 (define-public r-fracdiff
19381 (name "r-fracdiff")
19386 (uri (cran-uri "fracdiff" version))
19389 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19390 (properties `((upstream-name . "fracdiff")))
19391 (build-system r-build-system)
19392 (home-page "https://github.com/mmaechler/fracdiff")
19394 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19396 "This package provides tools for the maximum likelihood estimation of the
19397 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19398 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19399 (license license:gpl2+)))
19401 (define-public r-forecast
19403 (name "r-forecast")
19408 (uri (cran-uri "forecast" version))
19411 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19412 (properties `((upstream-name . "forecast")))
19413 (build-system r-build-system)
19415 `(("r-colorspace" ,r-colorspace)
19416 ("r-fracdiff" ,r-fracdiff)
19417 ("r-ggplot2" ,r-ggplot2)
19418 ("r-lmtest" ,r-lmtest)
19419 ("r-magrittr" ,r-magrittr)
19422 ("r-rcpparmadillo" ,r-rcpparmadillo)
19423 ("r-timedate" ,r-timedate)
19424 ("r-tseries" ,r-tseries)
19428 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19429 (home-page "https://pkg.robjhyndman.com/forecast/")
19430 (synopsis "Forecasting functions for time series and linear models")
19432 "This package provides methods and tools for displaying and analysing
19433 univariate time series forecasts including exponential smoothing via state
19434 space models and automatic ARIMA modelling.")
19435 (license license:gpl3)))
19437 (define-public r-xmisc
19444 (uri (cran-uri "Xmisc" version))
19447 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
19448 (properties `((upstream-name . "Xmisc")))
19449 (build-system r-build-system)
19450 (home-page "https://cran.r-project.org/package=Xmisc")
19452 "Xiaobei's miscellaneous classes and functions")
19454 "This package provides Xiaobei's miscellaneous classes and functions,
19455 which are useful when developing R packages for @dfn{object oriented
19456 programming} (OOP) using R Reference Class.")
19457 (license license:gpl2+)))
19459 (define-public r-proxyc
19466 (uri (cran-uri "proxyC" version))
19469 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
19470 (properties `((upstream-name . "proxyC")))
19471 (build-system r-build-system)
19473 `(("r-matrix" ,r-matrix)
19475 ("r-rcpparmadillo" ,r-rcpparmadillo)
19476 ("r-rcppparallel" ,r-rcppparallel)))
19477 (home-page "https://cran.r-project.org/package=proxyC")
19478 (synopsis "Compute proximity in large sparse matrices")
19480 "This package provides efficient tools to compute the proximity between
19481 rows or columns of large matrices. Functions are optimised for large sparse
19482 matrices using the Armadillo and Intel TBB libraries. Among several built-in
19483 similarity/distance measures, computation of correlation, cosine similarity
19484 and Euclidean distance is particularly fast.")
19485 (license license:gpl3)))
19487 (define-public r-isocodes
19489 (name "r-isocodes")
19490 (version "2020.03.16")
19494 (uri (cran-uri "ISOcodes" version))
19497 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
19498 (properties `((upstream-name . "ISOcodes")))
19499 (build-system r-build-system)
19500 (home-page "https://cran.r-project.org/package=ISOcodes")
19501 (synopsis "Selected ISO codes")
19503 "This package provides ISO language, territory, currency, script and
19504 character codes. It provides ISO 639 language codes, ISO 3166 territory
19505 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
19506 character codes as well as the UN M.49 area codes.")
19507 (license license:gpl2)))
19509 (define-public r-stopwords
19511 (name "r-stopwords")
19516 (uri (cran-uri "stopwords" version))
19519 "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
19520 (properties `((upstream-name . "stopwords")))
19521 (build-system r-build-system)
19522 (propagated-inputs `(("r-isocodes" ,r-isocodes)))
19523 (home-page "https://github.com/quanteda/stopwords")
19524 (synopsis "Multilingual stopword lists")
19526 "This package provides multiple sources of stopwords, for use in text
19527 analysis and natural language processing.")
19528 (license license:expat)))
19530 (define-public r-spacyr
19537 (uri (cran-uri "spacyr" version))
19540 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
19541 (properties `((upstream-name . "spacyr")))
19542 (build-system r-build-system)
19544 `(("r-data-table" ,r-data-table)
19545 ("r-reticulate" ,r-reticulate)))
19546 (home-page "https://spacyr.quanteda.io")
19547 (synopsis "R wrapper for the spaCy NLP library")
19549 "This package provides an R wrapper to the Python @dfn{natural language
19550 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
19551 (license license:gpl3)))
19553 (define-public r-snowballc
19555 (name "r-snowballc")
19560 (uri (cran-uri "SnowballC" version))
19563 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
19564 (properties `((upstream-name . "SnowballC")))
19565 (build-system r-build-system)
19566 (home-page "https://r-forge.r-project.org/projects/r-temis/")
19567 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
19569 "This package provides an R interface to the C @code{libstemmer} library
19570 that implements Porter's word stemming algorithm for collapsing words to a
19571 common root to aid comparison of vocabulary. Currently supported languages
19572 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
19573 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
19574 (license license:bsd-3)))
19576 (define-public r-quanteda
19578 (name "r-quanteda")
19583 (uri (cran-uri "quanteda" version))
19586 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
19587 (properties `((upstream-name . "quanteda")))
19588 (build-system r-build-system)
19590 `(("r-data-table" ,r-data-table)
19591 ("r-extrafont" ,r-extrafont)
19592 ("r-fastmatch" ,r-fastmatch)
19593 ("r-ggplot2" ,r-ggplot2)
19594 ("r-ggrepel" ,r-ggrepel)
19595 ("r-jsonlite" ,r-jsonlite)
19596 ("r-magrittr" ,r-magrittr)
19597 ("r-matrix" ,r-matrix)
19598 ("r-network" ,r-network)
19599 ("r-proxyc" ,r-proxyc)
19601 ("r-rcpparmadillo" ,r-rcpparmadillo)
19602 ("r-rcppparallel" ,r-rcppparallel)
19604 ("r-snowballc" ,r-snowballc)
19605 ("r-stopwords" ,r-stopwords)
19606 ("r-stringi" ,r-stringi)
19608 ("r-yaml" ,r-yaml)))
19610 `(("r-knitr" ,r-knitr)))
19611 (home-page "https://quanteda.io")
19612 (synopsis "Quantitative analysis of textual data")
19614 "This package provides a fast, flexible, and comprehensive framework for
19615 quantitative text analysis in R. It provides functionality for corpus
19616 management, creating and manipulating tokens and ngrams, exploring keywords in
19617 context, forming and manipulating sparse matrices of documents by features and
19618 feature co-occurrences, analyzing keywords, computing feature similarities and
19619 distances, applying content dictionaries, applying supervised and unsupervised
19620 machine learning, visually representing text and text analyses, and more.")
19621 (license license:gpl3)))
19623 (define-public r-topicmodels
19625 (name "r-topicmodels")
19630 (uri (cran-uri "topicmodels" version))
19633 "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
19634 (properties `((upstream-name . "topicmodels")))
19635 (build-system r-build-system)
19639 `(("r-modeltools" ,r-modeltools)
19642 (home-page "https://cran.r-project.org/package=topicmodels")
19643 (synopsis "Topic models")
19645 "This package provides an interface to the C code for @dfn{Latent
19646 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
19647 David M. Blei and co-authors and the C++ code for fitting LDA models using
19648 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
19649 (license license:gpl2)))
19651 (define-public r-stm
19658 (uri (cran-uri "stm" version))
19661 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
19662 (properties `((upstream-name . "stm")))
19663 (build-system r-build-system)
19665 `(("r-data-table" ,r-data-table)
19666 ("r-glmnet" ,r-glmnet)
19668 ("r-matrix" ,r-matrix)
19669 ("r-matrixstats" ,r-matrixstats)
19670 ("r-quadprog" ,r-quadprog)
19671 ("r-quanteda" ,r-quanteda)
19673 ("r-rcpparmadillo" ,r-rcpparmadillo)
19675 ("r-stringr" ,r-stringr)))
19676 (home-page "http://www.structuraltopicmodel.com/")
19677 (synopsis "Estimation of the Structural Topic Model")
19679 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
19680 topic models with document-level covariates. The package also includes tools
19681 for model selection, visualization, and estimation of topic-covariate
19683 (license license:expat)))
19685 (define-public r-polycor
19692 (uri (cran-uri "polycor" version))
19695 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
19696 (properties `((upstream-name . "polycor")))
19697 (build-system r-build-system)
19699 `(("r-matrix" ,r-matrix)
19700 ("r-mvtnorm" ,r-mvtnorm)))
19701 (home-page "https://r-forge.r-project.org/projects/polycor/")
19702 (synopsis "Polychoric and polyserial correlations")
19704 "This package provides tools to compute polychoric and polyserial
19705 correlations by quick \"two-step\" methods or ML, optionally with standard
19706 errors; tetrachoric and biserial correlations are special cases.")
19707 (license license:gpl2+)))
19709 (define-public r-msm
19716 (uri (cran-uri "msm" version))
19719 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
19720 (properties `((upstream-name . "msm")))
19721 (build-system r-build-system)
19723 `(("r-expm" ,r-expm)
19724 ("r-mvtnorm" ,r-mvtnorm)
19725 ("r-survival" ,r-survival)))
19726 (home-page "https://github.com/chjackson/msm")
19727 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
19729 "This package provides functions for fitting continuous-time Markov and
19730 hidden Markov multi-state models to longitudinal data. It was designed for
19731 processes observed at arbitrary times in continuous time (panel data) but some
19732 other observation schemes are supported. Both Markov transition rates and the
19733 hidden Markov output process can be modelled in terms of covariates, which may
19734 be constant or piecewise-constant in time.")
19735 (license license:gpl2+)))
19737 (define-public r-ltm
19744 (uri (cran-uri "ltm" version))
19747 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
19748 (properties `((upstream-name . "ltm")))
19749 (build-system r-build-system)
19751 `(("r-mass" ,r-mass)
19753 ("r-polycor" ,r-polycor)))
19754 (home-page "https://github.com/drizopoulos/ltm")
19755 (synopsis "Latent trait models under IRT")
19757 "This is a package supporting the analysis of multivariate dichotomous
19758 and polytomous data using latent trait models under the Item Response Theory
19759 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
19760 Three-Parameter, the Graded Response, and the Generalized Partial Credit
19762 (license license:gpl2+)))
19764 (define-public r-mi
19771 (uri (cran-uri "mi" version))
19774 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
19775 (properties `((upstream-name . "mi")))
19776 (build-system r-build-system)
19779 ("r-matrix" ,r-matrix)))
19780 (home-page "http://www.stat.columbia.edu/~gelman/")
19781 (synopsis "Missing data imputation and model checking")
19783 "This package provides functions for data manipulation, imputing missing
19784 values in an approximate Bayesian framework, diagnostics of the models used to
19785 generate the imputations, confidence-building mechanisms to validate some of
19786 the assumptions of the imputation algorithm, and functions to analyze multiply
19787 imputed data sets with the appropriate degree of sampling uncertainty.")
19788 (license license:gpl2+)))
19790 (define-public r-matrixcalc
19792 (name "r-matrixcalc")
19797 (uri (cran-uri "matrixcalc" version))
19800 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
19801 (properties `((upstream-name . "matrixcalc")))
19802 (build-system r-build-system)
19803 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
19804 (synopsis "Collection of functions for matrix calculations")
19806 "This package provides a collection of functions to support matrix
19807 calculations for probability, econometric and numerical analysis. There are
19808 additional functions that are comparable to APL functions which are useful for
19809 actuarial models such as pension mathematics.")
19810 (license license:gpl2+)))
19812 (define-public r-sem
19819 (uri (cran-uri "sem" version))
19822 "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
19823 (properties `((upstream-name . "sem")))
19824 (build-system r-build-system)
19826 `(("r-boot" ,r-boot)
19828 ("r-matrixcalc" ,r-matrixcalc)
19830 (home-page "https://cran.r-project.org/package=sem")
19831 (synopsis "Structural equation models")
19833 "This package provides functions for fitting general linear structural
19834 equation models (with observed and latent variables) using the RAM approach,
19835 and for fitting structural equations in observed-variable models by two-stage
19837 (license license:gpl2+)))
19839 (define-public r-semtools
19841 (name "r-semtools")
19846 (uri (cran-uri "semTools" version))
19849 "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
19850 (properties `((upstream-name . "semTools")))
19851 (build-system r-build-system)
19853 `(("r-lavaan" ,r-lavaan)))
19854 (home-page "https://github.com/simsem/semTools/wiki")
19855 (synopsis "Useful tools for structural equation modeling")
19857 "This package provides useful tools for structural equation modeling.")
19858 (license license:gpl2+)))
19860 (define-public r-regsem
19867 (uri (cran-uri "regsem" version))
19870 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
19871 (properties `((upstream-name . "regsem")))
19872 (build-system r-build-system)
19874 `(("r-lavaan" ,r-lavaan)
19876 ("r-rcpparmadillo" ,r-rcpparmadillo)
19877 ("r-rsolnp" ,r-rsolnp)))
19878 (home-page "https://cran.r-project.org/package=regsem")
19879 (synopsis "Regularized structural equation modeling")
19881 "This package uses both ridge and lasso penalties (and extensions) to
19882 penalize specific parameters in structural equation models. The package
19883 offers additional cost functions, cross validation, and other extensions
19884 beyond traditional structural equation models. It also contains a function to
19885 perform @dfn{exploratory mediation} (XMed).")
19886 (license license:gpl2+)))
19888 (define-public r-stanheaders
19890 (name "r-stanheaders")
19895 (uri (cran-uri "StanHeaders" version))
19898 "0cmk0fzczx7dcywcw1dhm6gfq84qlsx77qrsk4z3bf3dhr4bznam"))))
19899 (properties `((upstream-name . "StanHeaders")))
19900 (build-system r-build-system)
19901 (inputs `(("pandoc" ,ghc-pandoc)))
19903 `(("gfortran" ,gfortran)
19904 ("r-knitr" ,r-knitr))) ; for vignettes
19905 (home-page "https://mc-stan.org/")
19906 (synopsis "C++ header files for Stan")
19908 "The C++ header files of the Stan project are provided by this package.
19909 There is a shared object containing part of the @code{CVODES} library, but it
19910 is not accessible from R. @code{r-stanheaders} is only useful for developers
19911 who want to utilize the @code{LinkingTo} directive of their package's
19912 DESCRIPTION file to build on the Stan library without incurring unnecessary
19915 The Stan project develops a probabilistic programming language that implements
19916 full or approximate Bayesian statistical inference via Markov Chain Monte
19917 Carlo or variational methods and implements (optionally penalized) maximum
19918 likelihood estimation via optimization. The Stan library includes an advanced
19919 automatic differentiation scheme, templated statistical and linear algebra
19920 functions that can handle the automatically differentiable scalar types (and
19921 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
19922 package provides user-facing R functions to parse, compile, test, estimate,
19923 and analyze Stan models.")
19924 (license license:bsd-3)))
19926 (define-public r-rpf
19933 (uri (cran-uri "rpf" version))
19936 "1i2kqd7nx55nn35qnw89xmnqk23x9c8xhkh736c2xg7k2ai84ybl"))))
19937 (properties `((upstream-name . "rpf")))
19938 (build-system r-build-system)
19940 `(("r-lifecycle" ,r-lifecycle)
19941 ("r-mvtnorm" ,r-mvtnorm)
19943 ("r-rcppeigen" ,r-rcppeigen)))
19944 (home-page "https://github.com/jpritikin/rpf")
19945 (synopsis "Response probability functions")
19947 "The purpose of this package is to factor out logic and math common to
19948 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
19949 core support code suitable for more specialized IRT packages to build upon.
19950 Complete access to optimized C functions is made available with
19951 @code{R_RegisterCCallable()}.")
19952 (license license:gpl3+)))
19954 (define-public r-openmx
19961 (uri (cran-uri "OpenMx" version))
19964 "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc"))))
19965 (properties `((upstream-name . "OpenMx")))
19966 (build-system r-build-system)
19969 ("r-digest" ,r-digest)
19971 ("r-matrix" ,r-matrix)
19973 ("r-rcppeigen" ,r-rcppeigen)
19975 ("r-stanheaders" ,r-stanheaders)))
19976 (native-inputs `(("gfortran" ,gfortran)))
19977 (home-page "http://openmx.ssri.psu.edu")
19978 (synopsis "Extended structural equation modelling")
19980 "This package allows for the estimation of a wide variety of advanced
19981 multivariate statistical models. It consists of a library of functions and
19982 optimizers that allow you to quickly and flexibly define an SEM model and
19983 estimate parameters given observed data.")
19984 (license license:asl2.0)))
19986 (define-public r-kutils
19993 (uri (cran-uri "kutils" version))
19996 "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
19997 (properties `((upstream-name . "kutils")))
19998 (build-system r-build-system)
20000 `(("r-foreign" ,r-foreign)
20001 ("r-lavaan" ,r-lavaan)
20002 ("r-openxlsx" ,r-openxlsx)
20004 ("r-runit" ,r-runit)
20005 ("r-xtable" ,r-xtable)))
20006 (home-page "https://cran.r-project.org/package=kutils")
20007 (synopsis "Project management tools")
20009 "This package provides tools for data importation, recoding, and
20010 inspection. There are functions to create new project folders, R code
20011 templates, create uniquely named output directories, and to quickly obtain a
20012 visual summary for each variable in a data frame. The main feature here is
20013 the systematic implementation of the \"variable key\" framework for data
20014 importation and recoding.")
20015 (license license:gpl2)))
20017 (define-public r-rockchalk
20019 (name "r-rockchalk")
20020 (version "1.8.144")
20024 (uri (cran-uri "rockchalk" version))
20027 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20028 (properties `((upstream-name . "rockchalk")))
20029 (build-system r-build-system)
20031 `(("r-cardata" ,r-cardata)
20032 ("r-kutils" ,r-kutils)
20034 ("r-mass" ,r-mass)))
20035 (home-page "https://cran.r-project.org/package=rockchalk")
20036 (synopsis "Regression estimation and presentation")
20038 "This package provides a collection of functions for interpretation and
20039 presentation of regression analysis. These functions are used to produce the
20040 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20041 includes regression diagnostics, regression tables, and plots of interactions
20042 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20043 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20044 fairly comprehensive overview.")
20045 (license license:gpl3+)))
20047 (define-public r-lisreltor
20049 (name "r-lisreltor")
20054 (uri (cran-uri "lisrelToR" version))
20057 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20058 (properties `((upstream-name . "lisrelToR")))
20059 (build-system r-build-system)
20060 (home-page "https://cran.r-project.org/package=lisrelToR")
20061 (synopsis "Import output from LISREL into R")
20063 "This is an unofficial package aimed at automating the import of LISREL
20065 (license license:gpl2)))
20067 (define-public r-bdgraph
20074 (uri (cran-uri "BDgraph" version))
20077 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20078 (properties `((upstream-name . "BDgraph")))
20079 (build-system r-build-system)
20081 `(("r-igraph" ,r-igraph)))
20082 (home-page "https://www.uva.nl/profile/a.mohammadi")
20083 (synopsis "Bayesian structure learning in graphical models")
20085 "This package provides statistical tools for Bayesian structure learning
20086 in undirected graphical models for continuous, discrete, and mixed data. It
20087 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20088 on a continuous-time birth-death process.")
20089 (license license:gpl2+)))
20091 (define-public r-d3network
20093 (name "r-d3network")
20094 (version "0.5.2.1")
20098 (uri (cran-uri "d3Network" version))
20101 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20102 (properties `((upstream-name . "d3Network")))
20103 (build-system r-build-system)
20105 `(("r-plyr" ,r-plyr)
20106 ("r-rjson" ,r-rjson)
20107 ("r-whisker" ,r-whisker)))
20108 (home-page "http://christophergandrud.github.io/d3Network/")
20109 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20111 "This package is intended to make it easy to create D3 JavaScript
20112 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20113 (license license:gpl3+)))
20115 (define-public r-qgraph
20122 (uri (cran-uri "qgraph" version))
20125 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20126 (properties `((upstream-name . "qgraph")))
20127 (build-system r-build-system)
20129 `(("r-abind" ,r-abind)
20130 ("r-bdgraph" ,r-bdgraph)
20131 ("r-colorspace" ,r-colorspace)
20132 ("r-corpcor" ,r-corpcor)
20133 ("r-d3network" ,r-d3network)
20134 ("r-dplyr" ,r-dplyr)
20135 ("r-fdrtool" ,r-fdrtool)
20136 ("r-ggplot2" ,r-ggplot2)
20137 ("r-ggraph" ,r-ggraph)
20138 ("r-glasso" ,r-glasso)
20139 ("r-gtools" ,r-gtools)
20140 ("r-hmisc" ,r-hmisc)
20142 ("r-igraph" ,r-igraph)
20144 ("r-lavaan" ,r-lavaan)
20145 ("r-matrix" ,r-matrix)
20146 ("r-pbapply" ,r-pbapply)
20149 ("r-psych" ,r-psych)
20151 ("r-reshape2" ,r-reshape2)
20152 ("r-tidygraph" ,r-tidygraph)))
20153 (home-page "http://sachaepskamp.com/qgraph/")
20154 (synopsis "Weighted network visualization and analysis")
20156 "This package implements tools for weighted network visualization and
20157 analysis, as well as Gaussian graphical model computation. It contains graph
20158 plotting methods, and tools for psychometric data visualization and graphical
20159 model estimation. See Epskamp et al. (2012)
20160 @url{doi:10.18637/jss.v048.i04}.")
20161 (license license:gpl2)))
20163 (define-public r-semplot
20170 (uri (cran-uri "semPlot" version))
20173 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20174 (properties `((upstream-name . "semPlot")))
20175 (build-system r-build-system)
20177 `(("r-colorspace" ,r-colorspace)
20178 ("r-corpcor" ,r-corpcor)
20179 ("r-igraph" ,r-igraph)
20180 ("r-lavaan" ,r-lavaan)
20181 ("r-lisreltor" ,r-lisreltor)
20182 ("r-openmx" ,r-openmx)
20184 ("r-qgraph" ,r-qgraph)
20185 ("r-regsem" ,r-regsem)
20186 ("r-rockchalk" ,r-rockchalk)
20189 (home-page "https://github.com/SachaEpskamp/semPlot")
20190 (synopsis "Unified visualizations of structural equation models")
20192 "Structural equation modeling (SEM) has a long history of representing
20193 models graphically as path diagrams. The semPlot package for R fills the gap
20194 between advanced, but time-consuming, graphical software and the limited
20195 graphics produced automatically by SEM software. In addition, semPlot offers
20196 more functionality than drawing path diagrams: it can act as a common ground
20197 for importing SEM results into R. Any result usable as input to semPlot can
20198 also be represented in any of the three popular SEM frame-works, as well as
20199 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20200 (license license:gpl2)))
20202 (define-public r-cdm
20209 (uri (cran-uri "CDM" version))
20212 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20213 (properties `((upstream-name . "CDM")))
20214 (build-system r-build-system)
20216 `(("r-mvtnorm" ,r-mvtnorm)
20217 ("r-polycor" ,r-polycor)
20219 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20221 "https://github.com/alexanderrobitzsch/CDM")
20222 (synopsis "Cognitive diagnosis modeling")
20224 "This package provides functions for cognitive diagnosis modeling and
20225 multidimensional item response modeling for dichotomous and polytomous item
20226 responses. It enables the estimation of the DINA and DINO model, the multiple
20227 group (polytomous) GDINA model, the multiple choice DINA model, the general
20228 diagnostic model (GDM), the structured latent class model (SLCA), and
20229 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20230 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20231 estimation and the package structure. For tutorials on how to use the CDM
20232 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20233 well as Ravand and Robitzsch (2015).")
20234 (license license:gpl2+)))
20236 (define-public r-tam
20243 (uri (cran-uri "TAM" version))
20246 "111d7qkxhwh1lfvldyh9d61pdb5vb6x8lr8n9h95ssvw07vjqvk9"))))
20247 (properties `((upstream-name . "TAM")))
20248 (build-system r-build-system)
20252 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20253 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20254 (synopsis "Test analysis modules")
20256 "This package includes tools for marginal maximum likelihood estimation
20257 and joint maximum likelihood estimation for unidimensional and
20258 multidimensional item response models. The package functionality covers the
20259 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20260 multi-faceted Rasch model, nominal item response model, structured latent
20261 class model, mixture distribution IRT models, and located latent class models.
20262 Latent regression models and plausible value imputation are also supported.")
20263 (license license:gpl2+)))
20265 (define-public r-erm
20272 (uri (cran-uri "eRm" version))
20275 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20276 (properties `((upstream-name . "eRm")))
20277 (build-system r-build-system)
20279 `(("r-colorspace" ,r-colorspace)
20280 ("r-lattice" ,r-lattice)
20282 ("r-matrix" ,r-matrix)
20283 ("r-psych" ,r-psych)))
20284 (native-inputs `(("gfortran" ,gfortran)))
20285 (home-page "https://cran.r-project.org/package=eRm")
20286 (synopsis "Extended Rasch modeling")
20288 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20289 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20290 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20291 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20292 data matrix. Additional features are the ML estimation of the person
20293 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20294 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20295 infit and outfit measures, ICC and other plots, automated stepwise item
20296 elimination, and a simulation module for various binary data matrices.")
20297 (license license:gpl3)))
20299 (define-public r-irtoys
20306 (uri (cran-uri "irtoys" version))
20309 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20310 (properties `((upstream-name . "irtoys")))
20311 (build-system r-build-system)
20315 (home-page "https://cran.r-project.org/package=irtoys")
20316 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20318 "This package provides a collection of functions useful in learning and
20319 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20320 programs. It provides basic CTT analysis, a simple common interface to the
20321 estimation of item parameters in IRT models for binary responses with three
20322 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20323 EAP, WLE, plausible values), item and person fit statistics, scaling
20324 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20325 array of parametric and non-parametric (kernel) plots. It estimates and plots
20326 Haberman's interaction model when all items are dichotomously scored.")
20327 (license license:gpl2+)))
20329 (define-public r-iheatmapr
20331 (name "r-iheatmapr")
20336 (uri (cran-uri "iheatmapr" version))
20339 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20340 (properties `((upstream-name . "iheatmapr")))
20341 (build-system r-build-system)
20343 `(("r-fastcluster" ,r-fastcluster)
20344 ("r-ggdendro" ,r-ggdendro)
20345 ("r-htmlwidgets" ,r-htmlwidgets)
20346 ("r-jsonlite" ,r-jsonlite)
20347 ("r-knitr" ,r-knitr)
20348 ("r-magrittr" ,r-magrittr)
20350 ("r-rcolorbrewer" ,r-rcolorbrewer)
20351 ("r-s4vectors" ,r-s4vectors)
20352 ("r-scales" ,r-scales)))
20353 (home-page "https://docs.ropensci.org/iheatmapr")
20354 (synopsis "Interactive, Complex Heatmaps")
20356 "iheatmapr is an R package for building complex, interactive heatmaps
20357 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20358 subplots along the rows or columns of the main heatmap add more information
20359 about each row or column. For example, a one column additional heatmap may
20360 indicate what group a particular row or column belongs to. Complex heatmaps
20361 may also include multiple side by side heatmaps which show different types of
20362 data for the same conditions. Interactivity can improve complex heatmaps by
20363 providing tooltips with information about each cell and enabling zooming into
20364 interesting features. iheatmapr uses the plotly library for interactivity.")
20365 (license license:expat)))
20367 (define-public r-packrat
20374 (uri (cran-uri "packrat" version))
20377 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20378 (properties `((upstream-name . "packrat")))
20379 (build-system r-build-system)
20380 (home-page "https://github.com/rstudio/packrat/")
20381 (synopsis "Dependency management R projects")
20383 "This package provides a dependency manager for R projects that allows
20384 you to manage the R packages your project depends on in an isolated, portable,
20385 and reproducible way.")
20386 (license license:gpl2)))
20388 (define-public r-rsconnect
20390 (name "r-rsconnect")
20395 (uri (cran-uri "rsconnect" version))
20398 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20399 (properties `((upstream-name . "rsconnect")))
20400 (build-system r-build-system)
20402 `(("r-curl" ,r-curl)
20403 ("r-digest" ,r-digest)
20404 ("r-jsonlite" ,r-jsonlite)
20405 ("r-openssl" ,r-openssl)
20406 ("r-packrat" ,r-packrat)
20407 ("r-rstudioapi" ,r-rstudioapi)
20408 ("r-yaml" ,r-yaml)))
20409 (home-page "https://github.com/rstudio/rsconnect")
20410 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20412 "This package provides a programmatic deployment interface for RPubs,
20413 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20414 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20415 (license license:gpl2)))
20417 ;; This package includes minified JavaScript files. When upgrading please
20418 ;; check that there are no new minified JavaScript files.
20419 (define-public r-dygraphs
20421 (name "r-dygraphs")
20422 (version "1.1.1.6")
20426 (uri (cran-uri "dygraphs" version))
20429 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20430 (properties `((upstream-name . "dygraphs")))
20431 (build-system r-build-system)
20433 `(#:modules ((guix build utils)
20434 (guix build r-build-system)
20438 (modify-phases %standard-phases
20439 (add-after 'unpack 'process-javascript
20440 (lambda* (#:key inputs #:allow-other-keys)
20441 (with-directory-excursion "inst/htmlwidgets/lib/"
20445 `(("dygraphs/dygraph-combined-dev.js"
20446 "dygraph-combined.js")
20447 (,(assoc-ref inputs "js-jquery")
20448 "jquery/jquery.min.js")
20449 (,(assoc-ref inputs "js-fquarter")
20450 "fquarter/moment-fquarter.min.js"))))
20451 (lambda (sources targets)
20452 (for-each (lambda (source target)
20453 (format #t "Processing ~a --> ~a~%"
20455 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
20456 (call-with-output-file target
20458 (dump-port minified port)))))
20459 sources targets))))
20462 `(("uglify-js" ,uglify-js)
20463 ;; They actually use version 1.11.1, but this more recent version
20464 ;; should be just fine.
20468 (uri "https://code.jquery.com/jquery-1.12.4.js")
20471 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
20475 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
20476 "moment-fquarter/1.0.1/moment-fquarter.js"))
20479 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
20481 `(("r-htmltools" ,r-htmltools)
20482 ("r-htmlwidgets" ,r-htmlwidgets)
20483 ("r-magrittr" ,r-magrittr)
20486 (home-page "https://github.com/rstudio/dygraphs")
20487 (synopsis "Interface to Dygraphs interactive time series charting library")
20489 "This package provides an R interface to the dygraphs JavaScript charting
20490 library (a copy of which is included in the package). It provides rich
20491 facilities for charting time-series data in R, including highly configurable
20492 series- and axis-display and interactive features like zoom/pan and
20493 series/point highlighting.")
20494 (license license:expat)))
20496 (define-public r-shinystan
20498 (name "r-shinystan")
20503 (uri (cran-uri "shinystan" version))
20506 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
20507 (properties `((upstream-name . "shinystan")))
20508 (build-system r-build-system)
20510 `(("r-bayesplot" ,r-bayesplot)
20511 ("r-colourpicker" ,r-colourpicker)
20513 ("r-dygraphs" ,r-dygraphs)
20514 ("r-ggplot2" ,r-ggplot2)
20515 ("r-gridextra" ,r-gridextra)
20516 ("r-gtools" ,r-gtools)
20517 ("r-markdown" ,r-markdown)
20518 ("r-reshape2" ,r-reshape2)
20519 ("r-rsconnect" ,r-rsconnect)
20520 ("r-rstan" ,r-rstan)
20521 ("r-shiny" ,r-shiny)
20522 ("r-shinyjs" ,r-shinyjs)
20523 ("r-shinythemes" ,r-shinythemes)
20524 ("r-threejs" ,r-threejs)
20525 ("r-xtable" ,r-xtable)
20527 (home-page "https://mc-stan.org/")
20528 (synopsis "Interactive visual and numerical analysis for Bayesian models")
20530 "This package provides a graphical user interface for interactive
20531 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
20532 for analyzing a posterior sample. The interface is powered by the Shiny web
20533 application framework and works with the output of MCMC programs written in
20534 any programming language (and has extended functionality for Stan models fit
20535 using the @code{rstan} and @code{rstanarm} packages).")
20536 (license license:gpl3+)))
20538 (define-public r-rstantools
20540 (name "r-rstantools")
20545 (uri (cran-uri "rstantools" version))
20548 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
20549 (properties `((upstream-name . "rstantools")))
20550 (build-system r-build-system)
20551 (inputs `(("pandoc" ,ghc-pandoc)))
20553 `(("r-desc" ,r-desc)
20554 ("r-rcpp" ,r-rcpp)))
20555 (home-page "https://mc-stan.org/rstantools/")
20556 (synopsis "Tools for developing R packages interfacing with Stan")
20558 "This package provides various tools for developers of R packages
20559 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
20560 up the required package structure, S3 generics and default methods to unify
20561 function naming across Stan-based R packages, and vignettes with
20562 recommendations for developers.")
20563 (license license:gpl3+)))
20565 (define-public r-loo
20572 (uri (cran-uri "loo" version))
20575 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
20576 (properties `((upstream-name . "loo")))
20577 (build-system r-build-system)
20579 `(("pandoc" ,ghc-pandoc)
20580 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20582 `(("r-checkmate" ,r-checkmate)
20583 ("r-matrixstats" ,r-matrixstats)))
20584 (home-page "https://mc-stan.org/loo/")
20585 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
20587 "This package provides an implementation of efficient approximate
20588 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
20589 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
20590 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
20591 procedure for regularizing importance weights. As a byproduct of the
20592 calculations, we also obtain approximate standard errors for estimated
20593 predictive errors and for the comparison of predictive errors between models.
20594 The package also provides methods for using stacking and other model weighting
20595 techniques to average Bayesian predictive distributions.")
20596 (license license:gpl3+)))
20598 (define-public r-rstan
20605 (uri (cran-uri "rstan" version))
20608 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
20609 (properties `((upstream-name . "rstan")))
20610 (build-system r-build-system)
20613 (modify-phases %standard-phases
20614 (add-before 'install 'set-timezone
20615 ;; This package is picky about timezones.
20616 (lambda* (#:key inputs #:allow-other-keys)
20617 (setenv "TZ" "UTC+1")
20619 (string-append (assoc-ref inputs "tzdata")
20620 "/share/zoneinfo"))
20623 `(("tzdata" ,tzdata)
20624 ("pandoc" ,ghc-pandoc)))
20627 ("r-ggplot2" ,r-ggplot2)
20628 ("r-gridextra" ,r-gridextra)
20629 ("r-inline" ,r-inline)
20631 ("r-pkgbuild" ,r-pkgbuild)
20633 ("r-rcppeigen" ,r-rcppeigen)
20634 ("r-stanheaders" ,r-stanheaders)))
20635 (home-page "https://discourse.mc-stan.org/")
20636 (synopsis "R interface to Stan")
20638 "User-facing R functions are provided to parse, compile, test, estimate,
20639 and analyze Stan models by accessing the header-only Stan library provided by
20640 the StanHeaders package. The Stan project develops a probabilistic
20641 programming language that implements full Bayesian statistical inference via
20642 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
20643 approximation, and (optionally penalized) maximum likelihood estimation via
20644 optimization. In all three cases, automatic differentiation is used to
20645 quickly and accurately evaluate gradients without burdening the user with the
20646 need to derive the partial derivatives.")
20647 (license license:gpl3+)))
20649 (define-public r-rstanarm
20651 (name "r-rstanarm")
20656 (uri (cran-uri "rstanarm" version))
20659 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
20660 (properties `((upstream-name . "rstanarm")))
20661 (build-system r-build-system)
20663 `(("pandoc" ,ghc-pandoc)
20664 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20666 `(("r-bayesplot" ,r-bayesplot)
20668 ("r-ggplot2" ,r-ggplot2)
20671 ("r-matrix" ,r-matrix)
20674 ("r-rcppeigen" ,r-rcppeigen)
20675 ("r-rcppparallel" ,r-rcppparallel)
20676 ("r-rstan" ,r-rstan)
20677 ("r-rstantools" ,r-rstantools)
20678 ("r-shinystan" ,r-shinystan)
20679 ("r-stanheaders" ,r-stanheaders)
20680 ("r-survival" ,r-survival)))
20681 (home-page "https://mc-stan.org/rstanarm/")
20682 (synopsis "Bayesian applied regression modeling via Stan")
20684 "This package estimates previously compiled regression models using the
20685 @code{rstan} package, which provides the R interface to the Stan C++ library
20686 for Bayesian estimation. Users specify models via the customary R syntax with
20687 a formula and @code{data.frame} plus some additional arguments for priors.")
20688 (license license:gpl3+)))
20690 (define-public r-kendall
20697 (uri (cran-uri "Kendall" version))
20700 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
20701 (properties `((upstream-name . "Kendall")))
20702 (build-system r-build-system)
20704 `(("r-boot" ,r-boot)))
20706 `(("gfortran" ,gfortran)))
20707 (home-page "https://cran.r-project.org/web/packages/Kendall/")
20708 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
20710 "This package computes the Kendall rank correlation and Mann-Kendall
20712 (license license:gpl2+)))
20714 (define-public r-zyp
20717 (version "0.10-1.1")
20721 (uri (cran-uri "zyp" version))
20724 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
20725 (properties `((upstream-name . "zyp")))
20726 (build-system r-build-system)
20728 `(("r-kendall" ,r-kendall)))
20729 (home-page "https://cran.r-project.org/web/packages/zyp/")
20730 (synopsis "Zhang + Yue-Pilon Trends Package")
20732 "This package contains an efficient implementation of Sen's slope
20733 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
20734 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
20736 (license license:lgpl2.1)))
20738 (define-public r-zvcv
20745 (uri (cran-uri "ZVCV" version))
20748 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
20749 (properties `((upstream-name . "ZVCV")))
20750 (build-system r-build-system)
20752 `(("r-abind" ,r-abind)
20753 ("r-glmnet" ,r-glmnet)
20754 ("r-mvtnorm" ,r-mvtnorm)
20755 ("r-partitions" ,r-partitions)
20757 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20758 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
20759 (synopsis "Zero-Variance Control Variates")
20761 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
20762 to reduce the variance of Monte Carlo estimators of expectations using the
20763 derivatives of the log target. Once the derivatives are available, the only
20764 additional computational effort is in solving a linear regression problem.
20765 This method has been extended to higher dimensions using regularisation. This
20766 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
20767 samples, derivatives and function evaluations are available. Additional
20768 functions for applying ZV-CV to two estimators for the normalising constant of
20769 the posterior distribution in Bayesian statistics are also supplied.")
20770 (license license:gpl2+)))
20772 (define-public r-ztype
20779 (uri (cran-uri "ztype" version))
20782 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
20783 (properties `((upstream-name . "ztype")))
20784 (build-system r-build-system)
20786 `(("r-assertthat" ,r-assertthat)
20787 ("r-dplyr" ,r-dplyr)
20788 ("r-ggplot2" ,r-ggplot2)
20789 ("r-lubridate" ,r-lubridate)
20790 ("r-magrittr" ,r-magrittr)
20791 ("r-rvest" ,r-rvest)
20792 ("r-stringr" ,r-stringr)))
20793 (home-page "https://cran.r-project.org/web/packages/ztype/")
20794 (synopsis "Run a Ztype game loaded with R functions")
20796 "How fast can you type R functions on your keyboard? Find out by running
20797 a @code{zty.pe} game: export R functions as instructions to type to destroy
20798 opponents' vessels.")
20799 (license license:gpl3)))
20801 (define-public r-zseq
20808 (uri (cran-uri "Zseq" version))
20811 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
20812 (properties `((upstream-name . "Zseq")))
20813 (build-system r-build-system)
20815 `(("r-gmp" ,r-gmp)))
20816 (home-page "https://cran.r-project.org/web/packages/Zseq/")
20817 (synopsis "Integer sequence generator")
20819 "This package generates well-known integer sequences. The @code{gmp}
20820 package is adopted for computing with arbitrarily large numbers. Every
20821 function has a hyperlink to its corresponding item in the @dfn{On-Line
20822 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
20823 (license license:gpl3+)))
20825 (define-public r-isoband
20832 (uri (cran-uri "isoband" version))
20835 "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
20836 (properties `((upstream-name . "isoband")))
20837 (build-system r-build-system)
20839 `(("r-rcpp" ,r-rcpp)
20840 ("r-testthat" ,r-testthat)))
20842 `(("r-knitr" ,r-knitr)))
20843 (home-page "https://github.com/wilkelab/isoband")
20844 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
20846 "This package provides a fast C++ implementation to generate contour
20847 lines (isolines) and contour polygons (isobands) from regularly spaced grids
20848 containing elevation data.")
20849 (license license:expat)))
20851 (define-public r-ppcor
20858 (uri (cran-uri "ppcor" version))
20861 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
20862 (properties `((upstream-name . "ppcor")))
20863 (build-system r-build-system)
20865 `(("r-mass" ,r-mass)))
20866 (home-page "https://cran.r-project.org/web/packages/ppcor/")
20867 (synopsis "Partial and semi-partial correlation")
20869 "This package provides users not only with a function to readily
20870 calculate the higher-order partial and semi-partial correlations but also with
20871 statistics and p-values of the correlation coefficients.")
20872 (license license:gpl2)))
20874 (define-public r-hrbrthemes
20876 (name "r-hrbrthemes")
20881 (uri (cran-uri "hrbrthemes" version))
20883 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
20884 (properties `((upstream-name . "hrbrthemes")))
20885 (build-system r-build-system)
20887 `(("r-extrafont" ,r-extrafont)
20888 ("r-gdtools" ,r-gdtools)
20889 ("r-ggplot2" ,r-ggplot2)
20890 ("r-htmltools" ,r-htmltools)
20891 ("r-knitr" ,r-knitr)
20892 ("r-magrittr" ,r-magrittr)
20893 ("r-rmarkdown" ,r-rmarkdown)
20894 ("r-scales" ,r-scales)))
20896 `(("r-knitr" ,r-knitr)))
20897 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
20898 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
20900 "This package provides a compilation of extra @code{ggplot2} themes,
20901 scales and utilities, including a spell check function for plot label fields
20902 and an overall emphasis on typography.")
20903 (license license:expat)))
20905 (define-public r-crochet
20912 (uri (cran-uri "crochet" version))
20915 "1cbv79nyycxk6f8ldcsnn2pvgxqlnrj0qs19nhafnq2clxy863k6"))))
20916 (build-system r-build-system)
20917 (home-page "https://github.com/agrueneberg/crochet")
20918 (synopsis "Implementation Helper for Matrix-Like Types")
20920 "Functions to help implement the extraction / subsetting / indexing
20921 function @code{[} and replacement function @code{[<-} of custom matrix-like
20922 types (based on S3, S4, etc.), modeled as closely to the base matrix class
20923 as possible (with tests to prove it).")
20924 (license license:expat)))
20926 (define-public r-boa
20929 (version "1.1.8-2")
20933 (uri (cran-uri "boa" version))
20936 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
20937 (properties `((upstream-name . "boa")))
20938 (build-system r-build-system)
20939 (home-page "http://www.jstatsoft.org/v21/i11")
20940 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
20942 "This package provides a menu-driven program and library of functions for
20943 carrying out convergence diagnostics and statistical and graphical analysis of
20944 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
20945 (license license:gpl2+)))
20947 (define-public r-httpcode
20949 (name "r-httpcode")
20953 (uri (cran-uri "httpcode" version))
20956 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
20957 (build-system r-build-system)
20958 (home-page "https://github.com/sckott/httpcode")
20959 (synopsis "HTTP status code helper")
20960 (description "@code{httpcode} provides functionality for finding and
20961 explaining the meaning of @code{HTTP} status codes. Functions are included for
20962 searching for codes by full or partial number, by message, and to get
20963 appropriate dog and cat images for many status codes.")
20964 (license license:expat)))
20966 (define-public r-latex2exp
20968 (name "r-latex2exp")
20972 (uri (cran-uri "latex2exp" version))
20975 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
20976 (build-system r-build-system)
20978 `(("r-stringr" ,r-stringr)
20979 ("r-magrittr", r-magrittr)))
20980 (home-page "https://github.com/stefano-meschiari/latex2exp/")
20981 (synopsis "Use LaTeX expressions in plots")
20982 (description "@code{latex2exp} parses and converts LaTeX math formulas to
20983 R's plotmath expressions, used to enter mathematical formulas and symbols to be
20984 rendered as text, axis labels, etc. throughout R's plotting system.")
20985 (license license:expat)))
20987 (define-public r-oai
20993 (uri (cran-uri "oai" version))
20996 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
20997 (build-system r-build-system)
20999 `(("r-xml2" ,r-xml2)
21002 ("r-stringr" ,r-stringr)
21003 ("r-tibble" ,r-tibble)))
21004 (home-page "https://github.com/ropensci/oai/")
21005 (synopsis "General purpose OAI-PMH services client")
21006 (description "@code{oai} provides a general purpose client to work with
21007 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21008 service. Functions are provided to work with the OAI-PMH verbs:
21009 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21010 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21011 (license license:expat)))
21013 (define-public r-argon2
21020 (uri (cran-uri "argon2" version))
21023 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21024 (properties `((upstream-name . "argon2")))
21025 (build-system r-build-system)
21026 (home-page "https://github.com/wrathematics/argon2")
21027 (synopsis "Secure password hashing based on the argon2 algorithm")
21029 "This package provides utilities for secure password hashing via the
21030 argon2 algorithm.")
21031 (license license:bsd-2)))
21033 (define-public r-getpass
21040 (uri (cran-uri "getPass" version))
21043 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21044 (properties `((upstream-name . "getPass")))
21045 (build-system r-build-system)
21047 `(("r-rstudioapi" ,r-rstudioapi)))
21048 (home-page "https://github.com/wrathematics/getPass")
21049 (synopsis "Masked user input")
21051 "This package provides a micro-package for reading \"passwords\", i.e.
21052 reading user input with masking, so that the input is not displayed as it is
21053 typed. Currently, RStudio, the command line (every OS), and any platform
21054 where tcltk is present are supported.")
21055 (license license:bsd-2)))
21057 (define-public r-remoter
21064 (uri (cran-uri "remoter" version))
21067 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21068 (properties `((upstream-name . "remoter")))
21069 (build-system r-build-system)
21071 `(("r-argon2" ,r-argon2)
21072 ("r-getpass" ,r-getpass)
21073 ("r-pbdzmq" ,r-pbdzmq)
21075 (home-page "https://github.com/RBigData/remoter")
21076 (synopsis "Control a remote R session from a local one")
21078 "This package provides a set of utilities for client/server computing
21079 with R, controlling a remote R session (the server) from a local one (the
21081 (license license:bsd-2)))
21083 (define-public r-asd
21090 (uri (cran-uri "asd" version))
21093 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21094 (properties `((upstream-name . "asd")))
21095 (build-system r-build-system)
21097 `(("r-mvtnorm" ,r-mvtnorm)))
21098 (home-page "https://cran.r-project.org/web/packages/asd")
21099 (synopsis "Simulations for Adaptive Seamless Designs")
21101 "This package provdes means to run simulations for adaptive seamless
21102 designs with and without early outcomes for treatment selection and
21103 subpopulation type designs.")
21104 (license license:gpl3)))