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)))
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 "0alklqcf68kmccssp4j7a7fv553pyqyy6mkkfslav83inppm4d3g"))))
1570 (build-system r-build-system)
1571 (home-page "https://github.com/tidyverse/glue")
1572 (synopsis "Interpreted string literals")
1574 "This package provides an implementation of interpreted string literals,
1575 inspired by Python's Literal String Interpolation (PEP-0498) and
1576 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1577 (license license:expat)))
1579 (define-public r-pastecs
1585 (uri (cran-uri "pastecs" version))
1588 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1589 (build-system r-build-system)
1591 `(("r-boot" ,r-boot)))
1592 (home-page "http://www.sciviews.org/pastecs")
1593 (synopsis "Analysis of space-time ecological series")
1595 "This package provides functions for regulation, decomposition and analysis
1596 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1597 initiative to bring PASSTEC 2000 functionalities to R.")
1598 (license license:gpl2+)))
1600 (define-public r-plogr
1607 (uri (cran-uri "plogr" version))
1610 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1611 (build-system r-build-system)
1612 (home-page "https://github.com/krlmlr/plogr")
1613 (synopsis "R bindings for the plog C++ logging library")
1615 "This package provides the header files for a stripped-down version of
1616 the plog header-only C++ logging library, and a method to log to R's standard
1618 (license license:expat)))
1620 (define-public r-pls
1627 (uri (cran-uri "pls" version))
1629 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1630 (build-system r-build-system)
1631 (home-page "https://mevik.net/work/software/pls.html")
1632 (synopsis "Partial Least Squares and Principal Component Regression")
1634 "The pls package implements multivariate regression methods: Partial Least
1635 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1636 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1639 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1640 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1641 @item multi-response models (or @dfn{PLS2})
1642 @item flexible cross-validation
1643 @item Jackknife variance estimates of regression coefficients
1644 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1645 (R)MSEP, R², and correlation loadings
1646 @item formula interface, modelled after @code{lm()}, with methods for predict,
1647 print, summary, plot, update, etc.
1648 @item extraction functions for coefficients, scores, and loadings
1649 @item MSEP, RMSEP, and R² estimates
1650 @item multiplicative scatter correction (@dfn{MSC})
1652 (license license:gpl2)))
1661 (uri (cran-uri "ps" version))
1663 (base32 "0127q6pw9iw8hhcfp231gmdh29nahh2n5jzc38avrzy7yrm4bwl9"))))
1664 (build-system r-build-system)
1665 (home-page "https://ps.r-lib.org")
1666 (synopsis "List, query, and manipulate system processes")
1668 "The ps package implements an API to list, query, and manipulate system
1669 processes. Most of its code is based on the @code{psutil} Python package.")
1670 (license license:bsd-3)))
1672 (define-public r-pkgbuild
1679 (uri (cran-uri "pkgbuild" version))
1681 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1682 (build-system r-build-system)
1684 `(("r-callr" ,r-callr)
1686 ("r-crayon" ,r-crayon)
1688 ("r-prettyunits" ,r-prettyunits)
1690 ("r-rprojroot" ,r-rprojroot)
1691 ("r-withr" ,r-withr)))
1692 (home-page "https://github.com/r-pkgs/pkgbuild")
1693 (synopsis "Find tools needed to build R packages")
1695 "This package provides functions used to build R packages. It locates
1696 compilers needed to build R packages on various platforms and ensures the PATH
1697 is configured appropriately so R can use them.")
1698 (license license:gpl3)))
1700 (define-public r-pkgload
1707 (uri (cran-uri "pkgload" version))
1710 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1711 (build-system r-build-system)
1713 `(("r-desc" ,r-desc)
1714 ("r-pkgbuild" ,r-pkgbuild)
1715 ("r-rlang" ,r-rlang)
1716 ("r-rprojroot" ,r-rprojroot)
1717 ("r-rstudioapi" ,r-rstudioapi)
1718 ("r-withr" ,r-withr)))
1719 (home-page "https://github.com/r-lib/pkgload")
1720 (synopsis "Simulate package installation and attach")
1722 "This package simulates the process of installing a package and then
1723 attaching it. This is a key part of the @code{devtools} package as it allows
1724 you to rapidly iterate while developing a package.")
1725 (license license:gpl3)))
1727 (define-public r-rcpp
1734 (uri (cran-uri "Rcpp" version))
1736 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
1737 (build-system r-build-system)
1738 (home-page "http://www.rcpp.org")
1739 (synopsis "Seamless R and C++ integration")
1741 "The Rcpp package provides R functions as well as C++ classes which offer
1742 a seamless integration of R and C++. Many R data types and objects can be
1743 mapped back and forth to C++ equivalents which facilitates both writing of new
1744 code as well as easier integration of third-party libraries. Documentation
1745 about Rcpp is provided by several vignettes included in this package, via the
1746 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1747 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1748 @code{citation(\"Rcpp\")} for details on these last two.")
1749 (license license:gpl2+)))
1751 (define-public r-bindr
1758 (uri (cran-uri "bindr" version))
1761 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1762 (build-system r-build-system)
1763 (home-page "https://github.com/krlmlr/bindr")
1764 (synopsis "Parametrized active bindings")
1766 "This package provides a simple interface for creating active bindings
1767 where the bound function accepts additional arguments.")
1768 (license license:expat)))
1770 (define-public r-bindrcpp
1777 (uri (cran-uri "bindrcpp" version))
1780 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1781 (build-system r-build-system)
1783 `(("r-bindr" ,r-bindr)
1784 ("r-plogr" ,r-plogr)
1785 ("r-rcpp" ,r-rcpp)))
1786 (home-page "https://github.com/krlmlr/bindrcpp")
1787 (synopsis "Rcpp interface to active bindings")
1789 "This package provides an easy way to fill an environment with active
1790 bindings that call a C++ function.")
1791 (license license:expat)))
1793 (define-public r-auc
1800 (uri (cran-uri "AUC" version))
1803 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1804 (properties `((upstream-name . "AUC")))
1805 (build-system r-build-system)
1806 (home-page "https://cran.r-project.org/web/packages/AUC")
1807 (synopsis "Compute the area under the curve of selected measures")
1809 "This package includes functions to compute the area under the curve of
1810 selected measures: the area under the sensitivity curve (AUSEC), the area
1811 under the specificity curve (AUSPC), the area under the accuracy
1812 curve (AUACC), and the area under the receiver operating characteristic
1813 curve (AUROC). The curves can also be visualized. Support for partial areas
1815 (license license:gpl2+)))
1817 (define-public r-calibrate
1819 (name "r-calibrate")
1824 (uri (cran-uri "calibrate" version))
1826 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1827 (build-system r-build-system)
1829 `(("r-mass" ,r-mass)))
1830 (home-page "https://cran.r-project.org/web/packages/calibrate")
1831 (synopsis "Calibration of scatterplot and biplot axes")
1833 "This is a package for drawing calibrated scales with tick marks
1834 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1835 (license license:gpl2)))
1837 (define-public r-shape
1844 (uri (cran-uri "shape" version))
1847 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1848 (build-system r-build-system)
1849 (home-page "https://cran.r-project.org/web/packages/shape")
1850 (synopsis "Functions for plotting graphical shapes")
1852 "This package provides functions for plotting graphical shapes such as
1853 ellipses, circles, cylinders, arrows, ...")
1854 (license license:gpl3+)))
1856 (define-public r-globaloptions
1858 (name "r-globaloptions")
1863 (uri (cran-uri "GlobalOptions" version))
1865 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1866 (properties `((upstream-name . "GlobalOptions")))
1867 (build-system r-build-system)
1868 (home-page "https://github.com/jokergoo/GlobalOptions")
1869 (synopsis "Generate functions to get or set global options")
1871 "This package provides more controls on the option values such as
1872 validation and filtering on the values, making options invisible or private.")
1873 (license license:gpl2+)))
1875 (define-public r-circlize
1882 (uri (cran-uri "circlize" version))
1885 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1886 (build-system r-build-system)
1888 `(("r-colorspace" ,r-colorspace)
1889 ("r-globaloptions" ,r-globaloptions)
1890 ("r-shape" ,r-shape)))
1891 (home-page "https://github.com/jokergoo/circlize")
1892 (synopsis "Circular visualization")
1894 "Circular layout is an efficient way to visualise huge amounts of
1895 information. This package provides an implementation of circular layout
1896 generation in R as well as an enhancement of available software. Its
1897 flexibility is based on the usage of low-level graphics functions such that
1898 self-defined high-level graphics can be easily implemented by users for
1899 specific purposes. Together with the seamless connection between the powerful
1900 computational and visual environment in R, it gives users more convenience and
1901 freedom to design figures for better understanding complex patterns behind
1902 multi-dimensional data.")
1903 (license license:gpl2+)))
1905 (define-public r-powerlaw
1912 (uri (cran-uri "poweRlaw" version))
1914 (base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
1915 (properties `((upstream-name . "poweRlaw")))
1916 (build-system r-build-system)
1918 `(("r-vgam" ,r-vgam)))
1919 (home-page "https://github.com/csgillespie/poweRlaw")
1920 (synopsis "Tools for the analysis of heavy tailed distributions")
1922 "This package provides an implementation of maximum likelihood estimators
1923 for a variety of heavy tailed distributions, including both the discrete and
1924 continuous power law distributions. Additionally, a goodness-of-fit based
1925 approach is used to estimate the lower cut-off for the scaling region.")
1926 ;; Any of these GPL versions.
1927 (license (list license:gpl2 license:gpl3))))
1929 (define-public r-compare
1936 (uri (cran-uri "compare" version))
1939 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1940 (build-system r-build-system)
1941 (home-page "https://cran.r-project.org/web/packages/compare")
1942 (synopsis "Comparing objects for differences")
1944 "This package provides functions to compare a model object to a
1945 comparison object. If the objects are not identical, the functions can be
1946 instructed to explore various modifications of the objects (e.g., sorting
1947 rows, dropping names) to see if the modified versions are identical.")
1948 (license license:gpl2+)))
1950 (define-public r-dendextend
1952 (name "r-dendextend")
1957 (uri (cran-uri "dendextend" version))
1960 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
1961 (build-system r-build-system)
1963 `(("r-ggplot2" ,r-ggplot2)
1964 ("r-magrittr" ,r-magrittr)
1965 ("r-viridis" ,r-viridis)))
1966 (home-page "https://cran.r-project.org/web/packages/dendextend")
1967 (synopsis "Extending 'dendrogram' functionality in R")
1969 "This package offers a set of functions for extending @code{dendrogram}
1970 objects in R, letting you visualize and compare trees of hierarchical
1971 clusterings. You can adjust a tree's graphical parameters (the color, size,
1972 type, etc of its branches, nodes and labels) and visually and statistically
1973 compare different dendrograms to one another.")
1974 ;; Any of these versions
1975 (license (list license:gpl2 license:gpl3))))
1977 (define-public r-getoptlong
1979 (name "r-getoptlong")
1984 (uri (cran-uri "GetoptLong" version))
1987 "1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
1988 (properties `((upstream-name . "GetoptLong")))
1989 (build-system r-build-system)
1993 `(("r-globaloptions" ,r-globaloptions)
1994 ("r-rjson" ,r-rjson)))
1995 (home-page "https://github.com/jokergoo/GetoptLong")
1996 (synopsis "Parsing command-line arguments and variable interpolation")
1998 "This is yet another command-line argument parser which wraps the
1999 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2000 use in R. It also provides a simple way for variable interpolation in R.")
2001 (license license:gpl2+)))
2003 (define-public r-fastmatch
2005 (name "r-fastmatch")
2010 (uri (cran-uri "fastmatch" version))
2013 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2014 (build-system r-build-system)
2015 (home-page "https://www.rforge.net/fastmatch")
2016 (synopsis "Fast match function")
2018 "This package provides a fast @code{match} replacement for cases that
2019 require repeated look-ups. It is slightly faster that R's built-in
2020 @code{match} function on first match against a table, but extremely fast on
2021 any subsequent lookup as it keeps the hash table in memory.")
2022 (license license:gpl2)))
2031 (uri (cran-uri "ff" version))
2034 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
2035 (build-system r-build-system)
2036 (propagated-inputs `(("r-bit" ,r-bit)))
2037 (home-page "http://ff.r-forge.r-project.org/")
2038 (synopsis "Memory-efficient storage of large data on disk and access functions")
2040 "This package provides data structures that are stored on disk but
2041 behave (almost) as if they were in RAM by transparently mapping only a section
2043 ;; error Architecture not supported.
2044 (supported-systems (delete "aarch64-linux" %supported-systems))
2045 (license license:gpl2)))
2047 (define-public r-ffbase
2054 (uri (cran-uri "ffbase" version))
2057 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2058 (build-system r-build-system)
2061 ("r-fastmatch" ,r-fastmatch)
2063 (home-page "http://github.com/edwindj/ffbase")
2064 (synopsis "Basic statistical functions for package 'ff'")
2066 "This package extends the out of memory vectors of @code{ff} with
2067 statistical functions and other utilities to ease their usage.")
2068 (license license:gpl3)))
2070 (define-public r-prettyunits
2072 (name "r-prettyunits")
2077 (uri (cran-uri "prettyunits" version))
2080 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2081 (build-system r-build-system)
2082 (home-page "https://github.com/gaborcsardi/prettyunits")
2083 (synopsis "Pretty, human readable formatting of quantities")
2085 "This package provides tools for pretty, human readable formatting of
2087 (license license:expat)))
2089 (define-public r-reshape
2096 (uri (cran-uri "reshape" version))
2099 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2100 (build-system r-build-system)
2102 `(("r-plyr" ,r-plyr)
2103 ("r-rcpp" ,r-rcpp)))
2104 (home-page "http://had.co.nz/reshape")
2105 (synopsis "Flexibly reshape data")
2107 "Flexibly restructure and aggregate data using just two functions:
2108 @code{melt} and @code{cast}. This package provides them.")
2109 (license license:expat)))
2111 (define-public r-progress
2118 (uri (cran-uri "progress" version))
2121 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2122 (build-system r-build-system)
2124 `(("r-crayon" ,r-crayon)
2126 ("r-prettyunits" ,r-prettyunits)
2128 (home-page "https://github.com/gaborcsardi/progress")
2129 (synopsis "Terminal progress bars")
2131 "This package provides configurable progress bars. They may include
2132 percentage, elapsed time, and/or the estimated completion time. They work in
2133 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2134 package also provides a C++ API, that works with or without Rcpp.")
2135 (license license:expat)))
2137 (define-public r-ggally
2144 (uri (cran-uri "GGally" version))
2147 "082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
2148 (properties `((upstream-name . "GGally")))
2149 (build-system r-build-system)
2151 `(("libressl" ,libressl)))
2153 `(("r-ggplot2" ,r-ggplot2)
2154 ("r-gtable" ,r-gtable)
2156 ("r-progress" ,r-progress)
2157 ("r-rcolorbrewer" ,r-rcolorbrewer)
2158 ("r-reshape" ,r-reshape)
2159 ("r-rlang" ,r-rlang)))
2160 (home-page "https://ggobi.github.io/ggally")
2161 (synopsis "Extension to ggplot2")
2163 "The R package ggplot2 is a plotting system based on the grammar of
2164 graphics. GGally extends ggplot2 by adding several functions to reduce the
2165 complexity of combining geometric objects with transformed data. Some of
2166 these functions include a pairwise plot matrix, a two group pairwise plot
2167 matrix, a parallel coordinates plot, a survival plot, and several functions to
2169 (license license:gpl2+)))
2171 (define-public r-proxy
2178 (uri (cran-uri "proxy" version))
2181 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2182 (build-system r-build-system)
2183 (home-page "https://cran.r-project.org/web/packages/proxy")
2184 (synopsis "Distance and similarity measures")
2186 "This package provides an extensible framework for the efficient
2187 calculation of auto- and cross-proximities, along with implementations of the
2188 most popular ones.")
2189 (license license:gpl2)))
2198 (uri (cran-uri "sp" version))
2200 (base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg"))))
2201 (build-system r-build-system)
2203 `(("r-lattice" ,r-lattice)))
2204 (home-page "https://cran.r-project.org/web/packages/sp")
2205 (synopsis "Classes and methods for spatial data")
2207 "This package provides classes and methods for spatial data; the classes
2208 document where the spatial location information resides, for 2D or 3D data.
2209 Utility functions are provided, e.g. for plotting data as maps, spatial
2210 selection, as well as methods for retrieving coordinates, for subsetting,
2211 print, summary, etc.")
2212 (license license:gpl2+)))
2214 (define-public r-rmtstat
2221 (uri (cran-uri "RMTstat" version))
2224 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2225 (properties `((upstream-name . "RMTstat")))
2226 (build-system r-build-system)
2227 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2228 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2230 "This package provides functions for working with the Tracy-Widom laws
2231 and other distributions related to the eigenvalues of large Wishart
2233 (license license:bsd-3)))
2235 (define-public r-rmpi
2241 (uri (cran-uri "Rmpi" version))
2244 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2245 (properties `((upstream-name . "Rmpi")))
2246 (build-system r-build-system)
2248 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2249 #:phases (modify-phases %standard-phases
2250 (add-before 'install 'mpi-setup
2253 `(("openmpi" ,openmpi)))
2255 `(("pkg-config" ,pkg-config)))
2256 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2257 (synopsis "R interface to message-passing interface (MPI)")
2259 "This package provides an interface (wrapper) to MPI APIs. It also
2260 provides an interactive R manager and worker environment.")
2261 (license license:gpl2+)))
2263 (define-public r-lmoments
2270 (uri (cran-uri "Lmoments" version))
2273 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2274 (properties `((upstream-name . "Lmoments")))
2275 (build-system r-build-system)
2277 `(("r-rcpp" ,r-rcpp)
2278 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2279 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2280 (synopsis "L-moments and quantile mixtures")
2282 "This package contains functions to estimate L-moments and trimmed
2283 L-moments from the data. It also contains functions to estimate the
2284 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2285 quantile mixture from L-moments and trimmed L-moments.")
2286 (license license:gpl2)))
2288 (define-public r-distillery
2290 (name "r-distillery")
2295 (uri (cran-uri "distillery" version))
2298 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2299 (build-system r-build-system)
2300 (home-page "https://ral.ucar.edu/staff/ericg/")
2301 (synopsis "Functions for confidence intervals and object information")
2303 "This package provides some very simple method functions for confidence
2304 interval calculation and to distill pertinent information from a potentially
2305 complex object; primarily used in common with the packages extRemes and
2307 (license license:gpl2+)))
2309 (define-public r-extremes
2316 (uri (cran-uri "extRemes" version))
2319 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2320 (properties `((upstream-name . "extRemes")))
2321 (build-system r-build-system)
2323 `(("r-distillery" ,r-distillery)
2324 ("r-lmoments" ,r-lmoments)))
2325 (home-page "https://www.assessment.ucar.edu/toolkit/")
2326 (synopsis "Extreme value analysis")
2328 "ExtRemes is a suite of functions for carrying out analyses on the
2329 extreme values of a process of interest; be they block maxima over long blocks
2330 or excesses over a high threshold.")
2331 (license license:gpl2+)))
2333 (define-public r-lmtest
2340 (uri (cran-uri "lmtest" version))
2343 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2344 (build-system r-build-system)
2346 `(("r-zoo" ,r-zoo)))
2348 `(("gfortran" ,gfortran)))
2349 (home-page "https://cran.r-project.org/web/packages/lmtest")
2350 (synopsis "Testing linear regression models")
2352 "This package provides a collection of tests, data sets, and examples for
2353 diagnostic checking in linear regression models. Furthermore, some generic
2354 tools for inference in parametric models are provided.")
2355 ;; Either version is okay
2356 (license (list license:gpl2 license:gpl3))))
2358 (define-public r-idr
2364 (uri (cran-uri "idr" version))
2367 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2368 (build-system r-build-system)
2369 (home-page "https://cran.r-project.org/web/packages/idr/")
2370 (synopsis "Irreproducible discovery rate")
2372 "This is a package for estimating the copula mixture model and plotting
2373 correspondence curves in \"Measuring reproducibility of high-throughput
2374 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2375 by Li, Brown, Huang, and Bickel")
2376 (license license:gpl2+)))
2378 (define-public r-inline
2384 (uri (cran-uri "inline" version))
2387 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2388 (build-system r-build-system)
2389 (home-page "https://cran.r-project.org/web/packages/inline")
2390 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2392 "This package provides functionality to dynamically define R functions
2393 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2394 @code{.Call} calling conventions.")
2395 ;; Any version of the LGPL.
2396 (license license:lgpl3+)))
2398 (define-public r-bdsmatrix
2400 (name "r-bdsmatrix")
2405 (uri (cran-uri "bdsmatrix" version))
2408 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2409 (properties `((upstream-name . "bdsmatrix")))
2410 (build-system r-build-system)
2411 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2412 (synopsis "Routines for block diagonal symmetric matrices")
2414 "This package provides procedures to work with block diagonal symmetric
2415 matrices, a special case of sparse matrices.")
2416 (license license:lgpl2.0)))
2418 (define-public r-bbmle
2421 (version "1.0.23.1")
2425 (uri (cran-uri "bbmle" version))
2428 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2429 (build-system r-build-system)
2431 `(("r-bdsmatrix" ,r-bdsmatrix)
2432 ("r-lattice" ,r-lattice)
2434 ("r-matrix" ,r-matrix)
2435 ("r-mvtnorm" ,r-mvtnorm)
2436 ("r-numderiv" ,r-numderiv)))
2437 (home-page "https://cran.r-project.org/web/packages/bbmle")
2438 (synopsis "Tools for General Maximum Likelihood Estimation")
2440 "This package provides methods and functions for fitting maximum
2441 likelihood models in R. This package modifies and extends the @code{mle}
2442 classes in the @code{stats4} package.")
2443 ;; Any version of the GPL
2444 (license license:gpl2+)))
2446 (define-public r-emdbook
2453 (uri (cran-uri "emdbook" version))
2456 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2457 (build-system r-build-system)
2459 `(("r-bbmle" ,r-bbmle)
2461 ("r-lattice" ,r-lattice)
2463 ("r-plyr" ,r-plyr)))
2464 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2465 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2467 "This package provides auxiliary functions and data sets for \"Ecological
2468 Models and Data\", a book presenting maximum likelihood estimation and related
2469 topics for ecologists (ISBN 978-0-691-12522-0).")
2471 (license (list license:gpl2 license:gpl3))))
2473 (define-public r-lpsolve
2480 (uri (cran-uri "lpSolve" version))
2483 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2484 (properties `((upstream-name . "lpSolve")))
2485 (build-system r-build-system)
2486 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2487 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2489 "Lp_solve is software for solving linear, integer and mixed integer
2490 programs. This implementation supplies a \"wrapper\" function in C and some R
2491 functions that solve general linear/integer problems, assignment problems, and
2492 transportation problems.")
2493 (license license:lgpl2.0)))
2495 (define-public r-limsolve
2502 (uri (cran-uri "limSolve" version))
2505 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2506 (properties `((upstream-name . "limSolve")))
2507 (build-system r-build-system)
2509 `(("r-lpsolve" ,r-lpsolve)
2511 ("r-quadprog" ,r-quadprog)))
2512 (native-inputs `(("gfortran" ,gfortran)))
2513 (home-page "https://cran.r-project.org/web/packages/limSolve")
2514 (synopsis "Solving linear inverse models")
2516 "This package provides functions that:
2519 @item find the minimum/maximum of a linear or quadratic function,
2520 @item sample an underdetermined or overdetermined system,
2521 @item solve a linear system Ax=B for the unknown x.
2524 It includes banded and tridiagonal linear systems. The package calls Fortran
2525 functions from LINPACK.")
2527 (license (list license:gpl2+ license:gpl3+))))
2529 (define-public r-fitdistrplus
2531 (name "r-fitdistrplus")
2536 (uri (cran-uri "fitdistrplus" version))
2539 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2540 (build-system r-build-system)
2542 `(("r-mass" ,r-mass)
2543 ("r-npsurv" ,r-npsurv)
2544 ("r-survival" ,r-survival)))
2545 (home-page "http://riskassessment.r-forge.r-project.org")
2546 (synopsis "Fitting a parametric distribution from data")
2548 "This package extends the @code{fitdistr} function of the MASS package
2549 with several functions to help the fit of a parametric distribution to
2550 non-censored or censored data. Censored data may contain left-censored,
2551 right-censored and interval-censored values, with several lower and upper
2552 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2553 provides moment matching (MME), quantile matching (QME) and maximum
2554 goodness-of-fit estimation (MGE) methods (available only for non-censored
2555 data). Weighted versions of MLE, MME and QME are available.")
2556 (license license:gpl2+)))
2558 (define-public r-energy
2565 (uri (cran-uri "energy" version))
2568 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2569 (build-system r-build-system)
2571 `(("r-boot" ,r-boot)
2572 ("r-rcpp" ,r-rcpp)))
2573 (home-page "https://cran.r-project.org/web/packages/energy")
2574 (synopsis "Multivariate inference via the energy of data")
2576 "This package provides e-statistics (energy) tests and statistics for
2577 multivariate and univariate inference, including distance correlation,
2578 one-sample, two-sample, and multi-sample tests for comparing multivariate
2579 distributions, are implemented. Measuring and testing multivariate
2580 independence based on distance correlation, partial distance correlation,
2581 multivariate goodness-of-fit tests, clustering based on energy distance,
2582 testing for multivariate normality, distance components (disco) for
2583 non-parametric analysis of structured data, and other energy
2584 statistics/methods are implemented.")
2585 (license license:gpl2+)))
2587 (define-public r-suppdists
2589 (name "r-suppdists")
2594 (uri (cran-uri "SuppDists" version))
2597 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2598 (properties `((upstream-name . "SuppDists")))
2599 (build-system r-build-system)
2600 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2601 (synopsis "Supplementary distributions")
2603 "This package provides ten distributions supplementing those built into
2604 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2605 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2606 coefficient, Johnson distributions, normal scores and generalized
2607 hypergeometric distributions. In addition two random number generators of
2608 George Marsaglia are included.")
2609 (license license:gpl2+)))
2611 (define-public r-ksamples
2618 (uri (cran-uri "kSamples" version))
2621 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2622 (properties `((upstream-name . "kSamples")))
2623 (build-system r-build-system)
2625 `(("r-suppdists" ,r-suppdists)))
2626 (home-page "https://cran.r-project.org/web/packages/kSamples")
2627 (synopsis "K-Sample rank tests and their combinations")
2629 "This package provides tools to compares k samples using the
2630 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2631 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2632 test. It computes asymptotic, simulated or (limited) exact P-values, all
2633 valid under randomization, with or without ties, or conditionally under random
2634 sampling from populations, given the observed tie pattern. Except for Steel's
2635 test and the JT test it also combines these tests across several blocks of
2637 (license license:gpl2+)))
2639 (define-public r-cvst
2646 (uri (cran-uri "CVST" version))
2649 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2650 (properties `((upstream-name . "CVST")))
2651 (build-system r-build-system)
2653 `(("r-kernlab" ,r-kernlab)
2654 ("r-matrix" ,r-matrix)))
2655 (home-page "https://cran.r-project.org/web/packages/CVST")
2656 (synopsis "Fast cross-validation via sequential testing")
2658 "This package implements the fast cross-validation via sequential
2659 testing (CVST) procedure. CVST is an improved cross-validation procedure
2660 which uses non-parametric testing coupled with sequential analysis to
2661 determine the best parameter set on linearly increasing subsets of the data.
2662 Additionally to the CVST the package contains an implementation of the
2663 ordinary k-fold cross-validation with a flexible and powerful set of helper
2664 objects and methods to handle the overall model selection process. The
2665 implementations of the Cochran's Q test with permutations and the sequential
2666 testing framework of Wald are generic and can therefore also be used in other
2668 (license license:gpl2+)))
2670 (define-public r-squarem
2677 (uri (cran-uri "SQUAREM" version))
2680 "1j6sa93xjvynnzx9jx79a3fysbykmbqyknknsqif5bcha6xp6cvf"))))
2681 (properties `((upstream-name . "SQUAREM")))
2682 (build-system r-build-system)
2683 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2684 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2686 "This package provides algorithms for accelerating the convergence of
2687 slow, monotone sequences from smooth, contraction mapping such as the EM
2688 algorithm. It can be used to accelerate any smooth, linearly convergent
2689 acceleration scheme. A tutorial style introduction to this package is
2690 available in a vignette.")
2691 (license license:gpl2+)))
2693 (define-public r-lava
2700 (uri (cran-uri "lava" version))
2703 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2704 (build-system r-build-system)
2706 `(("r-numderiv" ,r-numderiv)
2707 ("r-squarem" ,r-squarem)
2708 ("r-survival" ,r-survival)))
2709 (home-page "https://github.com/kkholst/lava")
2710 (synopsis "Latent variable models")
2712 "This package provides tools for the estimation and simulation of latent
2714 (license license:gpl3)))
2716 (define-public r-drr
2723 (uri (cran-uri "DRR" version))
2726 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
2727 (properties `((upstream-name . "DRR")))
2728 (build-system r-build-system)
2730 `(("r-cvst" ,r-cvst)
2731 ("r-kernlab" ,r-kernlab)
2732 ("r-matrix" ,r-matrix)))
2733 (home-page "https://cran.r-project.org/web/packages/DRR")
2734 (synopsis "Dimensionality reduction via regression")
2736 "This package provides an implementation of dimensionality reduction via
2737 regression using Kernel Ridge Regression.")
2738 (license license:gpl3)))
2740 (define-public r-prodlim
2743 (version "2019.11.13")
2747 (uri (cran-uri "prodlim" version))
2750 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2751 (build-system r-build-system)
2753 `(("r-kernsmooth" ,r-kernsmooth)
2756 ("r-survival" ,r-survival)))
2757 (home-page "https://cran.r-project.org/web/packages/prodlim")
2758 (synopsis "Product-limit estimation for censored event history analysis")
2760 "This package provides a fast and user-friendly implementation of
2761 nonparametric estimators for censored event history (survival) analysis with
2762 the Kaplan-Meier and Aalen-Johansen methods.")
2763 (license license:gpl2+)))
2765 (define-public r-dimred
2772 (uri (cran-uri "dimRed" version))
2775 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2776 (properties `((upstream-name . "dimRed")))
2777 (build-system r-build-system)
2780 ("r-magrittr" ,r-magrittr)))
2781 (home-page "https://github.com/gdkrmr/dimRed")
2782 (synopsis "Framework for dimensionality reduction")
2784 "This package provides a collection of dimensionality reduction
2785 techniques from R packages and provides a common interface for calling the
2787 (license license:gpl3)))
2789 (define-public r-timedate
2792 (version "3043.102")
2796 (uri (cran-uri "timeDate" version))
2799 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2800 (properties `((upstream-name . "timeDate")))
2801 (build-system r-build-system)
2802 (home-page "https://www.rmetrics.org")
2803 (synopsis "Chronological and calendar objects")
2805 "This package provides an environment for teaching \"Financial
2806 Engineering and Computational Finance\" and for managing chronological and
2808 (license license:gpl2+)))
2810 (define-public r-magic
2817 (uri (cran-uri "magic" version))
2820 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2821 (build-system r-build-system)
2823 `(("r-abind" ,r-abind)))
2824 (home-page "https://github.com/RobinHankin/magic.git")
2825 (synopsis "Create and investigate magic squares")
2827 "This package provides a collection of efficient, vectorized algorithms
2828 for the creation and investigation of magic squares and hypercubes, including
2829 a variety of functions for the manipulation and analysis of arbitrarily
2830 dimensioned arrays.")
2831 (license license:gpl2)))
2833 (define-public r-rmysql
2840 (uri (cran-uri "RMySQL" version))
2843 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
2844 (properties `((upstream-name . "RMySQL")))
2845 (build-system r-build-system)
2847 `(("mariadb" ,mariadb "lib")
2848 ("mariadb-dev" ,mariadb "dev")
2851 `(("r-dbi" ,r-dbi)))
2852 (home-page "https://github.com/r-dbi/RMySQL")
2853 (synopsis "Database interface and MySQL driver for R")
2855 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2856 package contains an old implementation based on legacy code from S-PLUS which
2857 is being phased out. A modern MySQL client based on Rcpp is available from
2858 the RMariaDB package.")
2859 (license license:gpl2)))
2861 (define-public r-rpostgresql
2863 (name "r-rpostgresql")
2868 (uri (cran-uri "RPostgreSQL" version))
2871 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2872 (properties `((upstream-name . "RPostgreSQL")))
2873 (build-system r-build-system)
2875 `(("postgresql" ,postgresql)))
2877 `(("r-dbi" ,r-dbi)))
2878 (home-page "https://github.com/tomoakin/RPostgreSQL")
2879 (synopsis "R interface to the PostgreSQL database system")
2881 "This package provides a Database Interface (DBI) compliant driver for R
2882 to access PostgreSQL database systems.")
2883 ;; The whole package is released under GPL version 2. It includes code
2884 ;; under the PostgreSQL license.
2885 (license license:gpl2)))
2887 (define-public r-linprog
2894 (uri (cran-uri "linprog" version))
2897 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2898 (build-system r-build-system)
2899 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2900 (home-page "http://linprog.r-forge.r-project.org/")
2901 (synopsis "Linear programming and optimization")
2903 "This package can be used to solve Linear Programming / Linear
2904 Optimization problems by using the simplex algorithm.")
2905 (license license:gpl2+)))
2907 (define-public r-geometry
2914 (uri (cran-uri "geometry" version))
2917 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2918 (build-system r-build-system)
2920 `(("r-magic" ,r-magic)
2921 ("r-linprog" ,r-linprog)
2922 ("r-lpsolve" ,r-lpsolve)
2924 ("r-rcppprogress" ,r-rcppprogress)))
2925 (home-page "http://geometry.r-forge.r-project.org/")
2926 (synopsis "Mesh generation and surface tesselation")
2928 "This package makes the qhull library available in R, in a similar manner
2929 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2930 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2931 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2932 and higher dimensions. It implements the Quickhull algorithm for computing
2933 the convex hull. Qhull does not support constrained Delaunay triangulations,
2934 or mesh generation of non-convex objects, but the package does include some R
2935 functions that allow for this. Currently the package only gives access to
2936 Delaunay triangulation and convex hull computation.")
2937 ;; The Qhull sources are included and are distributed under a custom
2938 ;; non-copyleft license. The R sources are released under GPL version 2.
2939 (license (list license:gpl2
2940 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2942 (define-public r-ddalpha
2949 (uri (cran-uri "ddalpha" version))
2952 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
2953 (build-system r-build-system)
2956 ("r-class" ,r-class)
2957 ("r-geometry" ,r-geometry)
2960 ("r-robustbase" ,r-robustbase)
2961 ("r-sfsmisc" ,r-sfsmisc)))
2963 `(("gfortran" ,gfortran)))
2964 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2965 (synopsis "Depth-Based classification and calculation of data depth")
2967 "This package contains procedures for depth-based supervised learning,
2968 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2969 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2970 statistical depth function to a compact low-dimensional space, where the final
2971 classification is done. It also offers an extension to functional data and
2972 routines for calculating certain notions of statistical depth functions. 50
2973 multivariate and 5 functional classification problems are included.")
2974 (license license:gpl2)))
2976 (define-public r-gower
2983 (uri (cran-uri "gower" version))
2986 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2987 (build-system r-build-system)
2988 (home-page "https://github.com/markvanderloo/gower")
2989 (synopsis "Gower's distance")
2991 "This package provides tools to compute Gower's distance (or similarity)
2992 coefficient between records, and to compute the top-n matches between records.
2993 Core algorithms are executed in parallel on systems supporting OpenMP.")
2994 (license license:gpl3)))
2996 (define-public r-rcpproll
3003 (uri (cran-uri "RcppRoll" version))
3006 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3007 (properties `((upstream-name . "RcppRoll")))
3008 (build-system r-build-system)
3010 `(("r-rcpp" ,r-rcpp)))
3011 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3012 (synopsis "Efficient rolling and windowed operations")
3014 "This package provides fast and efficient routines for common rolling /
3015 windowed operations. Routines for the efficient computation of windowed mean,
3016 median, sum, product, minimum, maximum, standard deviation and variance are
3018 (license license:gpl2+)))
3020 (define-public r-ipred
3027 (uri (cran-uri "ipred" version))
3030 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3031 (build-system r-build-system)
3033 `(("r-class" ,r-class)
3036 ("r-prodlim" ,r-prodlim)
3037 ("r-rpart" ,r-rpart)
3038 ("r-survival" ,r-survival)))
3039 (home-page "https://cran.r-project.org/web/packages/ipred")
3040 (synopsis "Improved predictors")
3042 "This package provides improved predictive models by indirect
3043 classification and bagging for classification, regression and survival
3044 problems as well as resampling based estimators of prediction error.")
3045 (license license:gpl2+)))
3047 (define-public r-psych
3050 (version "1.9.12.31")
3054 (uri (cran-uri "psych" version))
3057 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3058 (build-system r-build-system)
3060 `(("r-lattice" ,r-lattice)
3061 ("r-mnormt" ,r-mnormt)
3062 ("r-nlme" ,r-nlme)))
3063 (home-page "https://cran.r-project.org/web/packages/psych/")
3064 (synopsis "Procedures for psychological, psychometric, and personality research")
3066 "This package provides a general purpose toolbox for personality,
3067 psychometric theory and experimental psychology. Functions are primarily for
3068 multivariate analysis and scale construction using factor analysis, principal
3069 component analysis, cluster analysis and reliability analysis, although others
3070 provide basic descriptive statistics. Item Response Theory is done using
3071 factor analysis of tetrachoric and polychoric correlations. Functions for
3072 analyzing data at multiple levels include within and between group statistics,
3073 including correlations and factor analysis. Functions for simulating and
3074 testing particular item and test structures are included. Several functions
3075 serve as a useful front end for structural equation modeling. Graphical
3076 displays of path diagrams, factor analysis and structural equation models are
3077 created using basic graphics.")
3078 (license license:gpl2+)))
3080 (define-public r-generics
3087 (uri (cran-uri "generics" version))
3090 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3091 (build-system r-build-system)
3092 (home-page "https://github.com/r-lib/generics")
3093 (synopsis "Common S3 generics not provided by base R methods")
3095 "In order to reduce potential package dependencies and conflicts,
3096 generics provides a number of commonly used S3 generics that are not provided
3097 by base R methods related to model fitting.")
3098 (license license:gpl2)))
3100 (define-public r-broom
3107 (uri (cran-uri "broom" version))
3110 "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
3111 (build-system r-build-system)
3113 `(("r-backports" ,r-backports)
3114 ("r-dplyr" ,r-dplyr)
3115 ("r-generics" ,r-generics)
3117 ("r-purrr" ,r-purrr)
3118 ("r-reshape2" ,r-reshape2)
3119 ("r-stringr" ,r-stringr)
3120 ("r-tibble" ,r-tibble)
3121 ("r-tidyr" ,r-tidyr)))
3122 (home-page "https://github.com/tidyverse/broom")
3123 (synopsis "Convert statistical analysis objects into tidy data frames")
3125 "This package provides tools to convert statistical analysis objects from
3126 R into tidy data frames, so that they can more easily be combined, reshaped
3127 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3128 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3129 summarizes a model's statistical findings such as coefficients of a
3130 regression; @code{augment}, which adds columns to the original data such as
3131 predictions, residuals and cluster assignments; and @code{glance}, which
3132 provides a one-row summary of model-level statistics.")
3133 (license license:expat)))
3135 (define-public r-recipes
3142 (uri (cran-uri "recipes" version))
3145 "11f96aanrzi2v6cn49fhvf9y4cmhra63wcy6nvpv6hcfaqqmwd2g"))))
3146 (build-system r-build-system)
3148 `(("r-dplyr" ,r-dplyr)
3149 ("r-generics" ,r-generics)
3151 ("r-gower" ,r-gower)
3152 ("r-ipred" ,r-ipred)
3153 ("r-lubridate" ,r-lubridate)
3154 ("r-magrittr" ,r-magrittr)
3155 ("r-matrix" ,r-matrix)
3156 ("r-purrr" ,r-purrr)
3157 ("r-rlang" ,r-rlang)
3158 ("r-tibble" ,r-tibble)
3159 ("r-tidyr" ,r-tidyr)
3160 ("r-tidyselect" ,r-tidyselect)
3161 ("r-timedate" ,r-timedate)
3162 ("r-withr" ,r-withr)))
3164 `(("r-knitr" ,r-knitr)))
3165 (home-page "https://github.com/topepo/recipes")
3166 (synopsis "Preprocessing tools to create design matrices")
3168 "Recipes is an extensible framework to create and preprocess design
3169 matrices. Recipes consist of one or more data manipulation and analysis
3170 \"steps\". Statistical parameters for the steps can be estimated from an
3171 initial data set and then applied to other data sets. The resulting design
3172 matrices can then be used as inputs into statistical or machine learning
3174 (license license:gpl2)))
3176 (define-public r-pdist
3183 (uri (cran-uri "pdist" version))
3186 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3187 (build-system r-build-system)
3188 (home-page "https://github.com/jeffwong/pdist")
3189 (synopsis "Partitioned distance function")
3191 "Pdist computes the euclidean distance between rows of a matrix X and
3192 rows of another matrix Y. Previously, this could be done by binding the two
3193 matrices together and calling @code{dist}, but this creates unnecessary
3194 computation by computing the distances between a row of X and another row of
3195 X, and likewise for Y. Pdist strictly computes distances across the two
3196 matrices, not within the same matrix, making computations significantly faster
3197 for certain use cases.")
3198 (license license:gpl3+)))
3200 (define-public r-ggrepel
3207 (uri (cran-uri "ggrepel" version))
3210 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3211 (build-system r-build-system)
3213 `(("r-ggplot2" ,r-ggplot2)
3215 ("r-scales" ,r-scales)))
3217 `(("r-knitr" ,r-knitr))) ; for vignettes
3218 (home-page "http://github.com/slowkow/ggrepel")
3219 (synopsis "Repulsive text and label geometries for ggplot2")
3221 "This package provides text and label geometries for ggplot2 that help to
3222 avoid overlapping text labels. Labels repel away from each other and away
3223 from the data points.")
3224 (license license:gpl3)))
3226 (define-public r-corrplot
3233 (uri (cran-uri "corrplot" version))
3236 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3237 (build-system r-build-system)
3238 (home-page "https://github.com/taiyun/corrplot")
3239 (synopsis "Visualization of a correlation matrix")
3241 "This package provides a graphical display of a correlation matrix or
3242 general matrix. It also contains some algorithms to do matrix reordering. In
3243 addition, corrplot is good at details, including choosing color, text labels,
3244 color labels, layout, etc.")
3245 ;; Any version of the GPL
3246 (license license:gpl2+)))
3248 (define-public r-stringdist
3250 (name "r-stringdist")
3255 (uri (cran-uri "stringdist" version))
3257 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3258 (build-system r-build-system)
3259 (home-page "https://github.com/markvanderloo/stringdist")
3260 (synopsis "Approximate string matching and string distance functions")
3262 "This package implements an approximate string matching version of R's
3263 native @code{match} function. It can calculate various string distances based
3264 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3265 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3266 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3267 can be computed between character vectors while taking proper care of encoding
3268 or between integer vectors representing generic sequences.")
3269 (license license:gpl3+)))
3271 (define-public r-ucminf
3278 (uri (cran-uri "ucminf" version))
3281 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3282 (build-system r-build-system)
3283 (native-inputs `(("gfortran" ,gfortran)))
3284 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3285 (synopsis "General-purpose unconstrained non-linear optimization")
3287 "This package provides an implementation of an algorithm for
3288 general-purpose unconstrained non-linear optimization. The algorithm is of
3289 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3290 search with a trust region type monitoring of the input to the line search
3291 algorithm. The interface of @code{ucminf} is designed for easy interchange
3292 with the package @code{optim}.")
3293 (license license:gpl2+)))
3295 (define-public r-ordinal
3298 (version "2019.12-10")
3302 (uri (cran-uri "ordinal" version))
3305 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3306 (build-system r-build-system)
3308 `(("r-mass" ,r-mass)
3309 ("r-matrix" ,r-matrix)
3310 ("r-numderiv" ,r-numderiv)
3311 ("r-ucminf" ,r-ucminf)))
3312 (home-page "https://github.com/runehaubo/ordinal")
3313 (synopsis "Regression models for ordinal data")
3315 "This package provides an implementation of cumulative link (mixed)
3316 models also known as ordered regression models, proportional odds models,
3317 proportional hazards models for grouped survival times and ordered models.
3318 Estimation is via maximum likelihood and mixed models are fitted with the
3319 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3320 (license license:gpl2+)))
3322 (define-public r-jomo
3329 (uri (cran-uri "jomo" version))
3332 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3333 (build-system r-build-system)
3335 `(("r-lme4" ,r-lme4)
3337 ("r-ordinal" ,r-ordinal)
3338 ("r-survival" ,r-survival)))
3339 (home-page "https://cran.r-project.org/web/packages/jomo/")
3340 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3342 "Similarly to Schafer's package pan, jomo is a package for multilevel
3343 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3344 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3345 possibility of handling binary and categorical data through latent normal
3346 variables, the option to use cluster-specific covariance matrices and to
3347 impute compatibly with the substantive model.")
3348 (license license:gpl2)))
3350 (define-public r-pan
3357 (uri (cran-uri "pan" version))
3360 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3361 (build-system r-build-system)
3362 (native-inputs `(("gfortran" ,gfortran)))
3363 (home-page "https://cran.r-project.org/web/packages/pan/")
3364 (synopsis "Multiple imputation for multivariate panel or clustered data")
3366 "This package implements multiple imputation for multivariate panel or
3368 (license license:gpl3)))
3370 (define-public r-mitml
3377 (uri (cran-uri "mitml" version))
3380 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3381 (build-system r-build-system)
3383 `(("r-haven" ,r-haven)
3386 (home-page "https://cran.r-project.org/web/packages/mitml/")
3387 (synopsis "Tools for multiple imputation in multilevel modeling")
3389 "This package provides tools for multiple imputation of missing data in
3390 multilevel modeling. It includes a user-friendly interface to the packages
3391 pan and jomo, and several functions for visualization, data management and the
3392 analysis of multiply imputed data sets.")
3393 (license license:gpl2+)))
3395 (define-public r-mice
3402 (uri (cran-uri "mice" version))
3405 "1ibybvigqkkla4xwhqs2w4m6c68alfcdsljx99nn4p92rzb1ig04"))))
3406 (build-system r-build-system)
3408 `(("r-broom" ,r-broom)
3409 ("r-dplyr" ,r-dplyr)
3410 ("r-lattice" ,r-lattice)
3412 ("r-tidyr" ,r-tidyr)))
3413 (home-page "https://cran.r-project.org/web/packages/mice/")
3414 (synopsis "Multivariate imputation by chained equations")
3416 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3417 implemented by the MICE algorithm as described in @url{Van Buuren and
3418 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3419 variable has its own imputation model. Built-in imputation models are
3420 provided for continuous data (predictive mean matching, normal), binary
3421 data (logistic regression), unordered categorical data (polytomous logistic
3422 regression) and ordered categorical data (proportional odds). MICE can also
3423 impute continuous two-level data (normal model, pan, second-level variables).
3424 Passive imputation can be used to maintain consistency between variables.
3425 Various diagnostic plots are available to inspect the quality of the
3427 ;; Any of these two versions.
3428 (license (list license:gpl2 license:gpl3))))
3430 (define-public r-truncnorm
3432 (name "r-truncnorm")
3437 (uri (cran-uri "truncnorm" version))
3440 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3441 (build-system r-build-system)
3442 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3443 (synopsis "Truncated normal distribution")
3444 (description "This package provides functions for the truncated normal
3445 distribution with mean equal to @code{mean} and standard deviation equal to
3446 @code{sd}. It includes density, distribution, quantile, and expected value
3447 functions, as well as a random generation function.")
3448 (license license:gpl2)))
3450 (define-public r-rsolnp
3457 (uri (cran-uri "Rsolnp" version))
3460 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3461 (properties `((upstream-name . "Rsolnp")))
3462 (build-system r-build-system)
3464 `(("r-truncnorm" ,r-truncnorm)))
3465 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3466 (synopsis "General non-linear optimization")
3467 (description "The Rsolnp package implements a general non-linear augmented
3468 Lagrange multiplier method solver, a @dfn{sequential quadratic
3469 programming} (SQP) based solver).")
3470 ;; Any version of the GPL.
3471 (license license:gpl2+)))
3473 (define-public r-hardyweinberg
3475 (name "r-hardyweinberg")
3480 (uri (cran-uri "HardyWeinberg" version))
3483 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3484 (properties `((upstream-name . "HardyWeinberg")))
3485 (build-system r-build-system)
3487 `(("r-mice" ,r-mice)
3489 ("r-rsolnp" ,r-rsolnp)))
3490 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3491 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3493 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3494 diallelic genetic marker data. All classical tests (chi-square, exact,
3495 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3496 included in the package, as well as functions for power computation and for
3497 the simulation of marker data under equilibrium and disequilibrium. Routines
3498 for dealing with markers on the X-chromosome are included. Functions for
3499 testing equilibrium in the presence of missing data by using multiple
3500 imputation are also provided. Implements several graphics for exploring the
3501 equilibrium status of a large set of diallelic markers: ternary plots with
3502 acceptance regions, log-ratio plots and Q-Q plots.")
3503 (license license:gpl2+)))
3512 (uri (cran-uri "sm" version))
3515 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3516 (build-system r-build-system)
3517 (native-inputs `(("gfortran" ,gfortran)))
3518 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3519 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3521 "This is software accompanying the book 'Applied Smoothing Techniques for
3522 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3523 University Press. It provides smoothing methods for nonparametric regression
3524 and density estimation")
3525 (license license:gpl2+)))
3527 (define-public r-venndiagram
3529 (name "r-venndiagram")
3533 (uri (cran-uri "VennDiagram" version))
3536 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3537 (properties `((upstream-name . "VennDiagram")))
3538 (build-system r-build-system)
3540 `(("r-futile-logger" ,r-futile-logger)))
3541 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3542 (synopsis "Generate High-Resolution Venn and Euler Plots")
3544 "This package provides a set of functions to generate high-resolution
3545 Venn and Euler plots. It includes handling for several special cases,
3546 including two-case scaling, and extensive customization of plot shape and
3548 (license license:gpl2+)))
3550 (define-public r-vioplot
3557 (uri (cran-uri "vioplot" version))
3560 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3561 (build-system r-build-system)
3565 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3566 (synopsis "Violin plot")
3568 "This package provides a violin plot, which is a combination of a box
3569 plot and a kernel density plot.")
3570 (license license:bsd-3)))
3572 (define-public r-rsofia
3578 ;; This package has been removed from CRAN, so we can
3579 ;; only fetch it from the archives.
3580 (uri (string-append "https://cran.r-project.org/src/"
3581 "contrib/Archive/RSofia/RSofia_"
3585 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3586 (properties `((upstream-name . "RSofia")))
3587 (build-system r-build-system)
3589 `(("r-rcpp" ,r-rcpp)))
3590 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3591 (synopsis "Port of sofia-ml to R")
3592 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3593 suite of fast incremental algorithms for machine learning that can be used for
3594 training models for classification or ranking.")
3595 (license license:asl2.0)))
3597 (define-public r-xts
3604 (uri (cran-uri "xts" version))
3607 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3608 (build-system r-build-system)
3609 (propagated-inputs `(("r-zoo" ,r-zoo)))
3610 (home-page "https://github.com/joshuaulrich/xts")
3611 (synopsis "Extensible time series")
3613 "This package provides for uniform handling of R's different time-based
3614 data classes by extending @code{zoo}, maximizing native format information
3615 preservation and allowing for user-level customization and extension, while
3616 simplifying cross-class interoperability.")
3617 (license license:gpl2+)))
3619 (define-public r-performanceanalytics
3621 (name "r-performanceanalytics")
3626 (uri (cran-uri "PerformanceAnalytics" version))
3629 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3631 `((upstream-name . "PerformanceAnalytics")))
3632 (build-system r-build-system)
3634 `(("r-quadprog" ,r-quadprog)
3637 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3638 (synopsis "Econometric tools for performance and risk analysis")
3639 (description "This is a collection of econometric functions for
3640 performance and risk analysis. This package aims to aid practitioners and
3641 researchers in utilizing the latest research in analysis of non-normal return
3642 streams. In general, it is most tested on return (rather than price) data on
3643 a regular scale, but most functions will work with irregular return data as
3644 well, and increasing numbers of functions will work with P&L or price data
3646 ;; Either version may be picked.
3647 (license (list license:gpl2 license:gpl3))))
3649 (define-public r-laeken
3656 (uri (cran-uri "laeken" version))
3659 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3660 (build-system r-build-system)
3662 `(("r-boot" ,r-boot)
3663 ("r-mass" ,r-mass)))
3664 (home-page "https://cran.r-project.org/web/packages/laeken/")
3665 (synopsis "Estimation of indicators on social exclusion and poverty")
3666 (description "This package provides tools for the estimation of indicators
3667 on social exclusion and poverty, as well as an implementation of Pareto tail
3668 modeling for empirical income distributions.")
3669 (license license:gpl2+)))
3671 (define-public r-vcd
3678 (uri (cran-uri "vcd" version))
3681 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3682 (build-system r-build-system)
3684 `(("r-colorspace" ,r-colorspace)
3685 ("r-lmtest" ,r-lmtest)
3686 ("r-mass" ,r-mass)))
3687 (home-page "https://cran.r-project.org/web/packages/vcd/")
3688 (synopsis "Visualizing categorical data")
3689 (description "This package provides visualization techniques, data sets,
3690 summary and inference procedures aimed particularly at categorical data.
3691 Special emphasis is given to highly extensible grid graphics. The package was
3692 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3693 Friendly and is now the main support package for a new book, \"Discrete Data
3694 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3695 (license license:gpl2)))
3697 (define-public r-ica
3704 (uri (cran-uri "ica" version))
3707 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3708 (build-system r-build-system)
3709 (home-page "https://cran.r-project.org/web/packages/ica/")
3710 (synopsis "Independent component analysis")
3711 (description "This package provides tools for @dfn{Independent Component
3712 Analysis} (ICA) using various algorithms: FastICA,
3713 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3714 of Eigenmatrices} (JADE).")
3715 (license license:gpl2+)))
3717 (define-public r-dtw
3724 (uri (cran-uri "dtw" version))
3727 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3728 (build-system r-build-system)
3729 (propagated-inputs `(("r-proxy" ,r-proxy)))
3730 (home-page "http://dtw.r-forge.r-project.org/")
3731 (synopsis "Dynamic Time Warping Algorithms")
3732 (description "This package provides a comprehensive implementation of
3733 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3734 optimal (least cumulative distance) alignment between points of two time
3735 series. Common DTW variants covered include local (slope) and global (window)
3736 constraints, subsequence matches, arbitrary distance definitions,
3737 normalizations, minimum variance matching, and so on.")
3738 (license license:gpl2+)))
3740 (define-public r-sdmtools
3743 (version "1.1-221.2")
3747 (uri (cran-uri "SDMTools" version))
3750 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3751 (properties `((upstream-name . "SDMTools")))
3752 (build-system r-build-system)
3753 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3754 (home-page "https://www.rforge.net/SDMTools/")
3755 (synopsis "Species distribution modelling tools")
3756 (description "This package provides a set of tools for post processing
3757 the outcomes of species distribution modeling exercises. It includes novel
3758 methods for comparing models and tracking changes in distributions through
3759 time. It further includes methods for visualizing outcomes, selecting
3760 thresholds, calculating measures of accuracy and landscape fragmentation
3762 (license license:gpl3+)))
3764 (define-public r-scatterplot3d
3766 (name "r-scatterplot3d")
3771 (uri (cran-uri "scatterplot3d" version))
3774 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3775 (build-system r-build-system)
3776 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3777 (synopsis "3D scatter plot")
3778 (description "This package provides an implementation of scatter plots for
3779 plotting. a three dimensional point cloud.")
3780 (license license:gpl2)))
3782 (define-public r-ggridges
3789 (uri (cran-uri "ggridges" version))
3792 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
3793 (build-system r-build-system)
3795 `(("r-ggplot2" ,r-ggplot2)
3797 ("r-scales" ,r-scales)
3798 ("r-withr" ,r-withr)))
3799 (home-page "https://github.com/clauswilke/ggridges")
3800 (synopsis "Ridgeline plots in ggplot2")
3802 "Ridgeline plots provide a convenient way of visualizing changes in
3803 distributions over time or space. This package enables the creation of such
3804 plots in @code{ggplot2}.")
3805 (license license:gpl2)))
3807 (define-public r-ggjoy
3814 (uri (cran-uri "ggjoy" version))
3817 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3818 (build-system r-build-system)
3820 `(("r-ggplot2" ,r-ggplot2)
3821 ("r-ggridges" ,r-ggridges)))
3822 (home-page "https://github.com/clauswilke/ggjoy")
3823 (synopsis "Joyplots in ggplot2")
3824 (description "Joyplots provide a convenient way of visualizing changes in
3825 distributions over time or space. This package enables the creation of such
3826 plots in @code{ggplot2}.")
3827 (license license:gpl2)))
3829 (define-public r-cli
3836 (uri (cran-uri "cli" version))
3839 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
3840 (build-system r-build-system)
3842 `(("r-assertthat" ,r-assertthat)
3843 ("r-crayon" ,r-crayon)
3844 ("r-fansi" ,r-fansi)
3845 ("r-glue" ,r-glue)))
3846 (home-page "https://github.com/r-lib/cli#readme")
3847 (synopsis "Helpers for developing command line interfaces")
3848 (description "This package provides a suite of tools designed to build
3849 attractive command line interfaces (CLIs). It includes tools for drawing
3850 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3851 (license license:expat)))
3853 (define-public r-argparser
3855 (name "r-argparser")
3860 (uri (cran-uri "argparser" version))
3863 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3864 (build-system r-build-system)
3865 (home-page "https://bitbucket.org/djhshih/argparser")
3866 (synopsis "Command-line argument parser")
3868 "This package provides a cross-platform command-line argument parser
3869 written purely in R with no external dependencies. It is useful with the
3870 Rscript front-end and facilitates turning an R script into an executable
3872 (license license:gpl3+)))
3874 (define-public r-debugme
3881 (uri (cran-uri "debugme" version))
3884 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3885 (build-system r-build-system)
3886 (propagated-inputs `(("r-crayon" ,r-crayon)))
3887 (home-page "https://github.com/r-lib/debugme#readme")
3888 (synopsis "Debug R packages")
3890 "This package allows the user to specify debug messages as special string
3891 constants, and control debugging of packages via environment variables.")
3892 (license license:expat)))
3894 (define-public r-processx
3901 (uri (cran-uri "processx" version))
3904 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
3905 (build-system r-build-system)
3909 (home-page "https://github.com/r-lib/processx3")
3910 (synopsis "Execute and control system processes")
3912 "This package provides portable tools to run system processes in the
3913 background. It can check if a background process is running; wait on a
3914 background process to finish; get the exit status of finished processes; kill
3915 background processes and their children; restart processes. It can read the
3916 standard output and error of the processes, using non-blocking connections.
3917 @code{processx} can poll a process for standard output or error, with a
3918 timeout. It can also poll several processes at once.")
3919 (license license:expat)))
3921 (define-public r-tsp
3928 (uri (cran-uri "TSP" version))
3931 "183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
3932 (properties `((upstream-name . "TSP")))
3933 (build-system r-build-system)
3934 (propagated-inputs `(("r-foreach" ,r-foreach)))
3935 (home-page "https://cran.r-project.org/web/packages/TSP/")
3936 (synopsis "Traveling salesperson problem (TSP)")
3937 (description "This package provides basic infrastructure and some
3938 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3939 traveling salesman problem).")
3940 (license license:gpl3)))
3942 (define-public r-qap
3949 (uri (cran-uri "qap" version))
3952 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3953 (build-system r-build-system)
3954 (native-inputs `(("gfortran" ,gfortran)))
3955 (home-page "https://cran.r-project.org/web/packages/qap/")
3956 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3957 (description "This package implements heuristics for the @dfn{quadratic
3958 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3960 (license license:gpl3)))
3962 (define-public r-gclus
3969 (uri (cran-uri "gclus" version))
3972 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3973 (build-system r-build-system)
3974 (propagated-inputs `(("r-cluster" ,r-cluster)))
3975 (home-page "https://cran.r-project.org/web/packages/gclus/")
3976 (synopsis "Clustering graphics")
3977 (description "This package orders panels in scatterplot matrices and
3978 parallel coordinate displays by some merit index. It contains various indices
3979 of merit, ordering functions, and enhanced versions of @code{pairs} and
3980 @code{parcoord} which color panels according to their merit level.")
3981 (license license:gpl2+)))
3983 (define-public r-webshot
3990 (uri (cran-uri "webshot" version))
3993 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3994 (build-system r-build-system)
3996 `(("r-callr" ,r-callr)
3997 ("r-jsonlite" ,r-jsonlite)
3998 ("r-magrittr" ,r-magrittr)))
3999 (home-page "https://github.com/wch/webshot/")
4000 (synopsis "Take screenshots of web pages")
4002 "Webshot makes it easy to take screenshots of web pages from within R.
4003 It can also run Shiny applications locally and take screenshots of the
4004 application; and it can render and screenshot static as well as interactive R
4005 Markdown documents.")
4006 (license license:gpl2)))
4008 (define-public r-seriation
4010 (name "r-seriation")
4015 (uri (cran-uri "seriation" version))
4018 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4019 (build-system r-build-system)
4021 `(("r-cluster" ,r-cluster)
4022 ("r-colorspace" ,r-colorspace)
4023 ("r-dendextend" ,r-dendextend)
4024 ("r-gclus" ,r-gclus)
4025 ("r-gplots" ,r-gplots)
4028 ("r-registry" ,r-registry)
4030 (native-inputs `(("gfortran" ,gfortran)))
4031 (home-page "https://s2.smu.edu/IDA/seriation/")
4032 (synopsis "Infrastructure for ordering objects using seriation")
4034 "This package provides infrastructure for seriation with an
4035 implementation of several seriation/sequencing techniques to reorder matrices,
4036 dissimilarity matrices, and dendrograms. It also provides (optimally)
4037 reordered heatmaps, color images and clustering visualizations like
4038 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4040 (license license:gpl3)))
4042 (define-public r-xfun
4049 (uri (cran-uri "xfun" version))
4051 (base32 "03iyqgx9mmdbd3qih70qzijjqcdg7k7ps5r1y6q8praanx9qvnm3"))))
4052 (build-system r-build-system)
4053 ;; knitr itself depends on xfun
4056 `(("r-knitr" ,r-knitr)))
4057 (home-page "https://github.com/yihui/xfun")
4058 (synopsis "Miscellaneous functions")
4060 "This package provides miscellaneous functions commonly used in other
4061 packages maintained by Yihui Xie.")
4062 (license license:expat)))
4064 (define-public r-utf8
4071 (uri (cran-uri "utf8" version))
4074 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4075 (build-system r-build-system)
4076 (home-page "https://github.com/patperry/r-utf8")
4077 (synopsis "Unicode text processing")
4079 "This package provides tools to process and print UTF-8 encoded
4080 international text (Unicode). Input, validate, normalize, encode, format, and
4082 (license license:asl2.0)))
4084 (define-public r-zeallot
4091 (uri (cran-uri "zeallot" version))
4094 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4095 (build-system r-build-system)
4096 (home-page "https://github.com/nteetor/zeallot")
4097 (synopsis "Multiple, unpacking, and destructuring assignment")
4099 "This package provides a @code{%<-%} operator to perform multiple,
4100 unpacking, and destructuring assignment in R. The operator unpacks the
4101 right-hand side of an assignment into multiple values and assigns these values
4102 to variables on the left-hand side of the assignment.")
4103 (license license:expat)))
4105 (define-public r-vctrs
4112 (uri (cran-uri "vctrs" version))
4115 "15sgzs6afvmhssk6jcg41rn3bvmzmbm4sgca6f6x8lfrsazvdj6w"))))
4116 (build-system r-build-system)
4118 `(("r-digest" ,r-digest)
4119 ("r-ellipsis" ,r-ellipsis)
4121 ("r-rlang" ,r-rlang)))
4123 `(("r-knitr" ,r-knitr)))
4124 (home-page "https://github.com/r-lib/vctrs")
4125 (synopsis "Vector helpers")
4127 "There are three main goals to the @code{vctrs} package:
4130 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4131 @code{length()} and @code{class()}. These definitions are paired with a
4132 framework for type-coercion and size-recycling.
4133 @item To define type- and size-stability as desirable function properties, use
4134 them to analyse existing base function, and to propose better alternatives.
4135 This work has been particularly motivated by thinking about the ideal
4136 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4137 @item To provide a new @code{vctr} base class that makes it easy to create new
4138 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4139 a few new @code{vctrs} generics, making implementation considerably simpler
4142 (license license:gpl3)))
4144 (define-public r-pillar
4151 (uri (cran-uri "pillar" version))
4154 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4155 (build-system r-build-system)
4158 ("r-crayon" ,r-crayon)
4159 ("r-fansi" ,r-fansi)
4160 ("r-rlang" ,r-rlang)
4162 ("r-vctrs" ,r-vctrs)))
4163 (home-page "https://github.com/r-lib/pillar")
4164 (synopsis "Coloured formatting for columns")
4166 "This package provides a @code{pillar} generic designed for formatting
4167 columns of data using the full range of colours provided by modern
4169 (license license:gpl3)))
4171 (define-public r-uuid
4178 (uri (cran-uri "uuid" version))
4181 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4182 (build-system r-build-system)
4183 (home-page "https://www.rforge.net/uuid")
4184 (synopsis "Tools for generating and handling of UUIDs")
4186 "This package provides tools for generating and handling of
4187 @dfn{Universally Unique Identifiers} (UUIDs).")
4188 (license license:expat)))
4190 (define-public r-tinytex
4197 (uri (cran-uri "tinytex" version))
4200 "088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9"))))
4201 (build-system r-build-system)
4203 `(("r-xfun" ,r-xfun)))
4204 (home-page "https://github.com/yihui/tinytex")
4205 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4207 "This package provides helper functions to install and maintain the LaTeX
4208 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4209 easy-to-maintain version of TeX Live. This package also contains helper
4210 functions to compile LaTeX documents, and install missing LaTeX packages
4212 (license license:expat)))
4214 (define-public r-network
4221 (uri (cran-uri "network" version))
4224 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4225 (build-system r-build-system)
4227 `(("r-magrittr" ,r-magrittr)
4228 ("r-tibble" ,r-tibble)))
4229 (home-page "https://statnet.org/")
4230 (synopsis "Classes for relational data")
4232 "This package provides tools to create and modify network objects. The
4233 @code{network} class can represent a range of relational data types, and
4234 supports arbitrary vertex/edge/graph attributes.")
4235 (license license:gpl2+)))
4237 (define-public r-statnet-common
4239 (name "r-statnet-common")
4244 (uri (cran-uri "statnet.common" version))
4247 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4249 `((upstream-name . "statnet.common")))
4250 (build-system r-build-system)
4252 `(("r-coda" ,r-coda)))
4253 (home-page "https://statnet.org")
4254 (synopsis "R scripts and utilities used by the Statnet software")
4255 (description "This package provides non-statistical utilities used by the
4256 software developed by the Statnet Project.")
4257 (license license:gpl3)))
4259 (define-public r-statcheck
4261 (name "r-statcheck")
4266 (uri (cran-uri "statcheck" version))
4269 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4270 (build-system r-build-system)
4272 `(("r-ggplot2" ,r-ggplot2)
4274 ("r-rmarkdown" ,r-rmarkdown)))
4275 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4276 (synopsis "Extract statistics from articles and recompute p-values")
4277 (description "This package can automatically extract statistical
4278 null-hypothesis significant testing (NHST) results from articles and recompute
4279 the p-values based on the reported test statistic and degrees of freedom to
4280 detect possible inconsistencies.")
4281 (license license:gpl2)))
4283 (define-public r-sna
4290 (uri (cran-uri "sna" version))
4293 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4294 (build-system r-build-system)
4296 `(("r-network" ,r-network)
4297 ("r-statnet-common" ,r-statnet-common)))
4298 (home-page "https://statnet.org")
4299 (synopsis "Tools for social network analysis")
4301 "This package provides a range of tools for social network analysis,
4302 including node and graph-level indices, structural distance and covariance
4303 methods, structural equivalence detection, network regression, random graph
4304 generation, and 2D/3D network visualization.")
4305 (license license:gpl2+)))
4307 (define-public r-tfisher
4314 (uri (cran-uri "TFisher" version))
4317 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4318 (properties `((upstream-name . "TFisher")))
4319 (build-system r-build-system)
4321 `(("r-matrix" ,r-matrix)
4322 ("r-mvtnorm" ,r-mvtnorm)
4324 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4325 (synopsis "Optimal thresholding Fisher's p-value combination method")
4327 "This package provides the @dfn{cumulative distribution function} (CDF),
4328 quantile, and statistical power calculator for a collection of thresholding
4329 Fisher's p-value combination methods, including Fisher's p-value combination
4330 method, truncated product method and, in particular, soft-thresholding
4331 Fisher's p-value combination method which is proven to be optimal in some
4332 context of signal detection. The p-value calculator for the omnibus version
4333 of these tests are also included.")
4334 (license license:gpl2)))
4336 (define-public r-ttr
4343 (uri (cran-uri "TTR" version))
4346 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4347 (properties `((upstream-name . "TTR")))
4348 (build-system r-build-system)
4350 `(("r-curl" ,r-curl)
4353 (home-page "https://github.com/joshuaulrich/TTR")
4354 (synopsis "Technical trading rules")
4356 "This package provides functions and data to construct technical trading
4358 (license license:gpl2)))
4360 (define-public r-leaps
4367 (uri (cran-uri "leaps" version))
4370 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4371 (build-system r-build-system)
4372 (native-inputs `(("gfortran" ,gfortran)))
4373 (home-page "https://cran.r-project.org/web/packages/leaps/")
4374 (synopsis "Regression subset selection")
4376 "This package provides tools for regression subset selection, including
4377 exhaustive search.")
4378 (license license:gpl2+)))
4380 (define-public r-splus2r
4387 (uri (cran-uri "splus2R" version))
4390 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4391 (properties `((upstream-name . "splus2R")))
4392 (build-system r-build-system)
4393 (native-inputs `(("gfortran" ,gfortran)))
4394 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4395 (synopsis "Supplemental S-PLUS functionality in R")
4397 "Currently there are many functions in S-PLUS that are missing in R. To
4398 facilitate the conversion of S-PLUS packages to R packages, this package
4399 provides some missing S-PLUS functionality in R.")
4400 (license license:gpl2)))
4402 (define-public r-ifultools
4404 (name "r-ifultools")
4409 (uri (cran-uri "ifultools" version))
4412 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4413 (build-system r-build-system)
4415 `(("r-mass" ,r-mass)
4416 ("r-splus2r" ,r-splus2r)))
4417 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4418 (synopsis "Insightful research tools")
4419 (description "This package provides C code used by the wmtsa, fractal, and
4421 (license license:gpl2)))
4423 (define-public r-sapa
4430 (uri (cran-uri "sapa" version))
4433 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4434 (build-system r-build-system)
4436 `(("r-ifultools" ,r-ifultools)
4437 ("r-splus2r" ,r-splus2r)))
4438 (home-page "https://cran.r-project.org/web/packages/sapa/")
4439 (synopsis "Spectral analysis for physical applications")
4440 (description "This package provides software for the book Spectral
4441 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4442 Cambridge University Press, 1993.")
4443 (license license:gpl2)))
4445 (define-public r-aggregation
4447 (name "r-aggregation")
4452 (uri (cran-uri "aggregation" version))
4455 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4456 (build-system r-build-system)
4457 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4458 (synopsis "Methods for p-value aggregation")
4460 "This package contains functionality for performing the following methods
4461 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4462 Fisher's method), and Sidak correction.")
4463 (license license:gpl3)))
4465 (define-public r-quantmod
4472 (uri (cran-uri "quantmod" version))
4475 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4476 (build-system r-build-system)
4478 `(("r-curl" ,r-curl)
4482 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4483 (synopsis "Quantitative financial modelling framework")
4484 (description "This package provides a quantitative financial modelling
4485 framework to allow users to specify, build, trade, and analyse quantitative
4486 financial trading strategies.")
4487 (license license:gpl3)))
4489 (define-public r-tseries
4496 (uri (cran-uri "tseries" version))
4499 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4500 (build-system r-build-system)
4502 `(("r-quadprog" ,r-quadprog)
4503 ("r-quantmod" ,r-quantmod)
4506 `(("gfortran" ,gfortran)))
4507 (home-page "https://cran.r-project.org/web/packages/tseries/")
4508 (synopsis "Time series analysis and computational finance")
4510 "This package provides functions relating to time series analysis and
4511 computational finance.")
4512 (license license:gpl2)))
4514 (define-public r-wmtsa
4521 (uri (cran-uri "wmtsa" version))
4524 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4525 (build-system r-build-system)
4527 `(("r-ifultools" ,r-ifultools)
4529 ("r-splus2r" ,r-splus2r)))
4530 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4531 (synopsis "Wavelet methods for time series analysis")
4533 "This package provides software to accompany the book \"Wavelet Methods
4534 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4535 University Press, 2000.")
4536 (license license:gpl2)))
4538 (define-public r-tsa
4545 (uri (cran-uri "TSA" version))
4548 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4549 (properties `((upstream-name . "TSA")))
4550 (build-system r-build-system)
4552 `(("r-leaps" ,r-leaps)
4553 ("r-locfit" ,r-locfit)
4554 ("r-mgcv" ,r-mgcv)))
4555 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4556 (synopsis "Time series analysis")
4558 "This package contains R functions and datasets detailed in the book
4559 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4560 Cryer and Kung-Sik Chan.")
4561 (license license:gpl2+)))
4563 (define-public r-extradistr
4565 (name "r-extradistr")
4570 (uri (cran-uri "extraDistr" version))
4573 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4574 (properties `((upstream-name . "extraDistr")))
4575 (build-system r-build-system)
4577 `(("r-rcpp" ,r-rcpp)))
4578 (home-page "https://github.com/twolodzko/extraDistr")
4579 (synopsis "Additional univariate and multivariate distributions")
4581 "This package implements density, distribution functions, quantile
4582 functions and random generation functions for a large number of univariate and
4583 multivariate distributions.")
4584 (license license:gpl2)))
4586 (define-public r-fractal
4593 (uri (cran-uri "fractal" version))
4596 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4597 (build-system r-build-system)
4599 `(("r-ifultools" ,r-ifultools)
4602 ("r-scatterplot3d" ,r-scatterplot3d)
4603 ("r-splus2r" ,r-splus2r)
4604 ("r-wmtsa" ,r-wmtsa)))
4605 (home-page "https://cran.r-project.org/web/packages/fractal/")
4606 (synopsis "Fractal time series modeling and analysis")
4608 "This package provides tools for stochastic fractal and deterministic
4609 chaotic time series analysis.")
4610 (license license:gpl2)))
4612 (define-public r-urca
4619 (uri (cran-uri "urca" version))
4622 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4623 (build-system r-build-system)
4624 (propagated-inputs `(("r-nlme" ,r-nlme)))
4625 (native-inputs `(("gfortran" ,gfortran)))
4626 (home-page "https://cran.r-project.org/web/packages/urca/")
4627 (synopsis "Unit root and cointegration tests for time series data")
4629 "This package provides unit root and cointegration tests encountered in
4630 applied econometric analysis.")
4631 (license license:gpl2+)))
4633 (define-public r-cubature
4640 (uri (cran-uri "cubature" version))
4643 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4644 (build-system r-build-system)
4646 `(("r-rcpp" ,r-rcpp)))
4647 (home-page "https://github.com/bnaras/cubature")
4648 (synopsis "Adaptive multivariate integration over hypercubes")
4650 "This package is an R wrapper around the cubature C library for adaptive
4651 multivariate integration over hypercubes. This version provides both
4652 @code{hcubature} and @code{pcubature} routines in addition to a vector
4654 ;; The included cubature C library is released under GPLv2+, but the
4655 ;; wrapper declares the license to be GPLv3+.
4656 (license (list license:gpl2+ license:gpl3+))))
4658 (define-public r-trend
4665 (uri (cran-uri "trend" version))
4668 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4669 (build-system r-build-system)
4671 `(("r-extradistr" ,r-extradistr)))
4673 `(("gfortran" ,gfortran)))
4674 (home-page "https://cran.r-project.org/web/packages/trend/")
4675 (synopsis "Non-parametric trend tests and change-point detection")
4677 "The analysis of environmental data often requires the detection of
4678 trends and change-points. This package includes tests for trend
4679 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4680 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4681 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4682 correlation trend test), change-point detection (Lanzante's test procedures,
4683 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4684 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4685 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4686 sample Robust Rank-Order Distributional Test.")
4687 (license license:gpl3)))
4689 (define-public r-expm
4696 (uri (cran-uri "expm" version))
4699 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4700 (build-system r-build-system)
4701 (propagated-inputs `(("r-matrix" ,r-matrix)))
4702 (native-inputs `(("gfortran" ,gfortran)))
4703 (home-page "https://r-forge.r-project.org/projects/expm/")
4704 (synopsis "Tools for matrix exponentials and related quantities")
4706 "This package provides tools for the computation of the matrix
4707 exponential, logarithm, square root, and related quantities.")
4708 (license license:gpl2+)))
4710 (define-public r-complexplus
4712 (name "r-complexplus")
4717 (uri (cran-uri "complexplus" version))
4720 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4721 (build-system r-build-system)
4723 `(("r-expm" ,r-expm)
4724 ("r-matrix" ,r-matrix)))
4725 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4726 (synopsis "Functions of complex or real variables")
4728 "This package extends several functions to the complex domain, including
4729 the matrix exponential and logarithm, and the determinant.")
4730 (license license:gpl2)))
4732 (define-public r-phontools
4734 (name "r-phontools")
4739 (uri (cran-uri "phonTools" version))
4742 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4743 (properties `((upstream-name . "phonTools")))
4744 (build-system r-build-system)
4745 (home-page "http://www.santiagobarreda.com/rscripts.html")
4746 (synopsis "Tools for phonetic and acoustic analyses")
4748 "This package contains tools for the organization, display, and analysis
4749 of the sorts of data frequently encountered in phonetics research and
4750 experimentation, including the easy creation of IPA vowel plots, and the
4751 creation and manipulation of WAVE audio files.")
4752 (license license:bsd-2)))
4761 (uri (cran-uri "np" version))
4764 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
4765 (build-system r-build-system)
4767 `(("r-boot" ,r-boot)
4768 ("r-cubature" ,r-cubature)
4769 ("r-quadprog" ,r-quadprog)
4770 ("r-quantreg" ,r-quantreg)))
4771 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4772 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4773 (description "This package provides non-parametric (and semi-parametric)
4774 kernel methods that seamlessly handle a mix of continuous, unordered, and
4775 ordered factor data types.")
4776 ;; Any version of the GPL.
4777 (license license:gpl3+)))
4779 (define-public r-powerplus
4781 (name "r-powerplus")
4786 (uri (cran-uri "powerplus" version))
4789 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4790 (build-system r-build-system)
4792 `(("r-complexplus" ,r-complexplus)
4795 ("r-matrix" ,r-matrix)
4796 ("r-phontools" ,r-phontools)))
4797 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4798 (synopsis "Exponentiation operations")
4800 "This package provides tools for the computation of matrix and scalar
4802 (license license:gpl2)))
4804 (define-public r-egg
4811 (uri (cran-uri "egg" version))
4814 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4815 (properties `((upstream-name . "egg")))
4816 (build-system r-build-system)
4818 `(("r-ggplot2" ,r-ggplot2)
4819 ("r-gridextra" ,r-gridextra)
4820 ("r-gtable" ,r-gtable)))
4821 (home-page "https://cran.r-project.org/web/packages/egg")
4822 (synopsis "Extensions for ggplot2")
4824 "This package provides miscellaneous functions to help customize ggplot2
4825 objects. High-level functions are provided to post-process ggplot2 layouts
4826 and allow alignment between plot panels, as well as setting panel sizes to
4827 fixed values. Other functions include a custom @code{geom}, and helper
4828 functions to enforce symmetric scales or add tags to facetted plots.")
4829 (license license:gpl3)))
4831 (define-public r-heatmaply
4833 (name "r-heatmaply")
4838 (uri (cran-uri "heatmaply" version))
4841 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
4842 (build-system r-build-system)
4844 `(("r-assertthat" ,r-assertthat)
4845 ("r-colorspace" ,r-colorspace)
4846 ("r-dendextend" ,r-dendextend)
4848 ("r-ggplot2" ,r-ggplot2)
4849 ("r-htmlwidgets" ,r-htmlwidgets)
4850 ("r-magrittr" ,r-magrittr)
4851 ("r-plotly" ,r-plotly)
4852 ("r-rcolorbrewer" ,r-rcolorbrewer)
4853 ("r-reshape2" ,r-reshape2)
4854 ("r-scales" ,r-scales)
4855 ("r-seriation" ,r-seriation)
4856 ("r-viridis" ,r-viridis)
4857 ("r-webshot" ,r-webshot)))
4859 `(("r-knitr" ,r-knitr)))
4860 (home-page "https://cran.r-project.org/package=heatmaply")
4861 (synopsis "Interactive cluster heat maps using plotly")
4863 "This package enables you to create interactive cluster heatmaps that can
4864 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4865 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4866 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4867 a popular graphical method for visualizing high-dimensional data, in which a
4868 table of numbers is encoded as a grid of colored cells. The rows and columns
4869 of the matrix are ordered to highlight patterns and are often accompanied by
4871 ;; Either version of the license.
4872 (license (list license:gpl2 license:gpl3))))
4881 (uri (cran-uri "h5" version))
4884 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4885 (build-system r-build-system)
4890 `(("which" ,which)))
4892 `(("r-rcpp" ,r-rcpp)))
4893 (home-page "https://github.com/mannau/h5")
4894 (synopsis "Interface to the HDF5 Library")
4896 "This package provides an S4 interface to the HDF5 library supporting
4897 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4898 binary files in a language independent format. The HDF5 format can therefore
4899 be used as an alternative to R's save/load mechanism. Since h5 is able to
4900 access only subsets of stored data it can also handle data sets which do not
4902 (license license:bsd-2)))
4904 (define-public r-cgdsr
4911 (uri (cran-uri "cgdsr" version))
4914 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4915 (build-system r-build-system)
4917 `(("r-httr" ,r-httr)
4918 ("r-r-methodss3" ,r-r-methodss3)
4919 ("r-r-oo" ,r-r-oo)))
4920 (home-page "https://github.com/cBioPortal/cgdsr")
4921 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4923 "This package provides a basic set of R functions for querying the Cancer
4924 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4925 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4926 (license license:lgpl3)))
4928 (define-public r-import
4935 (uri (cran-uri "import" version))
4938 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4939 (build-system r-build-system)
4940 (home-page "https://github.com/smbache/import")
4941 (synopsis "Import mechanism for R")
4943 "This is an alternative mechanism for importing objects from packages.
4944 The syntax allows for importing multiple objects from a package with a single
4945 command in an expressive way. The import package bridges some of the gap
4946 between using @code{library} (or @code{require}) and direct (single-object)
4947 imports. Furthermore the imported objects are not placed in the current
4948 environment. It is also possible to import objects from stand-alone @code{.R}
4950 (license license:expat)))
4952 (define-public r-shinyace
4959 (uri (cran-uri "shinyAce" version))
4962 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4963 (properties `((upstream-name . "shinyAce")))
4964 (build-system r-build-system)
4966 `(("r-shiny" ,r-shiny)
4967 ("r-jsonlite" ,r-jsonlite)))
4968 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
4969 (synopsis "Ace editor bindings for Shiny")
4971 "This package provides Ace editor bindings to enable a rich text editing
4972 environment within Shiny.")
4973 (license license:expat)))
4975 (define-public r-randomizr
4977 (name "r-randomizr")
4982 (uri (cran-uri "randomizr" version))
4985 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
4986 (properties `((upstream-name . "randomizr")))
4987 (build-system r-build-system)
4989 `(("r-knitr" ,r-knitr)))
4990 (home-page "https://declaredesign.org/r/randomizr/")
4991 (synopsis "Tools for common forms of random assignment and sampling")
4993 "This package provides tools for generating random assignments for common
4994 experimental designs and random samples for common sampling designs.")
4995 (license license:expat)))
4997 (define-public r-base64url
4999 (name "r-base64url")
5004 (uri (cran-uri "base64url" version))
5007 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5008 (build-system r-build-system)
5010 `(("r-backports" ,r-backports)))
5011 (home-page "https://github.com/mllg/base64url")
5012 (synopsis "Fast and URL-safe base64 encoder and decoder")
5014 "This package provides a URL-safe base64 encoder and decoder. In
5015 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5016 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5017 encoder does not fill the string with trailing @code{=}. The resulting
5018 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5019 and thus are safe to use in URLs or for file names. The package also comes
5020 with a simple base32 encoder/decoder suited for case insensitive file
5022 (license license:gpl3)))
5024 (define-public r-radiant-data
5026 (name "r-radiant-data")
5031 (uri (cran-uri "radiant.data" version))
5034 "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs"))
5035 (modules '((guix build utils)))
5038 ;; Delete files that are under CC-NC-SA.
5039 (delete-file-recursively "inst/app/tools/help")
5041 (properties `((upstream-name . "radiant.data")))
5042 (build-system r-build-system)
5044 `(("r-base64enc" ,r-base64enc)
5045 ("r-broom" ,r-broom)
5048 ("r-dplyr" ,r-dplyr)
5051 ("r-ggplot2" ,r-ggplot2)
5052 ("r-import" ,r-import)
5053 ("r-jsonlite" ,r-jsonlite)
5054 ("r-knitr" ,r-knitr)
5055 ("r-lubridate" ,r-lubridate)
5056 ("r-magrittr" ,r-magrittr)
5057 ("r-markdown" ,r-markdown)
5059 ("r-patchwork" ,r-patchwork)
5060 ("r-plotly" ,r-plotly)
5061 ("r-psych" ,r-psych)
5062 ("r-randomizr" ,r-randomizr)
5063 ("r-readr" ,r-readr)
5064 ("r-readxl" ,r-readxl)
5065 ("r-rlang" ,r-rlang)
5066 ("r-rmarkdown" ,r-rmarkdown)
5067 ("r-rstudioapi" ,r-rstudioapi)
5068 ("r-scales" ,r-scales)
5069 ("r-shiny" ,r-shiny)
5070 ("r-shinyfiles" ,r-shinyfiles)
5071 ("r-shinyace" ,r-shinyace)
5072 ("r-stringi" ,r-stringi)
5073 ("r-tibble" ,r-tibble)
5074 ("r-tidyr" ,r-tidyr)
5075 ("r-writexl" ,r-writexl)))
5076 (home-page "https://github.com/radiant-rstats/radiant.data")
5077 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5079 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5080 visualizing, summarizing, transforming, and combining data. It also contains
5081 functionality to generate reproducible reports of the analyses conducted in
5083 (license license:agpl3)))
5085 (define-public r-algdesign
5087 (name "r-algdesign")
5092 (uri (cran-uri "AlgDesign" version))
5094 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5095 (properties `((upstream-name . "AlgDesign")))
5096 (build-system r-build-system)
5097 (home-page "https://github.com/jvbraun/AlgDesign")
5098 (synopsis "Algorithmic experimental design")
5100 "This package provides tools to calculate exact and approximate theory
5101 experimental designs for D, A, and I criteria. Very large designs may be
5102 created. Experimental designs may be blocked or blocked designs created from
5103 a candidate list, using several criteria. The blocking can be done when whole
5104 and within plot factors interact.")
5105 (license license:gpl2+)))
5107 (define-public r-signal
5114 (uri (cran-uri "signal" version))
5117 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5118 (build-system r-build-system)
5119 (propagated-inputs `(("r-mass" ,r-mass)))
5120 (native-inputs `(("gfortran" ,gfortran)))
5121 (home-page "https://cran.r-project.org/web/packages/signal/")
5122 (synopsis "Signal processing")
5124 "This package provides a set of signal processing functions originally
5125 written for Matlab and GNU Octave. It includes filter generation utilities,
5126 filtering functions, resampling routines, and visualization of filter models.
5127 It also includes interpolation functions.")
5128 (license license:gpl2)))
5130 (define-public r-gsubfn
5137 (uri (cran-uri "gsubfn" version))
5140 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5141 (build-system r-build-system)
5142 (propagated-inputs `(("r-proto" ,r-proto)))
5143 (home-page "https://code.google.com/archive/p/gsubfn/")
5144 (synopsis "Utilities for strings and function arguments.")
5146 "This package provides @code{gsubfn} which is like @code{gsub} but can
5147 take a replacement function or certain other objects instead of the
5148 replacement string. Matches and back references are input to the replacement
5149 function and replaced by the function output. @code{gsubfn} can be used to
5150 split strings based on content rather than delimiters and for quasi-perl-style
5151 string interpolation. The package also has facilities for translating
5152 formulas to functions and allowing such formulas in function calls instead of
5154 (license license:gpl2+)))
5156 (define-public r-sqldf
5163 (uri (cran-uri "sqldf" version))
5166 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5167 (build-system r-build-system)
5169 `(("r-chron" ,r-chron)
5171 ("r-gsubfn" ,r-gsubfn)
5172 ("r-proto" ,r-proto)
5173 ("r-rsqlite" ,r-rsqlite)))
5174 (home-page "https://github.com/ggrothendieck/sqldf")
5175 (synopsis "Manipulate R data frames using SQL")
5177 "The @code{sqldf} function is typically passed a single argument which is
5178 an SQL select statement where the table names are ordinary R data frame names.
5179 @code{sqldf} transparently sets up a database, imports the data frames into
5180 that database, performs the SQL statement and returns the result using a
5181 heuristic to determine which class to assign to each column of the returned
5182 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5183 used to read filtered files into R even if the original files are larger than
5184 R itself can handle.")
5185 (license license:gpl2)))
5187 (define-public r-abind
5194 (uri (cran-uri "abind" version))
5197 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5198 (build-system r-build-system)
5199 (home-page "https://cran.r-project.org/web/packages/abind/")
5200 (synopsis "Combine multidimensional arrays")
5202 "This package provides tools to combine multidimensional arrays into a
5203 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5204 works with vectors, matrices, and higher-dimensional arrays. It also provides
5205 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5206 extracting and replacing data in arrays.")
5207 (license license:lgpl2.0+)))
5209 (define-public r-prroc
5216 (uri (cran-uri "PRROC" version))
5219 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5220 (properties `((upstream-name . "PRROC")))
5221 (build-system r-build-system)
5222 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5223 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5225 "This package computes the areas under the @dfn{precision-recall} (PR)
5226 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5227 contrast to other implementations, the interpolation between points of the PR
5228 curve is done by a non-linear piecewise function. In addition to the areas
5229 under the curves, the curves themselves can also be computed and plotted by a
5230 specific S3-method.")
5231 (license license:gpl3)))
5233 (define-public r-vim
5240 (uri (cran-uri "VIM" version))
5243 "0w22ir0gvym7gqd6nw2j7w5ivlb3az1dkfxv33imimkb7c83056a"))))
5244 (properties `((upstream-name . "VIM")))
5245 (build-system r-build-system)
5248 ("r-colorspace" ,r-colorspace)
5249 ("r-data-table" ,r-data-table)
5250 ("r-e1071" ,r-e1071)
5251 ("r-laeken" ,r-laeken)
5252 ("r-magrittr" ,r-magrittr)
5255 ("r-ranger" ,r-ranger)
5257 ("r-robustbase" ,r-robustbase)
5260 (home-page "https://github.com/alexkowa/VIM")
5261 (synopsis "Visualization and imputation of missing values")
5263 "This package provides tools for the visualization of missing and/or
5264 imputed values are introduced, which can be used for exploring the data and
5265 the structure of the missing and/or imputed values. Depending on this
5266 structure of the missing values, the corresponding methods may help to
5267 identify the mechanism generating the missing values and allows to explore the
5268 data including missing values. In addition, the quality of imputation can be
5269 visually explored using various univariate, bivariate, multiple and
5270 multivariate plot methods.")
5271 (license license:gpl2+)))
5273 (define-public r-fnn
5280 (uri (cran-uri "FNN" version))
5283 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5284 (properties `((upstream-name . "FNN")))
5285 (build-system r-build-system)
5286 (home-page "https://cran.r-project.org/web/packages/FNN")
5287 (synopsis "Fast nearest neighbor search algorithms and applications")
5289 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5290 search algorithms. Related applications including KNN classification,
5291 regression and information measures are implemented.")
5292 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5293 ;; later can be used.
5294 (license license:gpl2+)))
5296 (define-public r-smoother
5303 (uri (cran-uri "smoother" version))
5306 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5307 (build-system r-build-system)
5309 `(("r-ttr" ,r-ttr)))
5310 (home-page "https://cran.r-project.org/web/packages/smoother")
5311 (synopsis "Functions relating to the smoothing of numerical data")
5313 "This package provides a collection of methods for smoothing numerical
5314 data, commencing with a port of the Matlab gaussian window smoothing function.
5315 In addition, several functions typically used in smoothing of financial data
5317 (license license:gpl2)))
5319 (define-public r-riverplot
5321 (name "r-riverplot")
5326 (uri (cran-uri "riverplot" version))
5329 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5330 (build-system r-build-system)
5331 (home-page "https://logfc.wordpress.com")
5332 (synopsis "Sankey or ribbon plots")
5334 "Sankey plots are a type of diagram that is convenient to illustrate how
5335 flow of information, resources etc. separates and joins, much like observing
5336 how rivers split and merge. For example, they can be used to compare
5337 different clusterings. This package provides an implementation of Sankey
5339 (license license:gpl2+)))
5341 (define-public r-dyn
5348 (uri (cran-uri "dyn" version))
5351 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5352 (build-system r-build-system)
5354 `(("r-zoo" ,r-zoo)))
5355 (home-page "https://cran.r-project.org/web/packages/dyn")
5356 (synopsis "Time series regression")
5358 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5359 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5360 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5361 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5362 @code{randomForest::randomForest()} and other regression functions, allowing
5363 those functions to be used with time series including specifications that may
5364 contain lags, diffs and missing values.")
5366 (license license:gpl2+)))
5368 (define-public r-catdap
5375 (uri (cran-uri "catdap" version))
5378 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5379 (build-system r-build-system)
5381 `(("gfortran" ,gfortran)))
5382 (home-page "https://cran.r-project.org/web/packages/catdap/")
5383 (synopsis "Tools for categorical data analysis")
5385 "This package provides functions for analyzing multivariate data.
5386 Dependencies of the distribution of the specified variable (response
5387 variable) to other variables (explanatory variables) are derived and
5388 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5389 (license license:gpl2+)))
5391 (define-public r-arules
5398 (uri (cran-uri "arules" version))
5401 "0bcvfn8lvcv74vv9z3kgg7yq5hm7wjqhmzadi55cbm8zxd76g84v"))))
5402 (build-system r-build-system)
5404 `(("r-matrix" ,r-matrix)))
5405 (home-page "https://github.com/mhahsler/arules")
5406 (synopsis "Mining association rules and frequent itemsets")
5408 "This package provides an infrastructure for representing, manipulating
5409 and analyzing transaction data and patterns (frequent itemsets and association rules).
5410 It also provides C implementations of the association mining algorithms Apriori
5412 (license license:gpl3)))
5414 (define-public r-parsedate
5416 (name "r-parsedate")
5421 (uri (cran-uri "parsedate" version))
5424 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5425 (build-system r-build-system)
5427 `(("r-rematch2" ,r-rematch2)))
5428 (home-page "https://github.com/gaborcsardi/parsedate")
5430 "Recognize and parse dates in various formats")
5432 "This package provides three functions for dealing with dates:
5433 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5434 time formats, @code{parse_date} parses dates in unspecified formats,
5435 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5436 (license license:gpl2)))
5438 (define-public r-abc-data
5445 (uri (cran-uri "abc.data" version))
5448 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5449 (properties `((upstream-name . "abc.data")))
5450 (build-system r-build-system)
5451 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5452 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5454 "This package contains data which are used by functions of the abc
5455 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5456 algorithms for performing parameter estimation, model selection, and
5458 (license license:gpl3+)))
5460 (define-public r-abc
5467 (uri (cran-uri "abc" version))
5470 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5471 (build-system r-build-system)
5473 `(("r-abc-data" ,r-abc-data)
5474 ("r-locfit" ,r-locfit)
5477 ("r-quantreg" ,r-quantreg)))
5478 (home-page "https://cran.r-project.org/web/packages/abc/")
5479 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5481 "This package implements several @dfn{Approximate Bayesian
5482 Computation} (ABC) algorithms for performing parameter estimation, model
5483 selection, and goodness-of-fit. Cross-validation tools are also available for
5484 measuring the accuracy of ABC estimates, and to calculate the
5485 misclassification probabilities of different models.")
5486 (license license:gpl3+)))
5488 (define-public r-zip
5495 (uri (cran-uri "zip" version))
5498 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5499 (build-system r-build-system)
5500 (home-page "https://github.com/gaborcsardi/zip")
5501 (synopsis "Cross-platform Zip compression")
5503 "This package provides a cross-platform Zip compression library for R.
5504 It is a replacement for the @code{zip} function, that does not require any
5505 additional external tools on any platform.")
5506 (license license:cc0)))
5508 (define-public r-openxlsx
5515 (uri (cran-uri "openxlsx" version))
5518 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5519 (build-system r-build-system)
5521 `(("r-rcpp" ,r-rcpp)
5522 ("r-stringi" ,r-stringi)
5524 (home-page "https://github.com/awalker89/openxlsx")
5525 (synopsis "Read, write and edit XLSX files")
5527 "This package simplifies the creation of Excel @code{.xlsx} files by
5528 providing a high level interface to writing, styling and editing worksheets.
5529 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5530 and @code{XLConnect} packages with the added benefit of removing the
5531 dependency on Java.")
5532 (license license:gpl3)))
5534 (define-public r-rio
5541 (uri (cran-uri "rio" version))
5544 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5545 (build-system r-build-system)
5547 `(("r-curl" ,r-curl)
5548 ("r-data-table" ,r-data-table)
5549 ("r-foreign" ,r-foreign)
5550 ("r-haven" ,r-haven)
5551 ("r-openxlsx" ,r-openxlsx)
5552 ("r-readxl" ,r-readxl)
5553 ("r-tibble" ,r-tibble)))
5554 (home-page "https://github.com/leeper/rio")
5555 (synopsis "Swiss-army knife for data I/O")
5557 "This package provides streamlined data import and export infrastructure
5558 by making assumptions that the user is probably willing to make: @code{import}
5559 and @code{export} determine the data structure from the file extension,
5560 reasonable defaults are used for data import and export (e.g.,
5561 @code{stringsAsFactors=FALSE}), web-based import is natively
5562 supported (including from SSL/HTTPS), compressed files can be read directly
5563 without explicit decompression, and fast import packages are used where
5564 appropriate. An additional convenience function, @code{convert}, provides a
5565 simple method for converting between file types.")
5566 (license license:gpl2)))
5568 (define-public r-maptools
5575 (uri (cran-uri "maptools" version))
5578 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5579 (build-system r-build-system)
5581 `(("r-foreign" ,r-foreign)
5582 ("r-lattice" ,r-lattice)
5584 (home-page "https://r-forge.r-project.org/projects/maptools/")
5585 (synopsis "Tools for reading and handling spatial objects")
5587 "This package provides a set of tools for manipulating and reading
5588 geographic data, in particular ESRI Shapefiles. It includes binary access to
5589 GSHHG shoreline files. The package also provides interface wrappers for
5590 exchanging spatial objects with other R packages.")
5591 ;; The C source files from shapelib are released under the Expat license.
5592 ;; The R code is released under GPL version 2 or later.
5593 (license (list license:gpl2+
5596 (define-public r-later
5603 (uri (cran-uri "later" version))
5606 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5607 (build-system r-build-system)
5611 ("r-rlang" ,r-rlang)))
5612 (home-page "https://github.com/r-lib/later")
5613 (synopsis "Utilities for delaying function execution")
5615 "This package provides tools to execute arbitrary R or C functions some
5616 time after the current time, after the R execution stack has emptied.")
5617 (license license:gpl2+)))
5619 (define-public r-promises
5626 (uri (cran-uri "promises" version))
5629 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5630 (build-system r-build-system)
5632 `(("r-later" ,r-later)
5633 ("r-magrittr" ,r-magrittr)
5636 ("r-rlang" ,r-rlang)))
5637 (home-page "https://rstudio.github.io/promises")
5638 (synopsis "Abstractions for promise-based asynchronous programming")
5640 "This package provides fundamental abstractions for doing asynchronous
5641 programming in R using promises. Asynchronous programming is useful for
5642 allowing a single R process to orchestrate multiple tasks in the background
5643 while also attending to something else. Semantics are similar to JavaScript
5644 promises, but with a syntax that is idiomatic R.")
5645 (license license:expat)))
5647 (define-public r-dosnow
5654 (uri (cran-uri "doSNOW" version))
5657 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5658 (properties `((upstream-name . "doSNOW")))
5659 (build-system r-build-system)
5661 `(("r-foreach" ,r-foreach)
5662 ("r-iterators" ,r-iterators)
5663 ("r-snow" ,r-snow)))
5664 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5665 (synopsis "Foreach parallel adaptor for the snow package")
5667 "This package provides a parallel backend for the @code{%dopar%} function
5668 using the @code{snow} package.")
5669 (license license:gpl2)))
5671 (define-public r-snowfall
5674 (version "1.84-6.1")
5677 (uri (cran-uri "snowfall" version))
5679 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5680 (build-system r-build-system)
5682 `(("r-snow" ,r-snow)))
5683 (home-page "https://cran.r-project.org/web/packages/snowfall/")
5684 (synopsis "Easier cluster computing")
5685 (description "This package is a usability wrapper around snow for easier
5686 development of parallel R programs. This package offers e.g. extended error
5687 checks, and additional functions. All functions work in sequential mode, too,
5688 if no cluster is present or wished. The package is also designed as connector
5689 to the cluster management tool @code{sfCluster}, but can also used without
5691 (license license:gpl2+)))
5693 (define-public r-rappdirs
5700 (uri (cran-uri "rappdirs" version))
5703 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5704 (build-system r-build-system)
5705 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5706 (synopsis "Determine where to save data, caches, and logs")
5708 "This package provides an easy way to determine which directories on the
5709 user's computer should be used to save data, caches and logs. It is a port of
5710 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5711 (license license:expat)))
5713 (define-public r-renv
5720 (uri (cran-uri "renv" version))
5723 "02ayfgbpw4b58148dcxz31anaxncwczmxs1zzkskwj0rzhb2x60r"))))
5724 (properties `((upstream-name . "renv")))
5725 (build-system r-build-system)
5726 (home-page "https://rstudio.github.io/renv")
5727 (synopsis "Project environments")
5729 "This package provides a dependency management toolkit for R. Using
5730 renv, you can create and manage project-local R libraries, save the state of
5731 these libraries to a lockfile, and later restore your library as required.
5732 Together, these tools can help make your projects more isolated, portable, and
5734 (license license:expat)))
5736 (define-public r-learnr
5743 (uri (cran-uri "learnr" version))
5746 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
5747 (build-system r-build-system)
5749 `(("r-checkmate" ,r-checkmate)
5750 ("r-ellipsis" ,r-ellipsis)
5751 ("r-evaluate" ,r-evaluate)
5752 ("r-htmltools" ,r-htmltools)
5753 ("r-htmlwidgets" ,r-htmlwidgets)
5754 ("r-jsonlite" ,r-jsonlite)
5755 ("r-knitr" ,r-knitr)
5756 ("r-markdown" ,r-markdown)
5757 ("r-rappdirs" ,r-rappdirs)
5759 ("r-rmarkdown" ,r-rmarkdown)
5760 ("r-rprojroot" ,r-rprojroot)
5761 ("r-shiny" ,r-shiny)
5762 ("r-withr" ,r-withr)))
5763 (home-page "https://rstudio.github.io/learnr/")
5764 (synopsis "Interactive tutorials for R")
5766 "This package provides tools to create interactive tutorials using R
5767 Markdown. Use a combination of narrative, figures, videos, exercises, and
5768 quizzes to create self-paced tutorials for learning about R and R packages.")
5769 (license license:asl2.0)))
5771 (define-public r-analytics
5773 (name "r-analytics")
5778 (uri (cran-uri "analytics" version))
5781 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5782 (build-system r-build-system)
5785 ("r-cluster" ,r-cluster)
5786 ("r-fractal" ,r-fractal)
5787 ("r-lmtest" ,r-lmtest)
5790 ("r-powerplus" ,r-powerplus)
5791 ("r-robust" ,r-robust)
5792 ("r-trend" ,r-trend)
5796 (home-page "https://cran.r-project.org/web/packages/analytics/")
5797 (synopsis "Collection of data analysis tools")
5799 "This package is a collection of data analysis tools. It includes tools
5800 for regression outlier detection in a fitted linear model, stationary
5801 bootstrap using a truncated geometric distribution, a comprehensive test for
5802 weak stationarity, column means by group, weighted biplots, and a heuristic to
5803 obtain a better initial configuration in non-metric MDS.")
5804 (license license:gpl2)))
5806 (define-public r-reticulate
5808 (name "r-reticulate")
5813 (uri (cran-uri "reticulate" version))
5816 "03dmnx9jhxx6vfbv2i5n6sln38kb9zkshz982pg3l9i4jjf3xns7"))))
5817 (build-system r-build-system)
5818 (inputs `(("python" ,python)))
5820 `(("r-rappdirs" ,r-rappdirs)
5821 ("r-jsonlite" ,r-jsonlite)
5822 ("r-matrix" ,r-matrix)
5823 ("r-rcpp" ,r-rcpp)))
5825 `(("r-knitr" ,r-knitr)))
5826 (home-page "https://github.com/rstudio/reticulate")
5827 (synopsis "R interface to Python")
5829 "This package provides an interface from R to Python modules, classes,
5830 and functions. When calling into Python, R data types are automatically
5831 converted to their equivalent Python types. When values are returned from
5832 Python to R they are converted back to R types.")
5833 (license license:asl2.0)))
5835 (define-public r-bibtex
5842 (uri (cran-uri "bibtex" version))
5845 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
5846 (build-system r-build-system)
5847 (propagated-inputs `(("r-stringr" ,r-stringr)))
5848 (home-page "https://github.com/romainfrancois/bibtex")
5849 (synopsis "Bibtex parser")
5850 (description "This package provides a utility for R to parse a bibtex
5852 (license license:gpl2+)))
5854 (define-public r-ggseqlogo
5856 (name "r-ggseqlogo")
5861 (uri (cran-uri "ggseqlogo" version))
5864 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5865 (build-system r-build-system)
5866 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5867 (home-page "https://github.com/omarwagih/ggseqlogo")
5868 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5870 "The range of functions provided by this package makes it possible to
5871 draw highly versatile genomic sequence logos. Features include, but are not
5872 limited to, modifying colour schemes and fonts used to draw the logo,
5873 generating multiple logo plots, and aiding the visualisation with annotations.
5874 Sequence logos can easily be combined with other ggplot2 plots.")
5875 ;; Unspecified version of the LGPL.
5876 (license license:lgpl3+)))
5878 (define-public r-ggsci
5885 (uri (cran-uri "ggsci" version))
5888 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5889 (build-system r-build-system)
5891 `(("r-ggplot2" ,r-ggplot2)
5892 ("r-scales" ,r-scales)))
5893 (home-page "https://nanx.me/ggsci/")
5894 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5896 "This package provides a collection of ggplot2 color palettes inspired by
5897 plots in scientific journals, data visualization libraries, science fiction
5898 movies, and TV shows.")
5899 (license license:gpl3)))
5901 (define-public r-ggsignif
5908 (uri (cran-uri "ggsignif" version))
5911 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5912 (build-system r-build-system)
5914 `(("r-knitr" ,r-knitr)))
5916 `(("r-ggplot2" ,r-ggplot2)))
5917 (home-page "https://github.com/const-ae/ggsignif")
5918 (synopsis "Significance brackets for ggplot2")
5920 "Enrich your ggplots with group-wise comparisons. This package provides
5921 an easy way to indicate if two groups are significantly different. Commonly
5922 this is shown by a bracket on top connecting the groups of interest which
5923 itself is annotated with the level of significance. The package provides a
5924 single layer that takes the groups for comparison and the test as arguments
5925 and adds the annotation to the plot.")
5926 (license license:gpl3)))
5928 (define-public r-ggpubr
5935 (uri (cran-uri "ggpubr" version))
5938 "0kb3hpmnhj4mkbx1kx0kv5y22himr8dijqx7ra0h8hi0pf2l2ha7"))))
5939 (build-system r-build-system)
5941 `(("r-cowplot" ,r-cowplot)
5942 ("r-dplyr" ,r-dplyr)
5943 ("r-ggplot2" ,r-ggplot2)
5944 ("r-ggrepel" ,r-ggrepel)
5945 ("r-ggsci" ,r-ggsci)
5946 ("r-ggsignif" ,r-ggsignif)
5948 ("r-gridextra" ,r-gridextra)
5949 ("r-magrittr" ,r-magrittr)
5950 ("r-polynom" ,r-polynom)
5951 ("r-purrr" ,r-purrr)
5952 ("r-rlang" ,r-rlang)
5953 ("r-scales" ,r-scales)
5954 ("r-tidyr" ,r-tidyr)))
5955 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5956 (synopsis "ggplot2-based publication-ready plots")
5958 "The ggplot2 package is an excellent and flexible package for elegant
5959 data visualization in R. However the default generated plots require some
5960 formatting before we can send them for publication. The ggpubr package
5961 provides some easy-to-use functions for creating and customizing ggplot2-based
5962 publication-ready plots.")
5963 (license license:gpl2)))
5965 (define-public r-ellipse
5972 (uri (cran-uri "ellipse" version))
5975 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5976 (build-system r-build-system)
5977 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5978 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5980 "This package contains various routines for drawing ellipses and
5981 ellipse-like confidence regions, implementing the plots described in Murdoch
5982 and Chow (1996), A graphical display of large correlation matrices, The
5983 American Statistician 50, 178-180. There are also routines implementing the
5984 profile plots described in Bates and Watts (1988), Nonlinear Regression
5985 Analysis and its Applications.")
5986 (license license:gpl2+)))
5988 (define-public r-flashclust
5990 (name "r-flashclust")
5995 (uri (cran-uri "flashClust" version))
5998 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5999 (properties `((upstream-name . "flashClust")))
6000 (build-system r-build-system)
6001 (native-inputs `(("gfortran" ,gfortran)))
6002 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6003 (synopsis "Implementation of optimal hierarchical clustering")
6005 "This package provides a fast implementation of hierarchical
6007 (license license:gpl2+)))
6009 (define-public r-factominer
6011 (name "r-factominer")
6016 (uri (cran-uri "FactoMineR" version))
6019 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6020 (properties `((upstream-name . "FactoMineR")))
6021 (build-system r-build-system)
6024 ("r-cluster" ,r-cluster)
6025 ("r-ellipse" ,r-ellipse)
6026 ("r-flashclust" ,r-flashclust)
6027 ("r-ggplot2" ,r-ggplot2)
6028 ("r-ggrepel" ,r-ggrepel)
6029 ("r-lattice" ,r-lattice)
6030 ("r-leaps" ,r-leaps)
6032 ("r-scatterplot3d" ,r-scatterplot3d)))
6033 (home-page "http://factominer.free.fr")
6034 (synopsis "Multivariate exploratory data analysis and data mining")
6036 "This package provides exploratory data analysis methods to summarize,
6037 visualize and describe datasets. The main principal component methods are
6038 available, those with the largest potential in terms of applications:
6039 principal component analysis (PCA) when variables are quantitative,
6040 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6041 variables are categorical, Multiple Factor Analysis when variables are
6042 structured in groups, etc. and hierarchical cluster analysis.")
6043 (license license:gpl2+)))
6045 (define-public r-factoextra
6047 (name "r-factoextra")
6052 (uri (cran-uri "factoextra" version))
6055 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6056 (build-system r-build-system)
6058 `(("r-abind" ,r-abind)
6059 ("r-cluster" ,r-cluster)
6060 ("r-dendextend" ,r-dendextend)
6061 ("r-factominer" ,r-factominer)
6062 ("r-ggplot2" ,r-ggplot2)
6063 ("r-ggpubr" ,r-ggpubr)
6064 ("r-ggrepel" ,r-ggrepel)
6065 ("r-reshape2" ,r-reshape2)
6066 ("r-tidyr" ,r-tidyr)))
6067 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6068 (synopsis "Extract and visualize the results of multivariate data analyses")
6070 "This package provides some easy-to-use functions to extract and
6071 visualize the output of multivariate data analyses, including
6072 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6073 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6074 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6075 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6076 packages. It contains also functions for simplifying some clustering analysis
6077 steps and provides ggplot2-based elegant data visualization.")
6078 (license license:gpl2)))
6080 (define-public r-fansi
6087 (uri (cran-uri "fansi" version))
6090 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6091 (build-system r-build-system)
6093 `(("r-knitr" ,r-knitr))) ; for vignettes
6094 (home-page "https://github.com/brodieG/fansi")
6095 (synopsis "ANSI control sequence aware string functions")
6097 "This package provides counterparts to R string manipulation functions
6098 that account for the effects of ANSI text formatting control sequences.")
6099 (license license:gpl2+)))
6101 (define-public r-nbclust
6108 (uri (cran-uri "NbClust" version))
6111 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6112 (properties `((upstream-name . "NbClust")))
6113 (build-system r-build-system)
6114 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6115 (synopsis "Determine the best number of clusters in a data set")
6117 "NbClust provides 30 indexes for determining the optimal number of
6118 clusters in a data set and offers the best clustering scheme from different
6119 results to the user.")
6120 (license license:gpl2)))
6122 (define-public r-hdf5r
6129 (uri (cran-uri "hdf5r" version))
6132 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6133 (build-system r-build-system)
6138 `(("r-bit64" ,r-bit64)
6141 `(("r-knitr" ,r-knitr)))
6142 (home-page "https://hhoeflin.github.io/hdf5r")
6143 (synopsis "Interface to the HDF5 binary data format")
6145 "HDF5 is a data model, library and file format for storing and managing
6146 large amounts of data. This package provides a nearly feature complete,
6147 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6148 functionality is added so that HDF5 objects behave very similar to their
6149 corresponding R counterparts.")
6150 (license license:asl2.0)))
6152 (define-public r-itertools
6154 (name "r-itertools")
6159 (uri (cran-uri "itertools" version))
6162 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6163 (build-system r-build-system)
6165 `(("r-iterators" ,r-iterators)))
6166 (home-page "https://cran.r-project.org/web/packages/itertools/")
6167 (synopsis "Iterator tools")
6169 "This package provides various tools for creating iterators, many
6170 patterned after functions in the Python @code{itertools} module, and others
6171 patterned after functions in the snow package.")
6172 (license license:gpl2)))
6174 (define-public r-polynom
6181 (uri (cran-uri "polynom" version))
6184 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6185 (build-system r-build-system)
6186 (home-page "https://cran.r-project.org/web/packages/polynom/")
6187 (synopsis "Functions for univariate polynomial manipulations")
6189 "This package provides a collection of functions to implement a class for
6190 univariate polynomial manipulations.")
6191 (license license:gpl2)))
6193 (define-public r-gbrd
6200 (uri (cran-uri "gbRd" version))
6203 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6204 (properties `((upstream-name . "gbRd")))
6205 (build-system r-build-system)
6206 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6207 (synopsis "Utilities for processing Rd objects and files")
6209 "This package provides utilities for processing Rd objects and files.
6210 Extract argument descriptions and other parts of the help pages of
6212 (license license:gpl2+)))
6214 (define-public r-rjags
6221 (uri (cran-uri "rjags" version))
6224 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6225 (build-system r-build-system)
6227 `(("r-coda" ,r-coda)))
6231 `(("pkg-config" ,pkg-config)))
6232 (home-page "http://mcmc-jags.sourceforge.net")
6233 (synopsis "Bayesian graphical models using MCMC")
6235 "This package provides an R interface to the JAGS MCMC library. JAGS is
6236 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6237 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6238 (license license:gpl2)))
6240 (define-public r-rdpack
6247 (uri (cran-uri "Rdpack" version))
6250 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6251 (properties `((upstream-name . "Rdpack")))
6252 (build-system r-build-system)
6254 `(("r-bibtex" ,r-bibtex)
6255 ("r-gbrd" ,r-gbrd)))
6256 (home-page "https://github.com/GeoBosh/Rdpack")
6257 (synopsis "Update and manipulate Rd documentation objects")
6259 "This package provides functions for manipulation of R documentation
6260 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6261 updating Rd documentation for functions, methods and classes; it also includes
6262 Rd macros for citations and import of references from bibtex files for use in
6263 Rd files and roxygen2 comments, as well as many functions for manipulation of
6264 references and Rd files.")
6265 (license license:gpl2+)))
6267 (define-public r-officer
6274 (uri (cran-uri "officer" version))
6277 "0xhx5n6qksyh2s9hvwhnc8y0hn362asc5y94ld06snad786hz0rw"))))
6278 (build-system r-build-system)
6280 `(("r-magrittr" ,r-magrittr)
6286 `(("r-knitr" ,r-knitr)))
6287 (home-page "https://davidgohel.github.io/officer")
6288 (synopsis "Manipulation of Word and PowerPoint documents")
6290 "This package provides tools to access and manipulate Word and PowerPoint
6291 documents from R. The package focuses on tabular and graphical reporting from
6292 R; it also provides two functions that let users get document content into
6293 data objects. A set of functions lets add and remove images, tables and
6294 paragraphs of text in new or existing documents. When working with PowerPoint
6295 presentations, slides can be added or removed; shapes inside slides can also
6296 be added or removed. When working with Word documents, a cursor can be used
6297 to help insert or delete content at a specific location in the document.")
6298 (license license:gpl3)))
6300 (define-public r-abn
6307 (uri (cran-uri "abn" version))
6310 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6311 (build-system r-build-system)
6315 `(("r-lme4" ,r-lme4)
6319 ("r-rcpparmadillo" ,r-rcpparmadillo)
6320 ("r-rjags" ,r-rjags)))
6321 (home-page "https://r-bayesian-networks.org/")
6322 (synopsis "Modelling multivariate data with additive bayesian networks")
6324 "Bayesian network analysis is a form of probabilistic graphical models
6325 which derives from empirical data a directed acyclic graph, DAG, describing
6326 the dependency structure between random variables. An additive Bayesian
6327 network model consists of a form of a DAG where each node comprises a
6328 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6329 equivalent to Bayesian multivariate regression using graphical modelling, they
6330 generalises the usual multivariable regression, GLM, to multiple dependent
6331 variables. This package provides routines to help determine optimal Bayesian
6332 network models for a given data set, where these models are used to identify
6333 statistical dependencies in messy, complex data.")
6334 (license license:gpl2+)))
6336 (define-public r-acd
6343 (uri (cran-uri "ACD" version))
6346 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6347 (properties `((upstream-name . "ACD")))
6348 (build-system r-build-system)
6349 (home-page "https://cran.r-project.org/web/packages/ACD/")
6350 (synopsis "Categorical data analysis with complete or missing responses")
6352 "This package provides tools for categorical data analysis with complete
6353 or missing responses.")
6354 (license license:gpl2+)))
6356 (define-public r-acdm
6363 (uri (cran-uri "ACDm" version))
6366 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6367 (properties `((upstream-name . "ACDm")))
6368 (build-system r-build-system)
6370 `(("r-dplyr" ,r-dplyr)
6371 ("r-ggplot2" ,r-ggplot2)
6373 ("r-rsolnp" ,r-rsolnp)
6375 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6376 (synopsis "Tools for Autoregressive Conditional Duration Models")
6378 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6379 and Russell, 1998) models. It creates trade, price or volume durations from
6380 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6382 (license license:gpl2+)))
6384 (define-public r-overlap
6391 (uri (cran-uri "overlap" version))
6394 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6395 (build-system r-build-system)
6396 (home-page "https://cran.r-project.org/web/packages/overlap/")
6397 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6399 "This package provides functions to fit kernel density functions to data
6400 on temporal activity patterns of animals; estimate coefficients of overlapping
6401 of densities for two species; and calculate bootstrap estimates of confidence
6403 (license license:gpl3+)))
6405 (define-public r-snakecase
6407 (name "r-snakecase")
6412 (uri (cran-uri "snakecase" version))
6415 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6416 (build-system r-build-system)
6418 `(("r-stringi" ,r-stringi)
6419 ("r-stringr" ,r-stringr)))
6420 (home-page "https://github.com/Tazinho/snakecase")
6421 (synopsis "Convert strings into any case")
6423 "This package provides a consistent, flexible and easy to use tool to
6424 parse and convert strings into cases like snake or camel among others.")
6425 (license license:gpl3)))
6427 (define-public r-prediction
6429 (name "r-prediction")
6434 (uri (cran-uri "prediction" version))
6437 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6438 (build-system r-build-system)
6440 `(("r-data-table" ,r-data-table)))
6441 (home-page "https://github.com/leeper/prediction")
6442 (synopsis "Tidy, type-safe prediction methods")
6444 "This package provides the @code{prediction()} function, a type-safe
6445 alternative to @code{predict()} that always returns a data frame. The package
6446 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6447 from the @code{stats} package, as well as numerous other model classes from
6448 other add-on packages.")
6449 (license license:expat)))
6451 (define-public r-insight
6458 (uri (cran-uri "insight" version))
6461 "0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
6462 (build-system r-build-system)
6464 `(("r-knitr" ,r-knitr)))
6465 (home-page "https://easystats.github.io/insight/")
6466 (synopsis "Easy access to model information for various model objects")
6468 "This package provides a tool to provide an easy, intuitive and
6469 consistent access to information contained in various R models, like model
6470 formulas, model terms, information about random effects, data that was used to
6471 fit the model or data from response variables. The package mainly revolves
6472 around two types of functions: Functions that find (the names of) information,
6473 starting with @code{find_}, and functions that get the underlying data,
6474 starting with @code{get_}. The package has a consistent syntax and works with
6475 many different model objects, where otherwise functions to access these
6476 information are missing.")
6477 (license license:gpl3)))
6479 (define-public r-sjlabelled
6481 (name "r-sjlabelled")
6486 (uri (cran-uri "sjlabelled" version))
6489 "1amq7i9sxf0pkxhskqc53xq5wvc9rdxm7cxyb4b6xh6qsskjnlsj"))))
6490 (build-system r-build-system)
6492 `(("r-haven" ,r-haven)
6493 ("r-insight" ,r-insight)))
6494 (home-page "https://github.com/strengejacke/sjlabelled")
6495 (synopsis "Labelled data utility functions")
6497 "This package provides a collection of functions dealing with labelled
6498 data, like reading and writing data between R and other statistical software
6499 packages. This includes easy ways to get, set or change value and variable
6500 label attributes, to convert labelled vectors into factors or numeric (and
6501 vice versa), or to deal with multiple declared missing values.")
6502 (license license:gpl3)))
6504 (define-public r-sjmisc
6511 (uri (cran-uri "sjmisc" version))
6514 "1ad7ca71w0v9ja4wb47aygczc987zz1lnjljhh2n497nzrpzzv64"))))
6515 (build-system r-build-system)
6517 `(("r-dplyr" ,r-dplyr)
6518 ("r-insight" ,r-insight)
6519 ("r-magrittr" ,r-magrittr)
6520 ("r-purrr" ,r-purrr)
6521 ("r-rlang" ,r-rlang)
6522 ("r-sjlabelled" ,r-sjlabelled)
6523 ("r-tidyselect" ,r-tidyselect)))
6525 `(("r-knitr" ,r-knitr)))
6526 (home-page "https://github.com/strengejacke/sjmisc")
6527 (synopsis "Data and variable transformation functions")
6529 "This package is a collection of miscellaneous utility functions,
6530 supporting data transformation tasks like recoding, dichotomizing or grouping
6531 variables, setting and replacing missing values. The data transformation
6532 functions also support labelled data, and all integrate seamlessly into a
6533 tidyverse workflow.")
6534 (license license:gpl3)))
6536 (define-public r-nortest
6543 (uri (cran-uri "nortest" version))
6546 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6547 (build-system r-build-system)
6548 (home-page "https://cran.r-project.org/web/packages/nortest/")
6549 (synopsis "Tests for normality")
6551 "This package provides five omnibus tests for testing the composite
6552 hypothesis of normality.")
6553 (license license:gpl2+)))
6555 (define-public r-moonbook
6562 (uri (cran-uri "moonBook" version))
6565 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6566 (properties `((upstream-name . "moonBook")))
6567 (build-system r-build-system)
6569 `(("r-magrittr" ,r-magrittr)
6570 ("r-nortest" ,r-nortest)
6571 ("r-purrr" ,r-purrr)
6572 ("r-sjmisc" ,r-sjmisc)
6573 ("r-stringr" ,r-stringr)
6574 ("r-survival" ,r-survival)))
6575 (home-page "https://github.com/cardiomoon/moonBook")
6576 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6578 "This package provides several analysis-related functions for the book
6579 entitled \"R statistics and graph for medical articles\" (written in Korean),
6580 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6582 (license license:gpl2)))
6584 (define-public r-flextable
6586 (name "r-flextable")
6591 (uri (cran-uri "flextable" version))
6594 "1rkz0nhwjy1l8sb0kmna5v492n2ydnk7gydswnmf88r8vfyjczhw"))))
6595 (build-system r-build-system)
6597 `(("r-base64enc" ,r-base64enc)
6598 ("r-data-table" ,r-data-table)
6599 ("r-gdtools" ,r-gdtools)
6600 ("r-htmltools" ,r-htmltools)
6601 ("r-knitr" ,r-knitr)
6602 ("r-officer" ,r-officer)
6603 ("r-rlang" ,r-rlang)
6604 ("r-rmarkdown" ,r-rmarkdown)
6605 ("r-xml2" ,r-xml2)))
6606 (home-page "https://davidgohel.github.io/flextable")
6607 (synopsis "Functions for tabular reporting")
6609 "This package provides tools to create pretty tables for HTML documents
6610 and other formats. Functions are provided to let users create tables, modify
6611 and format their content. It extends the @code{officer} package and can be
6612 used within R markdown documents when rendering to HTML and to Word
6614 (license license:gpl3)))
6616 (define-public r-writexl
6623 (uri (cran-uri "writexl" version))
6626 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6627 (build-system r-build-system)
6628 (inputs `(("zlib" ,zlib)))
6629 (home-page "https://github.com/ropensci/writexl")
6630 (synopsis "Export data frames to xlsx format")
6632 "This package provides a data frame to xlsx exporter based on
6634 (license license:bsd-2)))
6636 (define-public r-biasedurn
6638 (name "r-biasedurn")
6643 (uri (cran-uri "BiasedUrn" version))
6646 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6647 (properties `((upstream-name . "BiasedUrn")))
6648 (build-system r-build-system)
6649 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6650 (synopsis "Biased Urn model distributions")
6652 "This package provides statistical models of biased sampling in the form
6653 of univariate and multivariate noncentral hypergeometric distributions,
6654 including Wallenius' noncentral hypergeometric distribution and Fisher's
6655 noncentral hypergeometric distribution (also called extended hypergeometric
6657 (license license:gpl3)))
6659 (define-public r-goplot
6666 (uri (cran-uri "GOplot" version))
6669 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6670 (properties `((upstream-name . "GOplot")))
6671 (build-system r-build-system)
6673 `(("r-ggdendro" ,r-ggdendro)
6674 ("r-ggplot2" ,r-ggplot2)
6675 ("r-gridextra" ,r-gridextra)
6676 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6677 (home-page "https://github.com/wencke/wencke.github.io")
6678 (synopsis "Visualization of functional analysis data")
6680 "This package provides an implementation of multilayered visualizations
6681 for enhanced graphical representation of functional analysis data. It
6682 combines and integrates omics data derived from expression and functional
6683 annotation enrichment analyses. Its plotting functions have been developed
6684 with an hierarchical structure in mind: starting from a general overview to
6685 identify the most enriched categories (modified bar plot, bubble plot) to a
6686 more detailed one displaying different types of relevant information for the
6687 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6688 Venn diagram, heatmap).")
6689 (license license:gpl2)))
6691 (define-public r-getopt
6698 (uri (cran-uri "getopt" version))
6701 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6702 (build-system r-build-system)
6703 (home-page "https://github.com/trevorld/getopt")
6704 (synopsis "Command-line option processor for R")
6706 "This package is designed to be used with Rscript to write shebang
6707 scripts that accept short and long options. Many users will prefer to
6708 use the packages @code{optparse} or @code{argparse} which add extra
6709 features like automatically generated help options and usage texts,
6710 support for default values, positional argument support, etc.")
6711 (license license:gpl2+)))
6713 (define-public r-findpython
6715 (name "r-findpython")
6720 (uri (cran-uri "findpython" version))
6723 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6724 (build-system r-build-system)
6725 (home-page "https://github.com/trevorld/findpython")
6726 (synopsis "Functions to find an acceptable Python binary")
6728 "This package was designed to find an acceptable Python binary that
6729 matches version and feature constraints.")
6730 (license license:expat)))
6732 ;; This in not the same as "r-argparser"
6733 (define-public r-argparse
6740 (uri (cran-uri "argparse" version))
6743 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6744 (build-system r-build-system)
6745 (inputs `(("python" ,python)))
6747 `(("r-findpython" ,r-findpython)
6748 ("r-jsonlite" ,r-jsonlite)
6750 (home-page "https://github.com/trevorld/argparse")
6751 (synopsis "Command line optional and positional argument parser")
6753 "This package provides a command line parser to be used with Rscript to
6754 write shebang scripts that gracefully accept positional and optional arguments
6755 and automatically generate usage notices.")
6756 (license license:gpl2+)))
6758 (define-public r-hash
6765 (uri (cran-uri "hash" version))
6768 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6769 (build-system r-build-system)
6770 (home-page "https://cran.r-project.org/web/packages/hash/")
6771 (synopsis "Implementation of hash/associated arrays/dictionaries")
6773 "This package implements a data structure similar to hashes in Perl and
6774 dictionaries in Python but with a purposefully R flavor. For objects of
6775 appreciable size, access using hashes outperforms native named lists and
6777 (license license:gpl2+)))
6779 (define-public r-orddom
6786 (uri (cran-uri "orddom" version))
6789 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6790 (build-system r-build-system)
6791 (propagated-inputs `(("r-psych" ,r-psych)))
6792 (home-page "https://cran.r-project.org/web/packages/orddom/")
6793 (synopsis "Ordinal dominance statistics")
6795 "This package provides tools to compute ordinal, statistics and effect
6796 sizes as an alternative to mean comparison: Cliff's delta or success rate
6797 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6798 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6799 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6800 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6801 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6802 Group (Non-)Overlap considerations.")
6803 (license license:gpl2)))
6805 (define-public r-deriv
6812 (uri (cran-uri "Deriv" version))
6815 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6816 (properties `((upstream-name . "Deriv")))
6817 (build-system r-build-system)
6818 (home-page "https://cran.r-project.org/web/packages/Deriv")
6819 (synopsis "Symbolic differentiation")
6821 "This package provides an R-based solution for symbolic differentiation.
6822 It admits user-defined functions as well as function substitution in arguments
6823 of functions to be differentiated. Some symbolic simplification is part of
6825 (license license:gpl3+)))
6827 (define-public r-doby
6834 (uri (cran-uri "doBy" version))
6837 "1ckazh701b4ilg8bj17ji903538jmb49d997gm49ah5j5jc1x0g7"))))
6838 (properties `((upstream-name . "doBy")))
6839 (build-system r-build-system)
6841 `(("r-broom" ,r-broom)
6842 ("r-deriv" ,r-deriv)
6843 ("r-dplyr" ,r-dplyr)
6844 ("r-magrittr" ,r-magrittr)
6846 ("r-matrix" ,r-matrix)
6848 ("r-pbkrtest" ,r-pbkrtest)
6849 ("r-tibble" ,r-tibble)))
6850 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6851 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6853 "This package contains:
6856 @item facilities for working with grouped data: @code{do}
6857 something to data stratified @code{by} some variables.
6858 @item implementations of least-squares means, general linear contrasts, and
6859 @item miscellaneous other utilities.
6861 (license license:gpl2+)))
6863 (define-public r-refgenome
6865 (name "r-refgenome")
6870 (uri (cran-uri "refGenome" version))
6873 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6874 (properties `((upstream-name . "refGenome")))
6875 (build-system r-build-system)
6879 ("r-rsqlite" ,r-rsqlite)))
6880 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6882 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6884 "This package contains functionality for importing and managing of
6885 downloaded genome annotation data from the Ensembl genome browser (European
6886 Bioinformatics Institute) and from the UCSC genome browser (University of
6887 California, Santa Cruz) and annotation routines for genomic positions and
6888 splice site positions.")
6889 (license license:gpl2)))
6891 (define-public r-basix
6898 (uri (cran-uri "BASIX" version))
6901 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6902 (properties `((upstream-name . "BASIX")))
6903 (build-system r-build-system)
6904 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6905 (synopsis "Efficient C/C++ toolset for R")
6907 "BASIX provides some efficient C/C++ implementations of native R
6908 procedures to speed up calculations in R.")
6909 (license license:gpl2)))
6911 (define-public r-blockfest
6913 (name "r-blockfest")
6918 (uri (cran-uri "BlockFeST" version))
6921 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6922 (properties `((upstream-name . "BlockFeST")))
6923 (build-system r-build-system)
6924 (propagated-inputs `(("r-basix" ,r-basix)))
6925 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6926 (synopsis "Bayesian calculation of region-specific fixation index")
6928 "This package provides an R implementation of an extension of the
6929 BayeScan software for codominant markers, adding the option to group
6930 individual SNPs into pre-defined blocks. A typical application of this new
6931 approach is the identification of genomic regions, genes, or gene sets
6932 containing one or more SNPs that evolved under directional selection.")
6933 (license license:gpl2)))
6935 (define-public r-proc
6942 (uri (cran-uri "pROC" version))
6945 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
6946 (properties `((upstream-name . "pROC")))
6947 (build-system r-build-system)
6949 `(("r-plyr" ,r-plyr)
6950 ("r-rcpp" ,r-rcpp)))
6951 (home-page "https://web.expasy.org/pROC/")
6952 (synopsis "Display and analyze ROC curves")
6954 "This package provides tools for visualizing, smoothing and comparing
6955 receiver operating characteristic (ROC curves). The area under the
6956 curve (AUC) can be compared with statistical tests based on U-statistics or
6957 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6958 (license license:gpl3+)))
6960 (define-public r-rootsolve
6962 (name "r-rootsolve")
6967 (uri (cran-uri "rootSolve" version))
6970 "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
6971 (properties `((upstream-name . "rootSolve")))
6972 (build-system r-build-system)
6973 (native-inputs `(("gfortran" ,gfortran)))
6974 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6975 (synopsis "Tools for the analysis of ordinary differential equations")
6977 "This package provides routines to find the root of nonlinear functions,
6978 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6979 differential equations} (ODE). It includes routines that:
6982 @item generate gradient and jacobian matrices (full and banded),
6983 @item find roots of non-linear equations by the Newton-Raphson method,
6984 @item estimate steady-state conditions of a system of (differential) equations
6985 in full, banded or sparse form, using the Newton-Raphson method, or by
6986 dynamically running,
6987 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6988 and 3-D partial differential equations, that have been converted to ordinary
6989 differential equations by numerical differencing (using the method-of-lines
6992 (license license:gpl2+)))
6994 (define-public r-abcanalysis
6996 (name "r-abcanalysis")
7001 (uri (cran-uri "ABCanalysis" version))
7003 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7004 (properties `((upstream-name . "ABCanalysis")))
7005 (build-system r-build-system)
7006 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7007 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7008 (synopsis "Computed ABC Analysis")
7010 "Multivariate data sets often differ in several factors or derived statistical
7011 parameters, which have to be selected for a valid interpretation. Basing this
7012 selection on traditional statistical limits leads occasionally to the perception
7013 of losing information from a data set. This package provides tools to calculate
7014 these limits on the basis of the mathematical properties of the distribution of
7015 the analyzed items.")
7016 (license license:gpl3)))
7018 (define-public r-slam
7025 (uri (cran-uri "slam" version))
7027 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7028 (build-system r-build-system)
7029 (home-page "https://cran.r-project.org/web/packages/slam/")
7030 (synopsis "Sparse lightweight arrays and matrices")
7032 "This package contains data structures and algorithms for sparse arrays and matrices,
7033 based on index arrays and simple triplet representations, respectively.")
7034 (license license:gpl2)))
7036 (define-public r-manipulatewidget
7038 (name "r-manipulatewidget")
7043 (uri (cran-uri "manipulateWidget" version))
7045 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7047 `((upstream-name . "manipulateWidget")))
7048 (build-system r-build-system)
7050 `(("r-base64enc" ,r-base64enc)
7051 ("r-codetools" ,r-codetools)
7052 ("r-htmltools" ,r-htmltools)
7053 ("r-htmlwidgets" ,r-htmlwidgets)
7054 ("r-knitr" ,r-knitr)
7055 ("r-miniui" ,r-miniui)
7056 ("r-shiny" ,r-shiny)
7057 ("r-webshot" ,r-webshot)))
7058 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7059 (synopsis "Add even more interactivity to interactive charts")
7061 "This package lets you create in just a few lines of R code a nice user interface to
7062 modify the data or the graphical parameters of one or multiple interactive
7063 charts. It is useful to quickly explore visually some data or for package
7064 developers to generate user interfaces easy to maintain.")
7065 (license license:gpl2+)))
7074 (uri (cran-uri "A3" version))
7076 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7077 (properties `((upstream-name . "A3")))
7078 (build-system r-build-system)
7080 `(("r-pbapply" ,r-pbapply)
7081 ("r-xtable" ,r-xtable)))
7082 (home-page "https://cran.r-project.org/web/packages/A3/")
7083 (synopsis "Error metrics for predictive models")
7085 "This package supplies tools for tabulating and analyzing the results of predictive
7086 models. The methods employed are applicable to virtually any predictive model
7087 and make comparisons between different methodologies straightforward.")
7088 (license license:gpl2+)))
7090 (define-public r-infotheo
7097 (uri (cran-uri "infotheo" version))
7100 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7101 (build-system r-build-system)
7102 (home-page "http://homepage.meyerp.com/software")
7103 (synopsis "Information-theoretic measures")
7105 "This package implements various measures of information theory based on
7106 several entropy estimators.")
7107 (license license:gpl3+)))
7109 (define-public r-abcoptim
7116 (uri (cran-uri "ABCoptim" version))
7118 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7119 (properties `((upstream-name . "ABCoptim")))
7120 (build-system r-build-system)
7121 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7122 (home-page "https://github.com/gvegayon/ABCoptim/")
7123 (synopsis "Optimization of Artificial Bee Colony algorithm")
7125 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7126 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7127 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7128 algorithms, and uses only common control parameters such as colony size and
7129 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7130 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7131 This version is a work-in-progress and is written in R code.")
7132 (license license:expat)))
7134 (define-public r-abcp2
7141 (uri (cran-uri "ABCp2" version))
7143 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7144 (properties `((upstream-name . "ABCp2")))
7145 (build-system r-build-system)
7146 (propagated-inputs `(("r-mass" ,r-mass)))
7147 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7148 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7150 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7151 Poisson, and Gamma distribution and estimates the proportional paternity of the
7152 second male (P2) based on the best fit distribution.")
7153 (license license:gpl2)))
7155 (define-public r-abcrf
7162 (uri (cran-uri "abcrf" version))
7164 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7165 (build-system r-build-system)
7167 `(("r-doparallel" ,r-doparallel)
7168 ("r-foreach" ,r-foreach)
7170 ("r-matrixstats" ,r-matrixstats)
7171 ("r-ranger" ,r-ranger)
7173 ("r-rcpparmadillo" ,r-rcpparmadillo)
7174 ("r-readr" ,r-readr)
7175 ("r-stringr" ,r-stringr)))
7176 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7177 (synopsis "Approximate bayesian computation via random forests")
7179 "This package performs approximate bayesian computation (ABC) model choice and
7180 parameter inference via random forests. This machine learning tool named random
7181 forests (RF) can conduct selection among the highly complex models covered by
7183 (license license:gpl2+)))
7185 (define-public r-abctools
7192 (uri (cran-uri "abctools" version))
7194 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7195 (build-system r-build-system)
7198 ("r-abind" ,r-abind)
7199 ("r-hmisc" ,r-hmisc)
7200 ("r-plyr" ,r-plyr)))
7201 (home-page "https://github.com/dennisprangle/abctools/")
7202 (synopsis "Tools for ABC analyses")
7204 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7205 including summary statistic selection and assessing coverage. This includes
7206 recent dimension reduction algorithms to tune the choice of summary statistics,
7207 and coverage methods to tune the choice of threshold.")
7208 (license license:gpl2+)))
7210 (define-public r-ggstance
7217 (uri (cran-uri "ggstance" version))
7219 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7220 (build-system r-build-system)
7222 `(("r-ggplot2" ,r-ggplot2)
7224 ("r-rlang" ,r-rlang)
7225 ("r-withr" ,r-withr)))
7226 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7227 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7229 "This package is a @code{r-ggplot2} extension that provides flipped components:
7231 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7232 @item vertical versions of @code{r-ggplot2} positions.
7234 (license license:gpl3)))
7236 (define-public r-mosaiccore
7238 (name "r-mosaiccore")
7243 (uri (cran-uri "mosaicCore" version))
7245 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7246 (properties `((upstream-name . "mosaicCore")))
7247 (build-system r-build-system)
7249 `(("r-dplyr" ,r-dplyr)
7250 ("r-lazyeval" ,r-lazyeval)
7252 ("r-rlang" ,r-rlang)
7253 ("r-tidyr" ,r-tidyr)))
7254 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7255 (synopsis "Common utilities for mosaic family packages")
7257 "Common utilities used in other Mosaic family packages are collected here.")
7258 (license license:gpl2+)))
7260 (define-public r-ggformula
7262 (name "r-ggformula")
7267 (uri (cran-uri "ggformula" version))
7269 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7270 (build-system r-build-system)
7272 `(("r-ggforce" ,r-ggforce)
7273 ("r-ggplot2" ,r-ggplot2)
7274 ("r-ggstance" ,r-ggstance)
7275 ("r-magrittr" ,r-magrittr)
7276 ("r-mosaiccore" ,r-mosaiccore)
7277 ("r-rlang" ,r-rlang)
7278 ("r-stringr" ,r-stringr)
7279 ("r-tibble" ,r-tibble)))
7280 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7281 (synopsis "Formula interface for the @code{r-ggplot2}")
7283 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7284 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7285 and extends the excellent simplicity of the lattice-graphics formula interface,
7286 while providing the intuitive capabilities of @code{r-ggplot2}.")
7287 (license license:expat)))
7289 (define-public r-mosaicdata
7291 (name "r-mosaicdata")
7296 (uri (cran-uri "mosaicData" version))
7298 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7299 (properties `((upstream-name . "mosaicData")))
7300 (build-system r-build-system)
7301 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7302 (synopsis "Data sets for project Mosaic")
7304 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7305 used to teach mathematics, statistics, computation and modeling.")
7306 (license license:gpl2+)))
7308 (define-public r-raster
7315 (uri (cran-uri "raster" version))
7318 "0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
7319 (build-system r-build-system)
7321 `(("r-rcpp" ,r-rcpp)
7323 (home-page "https://www.rspatial.org/")
7324 (synopsis "Geographic data analysis and modeling")
7326 "The package implements basic and high-level functions for reading,
7327 writing, manipulating, analyzing and modeling of gridded spatial data.
7328 Processing of very large files is supported.")
7329 (license license:gpl3+)))
7331 (define-public r-mosaic
7338 (uri (cran-uri "mosaic" version))
7340 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7341 (build-system r-build-system)
7343 `(("r-broom" ,r-broom)
7344 ("r-dplyr" ,r-dplyr)
7345 ("r-ggdendro" ,r-ggdendro)
7346 ("r-ggformula" ,r-ggformula)
7347 ("r-ggplot2" ,r-ggplot2)
7348 ("r-ggrepel" ,r-ggrepel)
7350 ("r-gridextra" ,r-gridextra)
7351 ("r-lattice" ,r-lattice)
7352 ("r-latticeextra" ,r-latticeextra)
7353 ("r-lazyeval" ,r-lazyeval)
7355 ("r-matrix" ,r-matrix)
7356 ("r-mosaiccore" ,r-mosaiccore)
7357 ("r-mosaicdata" ,r-mosaicdata)
7358 ("r-readr" ,r-readr)
7359 ("r-tidyr" ,r-tidyr)))
7361 `(("r-knitr" ,r-knitr)))
7362 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7363 (synopsis "Mathematics, statistics, and computation teaching utilities")
7365 "This package contain data sets and utilities from
7366 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7367 statistics, computation and modeling. Project MOSAIC is a community of
7368 educators working to tie together aspects of quantitative work that students
7369 in science, technology, engineering and mathematics will need in their
7370 professional lives, but which are usually taught in isolation, if at all.")
7371 (license license:gpl2+)))
7373 (define-public r-abd
7380 (uri (cran-uri "abd" version))
7382 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7383 (build-system r-build-system)
7385 `(("r-lattice" ,r-lattice)
7386 ("r-mosaic" ,r-mosaic)
7387 ("r-nlme" ,r-nlme)))
7388 (home-page "https://cran.r-project.org/web/packages/abd/")
7389 (synopsis "Analysis of biological data")
7391 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7392 biological data by Michael Whitlock and Dolph Schluter.")
7393 (license license:gpl2)))
7395 (define-public r-svgui
7402 (uri (cran-uri "svGUI" version))
7404 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7405 (properties `((upstream-name . "svGUI")))
7406 (build-system r-build-system)
7407 (home-page "https://github.com/SciViews/svGUI/")
7408 (synopsis "Functions for managing GUI clients in R")
7410 "The SciViews @code{svGUI} package eases the management of Graphical User
7411 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7412 centralizes info about GUI elements currently used, and it dispatches GUI
7413 calls to the particular toolkits in use in function of the context.")
7414 (license license:gpl2)))
7416 (define-public r-svdialogs
7418 (name "r-svdialogs")
7423 (uri (cran-uri "svDialogs" version))
7425 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7426 (properties `((upstream-name . "svDialogs")))
7427 (build-system r-build-system)
7430 ("zenity" ,zenity)))
7432 `(("r-rstudioapi" ,r-rstudioapi)
7433 ("r-svgui" ,r-svgui)))
7434 (home-page "https://github.com/SciViews/svDialogs/")
7435 (synopsis "Portable dialog boxes")
7437 "This package helps to construct standard dialog boxes for your GUI, including
7438 message boxes, input boxes, list, file or directory selection, and others. In
7439 case R cannot display GUI dialog boxes, a simpler command line version of these
7440 interactive elements is also provided as a fallback solution.")
7441 (license license:gpl2)))
7443 (define-public r-abe
7450 (uri (cran-uri "abe" version))
7453 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7454 (build-system r-build-system)
7455 (home-page "https://cran.r-project.org/web/packages/abe/")
7456 (synopsis "Augmented backward elimination")
7458 "This package performs augmented backward elimination and checks the
7459 stability of the obtained model. Augmented backward elimination combines
7460 significance or information based criteria with the change in estimate to
7461 either select the optimal model for prediction purposes or to serve as a tool
7462 to obtain a practically sound, highly interpretable model.")
7463 (license license:gpl2+)))
7465 (define-public r-abf2
7472 (uri (cran-uri "abf2" version))
7474 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7475 (build-system r-build-system)
7476 (home-page "https://cran.r-project.org/web/packages/abf2/")
7477 (synopsis "Load gap-free axon @code{r-abf2} files")
7479 "This package loads electrophysiology data from ABF2 files, as created by
7480 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7481 mode are currently supported.")
7482 (license license:artistic2.0)))
7484 (define-public r-abhgenotyper
7486 (name "r-abhgenotyper")
7491 (uri (cran-uri "ABHgenotypeR" version))
7493 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7494 (properties `((upstream-name . "ABHgenotypeR")))
7495 (build-system r-build-system)
7497 `(("r-ggplot2" ,r-ggplot2)
7498 ("r-reshape2" ,r-reshape2)))
7499 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7500 (synopsis "Visualize and manipulate ABH genotypes")
7502 "The @code{r-abhgenotyper} package provides simple imputation,
7503 error-correction and plotting capacities for genotype data. The package is
7504 supposed to serve as an intermediate but independent analysis tool between the
7505 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7506 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7507 genotypes as \"graphical genotypes\".")
7508 (license license:gpl3)))
7510 (define-public r-furrr
7517 (uri (cran-uri "furrr" version))
7520 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7521 (build-system r-build-system)
7523 `(("r-future" ,r-future)
7524 ("r-globals" ,r-globals)
7525 ("r-purrr" ,r-purrr)
7526 ("r-rlang" ,r-rlang)))
7527 (home-page "https://github.com/DavisVaughan/furrr")
7528 (synopsis "Apply mapping functions in parallel using futures")
7530 "This package provides implementations of the family of @code{map()}
7531 functions from the @code{purrr} package that can be resolved using any
7532 @code{future}-supported backend, e.g. parallel on the local machine or
7533 distributed on a compute cluster.")
7534 (license license:lgpl2.1+)))
7536 (define-public r-abjutils
7543 (uri (cran-uri "abjutils" version))
7545 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7546 (build-system r-build-system)
7548 `(("r-devtools" ,r-devtools)
7549 ("r-dplyr" ,r-dplyr)
7550 ("r-furrr" ,r-furrr)
7551 ("r-future" ,r-future)
7554 ("r-magrittr" ,r-magrittr)
7555 ("r-progress" ,r-progress)
7556 ("r-purrr" ,r-purrr)
7557 ("r-readr" ,r-readr)
7558 ("r-rlang" ,r-rlang)
7559 ("r-rstudioapi" ,r-rstudioapi)
7560 ("r-scales" ,r-scales)
7561 ("r-stringi" ,r-stringi)
7562 ("r-stringr" ,r-stringr)
7563 ("r-tibble" ,r-tibble)
7564 ("r-tidyr" ,r-tidyr)))
7565 (home-page "https://github.com/abjur/abjutils/")
7566 (synopsis "Collection of tools for jurimetrical analysis")
7568 "This package implements general purpose tools, such as functions for
7569 sampling and basic manipulation of Brazilian lawsuits identification number.
7570 It also implements functions for text cleaning, such as accentuation
7572 (license license:expat)))
7574 (define-public r-abnormality
7576 (name "r-abnormality")
7581 (uri (cran-uri "abnormality" version))
7583 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7584 (build-system r-build-system)
7586 `(("r-mass" ,r-mass)
7587 ("r-matrix" ,r-matrix)))
7588 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7589 (synopsis "Measure a subject's abnormality with respect to a reference population")
7591 "This package contains functions to implement the methodology and
7592 considerations laid out by Marks et al. in the article \"Measuring abnormality
7593 in high dimensional spaces: applications in biomechanical gait analysis\".
7594 Using high-dimensional datasets to measure a subject's overall level of
7595 abnormality as compared to a reference population is often needed in outcomes
7597 (license license:expat)))
7599 (define-public r-abodoutlier
7601 (name "r-abodoutlier")
7606 (uri (cran-uri "abodOutlier" version))
7608 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7609 (properties `((upstream-name . "abodOutlier")))
7610 (build-system r-build-system)
7612 `(("r-cluster" ,r-cluster)))
7613 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7614 (synopsis "Angle-based outlier detection")
7616 "This package performs angle-based outlier detection on a given data
7617 frame. It offers three methods to process data:
7619 @item full but slow implementation using all the data that has cubic
7621 @item a fully randomized method;
7622 @item a method using k-nearest neighbours.
7624 These algorithms are well suited for high dimensional data outlier
7626 (license license:expat)))
7628 (define-public r-abps
7635 (uri (cran-uri "ABPS" version))
7637 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7638 (properties `((upstream-name . "ABPS")))
7639 (build-system r-build-system)
7640 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7641 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7642 (synopsis "Abnormal blood profile score to detect blood doping")
7644 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7645 The ABPS is a part of the Athlete biological passport program of the World
7646 anti-doping agency, which combines several blood parameters into a single
7647 score in order to detect blood doping. The package also contains functions to
7648 calculate other scores used in anti-doping programs, such as the ratio of
7649 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7650 (license license:gpl2+)))
7652 (define-public r-parmigene
7654 (name "r-parmigene")
7659 (uri (cran-uri "parmigene" version))
7662 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7663 (build-system r-build-system)
7664 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7665 (synopsis "Mutual information estimation for gene network reconstruction")
7667 "This package provides a parallel estimation of the mutual information
7668 based on entropy estimates from k-nearest neighbors distances and algorithms
7669 for the reconstruction of gene regulatory networks.")
7670 (license license:agpl3+)))
7672 (define-public r-pscl
7679 (uri (cran-uri "pscl" version))
7681 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
7682 (build-system r-build-system)
7684 `(("r-mass" ,r-mass)))
7685 (home-page "https://github.com/atahk/pscl/")
7686 (synopsis "Political science computational laboratory")
7688 "The @code{pscl} is an R package providing classes and methods for:
7690 @item Bayesian analysis of roll call data (item-response models);
7691 @item elementary Bayesian statistics;
7692 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7694 @item utility functions.
7696 (license license:gpl2)))
7698 (define-public r-accelmissing
7700 (name "r-accelmissing")
7705 (uri (cran-uri "accelmissing" version))
7707 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7708 (build-system r-build-system)
7710 `(("r-mice" ,r-mice)
7711 ("r-pscl" ,r-pscl)))
7712 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7713 (synopsis "Missing value imputation for accelerometer data")
7715 "This package provides a statistical method to impute the missing values in
7716 accelerometer data. The methodology includes both parametric and
7717 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7718 model. It also provides multiple functions to preprocess the accelerometer data
7719 previous to the missing data imputation. These include detecting the wearing
7720 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7721 (license license:gpl2+)))
7723 (define-public r-mhsmm
7730 (uri (cran-uri "mhsmm" version))
7732 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7733 (build-system r-build-system)
7734 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7735 (home-page "https://github.com/jaredo/mhsmm/")
7736 (synopsis "Inference for hidden Markov and semi-Markov models")
7738 "The @code{r-mhsmm} package implements estimation and prediction methods for
7739 hidden Markov and semi-Markov models for multiple observation sequences. Such
7740 techniques are of interest when observed data is thought to be dependent on some
7741 unobserved (or hidden) state. Also, this package is suitable for equidistant
7742 time series data, with multivariate and/or missing data. Allows user defined
7743 emission distributions.")
7744 (license license:gpl2+)))
7746 (define-public r-nleqslv
7753 (uri (cran-uri "nleqslv" version))
7755 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7756 (build-system r-build-system)
7757 (native-inputs `(("gfortran" ,gfortran)))
7758 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7759 (synopsis "Solve systems of nonlinear equations")
7761 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7762 Broyden or a Newton method with a choice of global strategies such as line
7763 search and trust region. There are options for using a numerical or user
7764 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7765 singular or ill-conditioned Jacobian.")
7766 (license license:gpl2+)))
7768 (define-public r-physicalactivity
7770 (name "r-physicalactivity")
7775 (uri (cran-uri "PhysicalActivity" version))
7777 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7779 `((upstream-name . "PhysicalActivity")))
7780 (build-system r-build-system)
7781 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7782 (synopsis "Procesing accelerometer data for physical activity measurement")
7784 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7785 for classification of monitor wear and nonwear time intervals in accelerometer
7786 data collected to assess physical activity. The package also contains functions
7787 for making plots of accelerometer data and obtaining the summary of various
7788 information including daily monitor wear time and the mean monitor wear time
7789 during valid days. The revised package version 0.2-1 improved the functions
7790 regarding speed, robustness and add better support for time zones and daylight
7791 saving. In addition, several functions were added:
7793 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7794 @item the @code{markPAI} can categorize physical activity intensity level based
7795 on user-defined cut-points of accelerometer counts.
7797 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7798 @code{queryActigraph} functions.")
7799 (license license:gpl3+)))
7801 (define-public r-acc
7808 (uri (cran-uri "acc" version))
7810 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7811 (build-system r-build-system)
7813 `(("r-circlize" ,r-circlize)
7815 ("r-ggplot2" ,r-ggplot2)
7816 ("r-iterators" ,r-iterators)
7817 ("r-mhsmm" ,r-mhsmm)
7818 ("r-nleqslv" ,r-nleqslv)
7819 ("r-physicalactivity" ,r-physicalactivity)
7821 ("r-r-utils" ,r-r-utils)
7823 ("r-rcpparmadillo" ,r-rcpparmadillo)
7824 ("r-rsqlite" ,r-rsqlite)
7826 (home-page "https://cran.r-project.org/web/packages/acc/")
7827 (synopsis "Exploring accelerometer data")
7829 "This package processes accelerometer data from uni-axial and tri-axial devices
7830 and generates data summaries. Also, includes functions to plot, analyze, and
7831 simulate accelerometer data.")
7832 (license license:gpl2+)))
7834 (define-public r-rbenchmark
7836 (name "r-rbenchmark")
7841 (uri (cran-uri "rbenchmark" version))
7843 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7844 (build-system r-build-system)
7845 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7846 (synopsis "Benchmarking routine for R")
7848 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7849 and is intended to facilitate benchmarking of arbitrary R code. The library
7850 consists of just one function, benchmark, which is a simple wrapper around
7851 system.time. Given a specification of the benchmarking process (counts of
7852 replications, evaluation environment) and an arbitrary number of expressions,
7853 benchmark evaluates each of the expressions in the specified environment,
7854 replicating the evaluation as many times as specified, and returning the results
7855 conveniently wrapped into a data frame.")
7856 (license license:gpl2+)))
7858 (define-public r-mitools
7865 (uri (cran-uri "mitools" version))
7868 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7869 (build-system r-build-system)
7870 (propagated-inputs `(("r-dbi" ,r-dbi)))
7871 (home-page "https://cran.r-project.org/web/packages/mitools/")
7872 (synopsis "Tools for multiple imputation of missing data")
7874 "This package provides tools to perform analyses and combine results from
7875 multiple-imputation datasets.")
7876 (license license:gpl2)))
7878 (define-public r-magick
7885 (uri (cran-uri "magick" version))
7888 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
7889 (build-system r-build-system)
7891 `(("imagemagick" ,imagemagick)
7894 `(("r-curl" ,r-curl)
7895 ("r-magrittr" ,r-magrittr)
7896 ("r-rcpp" ,r-rcpp)))
7898 `(("pkg-config" ,pkg-config)))
7899 (home-page "https://github.com/ropensci/magick")
7900 (synopsis "Advanced graphics and image-processing in R")
7902 "This package provides bindings to ImageMagick, a comprehensive image
7903 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7904 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7905 operations are vectorized via the Magick++ STL meaning they operate either on
7906 a single frame or a series of frames for working with layers, collages, or
7907 animation. In RStudio, images are automatically previewed when printed to the
7908 console, resulting in an interactive editing environment.")
7909 (license license:expat)))
7911 (define-public r-survey
7918 (uri (cran-uri "survey" version))
7921 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
7922 (build-system r-build-system)
7924 `(("r-lattice" ,r-lattice)
7925 ("r-matrix" ,r-matrix)
7926 ("r-minqa" ,r-minqa)
7927 ("r-mitools" ,r-mitools)
7928 ("r-numderiv" ,r-numderiv)
7929 ("r-survival" ,r-survival)))
7930 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7931 (synopsis "Analysis of complex survey samples")
7933 "This package provides tools for the analysis of complex survey samples.
7934 The provided features include: summary statistics, two-sample tests, rank
7935 tests, generalised linear models, cumulative link models, Cox models,
7936 loglinear models, and general maximum pseudolikelihood estimation for
7937 multistage stratified, cluster-sampled, unequally weighted survey samples;
7938 variances by Taylor series linearisation or replicate weights;
7939 post-stratification, calibration, and raking; two-phase subsampling designs;
7940 graphics; PPS sampling without replacement; principal components, and factor
7942 ;; Either version of the GPL.
7943 (license (list license:gpl2 license:gpl3))))
7945 (define-public r-gee
7952 (uri (cran-uri "gee" version))
7955 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
7956 (properties `((upstream-name . "gee")))
7957 (build-system r-build-system)
7959 `(("gfortran" ,gfortran)))
7960 (home-page "https://cran.r-project.org/web/packages/gee/")
7961 (synopsis "Generalized estimation equation solver")
7963 "This package provides a solver for generalized estimation equations.")
7964 (license license:gpl2)))
7966 (define-public r-tab
7973 (uri (cran-uri "tab" version))
7976 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
7977 (properties `((upstream-name . "tab")))
7978 (build-system r-build-system)
7980 `(("r-dplyr" ,r-dplyr)
7982 ("r-knitr" ,r-knitr)
7984 ("r-survey" ,r-survey)
7985 ("r-survival" ,r-survival)
7986 ("r-xtable" ,r-xtable)))
7987 (home-page "https://cran.r-project.org/web/packages/tab/")
7988 (synopsis "Create summary tables for statistical reports")
7990 "This package contains functions for creating various types of summary
7991 tables, e.g. comparing characteristics across levels of a categorical variable
7992 and summarizing fitted generalized linear models, generalized estimating
7993 equations, and Cox proportional hazards models. Functions are available to
7994 handle data from simple random samples as well as complex surveys.")
7995 (license license:gpl3+)))
7997 (define-public r-dvmisc
8004 (uri (cran-uri "dvmisc" version))
8006 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8007 (build-system r-build-system)
8009 `(("r-cubature" ,r-cubature)
8010 ("r-data-table" ,r-data-table)
8011 ("r-dplyr" ,r-dplyr)
8012 ("r-ggplot2" ,r-ggplot2)
8014 ("r-mvtnorm" ,r-mvtnorm)
8015 ("r-pracma" ,r-pracma)
8016 ("r-rbenchmark" ,r-rbenchmark)
8018 ("r-survey" ,r-survey)
8020 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8021 (synopsis "Faster computation of common statistics and miscellaneous functions")
8023 "This package implements faster versions of base R functions (e.g. mean, standard
8024 deviation, covariance, weighted mean), mostly written in C++, along with
8025 miscellaneous functions for various purposes (e.g. create the histogram with
8026 fitted probability density function or probability mass function curve, create
8027 the body mass index groups, assess the linearity assumption in logistic
8029 (license license:gpl2)))
8031 (define-public r-accelerometry
8033 (name "r-accelerometry")
8038 (uri (cran-uri "accelerometry" version))
8040 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8041 (build-system r-build-system)
8043 `(("r-dvmisc" ,r-dvmisc)
8044 ("r-rcpp" ,r-rcpp)))
8045 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8046 (synopsis "Functions for processing accelerometer data")
8048 "This package provides a collection of functions that perform operations on
8049 time-series accelerometer data, such as identify the non-wear time, flag minutes
8050 that are part of an activity bout, and find the maximum 10-minute average count
8051 value. The functions are generally very flexible, allowing for a variety of
8052 algorithms to be implemented.")
8053 (license license:gpl3)))
8055 (define-public r-absim
8062 (uri (cran-uri "AbSim" version))
8064 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8065 (properties `((upstream-name . "AbSim")))
8066 (build-system r-build-system)
8069 ("r-powerlaw" ,r-powerlaw)))
8070 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8071 (synopsis "Time resolved simulations of antibody repertoires")
8073 "This package provides simulation methods for the evolution of antibody repertoires.
8074 The heavy and light chain variable region of both human and C57BL/6 mice can
8075 be simulated in a time-dependent fashion. Both single lineages using one set of
8076 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8077 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8078 Upon completion, the main loop of the algorithm begins, with each iteration
8079 representing one simulated time step. Various mutation events are possible at
8080 each time step, contributing to a diverse final repertoire.")
8081 (license license:gpl2)))
8083 (define-public r-quic
8090 (uri (cran-uri "QUIC" version))
8092 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8093 (properties `((upstream-name . "QUIC")))
8094 (build-system r-build-system)
8095 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8096 (synopsis "Regularized sparse inverse covariance matrix estimation")
8098 "This package implements the regularized Gaussian maximum likelihood
8099 estimation of the inverse of a covariance matrix. It uses Newton's method and
8100 coordinate descent to solve the regularized inverse covariance matrix
8101 estimation problem.")
8102 ;; The project home page states that the release is under GPLv3 or later.
8103 ;; The CRAN page only says GPL-3.
8104 (license license:gpl3+)))
8106 (define-public r-abundant
8113 (uri (cran-uri "abundant" version))
8115 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8116 (build-system r-build-system)
8118 `(("r-quic" ,r-quic)))
8119 (home-page "https://cran.r-project.org/web/packages/abundant/")
8120 (synopsis "Abundant regression and high-dimensional principal fitted components")
8122 "This package provides tools to fit and predict with the high-dimensional
8123 principal fitted components model. This model is described by Cook, Forzani,
8124 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8125 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8126 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8127 (license license:gpl2+)))
8129 (define-public r-ac3net
8136 (uri (cran-uri "Ac3net" version))
8138 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8139 (properties `((upstream-name . "Ac3net")))
8140 (build-system r-build-system)
8142 `(("r-data-table" ,r-data-table)))
8143 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8144 (synopsis "Inferring directional conservative causal core gene networks")
8145 (description "This package infers directional Conservative causal core
8146 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8147 directional network.")
8148 (license license:gpl3+)))
8150 (define-public r-aca
8157 (uri (cran-uri "ACA" version))
8159 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8160 (properties `((upstream-name . "ACA")))
8161 (build-system r-build-system)
8162 (home-page "https://cran.r-project.org/web/packages/ACA/")
8163 (synopsis "Abrupt change-point or aberration detection in point series")
8165 "This package offers an interactive function for the detection of breakpoints in
8167 ;; Any version of the GPL
8168 (license (list license:gpl2+ license:gpl3+))))
8170 (define-public r-acceptancesampling
8172 (name "r-acceptancesampling")
8177 (uri (cran-uri "AcceptanceSampling" version))
8179 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8181 `((upstream-name . "AcceptanceSampling")))
8182 (build-system r-build-system)
8183 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8184 (synopsis "Creation and evaluation of acceptance sampling plans")
8186 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8187 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8188 in quality control and improvement. International standards of acceptance
8189 sampling provide sampling plans for specific circumstances. The aim of this
8190 package is to provide an easy-to-use interface to visualize single, double or
8191 multiple sampling plans. In addition, methods have been provided to enable the
8192 user to assess sampling plans against pre-specified levels of performance, as
8193 measured by the probability of acceptance for a given level of quality in the
8195 (license license:gpl3+)))
8197 (define-public r-acclma
8204 (uri (cran-uri "ACCLMA" version))
8206 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8207 (properties `((upstream-name . "ACCLMA")))
8208 (build-system r-build-system)
8209 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8210 (synopsis "ACC & LMA graph plotting")
8212 "This package contains a function that imports data from a @acronym{CSV,
8213 Comma-Separated Values} file, or uses manually entered data from the format (x,
8214 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8215 Curve} vs @acronym{LOI, Line of Independence} graph and
8216 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8217 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8218 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8219 string) was passed, a manual data entry window is opened. The header parameter
8220 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8221 a header row or not. The dataset should contain only one independent variable
8222 (x) and one dependent variable (y) and can contain a weight for each
8224 (license license:gpl2)))
8226 (define-public r-aspi
8233 (uri (cran-uri "aspi" version))
8235 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8236 (build-system r-build-system)
8238 "https://cran.r-project.org/web/packages/aspi/")
8240 "Analysis of symmetry of parasitic infections")
8242 "This package provides tools for the analysis and visualization of bilateral
8243 asymmetry in parasitic infections.")
8244 (license license:gpl3+)))
8246 (define-public r-sandwich
8253 (uri (cran-uri "sandwich" version))
8256 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8257 (build-system r-build-system)
8259 `(("r-zoo" ,r-zoo)))
8260 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8261 (synopsis "Robust Covariance Matrix Estimators")
8263 "This package provides model-robust standard error estimators for
8264 cross-sectional, time series, clustered, panel, and longitudinal data.")
8265 ;; Either version of the license.
8266 (license (list license:gpl2 license:gpl3))))
8268 (define-public r-th-data
8275 (uri (cran-uri "TH.data" version))
8278 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8279 (properties `((upstream-name . "TH.data")))
8280 (build-system r-build-system)
8282 `(("r-mass" ,r-mass)
8283 ("r-survival" ,r-survival)))
8284 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8285 (synopsis "Shared data sets")
8287 "This package contains supporting data sets that are used in other
8288 packages maintained by Torsten Hothorn.")
8289 (license license:gpl3)))
8291 (define-public r-multcomp
8298 (uri (cran-uri "multcomp" version))
8301 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8302 (build-system r-build-system)
8304 `(("r-codetools" ,r-codetools)
8305 ("r-mvtnorm" ,r-mvtnorm)
8306 ("r-sandwich" ,r-sandwich)
8307 ("r-survival" ,r-survival)
8308 ("r-th-data" ,r-th-data)))
8309 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8310 (synopsis "Simultaneous inference in general parametric models")
8312 "Simultaneous tests and confidence intervals for general linear
8313 hypotheses in parametric models, including linear, generalized linear, linear
8314 mixed effects, and survival models. The package includes demos reproducing
8315 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8316 Hothorn, Westfall, 2010, CRC Press).")
8317 (license license:gpl2)))
8319 (define-public r-emmeans
8326 (uri (cran-uri "emmeans" version))
8329 "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
8330 (build-system r-build-system)
8332 `(("r-estimability" ,r-estimability)
8333 ("r-mvtnorm" ,r-mvtnorm)
8334 ("r-numderiv" ,r-numderiv)
8336 ("r-xtable" ,r-xtable)))
8337 (home-page "https://github.com/rvlenth/emmeans")
8338 (synopsis "Estimated marginal means, aka least-squares means")
8340 "This package provides tools to obtain @dfn{estimated marginal
8341 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8342 be used to compute contrasts or linear functions of EMMs, trends, and
8343 comparisons of slopes.")
8344 ;; Either version of the license.
8345 (license (list license:gpl2 license:gpl3))))
8347 (define-public r-pwr
8354 (uri (cran-uri "pwr" version))
8357 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8358 (build-system r-build-system)
8360 `(("r-knitr" ,r-knitr)))
8361 (home-page "https://github.com/heliosdrm/pwr")
8362 (synopsis "Basic functions for power analysis")
8364 "This package provides power analysis functions along the lines of
8366 (license license:gpl3+)))
8368 (define-public r-libcoin
8375 (uri (cran-uri "libcoin" version))
8378 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8379 (build-system r-build-system)
8380 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8381 (home-page "https://cran.r-project.org/web/packages/libcoin")
8382 (synopsis "Linear test statistics for permutation inference")
8384 "This package provides basic infrastructure for linear test statistics
8385 and permutation inference in the framework of Strasser and Weber (1999).")
8386 (license license:gpl2)))
8388 (define-public r-coin
8395 (uri (cran-uri "coin" version))
8398 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8399 (build-system r-build-system)
8401 `(("r-libcoin" ,r-libcoin)
8402 ("r-matrixstats" ,r-matrixstats)
8403 ("r-modeltools" ,r-modeltools)
8404 ("r-multcomp" ,r-multcomp)
8405 ("r-mvtnorm" ,r-mvtnorm)
8406 ("r-survival" ,r-survival)))
8407 (home-page "http://coin.r-forge.r-project.org")
8408 (synopsis "Conditional inference procedures in a permutation test framework")
8410 "This package provides conditional inference procedures for the general
8411 independence problem including two-sample, K-sample (non-parametric ANOVA),
8412 correlation, censored, ordered and multivariate problems.")
8413 (license license:gpl2)))
8415 (define-public r-bayesplot
8417 (name "r-bayesplot")
8422 (uri (cran-uri "bayesplot" version))
8425 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8426 (build-system r-build-system)
8428 `(("pandoc" ,ghc-pandoc)
8429 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8431 `(("r-dplyr" ,r-dplyr)
8432 ("r-ggplot2" ,r-ggplot2)
8433 ("r-ggridges" ,r-ggridges)
8435 ("r-reshape2" ,r-reshape2)
8436 ("r-rlang" ,r-rlang)
8437 ("r-tibble" ,r-tibble)
8438 ("r-tidyselect" ,r-tidyselect)))
8439 (home-page "https://mc-stan.org/bayesplot")
8440 (synopsis "Plotting for Bayesian models")
8442 "This package provides plotting functions for posterior analysis, model
8443 checking, and MCMC diagnostics. The package is designed not only to provide
8444 convenient functionality for users, but also a common set of functions that
8445 can be easily used by developers working on a variety of R packages for
8446 Bayesian modeling.")
8447 (license license:gpl3+)))
8449 (define-public r-tmb
8456 (uri (cran-uri "TMB" version))
8459 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8460 (properties `((upstream-name . "TMB")))
8461 (build-system r-build-system)
8463 `(("r-matrix" ,r-matrix)
8464 ("r-rcppeigen" ,r-rcppeigen)))
8465 (home-page "http://tmb-project.org")
8466 (synopsis "Template model builder: a general random effect tool")
8468 "With this tool, a user should be able to quickly implement complex
8469 random effect models through simple C++ templates. The package combines
8470 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8471 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8472 from R) to obtain an efficient implementation of the applied Laplace
8473 approximation with exact derivatives. Key features are: Automatic sparseness
8474 detection, parallelism through BLAS and parallel user templates.")
8475 (license license:gpl2)))
8477 (define-public r-sjstats
8484 (uri (cran-uri "sjstats" version))
8486 (base32 "0938ac6ixvkif07azd2msa8g3qnn9rabj6jg17almbysl83kg4nm"))))
8487 (build-system r-build-system)
8489 `(("r-bayestestr" ,r-bayestestr)
8490 ("r-broom" ,r-broom)
8491 ("r-dplyr" ,r-dplyr)
8492 ("r-effectsize" ,r-effectsize)
8493 ("r-emmeans" ,r-emmeans)
8494 ("r-insight" ,r-insight)
8496 ("r-magrittr" ,r-magrittr)
8498 ("r-modelr" ,r-modelr)
8499 ("r-parameters" ,r-parameters)
8500 ("r-performance" ,r-performance)
8501 ("r-purrr" ,r-purrr)
8502 ("r-rlang" ,r-rlang)
8503 ("r-sjlabelled" ,r-sjlabelled)
8504 ("r-sjmisc" ,r-sjmisc)
8505 ("r-tidyr" ,r-tidyr)))
8506 (home-page "https://github.com/strengejacke/sjstats")
8507 (synopsis "Functions for common statistical computations")
8509 "This package provides a collection of convenient functions for common
8510 statistical computations, which are not directly provided by R's @code{base}
8511 or @code{stats} packages. This package aims at providing, first, shortcuts
8512 for statistical measures, which otherwise could only be calculated with
8513 additional effort. Second, these shortcut functions are generic, and can be
8514 applied not only to vectors, but also to other objects as well. The focus of
8515 most functions lies on summary statistics or fit measures for regression
8516 models, including generalized linear models, mixed effects models and Bayesian
8518 (license license:gpl3)))
8520 (define-public r-glmmtmb
8527 (uri (cran-uri "glmmTMB" version))
8530 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8531 (properties `((upstream-name . "glmmTMB")))
8532 (build-system r-build-system)
8534 `(("r-lme4" ,r-lme4)
8535 ("r-matrix" ,r-matrix)
8537 ("r-rcppeigen" ,r-rcppeigen)
8540 `(("r-knitr" ,r-knitr))) ; for vignettes
8541 (home-page "https://github.com/glmmTMB")
8542 (synopsis "Generalized linear mixed models")
8544 "Fit linear and generalized linear mixed models with various extensions,
8545 including zero-inflation. The models are fitted using maximum likelihood
8546 estimation via the Template Model Builder. Random effects are assumed to be
8547 Gaussian on the scale of the linear predictor and are integrated out using the
8548 Laplace approximation. Gradients are calculated using automatic
8550 (license license:agpl3+)))
8552 (define-public r-bayestestr
8554 (name "r-bayestestr")
8559 (uri (cran-uri "bayestestR" version))
8562 "1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz"))))
8563 (properties `((upstream-name . "bayestestR")))
8564 (build-system r-build-system)
8566 `(("r-insight" ,r-insight)))
8568 `(("r-knitr" ,r-knitr)))
8569 (home-page "https://github.com/easystats/bayestestR")
8570 (synopsis "Describe Bayesian models and posterior distributions")
8572 "This package provides utilities to understand and describe posterior
8573 distributions and Bayesian models. It includes point-estimates such as
8574 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8575 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8576 ROPE percentage and pd).")
8577 (license license:gpl3)))
8579 (define-public r-performance
8581 (name "r-performance")
8586 (uri (cran-uri "performance" version))
8589 "0j6wmnwhfdd3v1a17qmg491q50579knjzscmyr4yk3xr0jbsbg8x"))))
8590 (build-system r-build-system)
8592 `(("r-bayestestr" ,r-bayestestr)
8593 ("r-insight" ,r-insight)))
8594 (home-page "https://easystats.github.io/performance/")
8595 (synopsis "Assessment of regression models performance")
8597 "This package provides utilities for computing measures to assess model
8598 quality, which are not directly provided by R's @code{base} or @code{stats}
8599 packages. These include e.g. measures like r-squared, intraclass correlation
8600 coefficient, root mean squared error or functions to check models for
8601 overdispersion, singularity or zero-inflation and more. Functions apply to a
8602 large variety of regression models, including generalized linear models, mixed
8603 effects models and Bayesian models.")
8604 (license license:gpl3)))
8606 (define-public r-ggeffects
8608 (name "r-ggeffects")
8613 (uri (cran-uri "ggeffects" version))
8616 "1y3yfb07jrr6vkc8hk6rp52l70dj7042jvqgjzllslzy7hx2jhyw"))))
8617 (build-system r-build-system)
8619 `(("r-insight" ,r-insight)
8621 ("r-sjlabelled" ,r-sjlabelled)))
8623 `(("r-knitr" ,r-knitr)))
8624 (home-page "https://github.com/strengejacke/ggeffects")
8625 (synopsis "Create tidy data frames of marginal effects for ggplot")
8627 "This package provides tools to compute marginal effects from statistical
8628 models and return the result as tidy data frames. These data frames are ready
8629 to use with the @code{ggplot2} package. Marginal effects can be calculated
8630 for many different models. Interaction terms, splines and polynomial terms
8631 are also supported. The two main functions are @code{ggpredict()} and
8632 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8633 results using @code{ggplot2}.")
8634 (license license:gpl3)))
8636 (define-public r-effectsize
8638 (name "r-effectsize")
8643 (uri (cran-uri "effectsize" version))
8646 "0kijp4wamkidaxysc11dd4vhvnm4wnbi87871wcbwn27k5b6i5dg"))))
8647 (properties `((upstream-name . "effectsize")))
8648 (build-system r-build-system)
8650 `(("r-bayestestr" ,r-bayestestr)
8651 ("r-insight" ,r-insight)
8652 ("r-parameters" ,r-parameters)))
8654 `(("r-knitr" ,r-knitr)))
8655 (home-page "https://github.com/easystats/effectsize")
8656 (synopsis "Indices of effect size and standardized parameters")
8658 "This package provides utilities to work with indices of effect size and
8659 standardized parameters for a wide variety of models, allowing computation and
8660 conversion of indices such as Cohen's d, r, odds, etc.")
8661 (license license:gpl3)))
8663 (define-public r-sjplot
8670 (uri (cran-uri "sjPlot" version))
8672 (base32 "0ip1rkjlhyf3axlc8qqss1qq1f0xrda890c1jmcbhm98wwjw264f"))))
8673 (properties `((upstream-name . "sjPlot")))
8674 (build-system r-build-system)
8676 `(("r-bayestestr" ,r-bayestestr)
8677 ("r-dplyr" ,r-dplyr)
8678 ("r-effectsize" ,r-effectsize)
8679 ("r-ggeffects" ,r-ggeffects)
8680 ("r-ggplot2" ,r-ggplot2)
8681 ("r-insight" ,r-insight)
8682 ("r-knitr" ,r-knitr)
8684 ("r-parameters" ,r-parameters)
8685 ("r-performance" ,r-performance)
8686 ("r-purrr" ,r-purrr)
8687 ("r-rlang" ,r-rlang)
8688 ("r-scales" ,r-scales)
8689 ("r-sjlabelled" ,r-sjlabelled)
8690 ("r-sjmisc" ,r-sjmisc)
8691 ("r-sjstats" ,r-sjstats)
8692 ("r-tidyr" ,r-tidyr)))
8694 `(("r-knitr" ,r-knitr)))
8695 (home-page "https://strengejacke.github.io/sjPlot/")
8696 (synopsis "Data visualization for statistics in social science")
8698 "This package represents a collection of plotting and table output
8699 functions for data visualization. Results of various statistical
8700 analyses (that are commonly used in social sciences) can be visualized using
8701 this package, including simple and cross tabulated frequencies, histograms,
8702 box plots, (generalized) linear models, mixed effects models, principal
8703 component analysis and correlation matrices, cluster analyses, scatter plots,
8704 stacked scales, effects plots of regression models (including interaction
8705 terms) and much more. This package supports labelled data.")
8706 (license license:gpl3)))
8708 (define-public r-ini
8715 (uri (cran-uri "ini" version))
8718 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8719 (build-system r-build-system)
8720 (home-page "https://github.com/dvdscripter/ini")
8721 (synopsis "Read and write configuration files")
8723 "This package provides tools to parse simple @code{.ini} configuration
8724 files to an structured list. Users can manipulate this resulting list with
8725 @code{lapply()} functions. This same structured list can be used to write
8726 back to file after modifications.")
8727 (license license:gpl3)))
8736 (uri (cran-uri "gh" version))
8739 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
8740 (build-system r-build-system)
8745 ("r-jsonlite" ,r-jsonlite)))
8746 (home-page "https://github.com/r-lib/gh#readme")
8747 (synopsis "Access the GitHub API via R")
8749 "This package provides a minimal R client to access the GitHub API.")
8750 (license license:expat)))
8759 (uri (cran-uri "fs" version))
8762 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
8763 (build-system r-build-system)
8765 `(("pkg-config" ,pkg-config)
8766 ("r-knitr" ,r-knitr)))
8767 (home-page "https://fs.r-lib.org")
8768 (synopsis "Cross-platform file system operations based on libuv")
8770 "This package provides a cross-platform interface to file system
8771 operations, built on top of the libuv C library.")
8772 (license license:gpl3)))
8774 (define-public r-clisymbols
8776 (name "r-clisymbols")
8781 (uri (cran-uri "clisymbols" version))
8784 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8785 (build-system r-build-system)
8786 (home-page "https://github.com/gaborcsardi/clisymbols")
8787 (synopsis "Unicode symbols at the R prompt")
8789 "This package provides a small subset of Unicode symbols, that are useful
8790 when building command line applications. They fall back to alternatives on
8791 terminals that do not support Unicode.")
8792 (license license:expat)))
8794 (define-public r-usethis
8801 (uri (cran-uri "usethis" version))
8804 "12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
8805 (build-system r-build-system)
8808 ("r-clipr" ,r-clipr)
8809 ("r-crayon" ,r-crayon)
8814 ("r-git2r" ,r-git2r)
8816 ("r-purrr" ,r-purrr)
8817 ("r-rematch2" ,r-rematch2)
8818 ("r-rlang" ,r-rlang)
8819 ("r-rprojroot" ,r-rprojroot)
8820 ("r-rstudioapi" ,r-rstudioapi)
8821 ("r-whisker" ,r-whisker)
8822 ("r-withr" ,r-withr)
8823 ("r-yaml" ,r-yaml)))
8824 (home-page "https://github.com/r-lib/usethis")
8825 (synopsis "Automate R package and project setup")
8827 "This package helps you to automate R package and project setup tasks
8828 that are otherwise performed manually. This includes setting up unit testing,
8829 test coverage, continuous integration, Git, GitHub integration, licenses,
8830 Rcpp, RStudio projects, and more.")
8831 (license license:gpl3)))
8833 (define-public r-sessioninfo
8835 (name "r-sessioninfo")
8840 (uri (cran-uri "sessioninfo" version))
8843 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8844 (build-system r-build-system)
8847 ("r-withr" ,r-withr)))
8848 (home-page "https://github.com/r-lib/sessioninfo#readme")
8849 (synopsis "R session information")
8851 "This package provides tools to query and print information about the
8852 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8853 more information about packages, and where they were installed from.")
8854 (license license:gpl2)))
8856 (define-public r-remotes
8863 (uri (cran-uri "remotes" version))
8866 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
8867 (build-system r-build-system)
8868 (home-page "https://github.com/r-lib/remotes#readme")
8869 (synopsis "R package installation from remote repositories")
8871 "Download and install R packages stored in GitHub, BitBucket, or plain
8872 subversion or git repositories. This package is a lightweight replacement of
8873 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8874 the code was copied over from @code{devtools}.")
8875 (license license:gpl2+)))
8877 (define-public r-xopen
8884 (uri (cran-uri "xopen" version))
8887 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8888 (build-system r-build-system)
8890 `(("r-processx" ,r-processx)))
8891 (home-page "https://github.com/r-lib/xopen#readme")
8892 (synopsis "Open system files, URLs, anything")
8894 "This package provides a cross-platform solution to open files,
8895 directories or URLs with their associated programs.")
8896 (license license:expat)))
8898 (define-public r-rcmdcheck
8900 (name "r-rcmdcheck")
8905 (uri (cran-uri "rcmdcheck" version))
8908 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8909 (build-system r-build-system)
8911 `(("r-callr" ,r-callr)
8913 ("r-crayon" ,r-crayon)
8915 ("r-digest" ,r-digest)
8916 ("r-pkgbuild" ,r-pkgbuild)
8917 ("r-prettyunits" ,r-prettyunits)
8919 ("r-rprojroot" ,r-rprojroot)
8920 ("r-sessioninfo" ,r-sessioninfo)
8921 ("r-withr" ,r-withr)
8922 ("r-xopen" ,r-xopen)))
8923 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8924 (synopsis "Run R CMD check from R and capture results")
8926 "Run @code{R CMD check} from R programmatically, and capture the results
8927 of the individual checks.")
8928 (license license:expat)))
8930 (define-public r-rapportools
8932 (name "r-rapportools")
8937 (uri (cran-uri "rapportools" version))
8940 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8941 (build-system r-build-system)
8943 `(("r-pander" ,r-pander)
8945 ("r-reshape" ,r-reshape)))
8946 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8947 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8949 "This package provides helper functions that act as wrappers to more
8950 advanced statistical methods with the advantage of having sane defaults for
8952 (license license:agpl3+)))
8954 (define-public r-pander
8961 (uri (cran-uri "pander" version))
8964 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8965 (build-system r-build-system)
8967 `(("r-digest" ,r-digest)
8968 ("r-rcpp" ,r-rcpp)))
8969 (home-page "https://rapporter.github.io/pander")
8970 (synopsis "Render R objects into Pandoc's markdown")
8972 "The main aim of the pander R package is to provide a minimal and easy
8973 tool for rendering R objects into Pandoc's markdown. The package is also
8974 capable of exporting/converting complex Pandoc documents (reports) in various
8976 ;; This package is licensed under either the AGPLv3+ or the very rarely
8978 (license license:agpl3+)))
8980 (define-public r-summarytools
8982 (name "r-summarytools")
8987 (uri (cran-uri "summarytools" version))
8990 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
8991 (build-system r-build-system)
8993 `(("r-base64enc" ,r-base64enc)
8994 ("r-checkmate" ,r-checkmate)
8995 ("r-dplyr" ,r-dplyr)
8996 ("r-htmltools" ,r-htmltools)
8997 ("r-lubridate" ,r-lubridate)
8998 ("r-magick" ,r-magick)
8999 ("r-matrixstats" ,r-matrixstats)
9000 ("r-pander" ,r-pander)
9002 ("r-rapportools" ,r-rapportools)
9003 ("r-tibble" ,r-tibble)
9004 ("r-tidyr" ,r-tidyr)))
9005 (home-page "https://github.com/dcomtois/summarytools")
9006 (synopsis "Tools to quickly and neatly summarize data")
9008 "This package provides tools for data frame summaries, cross-tabulations,
9009 weight-enabled frequency tables and common univariate statistics in concise
9010 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9011 good point-of-entry for exploring data, both for experienced and new R
9013 (license license:gpl2)))
9015 (define-public r-lsei
9022 (uri (cran-uri "lsei" version))
9025 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
9026 (build-system r-build-system)
9028 `(("gfortran" ,gfortran)))
9029 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9030 (synopsis "Solve regression problems under equality/inequality constraints")
9032 "It contains functions that solve least squares linear regression
9033 problems under linear equality/inequality constraints. Functions for solving
9034 quadratic programming problems are also available, which transform such
9035 problems into least squares ones first.")
9036 (license license:gpl2+)))
9038 (define-public r-npsurv
9045 (uri (cran-uri "npsurv" version))
9048 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
9049 (build-system r-build-system)
9051 `(("r-lsei" ,r-lsei)))
9052 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9053 (synopsis "Nonparametric survival analysis")
9055 "This package contains functions for non-parametric survival analysis of
9056 exact and interval-censored observations.")
9057 (license license:gpl2+)))
9059 (define-public r-clusteval
9061 (name "r-clusteval")
9066 (uri (cran-uri "clusteval" version))
9069 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9070 (build-system r-build-system)
9072 `(("r-mvtnorm" ,r-mvtnorm)
9073 ("r-rcpp" ,r-rcpp)))
9074 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9075 (synopsis "Evaluation of clustering algorithms")
9077 "This R package provides a suite of tools to evaluate clustering
9078 algorithms, clusterings, and individual clusters.")
9079 (license license:expat)))
9081 (define-public r-tweedie
9088 (uri (cran-uri "tweedie" version))
9091 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9092 (build-system r-build-system)
9093 (native-inputs `(("gfortran" ,gfortran)))
9094 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9095 (synopsis "Evaluation of Tweedie exponential family models")
9097 "Maximum likelihood computations for Tweedie families, including the
9098 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9099 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9100 and related methods.")
9101 (license license:gpl2+)))
9103 (define-public r-rcppgsl
9110 (uri (cran-uri "RcppGSL" version))
9112 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9113 (properties `((upstream-name . "RcppGSL")))
9114 (build-system r-build-system)
9116 `(("r-rcpp" ,r-rcpp)
9119 `(("r-knitr" ,r-knitr))) ; for vignettes
9120 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9121 (synopsis "Rcpp integration for GSL vectors and matrices")
9123 "The GNU Scientific Library (or GSL) is a collection of numerical
9124 routines for scientific computing. It is particularly useful for C and C++
9125 programs as it provides a standard C interface to a wide range of mathematical
9126 routines. There are over 1000 functions in total with an extensive test
9127 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9128 structures and R using concepts from Rcpp which is itself a package that eases
9129 the interfaces between R and C++.")
9130 (license license:gpl2+)))
9132 (define-public r-mvabund
9139 (uri (cran-uri "mvabund" version))
9142 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9143 (build-system r-build-system)
9145 `(("r-mass" ,r-mass)
9147 ("r-rcppgsl" ,r-rcppgsl)
9148 ("r-statmod" ,r-statmod)
9149 ("r-tweedie" ,r-tweedie)))
9150 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9151 (synopsis "Statistical methods for analysing multivariate abundance data")
9153 "This package provides a set of tools for displaying, modeling and
9154 analysing multivariate abundance data in community ecology.")
9155 (license license:lgpl2.1+)))
9157 (define-public r-afex
9164 (uri (cran-uri "afex" version))
9167 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9168 (build-system r-build-system)
9172 ("r-lmertest" ,r-lmertest)
9173 ("r-pbkrtest" ,r-pbkrtest)
9174 ("r-reshape2" ,r-reshape2)))
9176 `(("r-knitr" ,r-knitr)))
9177 (home-page "https://afex.singmann.science/")
9178 (synopsis "Analysis of factorial experiments")
9180 "This package provides convenience functions for analyzing factorial
9181 experiments using ANOVA or mixed models.")
9182 (license license:gpl2+)))
9184 (define-public r-lmertest
9191 (uri (cran-uri "lmerTest" version))
9194 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9195 (properties `((upstream-name . "lmerTest")))
9196 (build-system r-build-system)
9198 `(("r-ggplot2" ,r-ggplot2)
9201 ("r-numderiv" ,r-numderiv)))
9202 (home-page "https://github.com/runehaubo/lmerTestR")
9203 (synopsis "Tests in linear mixed effects models")
9205 "This package provides p-values in type I, II or III anova and summary
9206 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9207 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9208 package. Model selection methods include step, drop1 and anova-like tables
9209 for random effects (ranova). Methods for Least-Square means (LS-means) and
9210 tests of linear contrasts of fixed effects are also available.")
9211 (license license:gpl2+)))
9213 (define-public r-r2glmm
9220 (uri (cran-uri "r2glmm" version))
9223 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9224 (build-system r-build-system)
9226 `(("r-afex" ,r-afex)
9227 ("r-data-table" ,r-data-table)
9228 ("r-dplyr" ,r-dplyr)
9229 ("r-ggplot2" ,r-ggplot2)
9230 ("r-gridextra" ,r-gridextra)
9231 ("r-lmertest" ,r-lmertest)
9233 ("r-matrix" ,r-matrix)
9235 ("r-pbkrtest" ,r-pbkrtest)))
9236 (home-page "https://github.com/bcjaeger/r2glmm")
9237 (synopsis "Compute R squared for mixed (multilevel) models")
9239 "This package computes model and semi partial R squared with confidence
9240 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9241 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9242 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9244 (license license:gpl2)))
9246 (define-public r-weights
9253 (uri (cran-uri "weights" version))
9256 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9257 (build-system r-build-system)
9259 `(("r-gdata" ,r-gdata)
9260 ("r-hmisc" ,r-hmisc)
9261 ("r-mice" ,r-mice)))
9263 "https://cran.r-project.org/web/packages/weights/")
9264 (synopsis "Weighting and weighted statistics")
9265 (description "This package Provides a variety of functions for producing
9266 simple weighted statistics, such as weighted Pearson's correlations, partial
9267 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9268 includes some software for quickly recoding survey data and plotting point
9269 estimates from interaction terms in regressions (and multiply imputed
9270 regressions). NOTE: Weighted partial correlation calculations pulled to
9272 (license license:gpl2+)))
9274 (define-public r-rcppannoy
9276 (name "r-rcppannoy")
9281 (uri (cran-uri "RcppAnnoy" version))
9284 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9285 (properties `((upstream-name . "RcppAnnoy")))
9286 (build-system r-build-system)
9288 `(("r-rcpp" ,r-rcpp)))
9289 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9290 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9292 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9293 for efficient memory usage as well an ability to load from and save to disk.
9294 This package provides an R interface.")
9295 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9297 (license (list license:gpl2+ license:asl2.0))))
9299 (define-public r-rcpphnsw
9306 (uri (cran-uri "RcppHNSW" version))
9309 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9310 (properties `((upstream-name . "RcppHNSW")))
9311 (build-system r-build-system)
9312 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9313 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9314 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9316 "Hnswlib is a C++ library for approximate nearest neighbors. This
9317 package provides a minimal R interface by relying on the Rcpp package.")
9318 ;; hnswlib is released under Version 2.0 of the Apache License.
9319 (license (list license:gpl3 license:asl2.0))))
9321 (define-public r-rcppparallel
9323 (name "r-rcppparallel")
9328 (uri (cran-uri "RcppParallel" version))
9331 "1mhd6vp47xmfw533h0pkvydv96m57fspvd85g8m7iqb5rcxvhhdb"))))
9332 (properties `((upstream-name . "RcppParallel")))
9333 (build-system r-build-system)
9334 (home-page "https://rcppcore.github.io/RcppParallel/")
9335 (synopsis "Parallel programming tools for Rcpp")
9337 "This package provides high level functions for parallel programming with
9338 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9339 the work of a standard serial @code{for} loop into a parallel one and the
9340 @code{parallelReduce()} function can be used for accumulating aggregates or
9342 (license license:gpl2)))
9344 (define-public r-ncdf4
9351 (uri (cran-uri "ncdf4" version))
9354 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9355 (build-system r-build-system)
9357 `(("netcdf" ,netcdf)
9359 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9360 (synopsis "R interface to Unidata netCDF format data files")
9362 "This package provides a high-level R interface to data files written
9363 using Unidata's netCDF library (version 4 or earlier), which are binary data
9364 files that are portable across platforms and include metadata information in
9365 addition to the data sets. Using this package, netCDF files can be opened and
9366 data sets read in easily. It is also easy to create new netCDF dimensions,
9367 variables, and files, in either version 3 or 4 format, and manipulate existing
9369 (license license:gpl3+)))
9371 (define-public r-biocmanager
9373 (name "r-biocmanager")
9378 (uri (cran-uri "BiocManager" version))
9380 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9381 (properties `((upstream-name . "BiocManager")))
9382 (build-system r-build-system)
9383 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9384 (synopsis "Access the Bioconductor project package repository")
9386 "This package provides a convenient tool to install and update
9387 Bioconductor packages.")
9388 (license license:artistic2.0)))
9390 (define-public r-rgl
9393 (version "0.100.50")
9397 (uri (cran-uri "rgl" version))
9400 "165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay"))))
9401 (build-system r-build-system)
9403 `(("pkg-config" ,pkg-config)))
9405 `(("freetype" ,freetype)
9409 ("ghc-pandoc" ,ghc-pandoc)
9412 `(("r-crosstalk" ,r-crosstalk)
9413 ("r-htmltools" ,r-htmltools)
9414 ("r-htmlwidgets" ,r-htmlwidgets)
9415 ("r-jsonlite" ,r-jsonlite)
9416 ("r-knitr" ,r-knitr)
9417 ("r-magrittr" ,r-magrittr)
9418 ("r-manipulatewidget" ,r-manipulatewidget)
9419 ("r-shiny" ,r-shiny)))
9420 (home-page "https://r-forge.r-project.org/projects/rgl/")
9421 (synopsis "3D visualization using OpenGL")
9423 "This package provides medium to high level functions for 3D interactive graphics,
9424 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9425 as functions for constructing representations of geometric
9426 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9427 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9428 image formats, including PNG, Postscript, SVG, PGF.")
9429 ;; Any version of the GPL.
9430 (license (list license:gpl2+ license:gpl3+))))
9432 (define-public r-multicool
9434 (name "r-multicool")
9439 (uri (cran-uri "multicool" version))
9442 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9443 (build-system r-build-system)
9444 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9445 (home-page "https://cran.r-project.org/web/packages/multicool/")
9446 (synopsis "Permutations of multisets in cool-lex order")
9448 "This package provides a set of tools to permute multisets without loops
9449 or hash tables and to generate integer partitions. Cool-lex order is similar
9450 to colexicographical order.")
9451 (license license:gpl2)))
9453 (define-public r-misc3d
9460 (uri (cran-uri "misc3d" version))
9463 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9464 (build-system r-build-system)
9465 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9466 (synopsis "Miscellaneous 3D Plots")
9468 "This package provides a collection of miscellaneous 3d plots, including
9470 ;; Any version of the GPL.
9471 (license (list license:gpl2+ license:gpl3+))))
9480 (uri (cran-uri "ks" version))
9482 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9483 (build-system r-build-system)
9486 ("r-kernlab" ,r-kernlab)
9487 ("r-kernsmooth" ,r-kernsmooth)
9488 ("r-matrix" ,r-matrix)
9489 ("r-mclust" ,r-mclust)
9491 ("r-multicool" ,r-multicool)
9492 ("r-mvtnorm" ,r-mvtnorm)))
9493 (home-page "http://www.mvstat.net/tduong/")
9494 (synopsis "Kernel smoothing")
9496 "This package provides kernel smoothers for univariate and multivariate
9497 data, including density functions, density derivatives, cumulative
9498 distributions, modal clustering, discriminant analysis, and two-sample
9499 hypothesis testing.")
9500 ;; Either version of the GPL.
9501 (license (list license:gpl2 license:gpl3))))
9503 (define-public r-feature
9510 (uri (cran-uri "feature" version))
9513 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9514 (build-system r-build-system)
9517 ("r-misc3d" ,r-misc3d)
9519 (home-page "http://www.mvstat.net/tduong/")
9520 (synopsis "Inferential feature significance for kernel density estimation")
9522 "The feature package contains functions to display and compute kernel
9523 density estimates, significant gradient and significant curvature regions.
9524 Significant gradient and/or curvature regions often correspond to significant
9525 features (e.g. local modes).")
9526 ;; Either version of the GPL.
9527 (license (list license:gpl2 license:gpl3))))
9529 (define-public r-arm
9536 (uri (cran-uri "arm" version))
9539 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9540 (build-system r-build-system)
9542 `(("r-abind" ,r-abind)
9546 ("r-matrix" ,r-matrix)
9547 ("r-nlme" ,r-nlme)))
9548 (home-page "https://cran.r-project.org/web/packages/arm/")
9549 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9551 "This package provides functions to accompany A. Gelman and J. Hill,
9552 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9553 University Press, 2007.")
9554 (license license:gpl3+)))
9556 (define-public r-circular
9563 (uri (cran-uri "circular" version))
9566 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9567 (build-system r-build-system)
9569 `(("r-boot" ,r-boot)
9570 ("r-mvtnorm" ,r-mvtnorm)))
9572 `(("gfortran" ,gfortran)))
9573 (home-page "https://cran.r-project.org/web/packages/circular/")
9574 (synopsis "Circular statistics")
9576 "This package provides tools for circular statistics, from \"Topics in
9577 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9579 (license license:gpl2+)))
9581 (define-public r-activity
9588 (uri (cran-uri "activity" version))
9591 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9592 (build-system r-build-system)
9594 `(("r-circular" ,r-circular)
9595 ("r-insol" ,r-insol)
9596 ("r-pbapply" ,r-pbapply)))
9597 (home-page "https://cran.r-project.org/web/packages/activity/")
9598 (synopsis "Animal activity statistics")
9600 "This package provides functions to fit kernel density functions to
9601 animal activity time data; plot activity distributions; quantify overall
9602 levels of activity; statistically compare activity metrics through
9603 bootstrapping; and evaluate variation in linear variables with time (or other
9604 circular variables).")
9605 (license license:gpl3)))
9607 (define-public r-ouch
9614 (uri (cran-uri "ouch" version))
9617 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9618 (build-system r-build-system)
9619 (propagated-inputs `(("r-subplex" ,r-subplex)))
9620 (home-page "https://kingaa.github.io/ouch/")
9621 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9623 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9624 for evolution along a phylogenetic tree.")
9625 (license license:gpl2+)))
9627 (define-public r-fmsb
9634 (uri (cran-uri "fmsb" version))
9637 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9638 (build-system r-build-system)
9639 (home-page "http://minato.sip21c.org/msb/")
9640 (synopsis "Functions for medical statistics book with demographic data")
9642 "This package provides several utility functions for the book entitled
9643 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9644 Japan, 2007) with Japanese demographic data and some demographic analysis
9645 related functions.")
9646 (license license:gpl2+)))
9648 (define-public r-stabledist
9650 (name "r-stabledist")
9655 (uri (cran-uri "stabledist" version))
9658 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9659 (build-system r-build-system)
9660 (home-page "https://www.rmetrics.org")
9661 (synopsis "Stable distribution functions")
9663 "This package provides density, probability and quantile functions, and
9664 random number generation for (skew) stable distributions, using the
9665 parametrizations of Nolan.")
9666 (license license:gpl2+)))
9668 (define-public r-gsl
9675 (uri (cran-uri "gsl" version))
9678 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9679 (build-system r-build-system)
9682 (home-page "https://cran.r-project.org/web/packages/gsl")
9683 (synopsis "Wrapper for the GNU Scientific Library")
9685 "This package provides an R wrapper for the special functions and quasi
9686 random number generators of the GNU Scientific Library.")
9687 (license license:gpl2+)))
9689 (define-public r-adgoftest
9691 (name "r-adgoftest")
9696 (uri (cran-uri "ADGofTest" version))
9699 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9700 (properties `((upstream-name . "ADGofTest")))
9701 (build-system r-build-system)
9702 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9703 (synopsis "Anderson-Darling GoF test")
9705 "This package provides an implementation of the Anderson-Darling GoF test
9706 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9707 Anderson-Darling Distribution\".")
9708 ;; Any version of the GPL.
9709 (license license:gpl3+)))
9711 (define-public r-softimpute
9713 (name "r-softimpute")
9718 (uri (cran-uri "softImpute" version))
9721 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9722 (properties `((upstream-name . "softImpute")))
9723 (build-system r-build-system)
9725 `(("r-matrix" ,r-matrix)))
9727 `(("gfortran" ,gfortran)))
9728 (home-page "https://cran.r-project.org/web/packages/softImpute")
9729 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9731 "This package provides iterative methods for matrix completion that use
9732 nuclear-norm regularization. The package includes procedures for centering
9733 and scaling rows, columns or both, and for computing low-rank @dfn{single
9734 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9736 (license license:gpl2)))
9738 (define-public r-fftwtools
9740 (name "r-fftwtools")
9745 (uri (cran-uri "fftwtools" version))
9748 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9749 (build-system r-build-system)
9750 (inputs `(("fftw" ,fftw)))
9751 (home-page "https://github.com/krahim/fftwtools")
9752 (synopsis "Wrapper for FFTW3")
9754 "This package provides a wrapper for several FFTW functions. It provides
9755 access to the two-dimensional FFT, the multivariate FFT, and the
9756 one-dimensional real to complex FFT using the FFTW3 library. The package
9757 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9758 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9759 The FFT functions have a parameter that allows them to not return the
9760 redundant complex conjugate when the input is real data.")
9761 (license license:gpl2+)))
9763 (define-public r-tiff
9770 (uri (cran-uri "tiff" version))
9773 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9774 (build-system r-build-system)
9776 `(("libtiff" ,libtiff)
9777 ("libjpeg" ,libjpeg)
9779 (home-page "https://www.rforge.net/tiff/")
9780 (synopsis "Read and write TIFF images")
9782 "This package provides an easy and simple way to read, write and display
9783 bitmap images stored in the TIFF format. It can read and write both files and
9784 in-memory raw vectors.")
9785 ;; Either of these two license versions.
9786 (license (list license:gpl2 license:gpl3))))
9788 (define-public r-nlp
9795 (uri (cran-uri "NLP" version))
9798 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9799 (properties `((upstream-name . "NLP")))
9800 (build-system r-build-system)
9801 (home-page "https://cran.r-project.org/web/packages/NLP/")
9802 (synopsis "Natural language processing infrastructure")
9804 "This package provides basic classes and methods for Natural Language
9806 (license license:gpl3)))
9815 (uri (cran-uri "tm" version))
9818 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9819 (properties `((upstream-name . "tm")))
9820 (build-system r-build-system)
9826 ("r-xml2" ,r-xml2)))
9827 (home-page "http://tm.r-forge.r-project.org/")
9828 (synopsis "Text mining package")
9830 "This package provides a framework for text mining applications within R.")
9831 (license license:gpl3)))
9833 (define-public r-waveslim
9840 (uri (cran-uri "waveslim" version))
9843 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
9844 (build-system r-build-system)
9846 `(("gfortran" ,gfortran)))
9847 (home-page "http://waveslim.blogspot.com")
9848 (synopsis "Basic wavelet routines for signal processing")
9850 "This package provides basic wavelet routines for time series (1D),
9851 image (2D) and array (3D) analysis. The code provided here is based on
9852 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9853 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9854 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9855 pairs (Selesnick 2001, 2002).")
9856 (license license:bsd-3)))
9858 (define-public r-wordcloud
9860 (name "r-wordcloud")
9865 (uri (cran-uri "wordcloud" version))
9868 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9869 (build-system r-build-system)
9871 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9873 ;; The "tm" package is only "suggested" according to CRAN, but the
9874 ;; wordcloud package cannot be loaded without it.
9876 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9877 (synopsis "Word clouds")
9879 "This package provides functionality to create pretty word clouds,
9880 visualize differences and similarity between documents, and avoid
9881 over-plotting in scatter plots with text.")
9882 (license license:lgpl2.1)))
9884 (define-public r-colorramps
9886 (name "r-colorramps")
9891 (uri (cran-uri "colorRamps" version))
9894 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9895 (properties `((upstream-name . "colorRamps")))
9896 (build-system r-build-system)
9897 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9898 (synopsis "Build color tables")
9899 (description "This package provides features to build gradient color
9901 ;; Any version of the GPL
9902 (license license:gpl3+)))
9904 (define-public r-tidytree
9911 (uri (cran-uri "tidytree" version))
9913 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
9914 (build-system r-build-system)
9917 ("r-dplyr" ,r-dplyr)
9918 ("r-lazyeval" ,r-lazyeval)
9919 ("r-magrittr" ,r-magrittr)
9920 ("r-rlang" ,r-rlang)
9921 ("r-tibble" ,r-tibble)))
9923 `(("r-knitr" ,r-knitr)))
9924 (home-page "https://github.com/GuangchuangYu/tidytree")
9925 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9927 "Phylogenetic trees generally contain multiple components including nodes,
9928 edges, branches and associated data. This package provides an approach to
9929 convert tree objects to tidy data frames. It also provides tidy interfaces to
9930 manipulate tree data.")
9931 (license license:artistic2.0)))
9933 (define-public r-rvcheck
9940 (uri (cran-uri "rvcheck" version))
9942 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
9943 (build-system r-build-system)
9945 `(("r-biocmanager" ,r-biocmanager)
9946 ("r-rlang" ,r-rlang)))
9947 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9948 (synopsis "R package version check")
9950 "This package provides tools to check the latest release version of R and
9951 R packages (on CRAN, Bioconductor or Github).")
9952 (license license:artistic2.0)))
9954 (define-public r-docopt
9961 (uri (cran-uri "docopt" version))
9964 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9965 (build-system r-build-system)
9966 (home-page "https://github.com/docopt/docopt.R")
9967 (synopsis "Command-line interface specification language")
9969 "This package enables you to define a command-line interface by just
9970 giving it a description in the specific format.")
9971 (license license:expat)))
9973 (define-public r-sparsesvd
9975 (name "r-sparsesvd")
9980 (uri (cran-uri "sparsesvd" version))
9983 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9984 (build-system r-build-system)
9985 (propagated-inputs `(("r-matrix" ,r-matrix)))
9986 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9987 (synopsis "Sparse truncated singular value decomposition")
9989 "This package provides a Wrapper around the SVDLIBC library
9990 for (truncated) singular value decomposition of a sparse matrix. Currently,
9991 only sparse real matrices in Matrix package format are supported.")
9992 ;; SVDLIBC is released under BSD-2. The R interface is released under
9994 (license (list license:bsd-3 license:bsd-2))))
9996 (define-public r-speedglm
10003 (uri (cran-uri "speedglm" version))
10006 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10007 (build-system r-build-system)
10009 `(("r-mass" ,r-mass)
10010 ("r-matrix" ,r-matrix)))
10011 (home-page "https://cran.r-project.org/web/packages/speedglm")
10012 (synopsis "Fit linear and generalized linear models to large data sets")
10014 "This package provides tools for fitting linear models and generalized
10015 linear models to large data sets by updating algorithms.")
10016 ;; Any version of the GPL
10017 (license license:gpl2+)))
10019 (define-public r-densityclust
10021 (name "r-densityclust")
10026 (uri (cran-uri "densityClust" version))
10029 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10030 (properties `((upstream-name . "densityClust")))
10031 (build-system r-build-system)
10034 ("r-ggplot2" ,r-ggplot2)
10035 ("r-ggrepel" ,r-ggrepel)
10036 ("r-gridextra" ,r-gridextra)
10037 ("r-rcolorbrewer" ,r-rcolorbrewer)
10039 ("r-rtsne" ,r-rtsne)))
10040 (home-page "https://cran.r-project.org/web/packages/densityClust")
10041 (synopsis "Clustering by fast search and find of density peaks")
10043 "This package provides an improved implementation (based on k-nearest
10044 neighbors) of the density peak clustering algorithm, originally described by
10045 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10046 large datasets (> 100,000 samples) very efficiently.")
10047 (license license:gpl2+)))
10049 (define-public r-combinat
10051 (name "r-combinat")
10056 (uri (cran-uri "combinat" version))
10059 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10060 (build-system r-build-system)
10061 (home-page "https://cran.r-project.org/web/packages/combinat")
10062 (synopsis "Combinatorics utilities")
10063 (description "This package provides assorted routines for combinatorics.")
10064 (license license:gpl2)))
10066 (define-public r-qlcmatrix
10068 (name "r-qlcmatrix")
10073 (uri (cran-uri "qlcMatrix" version))
10076 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10077 (properties `((upstream-name . "qlcMatrix")))
10078 (build-system r-build-system)
10080 `(("r-docopt" ,r-docopt)
10081 ("r-matrix" ,r-matrix)
10083 ("r-sparsesvd" ,r-sparsesvd)))
10084 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10085 (synopsis "Sparse matrix functions for quantitative language comparison")
10087 "This package provides an extension of the functionality of the Matrix
10088 package for using sparse matrices. Some of the functions are very general,
10089 while other are highly specific for the special data format used for
10090 @dfn{quantitative language comparison} (QLC).")
10091 (license license:gpl3)))
10093 (define-public r-ddrtree
10100 (uri (cran-uri "DDRTree" version))
10103 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10104 (properties `((upstream-name . "DDRTree")))
10105 (build-system r-build-system)
10108 ("r-irlba" ,r-irlba)
10110 ("r-rcppeigen" ,r-rcppeigen)))
10111 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10112 (synopsis "Learning principal graphs with DDRTree")
10114 "This package provides an implementation of the framework of
10115 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10116 dimensional space while constructs a principal tree which passes through the
10117 middle of the data simultaneously. DDRTree shows superiority to
10118 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10119 intrinsic structure of single cell genomics data. In general, it could be
10120 used to reconstruct the temporal progression as well as the bifurcation
10121 structure of any data type.")
10122 (license license:asl2.0)))
10124 (define-public r-corpcor
10131 (uri (cran-uri "corpcor" version))
10134 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10135 (build-system r-build-system)
10136 (home-page "http://strimmerlab.org/software/corpcor/")
10137 (synopsis "Efficient estimation of covariance and (partial) correlation")
10139 "This package implements a James-Stein-type shrinkage estimator for the
10140 covariance matrix, with separate shrinkage for variances and correlations.
10141 Furthermore, functions are available for fast singular value decomposition,
10142 for computing the pseudoinverse, and for checking the rank and positive
10143 definiteness of a matrix.")
10144 (license license:gpl3+)))
10146 (define-public r-rspectra
10148 (name "r-rspectra")
10153 (uri (cran-uri "RSpectra" version))
10156 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10157 (properties `((upstream-name . "RSpectra")))
10158 (build-system r-build-system)
10160 `(("r-matrix" ,r-matrix)
10162 ("r-rcppeigen" ,r-rcppeigen)))
10163 (home-page "https://github.com/yixuan/RSpectra")
10164 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10166 "This package provides an R interface to the Spectra library for
10167 large-scale eigenvalue and SVD problems. It is typically used to compute a
10168 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10169 which is usually more efficient than @code{eigen()} if k << n.")
10171 (license license:mpl2.0)))
10173 (define-public r-vbsr
10180 (uri (cran-uri "vbsr" version))
10183 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10184 (build-system r-build-system)
10185 (home-page "https://cran.r-project.org/web/packages/vbsr")
10186 (synopsis "Variational Bayes spike regression regularized linear models")
10188 "This package provides an efficient algorithm for solving ultra-sparse
10189 regularized regression models using a variational Bayes algorithm with a spike
10190 prior. The algorithm is solved on a path, with coordinate updates, and is
10191 capable of generating very sparse models. Very general model
10192 diagnostics for controlling type-1 errors are also provided.")
10193 (license license:gpl2)))
10195 (define-public r-flare
10198 (version "1.6.0.2")
10202 (uri (cran-uri "flare" version))
10205 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10206 (build-system r-build-system)
10208 `(("r-igraph" ,r-igraph)
10209 ("r-lattice" ,r-lattice)
10211 ("r-matrix" ,r-matrix)))
10212 (home-page "https://cran.r-project.org/web/packages/flare")
10213 (synopsis "Family of Lasso regression implementations")
10215 "This package provides implementations of a family of Lasso variants
10216 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10217 high dimensional sparse linear models.")
10218 (license license:gpl2)))
10220 (define-public r-lassopv
10227 (uri (cran-uri "lassopv" version))
10230 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10231 (build-system r-build-system)
10232 (propagated-inputs `(("r-lars" ,r-lars)))
10233 (home-page "https://github.com/lingfeiwang/lassopv")
10234 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10236 "This package enables you to estimate the p-values for predictors x
10237 against target variable y in Lasso regression, using the regularization
10238 strength when each predictor enters the active set of regularization path for
10239 the first time as the statistic.")
10240 (license license:gpl3)))
10242 (define-public r-splitstackshape
10244 (name "r-splitstackshape")
10249 (uri (cran-uri "splitstackshape" version))
10252 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10253 (build-system r-build-system)
10255 `(("r-data-table" ,r-data-table)))
10256 (home-page "https://github.com/mrdwab/splitstackshape")
10257 (synopsis "Stack and reshape datasets after splitting concatenated values")
10259 "Online data collection tools like Google Forms often export
10260 multiple-response questions with data concatenated in cells. The
10261 @code{concat.split} (cSplit) family of functions provided by this package
10262 splits such data into separate cells. This package also includes functions to
10263 stack groups of columns and to reshape wide data, even when the data are
10264 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10265 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10267 (license license:gpl3)))
10269 (define-public r-tfmpvalue
10271 (name "r-tfmpvalue")
10276 (uri (cran-uri "TFMPvalue" version))
10279 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10280 (properties `((upstream-name . "TFMPvalue")))
10281 (build-system r-build-system)
10282 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10283 (home-page "https://github.com/ge11232002/TFMPvalue")
10284 (synopsis "P-value computation for position weight matrices")
10286 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10287 identification from sequence/alignments, we are interested in the significance
10288 of certain match scores. TFMPvalue provides the accurate calculation of a
10289 p-value with a score threshold for position weight matrices, or the score with
10290 a given p-value. It is an interface to code originally made available by
10291 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10292 Touzet and Varre (2007).")
10293 (license license:gpl2)))
10295 (define-public r-rnifti
10302 (uri (cran-uri "RNifti" version))
10305 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10306 (properties `((upstream-name . "RNifti")))
10307 (build-system r-build-system)
10308 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10309 (home-page "https://github.com/jonclayden/RNifti")
10310 (synopsis "Fast R and C++ access to NIfTI images")
10312 "This package provides very fast read and write access to images stored
10313 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10314 compiled C and interpreted R code. It also provides a C/C++ API that can be
10315 used by other packages.")
10316 (license license:gpl2)))
10318 (define-public r-shades
10325 (uri (cran-uri "shades" version))
10328 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10329 (build-system r-build-system)
10330 (home-page "https://github.com/jonclayden/shades")
10331 (synopsis "Simple color manipulation")
10333 "This package provides functions for easily manipulating colors,
10334 creating color scales and calculating color distances.")
10335 (license license:bsd-3)))
10337 (define-public r-ore
10344 (uri (cran-uri "ore" version))
10346 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10347 (build-system r-build-system)
10348 (home-page "https://github.com/jonclayden/ore")
10349 (synopsis "R interface to the Onigmo regular expression library")
10351 "This package provides an alternative to R's built-in functionality for
10352 handling regular expressions, based on the Onigmo library. It offers
10353 first-class compiled regex objects, partial matching and function-based
10354 substitutions, amongst other features.")
10355 (license license:bsd-3)))
10357 (define-public r-reportr
10364 (uri (cran-uri "reportr" version))
10367 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10368 (build-system r-build-system)
10369 (propagated-inputs `(("r-ore" ,r-ore)))
10370 (home-page "https://github.com/jonclayden/reportr")
10371 (synopsis "General message and error reporting system")
10373 "This package provides a system for reporting messages, which offers
10374 certain useful features over the standard R system, such as the incorporation
10375 of output consolidation, message filtering, assertions, expression
10376 substitution, automatic generation of stack traces for debugging, and
10377 conditional reporting based on the current \"output level\".")
10378 (license license:gpl2)))
10380 (define-public r-tractor-base
10382 (name "r-tractor-base")
10387 (uri (cran-uri "tractor.base" version))
10390 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10391 (properties `((upstream-name . "tractor.base")))
10392 (build-system r-build-system)
10395 ("r-reportr" ,r-reportr)
10396 ("r-rnifti" ,r-rnifti)
10397 ("r-shades" ,r-shades)))
10398 (home-page "https://www.tractor-mri.org.uk")
10399 (synopsis "Read, manipulate and visualize magnetic resonance images")
10401 "This package provides functions for working with magnetic resonance
10402 images. It supports reading and writing of popular file formats (DICOM,
10403 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10404 visualization; flexible image manipulation; metadata and sparse image
10406 (license license:gpl2)))
10408 (define-public r-grimport
10410 (name "r-grimport")
10415 (uri (cran-uri "grImport" version))
10418 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10419 (properties `((upstream-name . "grImport")))
10420 (build-system r-build-system)
10422 `(("ghostscript" ,ghostscript)))
10424 `(("r-xml" ,r-xml)))
10425 (home-page "https://cran.r-project.org/web/packages/grImport")
10426 (synopsis "Convert, import, and draw PostScript pictures")
10428 "This package provides functions for converting, importing, and drawing
10429 PostScript pictures in R plots.")
10430 (license license:gpl2+)))
10432 (define-public r-grimport2
10434 (name "r-grimport2")
10439 (uri (cran-uri "grImport2" version))
10442 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10443 (properties `((upstream-name . "grImport2")))
10444 (build-system r-build-system)
10446 `(("r-base64enc" ,r-base64enc)
10450 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10451 (synopsis "Import SVG graphics")
10453 "This package provides functions for importing external vector images and
10454 drawing them as part of R plots. This package is different from the
10455 @code{grImport} package because, where that package imports PostScript format
10456 images, this package imports SVG format images. Furthermore, this package
10457 imports a specific subset of SVG, so external images must be preprocessed
10458 using a package like @code{rsvg} to produce SVG that this package can import.
10459 SVG features that are not supported by R graphics, such as gradient fills, can
10460 be imported and then exported via the @code{gridSVG} package.")
10461 (license license:gpl2+)))
10463 (define-public r-kohonen
10470 (uri (cran-uri "kohonen" version))
10473 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10474 (build-system r-build-system)
10476 `(("r-rcpp" ,r-rcpp)))
10477 (home-page "https://cran.r-project.org/web/packages/kohonen")
10478 (synopsis "Supervised and unsupervised self-organising maps")
10480 "This package provides functions to train @dfn{self-organising
10481 maps} (SOMs). Also interrogation of the maps and prediction using trained
10482 maps are supported. The name of the package refers to Teuvo Kohonen, the
10483 inventor of the SOM.")
10484 (license license:gpl2+)))
10486 (define-public r-nnls
10493 (uri (cran-uri "nnls" version))
10496 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10497 (build-system r-build-system)
10498 (native-inputs `(("gfortran" ,gfortran)))
10499 (home-page "https://cran.r-project.org/web/packages/nnls")
10500 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10502 "This package provides an R interface to the Lawson-Hanson implementation
10503 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10504 the combination of non-negative and non-positive constraints.")
10505 (license license:gpl2+)))
10507 (define-public r-iso
10514 (uri (cran-uri "Iso" version))
10517 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10518 (properties `((upstream-name . "Iso")))
10519 (build-system r-build-system)
10520 (native-inputs `(("gfortran" ,gfortran)))
10521 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10522 (synopsis "Functions to perform isotonic regression")
10524 "This package provides support for linear order and unimodal
10525 order (univariate) isotonic regression and bivariate isotonic regression with
10526 linear order on both variables.")
10527 (license license:gpl2+)))
10529 (define-public r-chemometricswithr
10531 (name "r-chemometricswithr")
10536 (uri (cran-uri "ChemometricsWithR" version))
10539 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10541 `((upstream-name . "ChemometricsWithR")))
10542 (build-system r-build-system)
10544 `(("r-devtools" ,r-devtools)
10545 ("r-kohonen" ,r-kohonen)
10548 (home-page "https://github.com/rwehrens/CWR")
10549 (synopsis "Chemometrics with R")
10551 "This package provides functions and scripts used in the book
10552 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10553 Life Sciences\" by Ron Wehrens, Springer (2011).")
10554 (license license:gpl2+)))
10556 (define-public r-als
10563 (uri (cran-uri "ALS" version))
10566 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10567 (properties `((upstream-name . "ALS")))
10568 (build-system r-build-system)
10571 ("r-nnls" ,r-nnls)))
10572 (home-page "https://cran.r-project.org/web/packages/ALS")
10573 (synopsis "Multivariate curve resolution alternating least squares")
10575 "Alternating least squares is often used to resolve components
10576 contributing to data with a bilinear structure; the basic technique may be
10577 extended to alternating constrained least squares. This package provides an
10578 implementation of @dfn{multivariate curve resolution alternating least
10579 squares} (MCR-ALS).
10581 Commonly applied constraints include unimodality, non-negativity, and
10582 normalization of components. Several data matrices may be decomposed
10583 simultaneously by assuming that one of the two matrices in the bilinear
10584 decomposition is shared between datasets.")
10585 (license license:gpl2+)))
10587 (define-public r-strucchange
10589 (name "r-strucchange")
10594 (uri (cran-uri "strucchange" version))
10597 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10598 (build-system r-build-system)
10600 `(("r-sandwich" ,r-sandwich)
10602 (home-page "https://cran.r-project.org/web/packages/strucchange")
10603 (synopsis "Testing, monitoring, and dating structural changes")
10605 "This package provides tools for testing, monitoring and dating
10606 structural changes in (linear) regression models. It features tests/methods
10607 from the generalized fluctuation test framework as well as from the F
10608 test (Chow test) framework. This includes methods to fit, plot and test
10609 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10610 statistics, respectively. It is possible to monitor incoming data online
10611 using fluctuation processes. Finally, the breakpoints in regression models
10612 with structural changes can be estimated together with confidence intervals.
10613 Emphasis is always given to methods for visualizing the data.")
10614 ;; Either of these two GPL versions
10615 (license (list license:gpl2 license:gpl3))))
10617 (define-public r-pixmap
10624 (uri (cran-uri "pixmap" version))
10627 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10628 (build-system r-build-system)
10629 (home-page "https://cran.r-project.org/web/packages/pixmap")
10630 (synopsis "Tools for bitmap images")
10632 "This package provides functions for importing, exporting, plotting and
10633 other manipulations of bitmapped images.")
10634 (license license:gpl2)))
10636 (define-public r-rapidjsonr
10638 (name "r-rapidjsonr")
10643 (uri (cran-uri "rapidjsonr" version))
10646 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
10647 (build-system r-build-system)
10648 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10649 (synopsis "JSON parser")
10651 "This package provides JSON parsing capability through the Rapidjson
10653 (license license:expat)))
10655 (define-public r-ontologyindex
10657 (name "r-ontologyindex")
10662 (uri (cran-uri "ontologyIndex" version))
10665 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10666 (properties `((upstream-name . "ontologyIndex")))
10667 (build-system r-build-system)
10668 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10669 (synopsis "Functions for processing ontologies in R")
10671 "This package provides functions for reading ontologies into R as lists
10672 and manipulating sets of ontological terms.")
10673 (license license:gpl2+)))
10675 (define-public r-gargle
10682 (uri (cran-uri "gargle" version))
10685 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10686 (build-system r-build-system)
10691 ("r-jsonlite" ,r-jsonlite)
10692 ("r-rlang" ,r-rlang)
10693 ("r-withr" ,r-withr)))
10694 (home-page "https://gargle.r-lib.org")
10695 (synopsis "Utilities for working with Google APIs")
10697 "This package provides utilities for working with Google APIs. This
10698 includes functions and classes for handling common credential types and for
10699 preparing, executing, and processing HTTP requests.")
10700 (license license:expat)))
10702 (define-public r-bigrquery
10704 (name "r-bigrquery")
10709 (uri (cran-uri "bigrquery" version))
10712 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10713 (build-system r-build-system)
10715 `(("r-assertthat" ,r-assertthat)
10716 ("r-bit64" ,r-bit64)
10719 ("r-gargle" ,r-gargle)
10722 ("r-jsonlite" ,r-jsonlite)
10723 ("r-prettyunits" ,r-prettyunits)
10724 ("r-progress" ,r-progress)
10725 ("r-rapidjsonr" ,r-rapidjsonr)
10727 ("r-rlang" ,r-rlang)
10728 ("r-tibble" ,r-tibble)))
10729 (home-page "https://github.com/rstats-db/bigrquery")
10730 (synopsis "R interface to Google's BigQuery API")
10732 "This package provides an R interface to Google's BigQuery database.")
10733 (license license:gpl3)))
10735 (define-public r-gmp
10738 (version "0.5-13.6")
10742 (uri (cran-uri "gmp" version))
10745 "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
10746 (build-system r-build-system)
10749 (modify-phases %standard-phases
10750 (add-after 'unpack 'set-CC
10751 (lambda _ (setenv "CC" "gcc") #t)))))
10752 (inputs `(("gmp" ,gmp)))
10753 (home-page "https://cran.r-project.org/web/packages/gmp")
10754 (synopsis "Multiple precision arithmetic")
10756 "This package supports multiple precision arithmetic (big integers and
10757 rationals, prime number tests, matrix computation), \"arithmetic without
10758 limitations\" using the GNU Multiple Precision library.")
10759 ;; Any version of the GPL.
10760 (license license:gpl3+)))
10762 (define-public r-rmpfr
10769 (uri (cran-uri "Rmpfr" version))
10772 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
10773 (properties `((upstream-name . "Rmpfr")))
10774 (build-system r-build-system)
10779 `(("r-gmp" ,r-gmp)))
10781 `(("pkg-config" ,pkg-config)))
10782 (home-page "http://rmpfr.r-forge.r-project.org/")
10783 (synopsis "R bindings to the MPFR library")
10785 "This package supports arithmetic (via S4 classes and methods) for
10786 arbitrary precision floating point numbers, including transcendental
10787 functions. To this end, the package interfaces with the @dfn{Multiple
10788 Precision Floating-Point Reliable} (MPFR) library.")
10789 (license license:gpl2+)))
10791 (define-public r-assertive-base
10793 (name "r-assertive-base")
10798 (uri (cran-uri "assertive.base" version))
10801 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10803 `((upstream-name . "assertive.base")))
10804 (build-system r-build-system)
10805 (home-page "https://bitbucket.org/richierocks/assertive.base")
10806 (synopsis "Core of the assertive package")
10808 "This package provides a minimal set of predicates and assertions used by
10809 the assertive package. This is mainly for use by other package developers who
10810 want to include run-time testing features in their own packages.")
10811 (license license:gpl3+)))
10813 (define-public r-assertive-properties
10815 (name "r-assertive-properties")
10820 (uri (cran-uri "assertive.properties" version))
10823 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10825 `((upstream-name . "assertive.properties")))
10826 (build-system r-build-system)
10828 `(("r-assertive-base" ,r-assertive-base)))
10829 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10830 (synopsis "Assertions to check properties of variables")
10832 "This package provides a set of predicates and assertions for checking
10833 the properties of variables, such as length, names and attributes. This is
10834 mainly for use by other package developers who want to include run-time
10835 testing features in their own packages.")
10836 (license license:gpl3+)))
10838 (define-public r-assertive-numbers
10840 (name "r-assertive-numbers")
10845 (uri (cran-uri "assertive.numbers" version))
10848 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10850 `((upstream-name . "assertive.numbers")))
10851 (build-system r-build-system)
10853 `(("r-assertive-base" ,r-assertive-base)))
10854 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10855 (synopsis "Assertions to check properties of numbers")
10857 "This package provides a set of predicates and assertions for checking
10858 the properties of numbers. This is mainly for use by other package developers
10859 who want to include run-time testing features in their own packages.")
10860 (license license:gpl3+)))
10862 (define-public r-assertive-sets
10864 (name "r-assertive-sets")
10869 (uri (cran-uri "assertive.sets" version))
10872 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10874 `((upstream-name . "assertive.sets")))
10875 (build-system r-build-system)
10877 `(("r-assertive-base" ,r-assertive-base)))
10878 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10879 (synopsis "Assertions to check properties of sets")
10881 "This package provides a set of predicates and assertions for checking
10882 the properties of sets. This is mainly for use by other package developers
10883 who want to include run-time testing features in their own packages.")
10884 (license license:gpl3+)))
10886 (define-public r-assertive-matrices
10888 (name "r-assertive-matrices")
10893 (uri (cran-uri "assertive.matrices" version))
10896 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10898 `((upstream-name . "assertive.matrices")))
10899 (build-system r-build-system)
10901 `(("r-assertive-base" ,r-assertive-base)))
10902 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10903 (synopsis "Assertions to check properties of matrices")
10905 "This package provides a set of predicates and assertions for checking
10906 the properties of matrices. This is mainly for use by other package
10907 developers who want to include run-time testing features in their own
10909 (license license:gpl3+)))
10911 (define-public r-assertive-models
10913 (name "r-assertive-models")
10918 (uri (cran-uri "assertive.models" version))
10921 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10923 `((upstream-name . "assertive.models")))
10924 (build-system r-build-system)
10926 `(("r-assertive-base" ,r-assertive-base)))
10927 (home-page "https://bitbucket.org/richierocks/assertive.models")
10928 (synopsis "Assertions to check properties of models")
10930 "This package provides a set of predicates and assertions for checking
10931 the properties of models. This is mainly for use by other package developers
10932 who want to include run-time testing features in their own packages.")
10933 (license license:gpl3+)))
10935 (define-public r-assertive-reflection
10937 (name "r-assertive-reflection")
10942 (uri (cran-uri "assertive.reflection" version))
10945 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10947 `((upstream-name . "assertive.reflection")))
10948 (build-system r-build-system)
10950 `(("r-assertive-base" ,r-assertive-base)))
10951 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10952 (synopsis "Assertions for checking the state of R")
10954 "This package provides a set of predicates and assertions for checking
10955 the state and capabilities of R, the operating system it is running on, and
10956 the IDE being used. This is mainly for use by other package developers who
10957 want to include run-time testing features in their own packages.")
10958 (license license:gpl3+)))
10960 (define-public r-assertive-types
10962 (name "r-assertive-types")
10967 (uri (cran-uri "assertive.types" version))
10970 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10972 `((upstream-name . "assertive.types")))
10973 (build-system r-build-system)
10975 `(("r-assertive-base" ,r-assertive-base)
10976 ("r-assertive-properties" ,r-assertive-properties)
10977 ("r-codetools" ,r-codetools)))
10978 (home-page "https://bitbucket.org/richierocks/assertive.types")
10979 (synopsis "Assertions to check types of variables")
10981 "This package provides a set of predicates and assertions for checking
10982 the types of variables. This is mainly for use by other package developers
10983 who want to include run-time testing features in their own packages.")
10984 (license license:gpl3+)))
10986 (define-public r-assertive-files
10988 (name "r-assertive-files")
10993 (uri (cran-uri "assertive.files" version))
10996 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10998 `((upstream-name . "assertive.files")))
10999 (build-system r-build-system)
11001 `(("r-assertive-base" ,r-assertive-base)
11002 ("r-assertive-numbers" ,r-assertive-numbers)))
11003 (home-page "https://bitbucket.org/richierocks/assertive.files")
11004 (synopsis "Assertions to check properties of files")
11006 "This package provides a set of predicates and assertions for checking
11007 the properties of files and connections. This is mainly for use by other
11008 package developers who want to include run-time testing features in their own
11010 (license license:gpl3+)))
11012 (define-public r-assertive-code
11014 (name "r-assertive-code")
11019 (uri (cran-uri "assertive.code" version))
11022 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11024 `((upstream-name . "assertive.code")))
11025 (build-system r-build-system)
11027 `(("r-assertive-base" ,r-assertive-base)
11028 ("r-assertive-properties" ,r-assertive-properties)
11029 ("r-assertive-types" ,r-assertive-types)))
11030 (home-page "https://bitbucket.org/richierocks/assertive.code")
11031 (synopsis "Assertions to check properties of code")
11033 "This package provides a set of predicates and assertions for checking
11034 the properties of code. This is mainly for use by other package developers
11035 who want to include run-time testing features in their own packages.")
11036 (license license:gpl3+)))
11038 (define-public r-assertive-datetimes
11040 (name "r-assertive-datetimes")
11045 (uri (cran-uri "assertive.datetimes" version))
11048 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11050 `((upstream-name . "assertive.datetimes")))
11051 (build-system r-build-system)
11053 `(("r-assertive-base" ,r-assertive-base)
11054 ("r-assertive-types" ,r-assertive-types)))
11055 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11056 (synopsis "Assertions to check properties of dates and times")
11058 "This package provides a set of predicates and assertions for checking
11059 the properties of dates and times. This is mainly for use by other package
11060 developers who want to include run-time testing features in their own
11062 (license license:gpl3+)))
11064 (define-public r-assertive-strings
11066 (name "r-assertive-strings")
11071 (uri (cran-uri "assertive.strings" version))
11074 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11076 `((upstream-name . "assertive.strings")))
11077 (build-system r-build-system)
11079 `(("r-assertive-base" ,r-assertive-base)
11080 ("r-assertive-types" ,r-assertive-types)
11081 ("r-stringi" ,r-stringi)))
11082 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11083 (synopsis "Assertions to check properties of strings")
11085 "This package provides a set of predicates and assertions for checking
11086 the properties of strings. This is mainly for use by other package developers
11087 who want to include run-time testing features in their own packages.")
11088 (license license:gpl3+)))
11090 (define-public r-assertive-data-us
11092 (name "r-assertive-data-us")
11097 (uri (cran-uri "assertive.data.us" version))
11100 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11102 `((upstream-name . "assertive.data.us")))
11103 (build-system r-build-system)
11105 `(("r-assertive-base" ,r-assertive-base)
11106 ("r-assertive-strings" ,r-assertive-strings)))
11107 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11108 (synopsis "Assertions to check properties of strings")
11110 "This package provides a set of predicates and assertions for checking
11111 the properties of US-specific complex data types. This is mainly for use by
11112 other package developers who want to include run-time testing features in
11113 their own packages.")
11114 (license license:gpl3+)))
11116 (define-public r-assertive-data-uk
11118 (name "r-assertive-data-uk")
11123 (uri (cran-uri "assertive.data.uk" version))
11126 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11128 `((upstream-name . "assertive.data.uk")))
11129 (build-system r-build-system)
11131 `(("r-assertive-base" ,r-assertive-base)
11132 ("r-assertive-strings" ,r-assertive-strings)))
11133 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11134 (synopsis "Assertions to check properties of strings")
11136 "This package provides a set of predicates and assertions for checking
11137 the properties of UK-specific complex data types. This is mainly for use by
11138 other package developers who want to include run-time testing features in
11139 their own packages.")
11140 (license license:gpl3+)))
11142 (define-public r-assertive-data
11144 (name "r-assertive-data")
11149 (uri (cran-uri "assertive.data" version))
11152 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11154 `((upstream-name . "assertive.data")))
11155 (build-system r-build-system)
11157 `(("r-assertive-base" ,r-assertive-base)
11158 ("r-assertive-strings" ,r-assertive-strings)))
11159 (home-page "https://bitbucket.org/richierocks/assertive.data")
11160 (synopsis "Assertions to check properties of data")
11162 "This package provides a set of predicates and assertions for checking
11163 the properties of (country independent) complex data types. This is mainly
11164 for use by other package developers who want to include run-time testing
11165 features in their own packages.")
11166 (license license:gpl3+)))
11168 (define-public r-assertive
11170 (name "r-assertive")
11175 (uri (cran-uri "assertive" version))
11178 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11179 (build-system r-build-system)
11181 `(("r-assertive-base" ,r-assertive-base)
11182 ("r-assertive-code" ,r-assertive-code)
11183 ("r-assertive-data" ,r-assertive-data)
11184 ("r-assertive-data-uk" ,r-assertive-data-uk)
11185 ("r-assertive-data-us" ,r-assertive-data-us)
11186 ("r-assertive-datetimes" ,r-assertive-datetimes)
11187 ("r-assertive-files" ,r-assertive-files)
11188 ("r-assertive-matrices" ,r-assertive-matrices)
11189 ("r-assertive-models" ,r-assertive-models)
11190 ("r-assertive-numbers" ,r-assertive-numbers)
11191 ("r-assertive-properties" ,r-assertive-properties)
11192 ("r-assertive-reflection" ,r-assertive-reflection)
11193 ("r-assertive-sets" ,r-assertive-sets)
11194 ("r-assertive-strings" ,r-assertive-strings)
11195 ("r-assertive-types" ,r-assertive-types)
11196 ("r-knitr" ,r-knitr)))
11197 (home-page "https://bitbucket.org/richierocks/assertive")
11198 (synopsis "Readable check functions to ensure code integrity")
11200 "This package provides lots of predicates (@code{is_*} functions) to
11201 check the state of your variables, and assertions (@code{assert_*} functions)
11202 to throw errors if they aren't in the right form.")
11203 (license license:gpl3+)))
11205 (define-public r-dotcall64
11207 (name "r-dotcall64")
11212 (uri (cran-uri "dotCall64" version))
11215 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11216 (properties `((upstream-name . "dotCall64")))
11217 (build-system r-build-system)
11218 (native-inputs `(("gfortran" ,gfortran)))
11219 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11220 (synopsis "Enhanced foreign function interface supporting long vectors")
11222 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11223 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11224 supports long vectors, arguments of type 64-bit integer, and provides a
11225 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11226 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11227 (license license:gpl2+)))
11229 (define-public r-spam
11236 (uri (cran-uri "spam" version))
11238 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11239 (build-system r-build-system)
11241 `(("r-dotcall64" ,r-dotcall64)))
11242 (native-inputs `(("gfortran" ,gfortran)))
11243 (home-page "https://www.math.uzh.ch/pages/spam/")
11244 (synopsis "Sparse matrix algebra")
11246 "This package provides a set of functions for sparse matrix algebra.
11247 Differences with other sparse matrix packages are:
11250 @item it only supports (essentially) one sparse matrix format;
11251 @item it is based on transparent and simple structure(s);
11252 @item it is tailored for MCMC calculations within G(M)RF;
11253 @item and it is fast and scalable (with the extension package @code{spam64}).
11255 ;; Either of these licenses
11256 (license (list license:bsd-3 license:lgpl2.0))))
11258 (define-public r-fields
11265 (uri (cran-uri "fields" version))
11267 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11268 (build-system r-build-system)
11270 `(("r-maps" ,r-maps)
11271 ("r-spam" ,r-spam)))
11273 `(("gfortran" ,gfortran)))
11274 (home-page "https://www.image.ucar.edu/fields")
11275 (synopsis "Tools for spatial data")
11277 "This is a package for curve, surface and function fitting with an
11278 emphasis on splines, spatial data and spatial statistics. The major methods
11279 include cubic, and thin plate splines, Kriging, and compactly supported
11280 covariance functions for large data sets.")
11281 (license license:gpl2+)))
11283 (define-public r-spatialextremes
11285 (name "r-spatialextremes")
11290 (uri (cran-uri "SpatialExtremes" version))
11293 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11295 `((upstream-name . "SpatialExtremes")))
11296 (build-system r-build-system)
11298 `(("r-fields" ,r-fields)
11299 ("r-maps" ,r-maps)))
11300 (home-page "http://spatialextremes.r-forge.r-project.org/")
11301 (synopsis "Modelling spatial extremes")
11303 "This package provides tools for the statistical modelling of spatial
11304 extremes using max-stable processes, copula or Bayesian hierarchical models.
11305 More precisely, this package allows (conditional) simulations from various
11306 parametric max-stable models, analysis of the extremal spatial dependence, the
11307 fitting of such processes using composite likelihoods or least square (simple
11308 max-stable processes only), model checking and selection and prediction.")
11309 (license license:gpl2+)))
11311 (define-public r-drc
11318 (uri (cran-uri "drc" version))
11321 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11322 (build-system r-build-system)
11325 ("r-gtools" ,r-gtools)
11327 ("r-multcomp" ,r-multcomp)
11328 ("r-plotrix" ,r-plotrix)
11329 ("r-scales" ,r-scales)))
11330 (home-page "https://cran.r-project.org/web/packages/drc")
11331 (synopsis "Analysis of dose-response curves")
11333 "This package provides a suite of flexible and versatile model fitting
11334 and after-fitting functions for the analysis of dose-response data.")
11335 (license license:gpl2+)))
11337 (define-public r-rmeta
11344 (uri (cran-uri "rmeta" version))
11347 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11348 (build-system r-build-system)
11349 (home-page "https://cran.r-project.org/web/packages/rmeta")
11350 (synopsis "Tools for meta-analysis")
11352 "This package provides functions for simple fixed and random effects
11353 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11354 draws standard summary plots, funnel plots, and computes summaries and tests
11355 for association and heterogeneity.")
11356 (license license:gpl2)))
11358 (define-public r-bootstrap
11360 (name "r-bootstrap")
11365 (uri (cran-uri "bootstrap" version))
11368 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11369 (build-system r-build-system)
11370 (native-inputs `(("gfortran" ,gfortran)))
11371 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11372 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11374 "This package provides software and data for the book \"An Introduction
11375 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11376 This package is primarily provided for projects already based on it, and for
11377 support of the book. New projects should preferentially use the recommended
11378 package \"boot\".")
11379 (license license:bsd-3)))
11381 (define-public r-survivalroc
11383 (name "r-survivalroc")
11388 (uri (cran-uri "survivalROC" version))
11391 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11392 (properties `((upstream-name . "survivalROC")))
11393 (build-system r-build-system)
11394 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11395 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11397 "Compute time-dependent ROC curve from censored survival data using
11398 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11399 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11400 (license license:gpl2+)))
11402 (define-public r-longitudinal
11404 (name "r-longitudinal")
11409 (uri (cran-uri "longitudinal" version))
11412 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11413 (build-system r-build-system)
11414 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11415 (home-page "http://strimmerlab.org/software/longitudinal/")
11416 (synopsis "Analysis of multiple time course data")
11418 "This package contains general data structures and functions for
11419 longitudinal data with multiple variables, repeated measurements, and
11420 irregularly spaced time points. It also implements a shrinkage estimator of
11421 dynamical correlation and dynamical covariance.")
11422 (license license:gpl3+)))
11424 (define-public r-genenet
11431 (uri (cran-uri "GeneNet" version))
11434 "0cdhrj15rz0w0pyw3r8mikrzsdh95y5i1c0pa3cn0c2bjnjx3x3n"))))
11435 (properties `((upstream-name . "GeneNet")))
11436 (build-system r-build-system)
11438 `(("r-corpcor" ,r-corpcor)
11439 ("r-fdrtool" ,r-fdrtool)
11440 ("r-longitudinal" ,r-longitudinal)))
11441 (home-page "http://strimmerlab.org/software/genenet/")
11442 (synopsis "Modeling and inferring gene networks")
11444 "This package analyzes gene expression (time series) data with focus on
11445 the inference of gene networks. In particular, GeneNet implements the methods
11446 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11447 for learning large-scale gene association networks (including assignment of
11448 putative directions).")
11449 (license license:gpl3+)))
11451 (define-public r-rbamtools
11453 (name "r-rbamtools")
11454 (version "2.16.17")
11458 (uri (cran-uri "rbamtools" version))
11461 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11462 (build-system r-build-system)
11463 (inputs `(("zlib" ,zlib)))
11465 `(("r-refgenome" ,r-refgenome)))
11466 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11467 (synopsis "Read and write BAM (binary alignment) files")
11469 "This package provides an R interface to functions of the SAMtools
11471 (license license:artistic2.0)))
11473 (define-public r-protviz
11480 (uri (cran-uri "protViz" version))
11483 "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7"))))
11484 (properties `((upstream-name . "protViz")))
11485 (build-system r-build-system)
11486 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11487 (home-page "https://github.com/protViz/protViz/")
11488 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11490 "This package helps with quality checks, visualizations and analysis of
11491 mass spectrometry data, coming from proteomics experiments. The package is
11492 developed, tested and used at the Functional Genomics Center Zurich, where it
11493 is used mainly for prototyping, teaching, and having fun with proteomics data.
11494 But it can also be used to do data analysis for small scale data sets.")
11495 (license license:gpl3)))
11497 (define-public r-cmprsk
11504 (uri (cran-uri "cmprsk" version))
11506 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11507 (build-system r-build-system)
11509 `(("r-survival" ,r-survival)))
11511 `(("gfortran" ,gfortran)))
11512 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11513 (synopsis "Subdistribution analysis of competing risks")
11515 "This package provides tool for estimation, testing and regression
11516 modeling of subdistribution functions in competing risks, as described in
11517 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11518 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11519 A proportional hazards model for the subdistribution of a competing risk,
11520 JASA, 94:496-509.")
11521 (license license:gpl2+)))
11523 (define-public r-etm
11526 (version "1.0.5.1")
11530 (uri (cran-uri "etm" version))
11533 "0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7"))))
11534 (build-system r-build-system)
11536 `(("r-data-table" ,r-data-table)
11537 ("r-lattice" ,r-lattice)
11539 ("r-rcpparmadillo" ,r-rcpparmadillo)
11540 ("r-survival" ,r-survival)))
11541 (home-page "https://cran.r-project.org/web/packages/etm")
11542 (synopsis "Empirical transition matrix")
11544 "The @dfn{empirical transition matrix} (etm) package estimates
11545 the matrix of transition probabilities for any time-inhomogeneous multistate
11546 model with finite state space using the Aalen-Johansen estimator.")
11547 (license license:expat)))
11549 (define-public r-epi
11556 (uri (cran-uri "Epi" version))
11559 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11560 (properties `((upstream-name . "Epi")))
11561 (build-system r-build-system)
11563 `(("r-cmprsk" ,r-cmprsk)
11564 ("r-data-table" ,r-data-table)
11567 ("r-matrix" ,r-matrix)
11569 ("r-numderiv" ,r-numderiv)
11571 ("r-survival" ,r-survival)
11573 (home-page "https://BendixCarstensen.com/Epi/")
11574 (synopsis "Statistical analysis in epidemiology")
11576 "This package provides functions for demographic and epidemiological
11577 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11578 particular representation, manipulation and simulation of multistate data -
11579 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11580 @code{etm} and @code{cmprsk} packages. It also contains functions for
11581 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11582 data and some useful functions for tabulation and plotting, as well as a
11583 number of epidemiological data sets.")
11584 (license license:gpl2)))
11586 (define-public r-ppls
11589 (version "1.6-1.1")
11593 (uri (cran-uri "ppls" version))
11596 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11597 (build-system r-build-system)
11598 (propagated-inputs `(("r-mass" ,r-mass)))
11599 (home-page "https://cran.r-project.org/web/packages/ppls")
11600 (synopsis "Penalized partial least squares")
11602 "This package contains linear and nonlinear regression methods based on
11603 partial least squares and penalization techniques. Model parameters are
11604 selected via cross-validation, and confidence intervals ans tests for the
11605 regression coefficients can be conducted via jackknifing.")
11606 (license license:gpl2+)))
11608 (define-public r-huge
11611 (version "1.3.4.1")
11615 (uri (cran-uri "huge" version))
11617 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
11618 (build-system r-build-system)
11620 `(("r-igraph" ,r-igraph)
11622 ("r-matrix" ,r-matrix)
11624 ("r-rcppeigen" ,r-rcppeigen)))
11625 (home-page "https://cran.r-project.org/web/packages/huge")
11626 (synopsis "High-dimensional undirected graph estimation")
11628 "This package provides a general framework for high-dimensional
11629 undirected graph estimation. It integrates data preprocessing, neighborhood
11630 screening, graph estimation, and model selection techniques into a pipeline.")
11631 (license license:gpl2)))
11633 (define-public r-parcor
11640 (uri (cran-uri "parcor" version))
11643 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11644 (build-system r-build-system)
11647 ("r-genenet" ,r-genenet)
11648 ("r-glmnet" ,r-glmnet)
11650 ("r-ppls" ,r-ppls)))
11651 (home-page "https://cran.r-project.org/web/packages/parcor")
11652 (synopsis "Regularized estimation of partial correlation matrices")
11654 "This package estimates the matrix of partial correlations based on
11655 different regularized regression methods: lasso, adaptive lasso, PLS, and
11656 Ridge Regression. In addition, the package provides model selection for
11657 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11658 (license license:gpl2+)))
11660 (define-public r-mcmc
11667 (uri (cran-uri "mcmc" version))
11670 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
11671 (build-system r-build-system)
11672 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
11673 (synopsis "Markov chain Monte Carlo")
11675 "This package simulates continuous distributions of random vectors using
11676 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11677 function that evaluates the log unnormalized density. Algorithms are random
11678 walk Metropolis algorithm (function @code{metrop}), simulated
11679 tempering (function @code{temper}), and morphometric random walk
11680 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11681 by change of variable.")
11682 (license license:expat)))
11684 (define-public r-listenv
11691 (uri (cran-uri "listenv" version))
11694 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11695 (build-system r-build-system)
11697 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11698 (home-page "https://github.com/HenrikBengtsson/listenv")
11699 (synopsis "Environments behaving (almost) as lists")
11701 "This package implements list environments. List environments are
11702 environments that have list-like properties. For instance, the elements of a
11703 list environment are ordered and can be accessed and iterated over using index
11705 (license license:lgpl2.1+)))
11707 (define-public r-globals
11714 (uri (cran-uri "globals" version))
11717 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11718 (build-system r-build-system)
11720 `(("r-codetools" ,r-codetools)))
11721 (home-page "https://github.com/HenrikBengtsson/globals")
11722 (synopsis "Identify global objects in R expressions")
11724 "This package provides tools to identify global (\"unknown\" or \"free\")
11725 objects in R expressions by code inspection using various strategies, e.g.
11726 conservative or liberal. The objective of this package is to make it as
11727 simple as possible to identify global objects for the purpose of exporting
11728 them in distributed compute environments.")
11729 (license license:lgpl2.1+)))
11731 (define-public r-future
11738 (uri (cran-uri "future" version))
11741 "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
11742 (build-system r-build-system)
11744 `(("r-digest" ,r-digest)
11745 ("r-globals" ,r-globals)
11746 ("r-listenv" ,r-listenv)))
11748 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11749 (home-page "https://github.com/HenrikBengtsson/future")
11750 (synopsis "Unified parallel and distributed processing in R")
11752 "The purpose of this package is to provide a lightweight and unified
11753 Future API for sequential and parallel processing of R expression via futures.
11754 This package implements sequential, multicore, multisession, and cluster
11755 futures. With these, R expressions can be evaluated on the local machine, in
11756 parallel a set of local machines, or distributed on a mix of local and remote
11757 machines. Extensions to this package implement additional backends for
11758 processing futures via compute cluster schedulers etc. Because of its unified
11759 API, there is no need to modify any code in order to switch from sequential on
11760 the local machine to, say, distributed processing on a remote compute cluster.")
11761 (license license:lgpl2.1+)))
11763 (define-public r-future-apply
11765 (name "r-future-apply")
11770 (uri (cran-uri "future.apply" version))
11773 "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
11774 (properties `((upstream-name . "future.apply")))
11775 (build-system r-build-system)
11777 `(("r-future" ,r-future)
11778 ("r-globals" ,r-globals)))
11780 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11781 (home-page "https://github.com/HenrikBengtsson/future.apply")
11782 (synopsis "Apply function to elements in parallel using futures")
11784 "This package provides implementations of @code{apply()},
11785 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11786 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11787 can be resolved using any future-supported backend, e.g. parallel on the local
11788 machine or distributed on a compute cluster.")
11789 (license license:gpl2+)))
11791 (define-public r-rsvd
11798 (uri (cran-uri "rsvd" version))
11801 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
11802 (build-system r-build-system)
11804 `(("r-matrix" ,r-matrix)))
11805 (home-page "https://github.com/erichson/rSVD")
11806 (synopsis "Randomized singular value decomposition")
11808 "Low-rank matrix decompositions are fundamental tools and widely used for
11809 data analysis, dimension reduction, and data compression. Classically, highly
11810 accurate deterministic matrix algorithms are used for this task. However, the
11811 emergence of large-scale data has severely challenged our computational
11812 ability to analyze big data. The concept of randomness has been demonstrated
11813 as an effective strategy to quickly produce approximate answers to familiar
11814 problems such as the @dfn{singular value decomposition} (SVD). This package
11815 provides several randomized matrix algorithms such as the randomized singular
11816 value decomposition (@code{rsvd}), randomized principal component
11817 analysis (@code{rpca}), randomized robust principal component
11818 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11819 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11820 functions are provided.")
11821 (license license:gpl3+)))
11823 (define-public r-sloop
11830 (uri (cran-uri "sloop" version))
11833 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11834 (build-system r-build-system)
11836 `(("r-codetools" ,r-codetools)
11837 ("r-crayon" ,r-crayon)
11838 ("r-purrr" ,r-purrr)
11839 ("r-rlang" ,r-rlang)
11840 ("r-tibble" ,r-tibble)))
11841 (home-page "https://github.com/r-lib/sloop")
11842 (synopsis "Helpers for object-oriented programming in R")
11844 "This package provides a collection of helper functions designed to
11845 help you to better understand object oriented programming in R, particularly
11847 (license license:gpl3)))
11849 (define-public r-capushe
11856 (uri (cran-uri "capushe" version))
11859 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11860 (build-system r-build-system)
11861 (propagated-inputs `(("r-mass" ,r-mass)))
11862 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11863 (synopsis "Calibrating penalties using slope heuristics")
11865 "This package provides tools for the calibration of penalized criteria
11866 for model selection. The calibration methods available are based on the slope
11868 (license license:gpl2+)))
11870 (define-public r-dorng
11877 (uri (cran-uri "doRNG" version))
11880 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
11881 (properties `((upstream-name . "doRNG")))
11882 (build-system r-build-system)
11884 `(("r-foreach" ,r-foreach)
11885 ("r-iterators" ,r-iterators)
11886 ("r-rngtools" ,r-rngtools)))
11887 (home-page "https://renozao.github.io/doRNG/")
11888 (synopsis "Generic reproducible parallel backend for foreach loops")
11890 "This package provides functions to perform reproducible parallel
11891 @code{foreach} loops, using independent random streams as generated by
11892 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11893 convert standard @code{%dopar%} loops into fully reproducible loops,
11894 independently of the number of workers, the task scheduling strategy, or the
11895 chosen parallel environment and associated foreach backend.")
11896 (license license:gpl2+)))
11898 (define-public r-blockmodeling
11900 (name "r-blockmodeling")
11905 (uri (cran-uri "blockmodeling" version))
11908 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
11909 (build-system r-build-system)
11911 `(("r-matrix" ,r-matrix)))
11912 (native-inputs `(("gfortran" ,gfortran)))
11913 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11914 (synopsis "Generalized and classical blockmodeling of valued networks")
11916 "This package is primarily meant as an implementation of generalized
11917 blockmodeling for valued networks. In addition, measures of similarity or
11918 dissimilarity based on structural equivalence and regular equivalence (REGE
11919 algorithms) can be computed and partitioned matrices can be plotted.")
11920 (license license:gpl2+)))
11922 (define-public r-upsetr
11929 (uri (cran-uri "UpSetR" version))
11932 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11933 (properties `((upstream-name . "UpSetR")))
11934 (build-system r-build-system)
11936 `(("r-ggplot2" ,r-ggplot2)
11937 ("r-gridextra" ,r-gridextra)
11939 ("r-scales" ,r-scales)))
11940 (home-page "https://github.com/hms-dbmi/UpSetR")
11941 (synopsis "Visualize intersecting sets")
11943 "This package provides a more scalable alternative to Venn and Euler
11944 diagrams for visualizing intersecting sets. Create visualizations of
11945 intersecting sets using a novel matrix design, along with visualizations of
11946 several common set, element and attribute related tasks.")
11947 (license license:expat)))
11949 ;; This package includes a JavaScript file, which is not minified. When
11950 ;; upgrading please check that there are no new minified JavaScript files.
11951 (define-public r-shinybs
11958 (uri (cran-uri "shinyBS" version))
11961 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11962 (properties `((upstream-name . "shinyBS")))
11963 (build-system r-build-system)
11964 ;; The tests spawn Shiny browser apps. They cannot be run
11965 ;; non-interactively.
11966 (arguments '(#:tests? #f))
11968 `(("r-htmltools" ,r-htmltools)
11969 ("r-shiny" ,r-shiny)))
11970 (home-page "https://ebailey78.github.io/shinyBS/")
11971 (synopsis "Twitter Bootstrap components for Shiny")
11973 "This package adds additional Twitter Bootstrap components to Shiny.")
11974 (license license:gpl3)))
11976 (define-public r-outliers
11978 (name "r-outliers")
11983 (uri (cran-uri "outliers" version))
11986 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11987 (build-system r-build-system)
11988 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11989 (synopsis "Tests for outliers")
11991 "This package provides a collection of some tests commonly used for
11992 identifying outliers.")
11993 (license license:gpl2+)))
11995 (define-public r-bayesm
12002 (uri (cran-uri "bayesm" version))
12004 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12005 (build-system r-build-system)
12007 `(("r-rcpp" ,r-rcpp)
12008 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12009 (home-page "http://www.perossi.org/home/bsm-1")
12010 (synopsis "Bayesian inference for marketing/micro-econometrics")
12012 "This package covers many important models used in marketing and
12013 micro-econometrics applications, including Bayes Regression (univariate or
12014 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12015 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12016 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12017 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12018 Estimation with normal base, Hierarchical Linear Models with normal prior and
12019 covariates, Hierarchical Linear Models with a mixture of normals prior and
12020 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12021 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12022 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12023 analysis of choice-based conjoint data, Bayesian treatment of linear
12024 instrumental variables models, Analysis of Multivariate Ordinal survey data
12025 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12026 Coefficient Logit Models.")
12027 (license license:gpl2+)))
12029 (define-public r-tensora
12036 (uri (cran-uri "tensorA" version))
12039 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12040 (properties `((upstream-name . "tensorA")))
12041 (build-system r-build-system)
12042 (home-page "http://www.stat.boogaart.de/tensorA")
12043 (synopsis "Advanced tensor arithmetic with named indices")
12045 "This package provides convenience functions for advanced linear algebra
12046 with tensors and computation with datasets of tensors on a higher level
12047 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12048 co- and contravariate indices, and parallel computations on sequences of
12050 (license license:gpl2+)))
12052 (define-public r-rarpack
12059 (uri (cran-uri "rARPACK" version))
12062 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12063 (properties `((upstream-name . "rARPACK")))
12064 (build-system r-build-system)
12065 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12066 (home-page "https://github.com/yixuan/rARPACK")
12067 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12069 "This package was previously an R wrapper of the ARPACK library, and now
12070 a shell of the R package RSpectra, an R interface to the Spectra library for
12071 solving large scale eigenvalue/vector problems. The current version of
12072 rARPACK simply imports and exports the functions provided by RSpectra. New
12073 users of rARPACK are advised to switch to the RSpectra package.")
12074 (license license:bsd-3)))
12076 (define-public r-compositions
12078 (name "r-compositions")
12083 (uri (cran-uri "compositions" version))
12086 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12087 (build-system r-build-system)
12089 `(("r-bayesm" ,r-bayesm)
12090 ("r-robustbase" ,r-robustbase)
12091 ("r-tensora" ,r-tensora)))
12092 (home-page "http://www.stat.boogaart.de/compositions")
12093 (synopsis "Compositional data analysis")
12095 "This package provides functions for the consistent analysis of
12096 compositional data (e.g. portions of substances) and positive
12097 numbers (e.g. concentrations).")
12098 (license license:gpl2+)))
12100 (define-public r-cobs
12107 (uri (cran-uri "cobs" version))
12110 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12111 (build-system r-build-system)
12113 `(("r-quantreg" ,r-quantreg)
12114 ("r-sparsem" ,r-sparsem)))
12115 (home-page "https://cran.r-project.org/web/packages/cobs")
12116 (synopsis "Constrained B-Splines (sparse matrix based)")
12118 "This package provides qualitatively constrained (regression) smoothing
12119 splines via linear programming and sparse matrices.")
12120 (license license:gpl2+)))
12122 (define-public r-drimpute
12124 (name "r-drimpute")
12129 (uri (cran-uri "DrImpute" version))
12132 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12133 (properties `((upstream-name . "DrImpute")))
12134 (build-system r-build-system)
12136 `(("r-rcpp" ,r-rcpp)
12137 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12138 (home-page "https://github.com/ikwak2/DrImpute")
12139 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12141 "This is an R package for imputing dropout events. Many statistical
12142 methods in cell type identification, visualization and lineage reconstruction
12143 do not account for dropout events. DrImpute can improve the performance of
12144 such software by imputing dropout events.")
12145 (license license:gpl3)))
12147 (define-public r-gamlss-dist
12149 (name "r-gamlss-dist")
12154 (uri (cran-uri "gamlss.dist" version))
12156 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12157 (properties `((upstream-name . "gamlss.dist")))
12158 (build-system r-build-system)
12159 (propagated-inputs `(("r-mass" ,r-mass)))
12160 (home-page "http://www.gamlss.org/")
12161 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12163 "This package provides a set of distributions which can be used for
12164 modelling the response variables in Generalized Additive Models for Location
12165 Scale and Shape. The distributions can be continuous, discrete or mixed
12166 distributions. Extra distributions can be created, by transforming, any
12167 continuous distribution defined on the real line, to a distribution defined on
12168 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12169 transformation, respectively.")
12170 ;; Either version of the GPL.
12171 (license (list license:gpl2 license:gpl3))))
12173 ;; This package includes JavaScript files, which are not minified. When
12174 ;; upgrading please check that there are no new minified JavaScript files.
12175 (define-public r-shinyjs
12182 (uri (cran-uri "shinyjs" version))
12185 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12186 (build-system r-build-system)
12188 `(("r-digest" ,r-digest)
12189 ("r-htmltools" ,r-htmltools)
12190 ("r-jsonlite" ,r-jsonlite)
12191 ("r-shiny" ,r-shiny)))
12192 (home-page "https://deanattali.com/shinyjs")
12193 (synopsis "Improve the user experience of your Shiny apps")
12195 "Perform common useful JavaScript operations in Shiny apps that will
12196 greatly improve your apps without having to know any JavaScript. Examples
12197 include: hiding an element, disabling an input, resetting an input back to its
12198 original value, delaying code execution by a few seconds, and many more useful
12199 functions for both the end user and the developer. Shinyjs can also be used
12200 to easily call your own custom JavaScript functions from R.")
12201 (license license:agpl3+)))
12203 ;; This package includes minified JavaScript files. When upgrading please
12204 ;; check that there are no new minified JavaScript files.
12205 (define-public r-colourpicker
12207 (name "r-colourpicker")
12212 (uri (cran-uri "colourpicker" version))
12215 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12216 (build-system r-build-system)
12218 `(#:modules ((guix build utils)
12219 (guix build r-build-system)
12223 (modify-phases %standard-phases
12224 (add-after 'unpack 'process-javascript
12225 (lambda* (#:key inputs #:allow-other-keys)
12226 (with-directory-excursion "inst"
12230 `((,(assoc-ref inputs "js-salvattore")
12231 "examples/colourInput/www/salvattore.min.js")
12232 (,(assoc-ref inputs "js-jquery")
12233 "htmlwidgets/lib/jquery/jquery.min.js")
12234 ("www/shared/colourpicker/js/colourpicker.js"
12235 "www/shared/colourpicker/js/colourpicker.min.js"))))
12236 (lambda (sources targets)
12237 (for-each (lambda (source target)
12238 (format #t "Processing ~a --> ~a~%"
12240 (delete-file target)
12241 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12242 (call-with-output-file target
12244 (dump-port minified port)))))
12245 sources targets))))
12248 `(("r-ggplot2" ,r-ggplot2)
12249 ("r-htmltools" ,r-htmltools)
12250 ("r-htmlwidgets" ,r-htmlwidgets)
12251 ("r-jsonlite" ,r-jsonlite)
12252 ("r-miniui" ,r-miniui)
12253 ("r-shiny" ,r-shiny)
12254 ("r-shinyjs" ,r-shinyjs)))
12256 `(("uglify-js" ,uglify-js)
12260 (uri "https://code.jquery.com/jquery-3.3.1.js")
12263 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12267 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12270 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12271 (home-page "https://github.com/daattali/colourpicker")
12272 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12274 "This package provides a color picker that can be used as an input in
12275 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12276 custom color palettes, and many more options. A plot color helper tool is
12277 available as an RStudio Addin, which helps you pick colors to use in your
12278 plots. A more generic color picker RStudio Addin is also provided to let you
12279 select colors to use in your R code.")
12280 (license license:expat)))
12282 (define-public r-ggextra
12289 (uri (cran-uri "ggExtra" version))
12292 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12293 (properties `((upstream-name . "ggExtra")))
12294 (build-system r-build-system)
12296 `(("r-colourpicker" ,r-colourpicker)
12297 ("r-ggplot2" ,r-ggplot2)
12298 ("r-gtable" ,r-gtable)
12299 ("r-miniui" ,r-miniui)
12301 ("r-scales" ,r-scales)
12302 ("r-shiny" ,r-shiny)
12303 ("r-shinyjs" ,r-shinyjs)))
12304 (home-page "https://github.com/daattali/ggExtra")
12305 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12307 "This package is a collection of functions and layers to enhance ggplot2.
12308 The flagship function is @code{ggMarginal()}, which can be used to add
12309 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12310 (license license:expat)))
12312 (define-public r-minpack-lm
12314 (name "r-minpack-lm")
12319 (uri (cran-uri "minpack.lm" version))
12322 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12323 (properties `((upstream-name . "minpack.lm")))
12324 (build-system r-build-system)
12325 (native-inputs `(("gfortran" ,gfortran)))
12326 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12327 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12329 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12330 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12331 problems by a modification of the Levenberg-Marquardt algorithm, with support
12332 for lower and upper parameter bounds. The implementation can be used via
12333 @code{nls}-like calls using the @code{nlsLM} function.")
12334 (license license:gpl3)))
12336 (define-public r-moments
12343 (uri (cran-uri "moments" version))
12346 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12347 (build-system r-build-system)
12348 (home-page "https://cran.r-project.org/web/packages/moments")
12349 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12351 "This package provides functions to calculate: moments, Pearson's
12352 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12353 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12354 (license license:gpl2+)))
12356 (define-public r-msir
12363 (uri (cran-uri "msir" version))
12366 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12367 (build-system r-build-system)
12369 `(("r-mclust" ,r-mclust)))
12370 (home-page "https://cran.r-project.org/web/packages/msir")
12371 (synopsis "Model-based sliced inverse regression")
12373 "This is an R package for dimension reduction based on finite Gaussian
12374 mixture modeling of inverse regression.")
12375 (license license:gpl2+)))
12377 (define-public r-pbivnorm
12379 (name "r-pbivnorm")
12384 (uri (cran-uri "pbivnorm" version))
12387 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12388 (build-system r-build-system)
12389 (native-inputs `(("gfortran" ,gfortran)))
12390 (home-page "https://github.com/brentonk/pbivnorm")
12391 (synopsis "Vectorized bivariate normal CDF")
12393 "This package provides a vectorized R function for calculating
12394 probabilities from a standard bivariate normal CDF.")
12395 (license license:gpl2+)))
12397 (define-public r-lavaan
12404 (uri (cran-uri "lavaan" version))
12407 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12408 (build-system r-build-system)
12410 `(("r-mass" ,r-mass)
12411 ("r-mnormt" ,r-mnormt)
12412 ("r-numderiv" ,r-numderiv)
12413 ("r-pbivnorm" ,r-pbivnorm)))
12414 (home-page "http://lavaan.ugent.be")
12415 (synopsis "Latent variable analysis")
12417 "This package provides tools to fit a variety of latent variable models,
12418 including confirmatory factor analysis, structural equation modeling and
12419 latent growth curve models.")
12420 (license license:gpl2+)))
12422 (define-public r-nonnest2
12424 (name "r-nonnest2")
12429 (uri (cran-uri "nonnest2" version))
12432 "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
12433 (build-system r-build-system)
12435 `(("r-compquadform" ,r-compquadform)
12436 ("r-lavaan" ,r-lavaan)
12437 ("r-mvtnorm" ,r-mvtnorm)
12438 ("r-sandwich" ,r-sandwich)))
12440 `(("r-knitr" ,r-knitr)))
12441 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12442 (synopsis "Tests of non-nested models")
12444 "This package allows for testing of non-nested models. It includes tests
12445 of model distinguishability and of model fit that can be applied to both
12446 nested and non-nested models. The package also includes functionality to
12447 obtain confidence intervals associated with AIC and BIC.")
12448 ;; Either version of the GPL.
12449 (license (list license:gpl2 license:gpl3))))
12451 (define-public r-penalized
12453 (name "r-penalized")
12458 (uri (cran-uri "penalized" version))
12461 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12462 (build-system r-build-system)
12464 `(("r-rcpp" ,r-rcpp)
12465 ("r-rcpparmadillo" ,r-rcpparmadillo)
12466 ("r-survival" ,r-survival)))
12467 (home-page "https://cran.r-project.org/web/packages/penalized/")
12468 (synopsis "Penalized estimation in GLMs and in the Cox model")
12470 "This package provides tools for fitting possibly high dimensional
12471 penalized regression models. The penalty structure can be any combination of
12472 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12473 constraint on the regression coefficients. The supported regression models
12474 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12475 model. Cross-validation routines allow optimization of the tuning
12477 (license license:gpl2+)))
12479 (define-public r-zim
12486 (uri (cran-uri "ZIM" version))
12489 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12490 (properties `((upstream-name . "ZIM")))
12491 (build-system r-build-system)
12492 (propagated-inputs `(("r-mass" ,r-mass)))
12493 (home-page "https://github.com/biostatstudio/ZIM")
12494 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12496 "Analyze count time series with excess zeros. Two types of statistical
12497 models are supported: Markov regression and state-space models. They are also
12498 known as observation-driven and parameter-driven models respectively in the
12499 time series literature. The functions used for Markov regression or
12500 observation-driven models can also be used to fit ordinary regression models
12501 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12502 negative binomial (ZINB) assumption. The package also contains miscellaneous
12503 functions to compute density, distribution, quantile, and generate random
12504 numbers from ZIP and ZINB distributions.")
12505 (license license:gpl3)))
12507 (define-public r-nor1mix
12514 (uri (cran-uri "nor1mix" version))
12517 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12518 (build-system r-build-system)
12519 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12520 (synopsis "Normal (1-d) mixture models")
12522 "This package provides S3 classes and methods for one-dimensional normal
12523 mixture models, for, e.g., density estimation or clustering algorithms
12524 research and teaching; it provides the widely used Marron-Wand densities. It
12525 also provides tools for efficient random number generation and graphics.")
12526 (license license:gpl2+)))
12528 (define-public r-beanplot
12530 (name "r-beanplot")
12535 (uri (cran-uri "beanplot" version))
12538 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12539 (build-system r-build-system)
12540 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12541 (synopsis "Visualization via beanplots")
12543 "This package provides beanplots, an alternative to
12544 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12546 (license license:gpl2)))
12548 (define-public r-pbdzmq
12555 (uri (cran-uri "pbdZMQ" version))
12558 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12559 (properties `((upstream-name . "pbdZMQ")))
12560 (build-system r-build-system)
12562 `(("zeromq" ,zeromq)
12565 `(("pkg-config" ,pkg-config)))
12566 (home-page "https://pbdr.org/")
12567 (synopsis "R interface to ZeroMQ")
12569 "ZeroMQ is a well-known library for high-performance asynchronous
12570 messaging in scalable, distributed applications. This package provides high
12571 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12572 interactive client/server programming frameworks. A few wrapper functions
12573 compatible with @code{rzmq} are also provided.")
12574 (license license:gpl3)))
12576 (define-public r-repr
12583 (uri (cran-uri "repr" version))
12586 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
12587 (build-system r-build-system)
12589 `(("r-base64enc" ,r-base64enc)
12590 ("r-htmltools" ,r-htmltools)
12591 ("r-jsonlite" ,r-jsonlite)
12592 ("r-pillar" ,r-pillar)))
12593 (home-page "https://cran.r-project.org/web/packages/repr/")
12594 (synopsis "Serializable representations")
12596 "This package provides string and binary representations of objects for
12597 several formats and MIME types.")
12598 (license license:gpl3)))
12600 (define-public r-irdisplay
12602 (name "r-irdisplay")
12607 (uri (cran-uri "IRdisplay" version))
12610 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12611 (properties `((upstream-name . "IRdisplay")))
12612 (build-system r-build-system)
12614 `(("r-repr" ,r-repr)))
12615 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12616 (synopsis "Jupyter display machinery")
12618 "This package provides an interface to the rich display capabilities of
12619 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12620 running IRkernel session.")
12621 (license license:expat)))
12623 (define-public r-irkernel
12625 (name "r-irkernel")
12630 (uri (cran-uri "IRkernel" version))
12633 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12634 (properties `((upstream-name . "IRkernel")))
12635 (build-system r-build-system)
12638 (modify-phases %standard-phases
12639 (add-after 'install 'install-kernelspec
12640 (lambda* (#:key outputs #:allow-other-keys)
12641 (let ((out (assoc-ref outputs "out")))
12642 (setenv "HOME" "/tmp")
12643 (invoke "jupyter" "kernelspec" "install"
12646 (string-append out "/site-library/IRkernel/kernelspec"))
12647 ;; Record the absolute file name of the 'R' executable in
12649 (substitute* (string-append out "/share/jupyter"
12650 "/kernels/ir/kernel.json")
12652 (string-append "[\"" (which "R") "\",")))
12655 `(("jupyter" ,jupyter)))
12657 `(("r-crayon" ,r-crayon)
12658 ("r-digest" ,r-digest)
12659 ("r-evaluate" ,r-evaluate)
12660 ("r-irdisplay" ,r-irdisplay)
12661 ("r-jsonlite" ,r-jsonlite)
12662 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12663 ("r-minimal" ,r-minimal)
12664 ("r-pbdzmq" ,r-pbdzmq)
12666 ("r-uuid" ,r-uuid)))
12667 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12668 (synopsis "Native R kernel for Jupyter")
12670 "The R kernel for the Jupyter environment executes R code which the
12671 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12673 (license license:expat)))
12675 (define-public r-gmodels
12682 (uri (cran-uri "gmodels" version))
12685 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12686 (build-system r-build-system)
12688 `(("r-gdata" ,r-gdata)
12689 ("r-mass" ,r-mass)))
12690 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12691 (synopsis "Various R programming tools for model fitting")
12693 "This package provides various R programming tools for model fitting.")
12694 (license license:gpl2)))
12696 (define-public r-apcluster
12698 (name "r-apcluster")
12703 (uri (cran-uri "apcluster" version))
12706 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12707 (build-system r-build-system)
12709 `(("r-matrix" ,r-matrix)
12710 ("r-rcpp" ,r-rcpp)))
12711 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12712 (synopsis "Affinity propagation clustering")
12714 "This package implements affinity propagation clustering introduced by
12715 Frey and Dueck (2007). The package further provides leveraged affinity
12716 propagation and an algorithm for exemplar-based agglomerative clustering that
12717 can also be used to join clusters obtained from affinity propagation. Various
12718 plotting functions are available for analyzing clustering results.")
12719 (license license:gpl2+)))
12721 (define-public r-valr
12728 (uri (cran-uri "valr" version))
12731 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12732 (build-system r-build-system)
12734 `(("r-broom" ,r-broom)
12735 ("r-dplyr" ,r-dplyr)
12736 ("r-ggplot2" ,r-ggplot2)
12738 ("r-readr" ,r-readr)
12739 ("r-rlang" ,r-rlang)
12740 ("r-stringr" ,r-stringr)
12741 ("r-tibble" ,r-tibble)))
12742 (home-page "http://github.com/rnabioco/valr")
12743 (synopsis "Genome interval arithmetic in R")
12745 "This package enables you to read and manipulate genome intervals and
12746 signals. It provides functionality similar to command-line tool suites within
12747 R, enabling interactive analysis and visualization of genome-scale data.")
12748 (license license:expat)))
12750 (define-public r-rematch2
12752 (name "r-rematch2")
12757 (uri (cran-uri "rematch2" version))
12760 "13siaa8s2ji9q6hykhb2r34ag76335ypmbqr90xaqilbir0klhnh"))))
12761 (build-system r-build-system)
12763 `(("r-tibble" ,r-tibble)))
12764 (home-page "https://github.com/r-lib/rematch2")
12765 (synopsis "Tidy output from regular expression matching")
12767 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12768 return the match results in tidy data frames.")
12769 (license license:expat)))
12771 (define-public r-picante
12778 (uri (cran-uri "picante" version))
12781 "1b16zm8zjjsl181b8krkdcrbcw347kf772c4w7y5332qmfi7jhz0"))))
12782 (build-system r-build-system)
12786 ("r-vegan" ,r-vegan)))
12787 (home-page "https://cran.r-project.org/web/packages/picante/")
12788 (synopsis "Integrating phylogenies and ecology")
12790 "This package provides functions for phylocom integration, community
12791 analyses, null-models, traits and evolution. It implements numerous
12792 ecophylogenetic approaches including measures of community phylogenetic and
12793 trait diversity, phylogenetic signal, estimation of trait values for
12794 unobserved taxa, null models for community and phylogeny randomizations, and
12795 utility functions for data input/output and phylogeny plotting. A full
12796 description of package functionality and methods are provided by Kembel et
12798 (license license:gpl2)))
12800 (define-public r-reinforcelearn
12802 (name "r-reinforcelearn")
12807 (uri (cran-uri "reinforcelearn" version))
12810 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12811 (build-system r-build-system)
12813 `(("r-checkmate" ,r-checkmate)
12815 ("r-purrr" ,r-purrr)
12817 (home-page "https://markusdumke.github.io/reinforcelearn")
12818 (synopsis "Reinforcement learning")
12820 "This package implements reinforcement learning environments and
12821 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12822 can be used with function approximation, eligibility traces (Singh & Sutton,
12823 1996) and experience replay (Mnih et al., 2013).")
12824 (license license:expat)))
12826 (define-public r-lemon
12833 (uri (cran-uri "lemon" version))
12836 "0m9hqwi709j9iwsxn8jh63741jiyr7ppwgqaw2zkv285p3m5wvd5"))))
12837 (build-system r-build-system)
12839 `(("r-ggplot2" ,r-ggplot2)
12840 ("r-gridextra" ,r-gridextra)
12841 ("r-gtable" ,r-gtable)
12842 ("r-knitr" ,r-knitr)
12843 ("r-lattice" ,r-lattice)
12845 ("r-rlang" ,r-rlang)
12846 ("r-scales" ,r-scales)))
12847 (home-page "https://github.com/stefanedwards/lemon")
12848 (synopsis "Freshen up your ggplot2 plots")
12850 "This package provides functions for working with legends and axis lines
12851 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12853 (license license:gpl3)))
12855 (define-public r-wgaim
12862 (uri (cran-uri "wgaim" version))
12864 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12865 (build-system r-build-system)
12867 `(("r-ggplot2" ,r-ggplot2)
12869 (home-page "https://cran.r-project.org/web/packages/wgaim")
12870 (synopsis "Whole genome average interval mapping for QTL detection")
12872 "This package integrates sophisticated mixed modelling methods with a
12873 whole genome approach to detecting significant QTL in linkage maps.")
12874 (license license:gpl2+)))
12876 (define-public r-bedr
12883 (uri (cran-uri "bedr" version))
12886 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12887 (build-system r-build-system)
12889 `(("r-data-table" ,r-data-table)
12890 ("r-r-utils" ,r-r-utils)
12891 ("r-testthat" ,r-testthat)
12892 ("r-venndiagram" ,r-venndiagram)
12895 ("bedtools" ,bedtools)
12896 ("htslib" ,htslib))) ; for tabix
12898 `(("r-knitr" ,r-knitr))) ; for vignettes
12899 (home-page "https://cran.r-project.org/web/packages/bedr")
12900 (synopsis "Genomic region processing")
12902 "This package is for genomic regions processing using command line tools
12903 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12904 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12905 The bedr package's API enhances access to these tools as well as offers
12906 additional utilities for genomic regions processing.")
12907 (license license:gpl2)))
12909 (define-public r-sets
12916 (uri (cran-uri "sets" version))
12919 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12920 (properties `((upstream-name . "sets")))
12921 (build-system r-build-system)
12922 (home-page "https://cran.r-project.org/web/packages/sets")
12923 (synopsis "Sets, generalized sets, customizable sets and intervals")
12925 "This package provides data structures and basic operations for ordinary
12926 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12927 customizable sets, and intervals.")
12928 (license license:gpl2)))
12930 (define-public r-partitions
12932 (name "r-partitions")
12937 (uri (cran-uri "partitions" version))
12940 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12941 (build-system r-build-system)
12944 ("r-polynom" ,r-polynom)
12945 ("r-sets" ,r-sets)))
12946 (home-page "https://cran.r-project.org/web/packages/partitions")
12947 (synopsis "Additive partitions of integers")
12949 "This package provides tools to enumerates the partitions, unequal
12950 partitions, and restricted partitions of an integer; the three corresponding
12951 partition functions are also given.")
12952 ;; Any version of the GPL
12953 (license license:gpl2+)))
12955 (define-public r-brobdingnag
12957 (name "r-brobdingnag")
12962 (uri (cran-uri "Brobdingnag" version))
12965 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12966 (properties `((upstream-name . "Brobdingnag")))
12967 (build-system r-build-system)
12968 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12969 (synopsis "Very large numbers in R")
12971 "This package handles very large numbers in R. Real numbers are held
12972 using their natural logarithms, plus a logical flag indicating sign. The
12973 package includes a vignette that gives a step-by-step introduction to using S4
12975 ;; Any version of the GPL
12976 (license license:gpl2+)))
12978 (define-public r-untb
12985 (uri (cran-uri "untb" version))
12988 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12989 (build-system r-build-system)
12991 `(("r-brobdingnag" ,r-brobdingnag)
12992 ("r-partitions" ,r-partitions)
12993 ("r-polynom" ,r-polynom)))
12994 (home-page "https://github.com/RobinHankin/untb.git")
12995 (synopsis "Ecological drift under the UNTB")
12997 "This package provides numerical simulations, and visualizations, of
12998 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12999 (license license:gpl2+)))
13001 (define-public r-stepwise
13003 (name "r-stepwise")
13008 (uri (cran-uri "stepwise" version))
13011 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13012 (build-system r-build-system)
13013 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13014 (synopsis "Stepwise detection of recombination breakpoints")
13016 "This package provides a stepwise approach to identifying recombination
13017 breakpoints in a genomic sequence alignment.")
13018 (license license:gpl2+)))
13020 (define-public r-snpmaxsel
13022 (name "r-snpmaxsel")
13027 (uri (cran-uri "SNPmaxsel" version))
13030 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13031 (properties `((upstream-name . "SNPmaxsel")))
13032 (build-system r-build-system)
13034 `(("r-combinat" ,r-combinat)
13035 ("r-mvtnorm" ,r-mvtnorm)))
13036 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13037 (synopsis "Maximally selected statistics for SNP data")
13039 "This package implements asymptotic methods related to maximally selected
13040 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13042 (license license:gpl2+)))
13044 (define-public r-acsnminer
13046 (name "r-acsnminer")
13047 (version "0.16.8.25")
13050 (uri (cran-uri "ACSNMineR" version))
13053 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13054 (properties `((upstream-name . "ACSNMineR")))
13055 (build-system r-build-system)
13057 `(("r-ggplot2" ,r-ggplot2)
13058 ("r-gridextra" ,r-gridextra)))
13059 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13060 (synopsis "Gene enrichment analysis")
13062 "This package provides tools to compute and represent gene set enrichment
13063 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13064 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13065 enrichment can be run with hypergeometric test or Fisher exact test, and can
13066 use multiple corrections. Visualization of data can be done either by
13067 barplots or heatmaps.")
13068 (license license:gpl2+)))
13070 (define-public r-seqinr
13077 (uri (cran-uri "seqinr" version))
13080 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13081 (build-system r-build-system)
13083 `(("r-ade4" ,r-ade4)
13084 ("r-segmented" ,r-segmented)))
13087 (home-page "http://seqinr.r-forge.r-project.org/")
13088 (synopsis "Biological sequences retrieval and analysis")
13090 "This package provides tools for exploratory data analysis and data
13091 visualization of biological sequence (DNA and protein) data. It also includes
13092 utilities for sequence data management under the ACNUC system.")
13093 (license license:gpl2+)))
13095 (define-public r-units
13102 (uri (cran-uri "units" version))
13105 "11x6xz1fbml28xmrhgn4sii9vfyj3gyfc1dfxahdg9cszdmcgdnh"))))
13106 (build-system r-build-system)
13108 `(("udunits" ,udunits)))
13110 `(("r-rcpp" ,r-rcpp)))
13112 `(("r-knitr" ,r-knitr)))
13113 (home-page "https://github.com/r-quantities/units/")
13114 (synopsis "Measurement Units for R Vectors")
13116 "This package provides support for measurement units in R vectors,
13117 matrices and arrays: automatic propagation, conversion, derivation and
13118 simplification of units; raising errors in case of unit incompatibility. It
13119 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13121 (license license:gpl2)))
13123 (define-public r-classint
13125 (name "r-classint")
13130 (uri (cran-uri "classInt" version))
13133 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13134 (properties `((upstream-name . "classInt")))
13135 (build-system r-build-system)
13137 `(("r-class" ,r-class)
13138 ("r-e1071" ,r-e1071)
13139 ("r-kernsmooth" ,r-kernsmooth)))
13141 `(("gfortran" ,gfortran)
13142 ("r-knitr" ,r-knitr)))
13143 (home-page "https://github.com/r-spatial/classInt/")
13144 (synopsis "Choose univariate class intervals")
13146 "This package provides selected commonly used methods for choosing
13147 univariate class intervals for mapping or other graphics purposes.")
13148 (license license:gpl2+)))
13150 (define-public r-spdata
13157 (uri (cran-uri "spData" version))
13160 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13161 (properties `((upstream-name . "spData")))
13162 (build-system r-build-system)
13164 `(("r-raster" ,r-raster)
13166 (home-page "https://github.com/Nowosad/spData")
13167 (synopsis "Datasets for spatial analysis")
13169 "This a package containing diverse spatial datasets for demonstrating,
13170 benchmarking and teaching spatial data analysis. It includes R data of class
13171 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13172 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13173 of the datasets are designed to illustrate specific analysis techniques.
13174 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13175 illustrate point pattern analysis techniques.")
13176 (license license:cc0)))
13178 (define-public r-learnbayes
13180 (name "r-learnbayes")
13185 (uri (cran-uri "LearnBayes" version))
13188 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13189 (properties `((upstream-name . "LearnBayes")))
13190 (build-system r-build-system)
13191 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13192 (synopsis "Functions for learning Bayesian inference")
13194 "This package provides a collection of functions helpful in learning the
13195 basic tenets of Bayesian statistical inference. It contains functions for
13196 summarizing basic one and two parameter posterior distributions and predictive
13197 distributions. It contains MCMC algorithms for summarizing posterior
13198 distributions defined by the user. It also contains functions for regression
13199 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13201 (license license:gpl2+)))
13203 (define-public r-deldir
13210 (uri (cran-uri "deldir" version))
13213 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13214 (build-system r-build-system)
13215 (native-inputs `(("gfortran" ,gfortran)))
13216 (home-page "https://cran.r-project.org/web/packages/deldir")
13217 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13219 "This package provides tools for calculating the Delaunay triangulation
13220 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13221 of a planar point set. It plots triangulations and tessellations in various
13222 ways, clips tessellations to sub-windows, calculates perimeters of
13223 tessellations, and summarizes information about the tiles of the
13225 (license license:gpl2+)))
13227 (define-public r-sf
13234 (uri (cran-uri "sf" version))
13237 "117r9l3v7nkdj9bfy6qr0yz0gd5bv0pwnkc9vk2gv3xqj0h1fpf6"))))
13238 (build-system r-build-system)
13245 `(("r-classint" ,r-classint)
13247 ("r-magrittr" ,r-magrittr)
13249 ("r-units" ,r-units)))
13251 `(("pkg-config" ,pkg-config)
13252 ("r-knitr" ,r-knitr)))
13253 (home-page "https://github.com/r-spatial/sf/")
13254 (synopsis "Simple features for R")
13256 "This package provides support for simple features, a standardized way to
13257 encode spatial vector data. It binds to GDAL for reading and writing data, to
13258 GEOS for geometrical operations, and to PROJ for projection conversions and
13259 datum transformations.")
13260 ;; Either of these licenses
13261 (license (list license:gpl2 license:expat))))
13263 (define-public r-spdep
13270 (uri (cran-uri "spdep" version))
13273 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13274 (build-system r-build-system)
13276 `(("r-boot" ,r-boot)
13278 ("r-deldir" ,r-deldir)
13280 ("r-gmodels" ,r-gmodels)
13281 ("r-learnbayes" ,r-learnbayes)
13283 ("r-matrix" ,r-matrix)
13287 ("r-spdata" ,r-spdata)))
13288 (home-page "https://github.com/r-spatial/spdep/")
13289 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13291 "This package provides a collection of functions to create spatial
13292 weights matrix objects from polygon contiguities, from point patterns by
13293 distance and tessellations, for summarizing these objects, and for permitting
13294 their use in spatial data analysis, including regional aggregation by minimum
13296 (license license:gpl2+)))
13298 (define-public r-adegenet
13300 (name "r-adegenet")
13305 (uri (cran-uri "adegenet" version))
13308 "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
13309 (build-system r-build-system)
13311 `(("r-ade4" ,r-ade4)
13314 ("r-dplyr" ,r-dplyr)
13315 ("r-ggplot2" ,r-ggplot2)
13316 ("r-igraph" ,r-igraph)
13318 ("r-reshape2" ,r-reshape2)
13319 ("r-seqinr" ,r-seqinr)
13320 ("r-shiny" ,r-shiny)
13321 ("r-spdep" ,r-spdep)
13322 ("r-vegan" ,r-vegan)))
13323 (home-page "https://github.com/thibautjombart/adegenet")
13324 (synopsis "Exploratory analysis of genetic and genomic data")
13326 "This package provides a toolset for the exploration of genetic and
13327 genomic data. Adegenet provides formal (S4) classes for storing and handling
13328 various genetic data, including genetic markers with varying ploidy and
13329 hierarchical population structure (@code{genind} class), alleles counts by
13330 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13331 also implements original multivariate methods (DAPC, sPCA), graphics,
13332 statistical tests, simulation tools, distance and similarity measures, and
13333 several spatial methods. A range of both empirical and simulated datasets is
13334 also provided to illustrate various methods.")
13335 (license license:gpl2+)))
13337 (define-public r-pegas
13344 (uri (cran-uri "pegas" version))
13346 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13347 (build-system r-build-system)
13349 `(("r-adegenet" ,r-adegenet)
13351 (home-page "http://ape-package.ird.fr/pegas.html")
13352 (synopsis "Population and evolutionary genetics analysis system")
13354 "This package provides functions for reading, writing, plotting,
13355 analysing, and manipulating allelic and haplotypic data, including from VCF
13356 files, and for the analysis of population nucleotide sequences and
13357 micro-satellites including coalescent analyses, linkage disequilibrium,
13358 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13359 minimum spanning tree and network, and median-joining networks.")
13360 (license license:gpl2+)))
13362 (define-public r-rmetasim
13364 (name "r-rmetasim")
13369 (uri (cran-uri "rmetasim" version))
13372 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13373 (build-system r-build-system)
13375 `(("r-ade4" ,r-ade4)
13376 ("r-adegenet" ,r-adegenet)
13377 ("r-gtools" ,r-gtools)
13378 ("r-pegas" ,r-pegas)))
13379 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13380 (synopsis "Individual-based population genetic simulation environment")
13382 "This package provides an interface between R and the metasim simulation
13383 engine. The simulation environment is documented in: Strand, A.(2002),
13384 Metasim 1.0: an individual-based environment for simulating population
13385 genetics of complex population dynamics.")
13387 (license license:gpl2+)))
13389 (define-public r-genetics
13391 (name "r-genetics")
13392 (version "1.3.8.1.2")
13396 (uri (cran-uri "genetics" version))
13399 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13400 (build-system r-build-system)
13402 `(("r-combinat" ,r-combinat)
13403 ("r-gdata" ,r-gdata)
13404 ("r-gtools" ,r-gtools)
13406 ("r-mvtnorm" ,r-mvtnorm)))
13407 (home-page "https://cran.r-project.org/web/packages/genetics/")
13408 (synopsis "Population genetics")
13410 "This package provides classes and methods for handling genetic data.
13411 It includes classes to represent genotypes and haplotypes at single markers up
13412 to multiple markers on multiple chromosomes. Function include allele
13413 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13414 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13415 and testing for linkage disequilibrium, ...")
13416 ;; Any GPL version.
13417 (license license:gpl2+)))
13419 (define-public r-snp-plotter
13421 (name "r-snp-plotter")
13426 (uri (cran-uri "snp.plotter" version))
13429 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13430 (properties `((upstream-name . "snp.plotter")))
13431 (build-system r-build-system)
13432 (propagated-inputs `(("r-genetics" ,r-genetics)))
13433 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13434 (synopsis "Plot p-values using single SNP and/or haplotype data")
13436 "This package helps you create plots of p-values using single SNP and/or
13437 haplotype data. Main features of the package include options to display a
13438 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13439 datasets simultaneously. Plots can be created using global and/or individual
13440 haplotype p-values along with single SNP p-values. Images are created as
13441 either PDF/EPS files.")
13442 (license license:gpl2+)))
13444 (define-public r-polspline
13446 (name "r-polspline")
13451 (uri (cran-uri "polspline" version))
13453 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13454 (build-system r-build-system)
13455 (native-inputs `(("gfortran" ,gfortran)))
13456 (home-page "https://cran.r-project.org/web/packages/polspline/")
13457 (synopsis "Polynomial spline routines")
13459 "This package provides routines for the polynomial spline fitting
13460 routines hazard regression, hazard estimation with flexible tails, logspline,
13461 lspec, polyclass, and polymars.")
13462 (license license:gpl2+)))
13464 (define-public r-rms
13471 (uri (cran-uri "rms" version))
13473 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13474 (build-system r-build-system)
13476 `(("r-ggplot2" ,r-ggplot2)
13477 ("r-hmisc" ,r-hmisc)
13478 ("r-htmltable" ,r-htmltable)
13479 ("r-htmltools" ,r-htmltools)
13480 ("r-lattice" ,r-lattice)
13481 ("r-multcomp" ,r-multcomp)
13483 ("r-polspline" ,r-polspline)
13484 ("r-quantreg" ,r-quantreg)
13485 ("r-rpart" ,r-rpart)
13486 ("r-sparsem" ,r-sparsem)
13487 ("r-survival" ,r-survival)))
13488 (native-inputs `(("gfortran" ,gfortran)))
13489 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13490 (synopsis "Regression modeling strategies")
13492 "This is a package for regression modeling, testing, estimation,
13493 validation, graphics, prediction, and typesetting by storing enhanced model
13494 design attributes in the fit. The rms package is a collection of functions
13495 that assist with and streamline modeling. It also contains functions for
13496 binary and ordinal logistic regression models, ordinal models for continuous Y
13497 with a variety of distribution families, and the Buckley-James multiple
13498 regression model for right-censored responses, and implements penalized
13499 maximum likelihood estimation for logistic and ordinary linear models. The
13500 package works with almost any regression model, but it was especially written
13501 to work with binary or ordinal regression models, Cox regression, accelerated
13502 failure time models, ordinary linear models, the Buckley-James model,
13503 generalized least squares for serially or spatially correlated observations,
13504 generalized linear models, and quantile regression.")
13505 (license license:gpl2+)))
13507 (define-public r-haplo-stats
13509 (name "r-haplo-stats")
13514 (uri (cran-uri "haplo.stats" version))
13517 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13518 (properties `((upstream-name . "haplo.stats")))
13519 (build-system r-build-system)
13521 `(("r-rms" ,r-rms)))
13523 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13524 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13525 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13527 "This package provides routines for the analysis of indirectly measured
13528 haplotypes. The statistical methods assume that all subjects are unrelated
13529 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13530 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13531 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13532 examples in the vignette.")
13533 (license license:gpl2+)))
13535 (define-public r-bqtl
13542 (uri (cran-uri "bqtl" version))
13545 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13546 (build-system r-build-system)
13547 (native-inputs `(("gfortran" ,gfortran)))
13548 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13549 (synopsis "Bayesian QTL mapping toolkit")
13551 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13552 lines. It includes maximum likelihood and Bayesian tools.")
13553 (license license:gpl2+)))
13555 (define-public r-ibdreg
13562 (uri (cran-uri "ibdreg" version))
13565 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13566 (build-system r-build-system)
13567 (home-page "https://www.mayo.edu/research/labs/\
13568 statistical-genetics-genetic-epidemiology/software")
13569 (synopsis "Regression methods for IBD linkage with covariates")
13571 "This package provides a method to test genetic linkage with covariates
13572 by regression methods with response IBD sharing for relative pairs. Account
13573 for correlations of IBD statistics and covariates for relative pairs within
13574 the same pedigree.")
13575 (license license:gpl2+)))
13577 (define-public r-dlmap
13584 (uri (cran-uri "dlmap" version))
13587 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13588 (build-system r-build-system)
13590 `(("r-ibdreg" ,r-ibdreg)
13594 ("r-wgaim" ,r-wgaim)))
13595 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13596 (synopsis "Detection localization mapping for QTL")
13598 "This is package for QTL mapping in a mixed model framework with separate
13599 detection and localization stages. The first stage detects the number of QTL
13600 on each chromosome based on the genetic variation due to grouped markers on
13601 the chromosome; the second stage uses this information to determine the most
13602 likely QTL positions. The mixed model can accommodate general fixed and
13603 random effects, including spatial effects in field trials and pedigree
13604 effects. It is applicable to backcrosses, doubled haploids, recombinant
13605 inbred lines, F2 intercrosses, and association mapping populations.")
13606 (license license:gpl2)))
13608 (define-public r-ldheatmap
13610 (name "r-ldheatmap")
13615 (uri (cran-uri "LDheatmap" version))
13618 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13619 (properties `((upstream-name . "LDheatmap")))
13620 (build-system r-build-system)
13622 `(("r-genetics" ,r-genetics)
13624 ("r-snpstats" ,r-snpstats)))
13625 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
13626 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13628 "This package provides tools to produce a graphical display, as a heat
13629 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13630 optionally include the physical locations or genetic map distances of each SNP
13632 (license license:gpl3)))
13634 (define-public r-hwde
13641 (uri (cran-uri "hwde" version))
13644 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13645 (build-system r-build-system)
13646 (home-page "https://cran.r-project.org/web/packages/hwde/")
13647 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13649 "This package fits models for genotypic disequilibria, as described in
13650 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13651 terms are available that account for first order interactions between loci.
13652 It also implements, for a single locus in a single population, a conditional
13653 exact test for Hardy-Weinberg equilibrium.")
13654 (license license:gpl2+)))
13656 (define-public r-tdthap
13663 (uri (cran-uri "tdthap" version))
13666 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13667 (build-system r-build-system)
13668 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13669 (synopsis "TDT tests for extended haplotypes")
13671 "Functions and examples are provided for transmission/disequilibrium
13672 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13673 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13674 (license license:artistic2.0)))
13676 (define-public r-sparql
13682 (uri (cran-uri "SPARQL" version))
13685 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13686 (properties `((upstream-name . "SPARQL")))
13687 (build-system r-build-system)
13689 `(("r-rcurl" ,r-rcurl)
13691 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13692 (synopsis "SPARQL client for R")
13693 (description "This package provides an interface to use SPARQL to pose
13694 SELECT or UPDATE queries to an end-point.")
13695 ;; The only license indication is found in the DESCRIPTION file,
13696 ;; which states GPL-3. So we cannot assume GPLv3+.
13697 (license license:gpl3)))
13699 (define-public r-bookdown
13701 (name "r-bookdown")
13705 (uri (cran-uri "bookdown" version))
13708 "1my6g16phx21v5cvfqcnjibh3zcv02xkix347aafd6a7r3hnxpq5"))))
13709 (build-system r-build-system)
13711 `(("r-htmltools" ,r-htmltools)
13712 ("r-knitr" ,r-knitr)
13713 ("r-rmarkdown" ,r-rmarkdown)
13714 ("r-tinytex" ,r-tinytex)
13716 ("pandoc" ,ghc-pandoc)))
13717 (home-page "https://github.com/rstudio/bookdown")
13718 (synopsis "Authoring books and technical documents with R markdown")
13719 (description "This package provides output formats and utilities for
13720 authoring books and technical documents with R Markdown.")
13721 (license license:gpl3)))
13723 (define-public r-optparse
13725 (name "r-optparse")
13730 (uri (cran-uri "optparse" version))
13733 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13734 (build-system r-build-system)
13736 `(("r-getopt" ,r-getopt)))
13737 (home-page "https://github.com/trevorld/optparse")
13738 (synopsis "Command line option parser")
13740 "This package provides a command line parser inspired by Python's
13741 @code{optparse} library to be used with Rscript to write shebang scripts
13742 that accept short and long options.")
13743 (license license:gpl2+)))
13745 (define-public r-wgcna
13752 (uri (cran-uri "WGCNA" version))
13755 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
13756 (properties `((upstream-name . "WGCNA")))
13757 (build-system r-build-system)
13759 `(("r-annotationdbi" ,r-annotationdbi)
13760 ("r-doparallel" ,r-doparallel)
13761 ("r-dynamictreecut" ,r-dynamictreecut)
13762 ("r-fastcluster" ,r-fastcluster)
13763 ("r-foreach" ,r-foreach)
13764 ("r-go-db" ,r-go-db)
13765 ("r-hmisc" ,r-hmisc)
13766 ("r-impute" ,r-impute)
13768 ("r-survival" ,r-survival)
13769 ("r-matrixstats" ,r-matrixstats)
13770 ("r-preprocesscore" ,r-preprocesscore)))
13772 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13773 (synopsis "Weighted correlation network analysis")
13775 "This package provides functions necessary to perform Weighted
13776 Correlation Network Analysis on high-dimensional data. It includes functions
13777 for rudimentary data cleaning, construction and summarization of correlation
13778 networks, module identification and functions for relating both variables and
13779 modules to sample traits. It also includes a number of utility functions for
13780 data manipulation and visualization.")
13781 (license license:gpl2+)))
13783 (define-public r-kernlab
13790 (uri (cran-uri "kernlab" version))
13792 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13793 (build-system r-build-system)
13794 (home-page "https://cran.r-project.org/web/packages/kernlab")
13795 (synopsis "Kernel-based machine learning tools")
13797 "This package provides kernel-based machine learning methods for
13798 classification, regression, clustering, novelty detection, quantile regression
13799 and dimensionality reduction. Among other methods @code{kernlab} includes
13800 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13802 (license license:gpl2)))
13804 (define-public r-hierfstat
13806 (name "r-hierfstat")
13807 (version "0.04-22")
13811 (uri (cran-uri "hierfstat" version))
13814 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13815 (build-system r-build-system)
13817 `(("r-ade4" ,r-ade4)
13818 ("r-adegenet" ,r-adegenet)
13819 ("r-gtools" ,r-gtools)))
13820 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13821 (synopsis "Estimation and tests of hierarchical F-statistics")
13823 "This package allows the estimation of hierarchical F-statistics from
13824 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13825 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13826 are also given to test via randomisations the significance of each F and
13827 variance components, using the likelihood-ratio statistics G.")
13828 (license license:gpl2+)))
13830 (define-public r-hapassoc
13832 (name "r-hapassoc")
13837 (uri (cran-uri "hapassoc" version))
13840 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13841 (build-system r-build-system)
13842 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
13843 (synopsis "Inference of trait associations with SNP haplotypes")
13845 "Hapassoc performs likelihood inference of trait associations with
13846 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13847 functions are developed primarily for data collected in cohort or
13848 cross-sectional studies. They can accommodate uncertain haplotype phase and
13849 handle missing genotypes at some SNPs.")
13850 (license license:gpl2)))
13852 (define-public r-sampling
13854 (name "r-sampling")
13859 (uri (cran-uri "sampling" version))
13862 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13863 (build-system r-build-system)
13865 `(("r-lpsolve" ,r-lpsolve)
13866 ("r-mass" ,r-mass)))
13867 (home-page "https://cran.r-project.org/web/packages/sampling/")
13868 (synopsis "Survey sampling")
13870 "This package provides functions for drawing and calibrating samples.")
13871 (license license:gpl2+)))
13873 (define-public r-r2html
13880 (uri (cran-uri "R2HTML" version))
13883 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13884 (properties `((upstream-name . "R2HTML")))
13885 (build-system r-build-system)
13886 (home-page "https://github.com/nalimilan/R2HTML")
13887 (synopsis "HTML export for R objects")
13889 "This package includes HTML functions and methods to write in an HTML
13890 file. Thus, making HTML reports is easy. It includes a function that allows
13891 redirection on the fly, which appears to be very useful for teaching purposes,
13892 as the student can keep a copy of the produced output to keep all that they
13893 did during the course. The package comes with a vignette describing how to
13894 write HTML reports for statistical analysis. Finally, a driver for Sweave
13895 parses HTML flat files containing R code and to automatically write
13896 the corresponding outputs (tables and graphs).")
13897 (license license:gpl2+)))
13899 (define-public r-rjava
13906 (uri (cran-uri "rJava" version))
13909 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
13910 (properties `((upstream-name . "rJava")))
13911 (build-system r-build-system)
13913 `(#:modules ((guix build utils)
13914 (guix build r-build-system)
13917 (modify-phases %standard-phases
13918 (add-after 'unpack 'set-JAVA_HOME
13919 (lambda* (#:key inputs #:allow-other-keys)
13920 (let ((jdk (assoc-ref inputs "jdk")))
13921 (setenv "JAVA_HOME" jdk)
13922 (setenv "JAVA" (which "java"))
13923 (setenv "JAR" (which "jar"))
13924 (setenv "JAVAC" (which "javac"))
13925 (setenv "JAVAH" (which "javah"))
13926 (setenv "JAVA_CPPFLAGS"
13927 (string-append "-I" jdk "/include "
13928 "-I" jdk "/include/linux"))
13929 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13930 ((lib) (setenv "JAVA_LIBS" lib))
13931 (_ (error "Could not find libjvm.so"))))
13935 ("jdk" ,icedtea-8 "jdk")
13938 (home-page "https://www.rforge.net/rJava/")
13939 (synopsis "Low-Level R to Java interface")
13941 "This package provides a low-level interface to the Java VM very much
13942 like .C/.Call and friends. It allows the creation of objects, calling methods
13943 and accessing fields.")
13944 (license license:gpl2)))
13946 (define-public r-svmisc
13953 (uri (cran-uri "svMisc" version))
13956 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13957 (properties `((upstream-name . "svMisc")))
13958 (build-system r-build-system)
13959 (home-page "https://github.com/SciViews/svMisc")
13960 (synopsis "Miscellaneous functions for SciViews")
13962 "This package provides miscellaneous functions for SciViews or general
13963 use, including tools to manage a temporary environment attached to the search
13964 path for temporary variables you do not want to @code{save()} or
13965 @code{load()}; test the current platform; showing progress bars, etc.")
13966 (license license:gpl2)))
13968 (define-public r-xyz
13975 (uri (cran-uri "xyz" version))
13978 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13979 (build-system r-build-system)
13981 `(("r-rcpp" ,r-rcpp)))
13982 (home-page "https://cran.r-project.org/web/packages/xyz/")
13983 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13985 "High dimensional interaction search by brute force requires a quadratic
13986 computational cost in the number of variables. The xyz algorithm provably
13987 finds strong interactions in almost linear time. For details of the algorithm
13988 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13989 interaction search in high-dimensional data.")
13990 ;; Any version of the GPL.
13991 (license license:gpl2+)))
13993 (define-public r-rttf2pt1
13995 (name "r-rttf2pt1")
14000 (uri (cran-uri "Rttf2pt1" version))
14003 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14004 (properties `((upstream-name . "Rttf2pt1")))
14005 (build-system r-build-system)
14006 (home-page "https://github.com/wch/Rttf2pt1")
14007 (synopsis "Font conversion utility")
14009 "This package contains the program @code{ttf2pt1}, for use with the
14010 @code{extrafont} package.")
14011 ;; Most of the files are covered under the Expat license. Some files are
14012 ;; covered under BSD-3. Deviations for individual files are recorded in
14013 ;; the LICENSE file.
14014 (license (list license:bsd-3 license:expat
14015 (license:non-copyleft "file://LICENSE")))))
14017 (define-public r-extrafontdb
14019 (name "r-extrafontdb")
14024 (uri (cran-uri "extrafontdb" version))
14027 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14028 (build-system r-build-system)
14029 (home-page "https://github.com/wch/extrafontdb")
14030 (synopsis "Database for the extrafont package")
14032 "This package holds the database for the @code{extrafont} package.")
14033 (license license:gpl2)))
14035 (define-public r-extrafont
14037 (name "r-extrafont")
14042 (uri (cran-uri "extrafont" version))
14045 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14046 (build-system r-build-system)
14048 `(("r-extrafontdb" ,r-extrafontdb)
14049 ("r-rttf2pt1" ,r-rttf2pt1)))
14050 (home-page "https://github.com/wch/extrafont")
14051 (synopsis "Tools for using fonts in R")
14053 "The extrafont package makes it easier to use fonts other than the basic
14054 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14055 used with PDF or PostScript output files. There are two hurdles for using
14056 fonts in PDF (or Postscript) output files:
14059 @item Making R aware of the font and the dimensions of the characters.
14060 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14061 properly on a device that doesn't have the font. This is usually needed if
14062 you want to print the PDF file or share it with others.
14065 The extrafont package makes both of these things easier.")
14066 (license license:gpl2)))
14068 (define-public r-xkcd
14075 (uri (cran-uri "xkcd" version))
14078 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14079 (build-system r-build-system)
14081 `(("r-extrafont" ,r-extrafont)
14082 ("r-ggplot2" ,r-ggplot2)
14083 ("r-hmisc" ,r-hmisc)))
14084 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14085 (synopsis "Plot ggplot2 graphics in the XKCD style")
14087 "This package provides the means to plot ggplot2 graphs in the style of
14088 the XKCD web comic.")
14089 (license license:gpl3)))
14091 (define-public r-msigdbr
14098 (uri (cran-uri "msigdbr" version))
14101 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14102 (build-system r-build-system)
14104 `(("r-dplyr" ,r-dplyr)
14105 ("r-magrittr" ,r-magrittr)
14106 ("r-rlang" ,r-rlang)
14107 ("r-tibble" ,r-tibble)))
14108 (home-page "https://github.com/igordot/msigdbr")
14109 (synopsis "MSigDB gene sets for multiple organisms")
14111 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14112 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14113 software in a standard R data frame with key-value pairs. Included are the
14114 original human gene symbols and Entrez IDs as well as the equivalents for
14115 various frequently studied model organisms such as mouse, rat, pig, fly, and
14117 ;; The package is covered under the Expat license, but the upstream MSigDB
14118 ;; files are made available under the Creative Commons Attribution 4.0
14119 ;; International license.
14120 (license (list license:expat license:cc-by4.0))))
14122 (define-public r-gridgraphics
14124 (name "r-gridgraphics")
14129 (uri (cran-uri "gridGraphics" version))
14132 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14133 (properties `((upstream-name . "gridGraphics")))
14134 (build-system r-build-system)
14135 (home-page "https://github.com/pmur002/gridgraphics")
14136 (synopsis "Redraw base graphics using @code{grid} graphics")
14138 "This package provides functions to convert a page of plots drawn with
14139 the @code{graphics} package into identical output drawn with the @code{grid}
14140 package. The result looks like the original @code{graphics}-based plot, but
14141 consists of @code{grid} grobs and viewports that can then be manipulated with
14142 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14143 (license license:gpl2+)))
14145 (define-public r-farver
14152 (uri (cran-uri "farver" version))
14155 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14156 (build-system r-build-system)
14157 (home-page "https://github.com/thomasp85/farver")
14158 (synopsis "Vectorized color conversion and comparison")
14160 "The encoding of color can be handled in many different ways, using
14161 different color spaces. As different color spaces have different uses,
14162 efficient conversion between these representations are important. This
14163 package provides a set of functions that gives access to very fast color space
14164 conversion and comparisons implemented in C++, and offers 100-fold speed
14165 improvements over the @code{convertColor} function in the @code{grDevices}
14167 (license license:expat)))
14169 (define-public r-ggplotify
14171 (name "r-ggplotify")
14176 (uri (cran-uri "ggplotify" version))
14179 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14180 (build-system r-build-system)
14182 `(("r-ggplot2" ,r-ggplot2)
14183 ("r-gridgraphics" ,r-gridgraphics)
14184 ("r-rvcheck" ,r-rvcheck)))
14186 `(("r-knitr" ,r-knitr)))
14187 (home-page "https://github.com/GuangchuangYu/ggplotify")
14188 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14190 "This package provides tools to convert plot function calls (using
14191 expression or formula) to @code{grob} or @code{ggplot} objects that are
14192 compatible with the @code{grid} and @code{ggplot2} environment. With this
14193 package, we are able to e.g. use @code{cowplot} to align plots produced by
14194 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14195 converting them to @code{ggplot} objects.")
14196 (license license:artistic2.0)))
14198 (define-public r-triebeard
14200 (name "r-triebeard")
14205 (uri (cran-uri "triebeard" version))
14208 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14209 (build-system r-build-system)
14210 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14211 (home-page "https://github.com/Ironholds/triebeard/")
14212 (synopsis "Radix trees in Rcpp")
14214 "Radix trees, or tries, are key-value data structures optimized for
14215 efficient lookups, similar in purpose to hash tables. This package provides
14216 an implementation of radix trees for use in R programming and in developing
14217 packages with Rcpp.")
14218 (license license:expat)))
14220 (define-public r-tweenr
14227 (uri (cran-uri "tweenr" version))
14230 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14231 (build-system r-build-system)
14233 `(("r-farver" ,r-farver)
14234 ("r-magrittr" ,r-magrittr)
14236 ("r-rlang" ,r-rlang)))
14237 (home-page "https://github.com/thomasp85/tweenr")
14238 (synopsis "Interpolate data for smooth animations")
14240 "In order to create smooth animation between states of data, tweening is
14241 necessary. This package provides a range of functions for creating tweened
14242 data that can be used as basis for animation. Furthermore it adds a number of
14243 vectorized interpolaters for common R data types such as numeric, date and
14245 (license license:expat)))
14247 (define-public r-polyclip
14249 (name "r-polyclip")
14254 (uri (cran-uri "polyclip" version))
14257 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14258 (build-system r-build-system)
14259 (native-inputs `(("pkg-config" ,pkg-config)))
14260 (home-page "http://www.angusj.com/delphi/clipper.php")
14261 (synopsis "Polygon clipping")
14263 "This package provides an R port of the library Clipper. It performs
14264 polygon clipping operations (intersection, union, set minus, set difference)
14265 for polygonal regions of arbitrary complexity, including holes. It computes
14266 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14267 dilations) for polygonal regions and polygonal lines. It computes the
14268 Minkowski Sum of general polygons. There is a function for removing
14269 self-intersections from polygon data.")
14270 (license license:boost1.0)))
14272 (define-public r-urltools
14274 (name "r-urltools")
14279 (uri (cran-uri "urltools" version))
14282 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14283 (build-system r-build-system)
14285 `(("r-rcpp" ,r-rcpp)
14286 ("r-triebeard" ,r-triebeard)))
14287 (home-page "https://github.com/Ironholds/urltools/")
14288 (synopsis "Vectorized tools for URL handling and parsing")
14290 "This package provides a toolkit for all URL-handling needs, including
14291 encoding and decoding, parsing, parameter extraction and modification. All
14292 functions are designed to be both fast and entirely vectorized. It is
14293 intended to be useful for people dealing with web-related datasets, such as
14294 server-side logs, although may be useful for other situations involving large
14296 (license license:expat)))
14298 (define-public r-ggforce
14305 (uri (cran-uri "ggforce" version))
14308 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14309 (build-system r-build-system)
14311 `(("r-ggplot2" ,r-ggplot2)
14312 ("r-gtable" ,r-gtable)
14314 ("r-polyclip" ,r-polyclip)
14316 ("r-rcppeigen" ,r-rcppeigen)
14317 ("r-rlang" ,r-rlang)
14318 ("r-scales" ,r-scales)
14319 ("r-tidyselect" ,r-tidyselect)
14320 ("r-tweenr" ,r-tweenr)
14321 ("r-withr" ,r-withr)))
14322 (home-page "https://ggforce.data-imaginist.com")
14323 (synopsis "Accelerating ggplot2")
14325 "The aim of the ggplot2 package is to aid in visual data investigations.
14326 This focus has led to a lack of facilities for composing specialized plots.
14327 Thi package aims to be a collection of mainly new statistics and geometries
14328 that fills this gap.")
14329 (license license:expat)))
14331 (define-public r-europepmc
14333 (name "r-europepmc")
14338 (uri (cran-uri "europepmc" version))
14341 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14342 (build-system r-build-system)
14344 `(("r-dplyr" ,r-dplyr)
14346 ("r-jsonlite" ,r-jsonlite)
14348 ("r-progress" ,r-progress)
14349 ("r-purrr" ,r-purrr)
14350 ("r-urltools" ,r-urltools)
14351 ("r-xml2" ,r-xml2)))
14352 (home-page "https://github.com/ropensci/europepmc/")
14353 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14355 "This package provides an R Client for the
14356 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14357 Service}. It gives access to both metadata on life science literature and
14358 open access full texts. Europe PMC indexes all PubMed content and other
14359 literature sources including Agricola, a bibliographic database of citations
14360 to the agricultural literature, or Biological Patents. In addition to
14361 bibliographic metadata, the client allows users to fetch citations and
14362 reference lists. Links between life-science literature and other EBI
14363 databases, including ENA, PDB or ChEMBL are also accessible.")
14364 (license license:gpl3)))
14366 (define-public r-ggraph
14373 (uri (cran-uri "ggraph" version))
14376 "1ckq82hg52vr2wydkqv2wrppgjyvddd6bwqzrngqlm7j71xapjl0"))))
14377 (build-system r-build-system)
14379 `(("r-digest" ,r-digest)
14380 ("r-dplyr" ,r-dplyr)
14381 ("r-ggforce" ,r-ggforce)
14382 ("r-ggplot2" ,r-ggplot2)
14383 ("r-ggrepel" ,r-ggrepel)
14384 ("r-graphlayouts" ,r-graphlayouts)
14385 ("r-gtable" ,r-gtable)
14386 ("r-igraph" ,r-igraph)
14389 ("r-rlang" ,r-rlang)
14390 ("r-scales" ,r-scales)
14391 ("r-tidygraph" ,r-tidygraph)
14392 ("r-viridis" ,r-viridis)))
14394 `(("r-knitr" ,r-knitr)))
14395 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14396 (synopsis "Implementation of grammar of graphics for graphs and networks")
14398 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14399 graph and network visualizations due to its reliance on tabular data input.
14400 The ggraph package is an extension of the ggplot2 API tailored to graph
14401 visualizations and provides the same flexible approach to building up plots
14403 (license license:gpl3)))
14405 (define-public r-varselrf
14407 (name "r-varselrf")
14412 (uri (cran-uri "varSelRF" version))
14415 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14416 (properties `((upstream-name . "varSelRF")))
14417 (build-system r-build-system)
14419 `(("r-randomforest" ,r-randomforest)))
14420 (home-page "https://www.ligarto.org/rdiaz/software/software")
14421 (synopsis "Variable selection using random forests")
14423 "This package provides tools for the variable selection from random
14424 forests using both backwards variable elimination (for the selection of small
14425 sets of non-redundant variables) and selection based on the importance
14426 spectrum (somewhat similar to scree plots; for the selection of large,
14427 potentially highly-correlated variables). The main applications are in
14428 high-dimensional data (e.g., microarray data, and other genomics and
14429 proteomics applications).")
14430 (license license:gpl2+)))
14432 (define-public r-pamr
14439 (uri (cran-uri "pamr" version))
14442 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14443 (build-system r-build-system)
14445 `(("r-cluster" ,r-cluster)
14446 ("r-survival" ,r-survival)))
14447 (native-inputs `(("gfortran" ,gfortran)))
14448 (home-page "https://cran.r-project.org/web/packages/pamr/")
14449 (synopsis "Prediction Analysis for Microarrays")
14451 "This package provides some functions for sample classification in
14453 (license license:gpl2)))
14455 (define-public r-rda
14458 (version "1.0.2-2.1")
14462 (uri (cran-uri "rda" version))
14465 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14466 (build-system r-build-system)
14467 (home-page "https://cran.r-project.org/web/packages/rda/")
14468 (synopsis "Shrunken centroids regularized discriminant analysis")
14470 "This package provides tools for shrunken centroids regularized
14471 discriminant analysis for the purpose of classifying high dimensional data.")
14472 (license license:gpl2+)))
14474 (define-public r-ggvis
14481 (uri (cran-uri "ggvis" version))
14484 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14485 (build-system r-build-system)
14487 `(("r-assertthat" ,r-assertthat)
14488 ("r-dplyr" ,r-dplyr)
14489 ("r-htmltools" ,r-htmltools)
14490 ("r-jsonlite" ,r-jsonlite)
14491 ("r-lazyeval" ,r-lazyeval)
14492 ("r-magrittr" ,r-magrittr)
14493 ("r-shiny" ,r-shiny)))
14494 (home-page "https://ggvis.rstudio.com/")
14495 (synopsis "Interactive grammar of graphics")
14497 "This package is a data visualization package for R providing an
14498 implementation of an interactive grammar of graphics, taking the best parts of
14499 ggplot2, combining them with the reactive framework of Shiny and drawing web
14500 graphics using Vega.")
14501 (license license:gpl2)))
14503 (define-public r-gbm
14510 (uri (cran-uri "gbm" version))
14513 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14514 (build-system r-build-system)
14516 `(("r-gridextra" ,r-gridextra)
14517 ("r-lattice" ,r-lattice)
14518 ("r-survival" ,r-survival)))
14519 (home-page "https://github.com/gbm-developers/gbm")
14520 (synopsis "Generalized boosted regression models")
14522 "This package is an implementation of extensions to Freund and Schapire's
14523 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14524 regression methods for least squares, absolute loss, t-distribution loss,
14525 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14526 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14527 and Learning to Rank measures (LambdaMart).")
14528 (license license:gpl2+)))
14530 (define-public r-threejs
14537 (uri (cran-uri "threejs" version))
14540 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14541 (build-system r-build-system)
14543 `(#:modules ((guix build utils)
14544 (guix build r-build-system)
14548 (modify-phases %standard-phases
14549 (add-after 'unpack 'process-javascript
14550 (lambda* (#:key inputs #:allow-other-keys)
14551 (with-directory-excursion "inst"
14555 `((,(assoc-ref inputs "js-jquery")
14556 "htmlwidgets/lib/jquery/jquery.min.js")
14557 (,(assoc-ref inputs "js-threejs-111")
14558 "htmlwidgets/lib/threejs-111/three.min.js"))))
14559 (lambda (sources targets)
14560 (for-each (lambda (source target)
14561 (format #t "Processing ~a --> ~a~%"
14563 (delete-file target)
14564 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14565 (call-with-output-file target
14567 (dump-port minified port)))))
14568 sources targets))))
14571 `(("r-base64enc" ,r-base64enc)
14572 ("r-crosstalk" ,r-crosstalk)
14573 ("r-htmlwidgets" ,r-htmlwidgets)
14574 ("r-igraph" ,r-igraph)))
14576 `(("uglify-js" ,uglify-js)
14580 (uri "https://code.jquery.com/jquery-1.12.4.js")
14583 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
14587 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
14590 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
14591 (home-page "https://bwlewis.github.io/rthreejs")
14592 (synopsis "Interactive 3D scatter plots, networks and globes")
14594 "Create interactive 3D scatter plots, network plots, and globes in R
14595 using the three.js visualization library.")
14596 (license license:expat)))
14598 (define-public r-mlbench
14605 (uri (cran-uri "mlbench" version))
14608 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14609 (build-system r-build-system)
14610 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14611 (synopsis "Machine learning benchmark problems")
14613 "This package provides a collection of artificial and real-world machine
14614 learning benchmark problems, including, e.g., several data sets from the UCI
14616 (license license:gpl2)))
14618 (define-public r-mpm
14625 (uri (cran-uri "mpm" version))
14628 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14629 (build-system r-build-system)
14631 `(("r-kernsmooth" ,r-kernsmooth)
14632 ("r-mass" ,r-mass)))
14633 (home-page "http://mpm.r-forge.r-project.org")
14634 (synopsis "Multivariate projection methods")
14636 "This is a package for exploratory graphical analysis of multivariate
14637 data, specifically gene expression data with different projection methods:
14638 principal component analysis, correspondence analysis, spectral map
14640 (license license:gpl2+)))
14642 (define-public r-png
14648 (uri (cran-uri "png" version))
14651 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14652 (build-system r-build-system)
14654 `(("libpng" ,libpng)
14656 (home-page "https://www.rforge.net/png/")
14657 (synopsis "Read and write PNG images")
14659 "This package provides an easy and simple way to read, write and display
14660 bitmap images stored in the PNG format. It can read and write both files and
14661 in-memory raw vectors.")
14662 ;; Any of these GPL versions.
14663 (license (list license:gpl2 license:gpl3))))
14665 (define-public r-ggcorrplot
14667 (name "r-ggcorrplot")
14672 (uri (cran-uri "ggcorrplot" version))
14675 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14676 (build-system r-build-system)
14678 `(("r-ggplot2" ,r-ggplot2)
14679 ("r-reshape2" ,r-reshape2)))
14680 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14681 (synopsis "Visualization of a correlation matrix using ggplot2")
14683 "The ggcorrplot package can be used to visualize easily a correlation
14684 matrix using ggplot2. It provides a solution for reordering the correlation
14685 matrix and displays the significance level on the plot. It also includes a
14686 function for computing a matrix of correlation p-values.")
14687 (license license:gpl2)))
14689 (define-public r-flexdashboard
14691 (name "r-flexdashboard")
14692 (version "0.5.1.1")
14696 (uri (cran-uri "flexdashboard" version))
14699 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14700 (build-system r-build-system)
14702 `(#:modules ((guix build utils)
14703 (guix build r-build-system)
14707 (ice-9 textual-ports))
14709 (modify-phases %standard-phases
14710 (add-after 'unpack 'process-javascript
14711 (lambda* (#:key inputs #:allow-other-keys)
14712 (with-directory-excursion "inst"
14713 ;; Concatenate all components of prism.js
14714 (let ((contents (string-join
14715 (map (lambda (name)
14716 (call-with-input-file
14717 (assoc-ref inputs name)
14721 "js-prism-line-numbers"))
14723 (call-with-output-file "prism-src.js"
14724 (cut display contents <>)))
14728 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14729 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14731 "www/sly/sly.min.js")
14733 "www/prism/prism.js")
14734 (,(assoc-ref inputs "js-raphael")
14735 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14736 (,(assoc-ref inputs "js-featherlight")
14737 "www/featherlight/featherlight.min.js"))))
14738 (lambda (sources targets)
14739 (for-each (lambda (source target)
14740 (format #t "Processing ~a --> ~a~%"
14742 (delete-file target)
14743 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14744 (call-with-output-file target
14746 (dump-port minified port)))))
14747 sources targets))))
14750 `(("r-htmltools" ,r-htmltools)
14751 ("r-htmlwidgets" ,r-htmlwidgets)
14752 ("r-jsonlite" ,r-jsonlite)
14753 ("r-knitr" ,r-knitr)
14754 ("r-rmarkdown" ,r-rmarkdown)
14755 ("r-shiny" ,r-shiny)))
14757 `(("uglify-js" ,uglify-js)
14761 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14764 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14768 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14771 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14775 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14778 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14779 ("js-prism-line-numbers"
14782 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14785 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14789 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14792 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14793 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14794 (synopsis "R Markdown format for flexible dashboards")
14796 "This package provides an R Markdown format for converting an R Markdown
14797 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14798 of its components to the containing web page.")
14799 (license license:expat)))
14801 (define-public r-preseqr
14808 (uri (cran-uri "preseqR" version))
14811 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14812 (properties `((upstream-name . "preseqR")))
14813 (build-system r-build-system)
14815 `(("r-polynom" ,r-polynom)))
14816 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14817 (synopsis "Predicting species accumulation curves")
14819 "This package can be used to predict the r-species accumulation
14820 curve (r-SAC), which is the number of species represented at least r times as
14821 a function of the sampling effort. When r = 1, the curve is known as the
14822 species accumulation curve, or the library complexity curve in high-throughput
14823 genomic sequencing. The package includes both parametric and nonparametric
14824 methods, as described by Deng C, et al. (2018).")
14825 (license license:gpl3)))
14827 (define-public r-mapplots
14829 (name "r-mapplots")
14834 (uri (cran-uri "mapplots" version))
14837 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14838 (build-system r-build-system)
14839 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14840 (synopsis "Data visualization on maps")
14842 "This package helps you create simple maps; add sub-plots like pie plots
14843 to a map or any other plot; format, plot and export gridded data. The package
14844 was developed for displaying fisheries data but most functions can be used for
14845 more generic data visualisation.")
14846 (license license:gpl2+)))
14848 (define-public r-pmcmr
14855 (uri (cran-uri "PMCMR" version))
14858 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14859 (properties `((upstream-name . "PMCMR")))
14860 (build-system r-build-system)
14861 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14862 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14864 "This is a deprecated package for calculating pairwise multiple
14865 comparisons of mean rank sums. This package is superseded by the novel
14866 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14867 compatibility of dependent packages for some time.")
14868 (license license:gpl3+)))
14870 (define-public r-downloader
14872 (name "r-downloader")
14877 (uri (cran-uri "downloader" version))
14880 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14881 (build-system r-build-system)
14883 `(("r-digest" ,r-digest)))
14884 (home-page "https://github.com/wch/downloader")
14885 (synopsis "Download files over HTTP and HTTPS")
14887 "This package provides a wrapper for the @code{download.file} function,
14888 making it possible to download files over HTTPS across platforms. The
14889 @code{RCurl} package provides this functionality (and much more) but has
14890 external dependencies. This package has is implemented purely in R.")
14891 (license license:gpl2)))
14893 (define-public r-rex
14900 (uri (cran-uri "rex" version))
14903 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14904 (build-system r-build-system)
14906 `(("r-lazyeval" ,r-lazyeval)
14907 ("r-magrittr" ,r-magrittr)))
14908 (home-page "https://github.com/kevinushey/rex")
14909 (synopsis "Friendly regular expressions")
14911 "This package provides a friendly interface for the construction of
14912 regular expressions. Regular expressions are a very powerful feature, however
14913 they are often difficult to interpret. Rex allows you to build complex
14914 regular expressions from human readable expressions")
14915 (license license:expat)))
14917 (define-public r-xmlparsedata
14919 (name "r-xmlparsedata")
14924 (uri (cran-uri "xmlparsedata" version))
14927 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14928 (properties `((upstream-name . "xmlparsedata")))
14929 (build-system r-build-system)
14930 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14931 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14933 "This package provides tools to convert the output of
14934 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14935 @code{XPath}, and is easier to manipulate in general.")
14936 (license license:expat)))
14938 (define-public r-cyclocomp
14940 (name "r-cyclocomp")
14945 (uri (cran-uri "cyclocomp" version))
14948 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14949 (properties `((upstream-name . "cyclocomp")))
14950 (build-system r-build-system)
14952 `(("r-callr" ,r-callr)
14953 ("r-crayon" ,r-crayon)
14955 ("r-remotes" ,r-remotes)
14956 ("r-withr" ,r-withr)))
14957 (home-page "https://github.com/MangoTheCat/cyclocomp")
14958 (synopsis "Cyclomatic complexity of R code")
14960 "Cyclomatic complexity is a software metric, used to indicate the
14961 complexity of a program. It is a quantitative measure of the number of
14962 linearly independent paths through a program's source code. This package
14963 provides tools to compute this metric.")
14964 (license license:expat)))
14966 (define-public r-lintr
14973 (uri (cran-uri "lintr" version))
14976 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
14977 (properties `((upstream-name . "lintr")))
14978 (build-system r-build-system)
14980 `(("r-codetools" ,r-codetools)
14981 ("r-crayon" ,r-crayon)
14982 ("r-cyclocomp" ,r-cyclocomp)
14983 ("r-digest" ,r-digest)
14985 ("r-jsonlite" ,r-jsonlite)
14986 ("r-knitr" ,r-knitr)
14988 ("r-rstudioapi" ,r-rstudioapi)
14989 ("r-testthat" ,r-testthat)
14991 ("r-xmlparsedata" ,r-xmlparsedata)))
14992 (home-page "https://github.com/jimhester/lintr")
14993 (synopsis "Linter for R code")
14994 (description "This package checks adherence to a given style, syntax
14995 errors and possible semantic issues. It supports on the fly checking of R
14996 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14997 (license license:expat)))
14999 (define-public r-sctransform
15001 (name "r-sctransform")
15006 (uri (cran-uri "sctransform" version))
15009 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15010 (build-system r-build-system)
15012 `(("r-future-apply" ,r-future-apply)
15013 ("r-ggplot2" ,r-ggplot2)
15014 ("r-gridextra" ,r-gridextra)
15016 ("r-matrix" ,r-matrix)
15018 ("r-rcppeigen" ,r-rcppeigen)
15019 ("r-reshape2" ,r-reshape2)))
15020 (home-page "https://github.com/ChristophH/sctransform")
15021 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15023 "This package provides a normalization method for single-cell UMI count
15024 data using a variance stabilizing transformation. The transformation is based
15025 on a negative binomial regression model with regularized parameters. As part
15026 of the same regression framework, this package also provides functions for
15027 batch correction, and data correction.")
15028 (license license:gpl3)))
15030 (define-public r-styler
15037 (uri (cran-uri "styler" version))
15040 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15041 (build-system r-build-system)
15043 `(("r-backports" ,r-backports)
15045 ("r-magrittr" ,r-magrittr)
15046 ("r-purrr" ,r-purrr)
15047 ("r-r-cache" ,r-r-cache)
15048 ("r-rematch2" ,r-rematch2)
15049 ("r-rlang" ,r-rlang)
15050 ("r-rprojroot" ,r-rprojroot)
15051 ("r-tibble" ,r-tibble)
15052 ("r-withr" ,r-withr)
15053 ("r-xfun" ,r-xfun)))
15054 (home-page "https://github.com/r-lib/styler")
15055 (synopsis "Non-invasive pretty printing of R code")
15057 "This is a package for pretty-printing R code without changing the user's
15058 formatting intent.")
15059 (license license:gpl3)))
15061 (define-public r-scrime
15068 (uri (cran-uri "scrime" version))
15071 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15072 (build-system r-build-system)
15073 (home-page "https://cran.r-project.org/web/packages/scrime/")
15074 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15076 "This package provides tools for the analysis of high-dimensional data
15077 developed/implemented at the group \"Statistical Complexity Reduction In
15078 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15079 the functions can also be applied to other types of categorical data.")
15080 (license license:gpl2)))
15082 (define-public r-pbmcapply
15084 (name "r-pbmcapply")
15089 (uri (cran-uri "pbmcapply" version))
15092 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15093 (build-system r-build-system)
15094 (home-page "https://github.com/kvnkuang/pbmcapply")
15095 (synopsis "Track the progress of apply procedures with a progress bar")
15097 "This light-weight package helps you track and visualize the progress of
15098 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15099 (license license:expat)))
15101 (define-public r-blme
15108 (uri (cran-uri "blme" version))
15111 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15112 (build-system r-build-system)
15113 (propagated-inputs `(("r-lme4" ,r-lme4)))
15114 (home-page "https://github.com/vdorie/blme")
15115 (synopsis "Bayesian linear mixed-effects models")
15117 "This package provides tools for maximum a posteriori estimation for
15118 linear and generalized linear mixed-effects models in a Bayesian setting. It
15119 extends the lme4 package.")
15120 (license license:gpl2+)))
15122 (define-public r-batchtools
15124 (name "r-batchtools")
15129 (uri (cran-uri "batchtools" version))
15132 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15133 (build-system r-build-system)
15135 `(("r-backports" ,r-backports)
15136 ("r-base64url" ,r-base64url)
15138 ("r-checkmate" ,r-checkmate)
15139 ("r-data-table" ,r-data-table)
15140 ("r-digest" ,r-digest)
15142 ("r-progress" ,r-progress)
15144 ("r-rappdirs" ,r-rappdirs)
15145 ("r-stringi" ,r-stringi)
15146 ("r-withr" ,r-withr)))
15148 `(("r-knitr" ,r-knitr)))
15149 (home-page "https://github.com/mllg/batchtools")
15150 (synopsis "Tools for computation on batch systems")
15152 "As a successor of the packages BatchJobs and BatchExperiments, this
15153 package provides a parallel implementation of the Map function for high
15154 performance computing systems managed by various schedulers. A multicore and
15155 socket mode allow the parallelization on a local machines, and multiple
15156 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15157 the package provides an abstraction mechanism to define large-scale computer
15158 experiments in a well-organized and reproducible way.")
15159 (license license:lgpl3)))
15161 (define-public r-clue
15168 (uri (cran-uri "clue" version))
15171 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15172 (build-system r-build-system)
15173 (propagated-inputs `(("r-cluster" ,r-cluster)))
15174 (home-page "https://cran.r-project.org/web/packages/clue/")
15175 (synopsis "Tools for analyzing cluster ensembles")
15176 (description "Cluster ensembles are collections of individual solutions to
15177 a given clustering problem which are useful or necessary to consider in a wide
15178 range of applications. This R package provides an extensible computational
15179 environment for creating and analyzing cluster ensembles, with basic data
15180 structures for representing partitions and hierarchies, and facilities for
15181 computing on them, including methods for measuring proximity and obtaining
15182 consensus and secondary clusterings.")
15183 (license license:gpl2)))
15185 (define-public r-sitmo
15192 (uri (cran-uri "sitmo" version))
15195 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15196 (build-system r-build-system)
15197 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15198 (home-page "https://github.com/coatless/sitmo/")
15199 (synopsis "Parallel pseudo random number generator header files")
15201 "This package provides two high quality and fast PPRNGs that may be used
15202 in an OpenMP parallel environment. In addition, there is a generator for one
15203 dimensional low-discrepancy sequence.")
15204 (license license:expat)))
15206 (define-public r-dqrng
15213 (uri (cran-uri "dqrng" version))
15216 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15217 (build-system r-build-system)
15221 ("r-sitmo" ,r-sitmo)))
15222 (home-page "https://www.daqana.org/dqrng")
15223 (synopsis "Fast pseudo random number generators")
15225 "Several fast random number generators are provided as C++ header-only
15226 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15227 Additionally, fast functions for generating random numbers according to a
15228 uniform, normal and exponential distribution are included. The latter two use
15229 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15230 functions are exported to R and as a C++ interface and are enabled for use
15231 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15232 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15233 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15234 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15235 ;; whole is distributed under the terms of the AGPL 3.
15236 (license license:agpl3)))
15238 (define-public r-dalex
15245 (uri (cran-uri "DALEX" version))
15248 "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0"))))
15249 (properties `((upstream-name . "DALEX")))
15250 (build-system r-build-system)
15251 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15252 (home-page "https://pbiecek.github.io/DALEX/")
15253 (synopsis "Descriptive machine learning explanations")
15255 "Machine Learning models are widely used and have various applications in
15256 classification or regression. Models created with boosting, bagging, stacking
15257 or similar techniques are often used due to their high performance, but such
15258 black-box models usually lack interpretability. The DALEX package contains
15259 various explainers that help to understand the link between input variables
15260 and model output.")
15261 ;; Any version of the GPL
15262 (license license:gpl3+)))
15264 (define-public r-enrichr
15271 (uri (cran-uri "enrichR" version))
15274 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15275 (properties `((upstream-name . "enrichR")))
15276 (build-system r-build-system)
15278 `(("r-httr" ,r-httr)
15279 ("r-rjson" ,r-rjson)))
15280 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15281 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15283 "This package provides an R interface to all Enrichr databases, a
15284 web-based tool for analyzing gene sets and returns any enrichment of common
15285 annotated biological functions.")
15286 (license license:gpl2+)))
15288 (define-public r-plot3d
15295 (uri (cran-uri "plot3D" version))
15298 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15299 (properties `((upstream-name . "plot3D")))
15300 (build-system r-build-system)
15301 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15302 (home-page "https://cran.r-project.org/web/packages/plot3D")
15303 (synopsis "Plot multi-dimensional data")
15305 "This package provides functions for viewing 2D and 3D data, including
15306 perspective plots, slice plots, surface plots, scatter plots, etc. It
15307 includes data sets from oceanography.")
15308 (license license:gpl3+)))
15310 (define-public r-ggfortify
15312 (name "r-ggfortify")
15317 (uri (cran-uri "ggfortify" version))
15320 "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5"))))
15321 (build-system r-build-system)
15323 `(("r-dplyr" ,r-dplyr)
15324 ("r-ggplot2" ,r-ggplot2)
15325 ("r-gridextra" ,r-gridextra)
15326 ("r-scales" ,r-scales)
15327 ("r-stringr" ,r-stringr)
15328 ("r-tibble" ,r-tibble)
15329 ("r-tidyr" ,r-tidyr)))
15331 `(("r-knitr" ,r-knitr)))
15332 (home-page "https://github.com/sinhrks/ggfortify")
15333 (synopsis "Data visualization tools for statistical analysis results")
15335 "This package provides unified plotting tools for statistics commonly
15336 used, such as GLM, time series, PCA families, clustering and survival
15337 analysis. The package offers a single plotting interface for these analysis
15338 results and plots in a unified style using the @code{ggplot2} package.")
15339 (license license:gpl2)))
15341 (define-public r-refmanager
15343 (name "r-refmanager")
15348 (uri (cran-uri "RefManageR" version))
15351 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15352 (properties `((upstream-name . "RefManageR")))
15353 (build-system r-build-system)
15355 `(("r-bibtex" ,r-bibtex)
15357 ("r-jsonlite" ,r-jsonlite)
15358 ("r-lubridate" ,r-lubridate)
15360 ("r-stringr" ,r-stringr)
15361 ("r-xml2" ,r-xml2)))
15362 (home-page "https://github.com/ropensci/RefManageR/")
15363 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15365 "This package provides tools for importing and working with bibliographic
15366 references. It greatly enhances the @code{bibentry} class by providing a
15367 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15368 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15369 by various formats for name lists (author by last names, translator by full
15370 names, etc.). Entries can be updated, combined, sorted, printed in a number
15371 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15372 into R and converted to @code{BibEntry} objects.")
15373 ;; Any of these licenses may be picked.
15374 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15376 (define-public r-citr
15383 (uri (cran-uri "citr" version))
15386 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15387 (build-system r-build-system)
15389 `(("r-assertthat" ,r-assertthat)
15392 ("r-miniui" ,r-miniui)
15393 ("r-refmanager" ,r-refmanager)
15394 ("r-rstudioapi" ,r-rstudioapi)
15395 ("r-shiny" ,r-shiny)
15396 ("r-shinyjs" ,r-shinyjs)
15397 ("r-yaml" ,r-yaml)))
15398 (home-page "https://github.com/crsh/citr")
15399 (synopsis "RStudio add-in to insert Markdown citations")
15401 "This package provides functions and an RStudio add-in that search a
15402 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15403 the current document.")
15404 (license license:expat)))
15406 (define-public r-xgboost
15409 (version "1.0.0.2")
15413 (uri (cran-uri "xgboost" version))
15416 "1ld2w51c5fy3bl0kvjn1iplffc4lmin9s9zz5xx7xsm44d6j6kzd"))))
15417 (build-system r-build-system)
15419 `(("r-data-table" ,r-data-table)
15420 ("r-magrittr" ,r-magrittr)
15421 ("r-matrix" ,r-matrix)
15422 ("r-stringi" ,r-stringi)))
15424 `(("r-knitr" ,r-knitr)))
15425 (home-page "https://github.com/dmlc/xgboost")
15426 (synopsis "Extreme gradient boosting")
15428 "This package provides an R interface to Extreme Gradient Boosting, which
15429 is an efficient implementation of the gradient boosting framework from Chen
15430 and Guestrin (2016). The package includes efficient linear model solver and
15431 tree learning algorithms. The package can automatically do parallel
15432 computation on a single machine. It supports various objective functions,
15433 including regression, classification and ranking. The package is made to be
15434 extensible, so that users are also allowed to define their own objectives
15436 (license license:asl2.0)))
15438 (define-public r-umap
15441 (version "0.2.5.0")
15445 (uri (cran-uri "umap" version))
15448 "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
15449 (build-system r-build-system)
15451 `(("r-openssl" ,r-openssl)
15453 ("r-reticulate" ,r-reticulate)
15454 ("r-rspectra" ,r-rspectra)))
15456 `(("r-knitr" ,r-knitr)))
15457 (home-page "https://github.com/tkonopka/umap")
15458 (synopsis "Uniform manifold approximation and projection")
15460 "Uniform manifold approximation and projection is a technique for
15461 dimension reduction. This package provides an interface to the UMAP algorithm
15462 in R, including a translation of the original algorithm into R.")
15463 (license license:expat)))
15465 (define-public r-uwot
15472 (uri (cran-uri "uwot" version))
15475 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
15476 (build-system r-build-system)
15478 `(("r-dqrng" ,r-dqrng)
15480 ("r-irlba" ,r-irlba)
15481 ("r-matrix" ,r-matrix)
15483 ("r-rcppannoy" ,r-rcppannoy)
15484 ("r-rcppprogress" ,r-rcppprogress)
15485 ("r-rspectra" ,r-rspectra)))
15486 (home-page "https://github.com/jlmelville/uwot")
15487 (synopsis "Uniform manifold approximation and projection")
15489 "This package provides an implementation of the Uniform Manifold
15490 Approximation and Projection dimensionality reduction by McInnes et
15491 al. (2018). It also provides means to transform new data and to carry out
15492 supervised dimensionality reduction. An implementation of the related
15493 LargeVis method of Tang et al. (2016) is also provided.")
15494 (license license:gpl3)))
15496 (define-public r-kableextra
15498 (name "r-kableextra")
15503 (uri (cran-uri "kableExtra" version))
15506 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15507 (properties `((upstream-name . "kableExtra")))
15508 (build-system r-build-system)
15510 `(("r-digest" ,r-digest)
15512 ("r-htmltools" ,r-htmltools)
15513 ("r-knitr" ,r-knitr)
15514 ("r-magrittr" ,r-magrittr)
15515 ("r-readr" ,r-readr)
15516 ("r-rmarkdown" ,r-rmarkdown)
15517 ("r-rstudioapi" ,r-rstudioapi)
15518 ("r-rvest" ,r-rvest)
15519 ("r-scales" ,r-scales)
15520 ("r-stringr" ,r-stringr)
15521 ("r-viridislite" ,r-viridislite)
15522 ("r-webshot" ,r-webshot)
15523 ("r-xml2" ,r-xml2)))
15524 (home-page "https://haozhu233.github.io/kableExtra/")
15525 (synopsis "Construct complex tables with pipe syntax")
15527 "Build complex HTML or LaTeX tables using @code{kable()} from
15528 @code{knitr} and the piping syntax from @code{magrittr}. The function
15529 @code{kable()} is a light weight table generator coming from @code{knitr}.
15530 This package simplifies the way to manipulate the HTML or LaTeX codes
15531 generated by @code{kable()} and allows users to construct complex tables and
15532 customize styles using a readable syntax.")
15533 (license license:expat)))
15535 (define-public r-glasso
15542 (uri (cran-uri "glasso" version))
15544 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15545 (build-system r-build-system)
15546 (native-inputs `(("gfortran" ,gfortran)))
15547 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
15548 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15550 "This is a package for estimation of a sparse inverse covariance matrix
15551 using a lasso (L1) penalty. Facilities are provided for estimates along a
15552 path of values for the regularization parameter.")
15553 (license license:gpl2)))
15555 (define-public r-rhpcblasctl
15557 (name "r-rhpcblasctl")
15558 (version "0.20-17")
15562 (uri (cran-uri "RhpcBLASctl" version))
15565 "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
15566 (properties `((upstream-name . "RhpcBLASctl")))
15567 (build-system r-build-system)
15568 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
15569 (synopsis "Control the number of threads on BLAS")
15571 "This package allows you to control the number of threads the BLAS
15572 library uses. It is also possible to control the number of threads in
15574 (license license:agpl3+)))
15576 (define-public r-lda
15583 (uri (cran-uri "lda" version))
15586 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15587 (build-system r-build-system)
15588 (home-page "https://cran.r-project.org/web/packages/lda/")
15589 (synopsis "Collapsed Gibbs sampling methods for topic models")
15591 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15592 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15593 mixed-membership stochastic blockmodel. Inference for all of these models is
15594 implemented via a fast collapsed Gibbs sampler written in C. Utility
15595 functions for reading/writing data typically used in topic models, as well as
15596 tools for examining posterior distributions are also included.")
15597 ;; Any version of the LGPL
15598 (license license:lgpl3+)))
15600 (define-public r-rann-l1
15607 (uri (cran-uri "RANN.L1" version))
15610 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15611 (properties `((upstream-name . "RANN.L1")))
15612 (build-system r-build-system)
15613 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15614 (synopsis "Fast nearest neighbour search using L1 metric")
15616 "This package provides tools to find the k nearest neighbours for every
15617 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15618 library. There is support for approximate as well as exact searches, fixed
15619 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15620 computed using the L1 (Manhattan, taxicab) metric.")
15621 (license license:gpl3+)))
15623 (define-public r-leiden
15630 (uri (cran-uri "leiden" version))
15633 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
15634 (properties `((upstream-name . "leiden")))
15635 (build-system r-build-system)
15637 `(("r-igraph" ,r-igraph)
15638 ("r-matrix" ,r-matrix)
15639 ("r-reticulate" ,r-reticulate)))
15640 (home-page "https://github.com/TomKellyGenetics/leiden")
15641 (synopsis "R implementation of Leiden clustering algorithm")
15643 "This package implements the Python @code{leidenalg} module to be called
15644 in R. It enables clustering using the Leiden algorithm for partitioning a
15645 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15646 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15647 (license license:gpl3)))
15649 (define-public r-patchwork
15651 (name "r-patchwork")
15656 (uri (cran-uri "patchwork" version))
15659 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
15660 (build-system r-build-system)
15662 `(("r-ggplot2" ,r-ggplot2)
15663 ("r-gtable" ,r-gtable)))
15665 `(("r-knitr" ,r-knitr)))
15666 (home-page "https://github.com/thomasp85/patchwork")
15667 (synopsis "Compose ggplot2 plots")
15669 "The @code{ggplot2} package provides a strong API for sequentially
15670 building up a plot, but does not concern itself with composition of multiple
15671 plots. Patchwork is a package that expands the API to allow for arbitrarily
15672 complex composition of plots by providing mathmatical operators for combining
15674 (license license:expat)))
15676 (define-public r-liger
15683 (uri (git-reference
15684 (url "https://github.com/MacoskoLab/liger.git")
15685 (commit (string-append "v" version))))
15686 (file-name (git-file-name name version))
15689 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15690 (modules '((guix build utils)))
15693 (delete-file "inst/java/ModularityOptimizer.jar")
15695 (build-system r-build-system)
15698 (modify-phases %standard-phases
15699 (add-after 'unpack 'build-java-part
15700 (lambda* (#:key inputs #:allow-other-keys)
15701 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15702 (for-each (lambda (file) (invoke "javac" file))
15703 (find-files "." "\\.java$"))
15704 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15705 (find-files "." "\\.class$"))
15708 `(("r-cowplot" ,r-cowplot)
15709 ("r-dosnow" ,r-dosnow)
15710 ("r-dplyr" ,r-dplyr)
15712 ("r-foreach" ,r-foreach)
15713 ("r-ggplot2" ,r-ggplot2)
15714 ("r-ggrepel" ,r-ggrepel)
15715 ("r-hmisc" ,r-hmisc)
15717 ("r-irlba" ,r-irlba)
15718 ("r-matrix" ,r-matrix)
15719 ("r-mclust" ,r-mclust)
15720 ("r-patchwork" ,r-patchwork)
15722 ("r-rann-l1" ,r-rann-l1)
15724 ("r-rcpparmadillo" ,r-rcpparmadillo)
15725 ("r-riverplot" ,r-riverplot)
15726 ("r-rtsne" ,r-rtsne)
15727 ("r-snow" ,r-snow)))
15729 `(("jdk" ,icedtea "jdk")
15730 ;; See https://github.com/MacoskoLab/liger/issues/96
15731 ;; The optimizer is released under the Expat license.
15735 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15738 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15740 ("r-knitr" ,r-knitr))) ; for vignettes
15741 (home-page "https://github.com/MacoskoLab/liger")
15742 (synopsis "Integrate and analyze multiple single-cell datasets")
15744 "LIGER is a package for integrating and analyzing multiple single-cell
15745 datasets, developed and maintained by the Macosko lab. It relies on
15746 integrative non-negative matrix factorization to identify shared and
15747 dataset-specific factors.")
15748 (license license:gpl3)))
15750 (define-public r-harmony
15757 (uri (git-reference
15758 (url "https://github.com/immunogenomics/harmony")
15760 (file-name (git-file-name name version))
15763 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
15764 (modules '((guix build utils)))
15767 (for-each delete-file '("config.status" "configure"))
15769 (build-system r-build-system)
15771 `(("r-cowplot" ,r-cowplot)
15772 ("r-dplyr" ,r-dplyr)
15773 ("r-ggplot2" ,r-ggplot2)
15774 ("r-irlba" ,r-irlba)
15775 ("r-matrix" ,r-matrix)
15777 ("r-rcpparmadillo" ,r-rcpparmadillo)
15778 ("r-rcppprogress" ,r-rcppprogress)
15779 ("r-rlang" ,r-rlang)
15780 ("r-tibble" ,r-tibble)
15781 ("r-tidyr" ,r-tidyr)))
15783 `(("autoconf" ,autoconf)))
15784 (home-page "https://github.com/immunogenomics/harmony")
15785 (synopsis "Integration of single cell sequencing data")
15787 "This package provides an implementation of the Harmony algorithm for
15788 single cell integration, described in Korsunsky et al
15789 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15790 function and interfaces to external frameworks.")
15791 (license license:gpl3)))
15793 (define-public r-covr
15800 (uri (cran-uri "covr" version))
15802 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
15803 (properties `((upstream-name . "covr")))
15804 (build-system r-build-system)
15806 `(("r-crayon" ,r-crayon)
15807 ("r-digest" ,r-digest)
15809 ("r-jsonlite" ,r-jsonlite)
15811 ("r-withr" ,r-withr)
15812 ("r-yaml" ,r-yaml)))
15814 `(("r-knitr" ,r-knitr))) ; for vignettes
15815 (home-page "https://github.com/r-lib/covr")
15816 (synopsis "Test coverage for R packages")
15818 "Thisp package enables you to track and report code coverage for your
15819 package and (optionally) upload the results to a coverage service. Code
15820 coverage is a measure of the amount of code being exercised by a set of tests.
15821 It is an indirect measure of test quality and completeness. This package is
15822 compatible with any testing methodology or framework and tracks coverage of
15823 both R code and compiled C/C++/FORTRAN code.")
15824 (license license:gpl3)))
15826 (define-public r-systemfonts
15828 (name "r-systemfonts")
15833 (uri (cran-uri "systemfonts" version))
15836 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15837 (properties `((upstream-name . "systemfonts")))
15838 (build-system r-build-system)
15840 `(("fontconfig" ,fontconfig)
15841 ("freetype" ,freetype)
15844 `(("pkg-config" ,pkg-config)))
15845 (home-page "https://github.com/r-lib/systemfonts")
15846 (synopsis "System native font finding")
15848 "This package provides system native access to the font catalogue. As
15849 font handling varies between systems it is difficult to correctly locate
15850 installed fonts across different operating systems. The 'systemfonts' package
15851 provides bindings to the native libraries for finding font files that can then
15852 be used further by e.g. graphic devices.")
15853 (license license:expat)))
15855 (define-public r-graphlayouts
15857 (name "r-graphlayouts")
15862 (uri (cran-uri "graphlayouts" version))
15865 "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0"))))
15866 (properties `((upstream-name . "graphlayouts")))
15867 (build-system r-build-system)
15869 `(("r-igraph" ,r-igraph)
15871 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15872 (home-page "https://github.com/schochastics/graphlayouts")
15873 (synopsis "Additional layout algorithms for network visualizations")
15875 "This package provides several layout algorithms to visualize networks
15876 which are not part of the igraph library. Most are based on the concept of
15877 stress majorization by Gansner et al. (2004)
15878 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
15879 emphasize hidden group structures in networks or focus on specific nodes.")
15880 (license license:expat)))
15882 (define-public r-tidygraph
15884 (name "r-tidygraph")
15889 (uri (cran-uri "tidygraph" version))
15892 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15893 (properties `((upstream-name . "tidygraph")))
15894 (build-system r-build-system)
15896 `(("r-dplyr" ,r-dplyr)
15897 ("r-igraph" ,r-igraph)
15898 ("r-magrittr" ,r-magrittr)
15899 ("r-pillar" ,r-pillar)
15902 ("r-rlang" ,r-rlang)
15903 ("r-tibble" ,r-tibble)
15904 ("r-tidyr" ,r-tidyr)))
15905 (home-page "https://github.com/thomasp85/tidygraph")
15906 (synopsis "Tidy API for graph manipulation")
15908 "This package provides a graph implementation that can be thought of as
15909 two tidy data frames describing node and edge data respectively. It provides
15910 an approach to manipulate these two virtual data frames using the API defined
15911 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15912 common graph algorithms.")
15913 (license license:expat)))
15915 (define-public r-soupx
15916 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15920 (version (git-version "0.3.1" revision commit))
15924 (uri (git-reference
15925 (url "https://github.com/constantAmateur/SoupX")
15927 (file-name (git-file-name name version))
15930 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15931 (properties `((upstream-name . "SoupX")))
15932 (build-system r-build-system)
15934 `(("r-ggplot2" ,r-ggplot2)
15935 ("r-matrix" ,r-matrix)
15936 ("r-seurat" ,r-seurat)))
15937 (home-page "https://github.com/constantAmateur/SoupX")
15938 (synopsis "Single cell mRNA Soup eXterminator")
15940 "This package provides a package for quantifying, profiling and
15941 removing cell free mRNA contamination (the \"soup\") from droplet based single
15942 cell RNA-seq experiments.")
15943 (license license:gpl2))))
15945 (define-public r-assertr
15952 (uri (cran-uri "assertr" version))
15955 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
15956 (build-system r-build-system)
15958 `(("r-dplyr" ,r-dplyr)
15960 ("r-rlang" ,r-rlang)))
15962 `(("r-knitr" ,r-knitr))) ; needed for vignette
15963 (home-page "https://github.com/ropensci/assertr")
15964 (synopsis "Assertive programming for R analysis pipelines")
15966 "This package provides functionality to assert conditions that have to be
15967 met so that errors in data used in analysis pipelines can fail quickly. It is
15968 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15970 (license license:expat)))
15972 (define-public r-parameters
15974 (name "r-parameters")
15979 (uri (cran-uri "parameters" version))
15982 "0zin3ikc013hc713n5zs0dbhc3m4nfw1vhc3924z0mrww8r241xn"))))
15983 (properties `((upstream-name . "parameters")))
15984 (build-system r-build-system)
15986 `(("r-bayestestr" ,r-bayestestr)
15987 ("r-insight" ,r-insight)))
15989 `(("r-knitr" ,r-knitr)))
15990 (home-page "https://cran.r-project.org/web/packages/parameters")
15991 (synopsis "Processing of model parameters")
15993 "This package provides utilities for processing the parameters of various
15994 statistical models. Beyond computing p values, CIs, and other indices for a
15995 wide variety of models, this package implements features like standardization
15996 or bootstrapping of parameters and models, feature reduction (feature
15997 extraction and variable selection) as well as conversion between indices of
15999 (license license:gpl3)))
16001 (define-public r-rgdal
16008 (uri (cran-uri "rgdal" version))
16010 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
16011 (properties `((upstream-name . "rgdal")))
16012 (build-system r-build-system)
16020 `(("pkg-config" ,pkg-config)))
16021 (home-page "http://rgdal.r-forge.r-project.org")
16022 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16024 "This package provides bindings to the Geospatial Data Abstraction
16025 Library (GDAL) and access to projection/transformation operations from the
16027 (license license:gpl2+)))
16029 (define-public r-insol
16036 (uri (cran-uri "insol" version))
16039 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16040 (properties `((upstream-name . "insol")))
16041 (build-system r-build-system)
16043 `(("r-raster" ,r-raster)))
16045 `(("gfortran" ,gfortran)))
16046 (home-page "https://meteoexploration.com/R/insol/index.html")
16047 (synopsis "Tools for calculating solar radiation")
16049 "This package provides functions to compute insolation on tilted
16050 surfaces, computes atmospheric transmittance and related parameters such as:
16051 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16052 time, vector in the direction of the sun, vector normal to surface, and some
16053 atmospheric physics.")
16054 (license license:gpl2+)))
16056 (define-public r-lifecycle
16058 (name "r-lifecycle")
16063 (uri (cran-uri "lifecycle" version))
16066 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16067 (properties `((upstream-name . "lifecycle")))
16068 (build-system r-build-system)
16070 `(("r-glue" ,r-glue)
16071 ("r-rlang" ,r-rlang)))
16073 `(("r-knitr" ,r-knitr))) ; for vignettes
16074 (home-page "https://github.com/r-lib/lifecycle")
16075 (synopsis "Manage the life cycle of your package functions")
16077 "Manage the life cycle of your exported functions with shared
16078 conventions, documentation badges, and non-invasive deprecation warnings. The
16079 lifecycle package defines four development stages (experimental, maturing,
16080 stable, and questioning) and three deprecation stages (soft-deprecated,
16081 deprecated, and defunct). It makes it easy to insert badges corresponding to
16082 these stages in your documentation. Usage of deprecated functions are
16083 signalled with increasing levels of non-invasive verbosity.")
16084 (license license:gpl3)))
16086 (define-public r-assertable
16088 (name "r-assertable")
16093 (uri (cran-uri "assertable" version))
16096 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16097 (build-system r-build-system)
16099 `(("r-data-table" ,r-data-table)))
16100 (home-page "https://cran.r-project.org/web/packages/assertable/")
16101 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16102 (description "This package provides simple, flexible assertions on
16103 data.frame or data.table objects with verbose output for vetting. While other
16104 assertion packages apply towards more general use-cases, @code{assertable} is
16105 tailored towards tabular data. It includes functions to check variable names
16106 and values, whether the dataset contains all combinations of a given set of
16107 unique identifiers, and whether it is a certain length. In addition,
16108 @code{assertable} includes utility functions to check the existence of target
16109 files and to efficiently import multiple tabular data files into one
16111 (license license:gpl3)))
16113 (define-public r-quadprog
16115 (name "r-quadprog")
16120 (uri (cran-uri "quadprog" version))
16122 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16123 (build-system r-build-system)
16125 `(("gfortran" ,gfortran)))
16126 (home-page "https://cran.r-project.org/web/packages/quadprog")
16127 (synopsis "Functions to solve quadratic programming problems")
16129 "This package contains routines and documentation for solving quadratic
16130 programming problems.")
16131 (license license:gpl3+)))
16133 (define-public r-desolve
16140 (uri (cran-uri "deSolve" version))
16142 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16143 (properties `((upstream-name . "deSolve")))
16144 (build-system r-build-system)
16146 `(("gfortran" ,gfortran)))
16147 (home-page "https://desolve.r-forge.r-project.org/")
16148 (synopsis "Solvers for initial value problems of differential equations")
16149 (description "This package provides functions that solve initial value
16150 problems of a system of first-order @dfn{ordinary differential
16151 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16152 @dfn{differential algebraic equations} (DAE), and of delay differential
16153 equations. The functions provide an interface to the FORTRAN functions
16154 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16155 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16156 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16157 time steps. The package contains routines designed for solving ODEs resulting
16158 from 1-D, 2-D and 3-D partial differential equations that have been converted
16159 to ODEs by numerical differencing.")
16160 (license license:gpl2+)))
16162 (define-public r-pracma
16168 (uri (cran-uri "pracma" version))
16170 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16171 (build-system r-build-system)
16172 (home-page "https://cran.r-project.org/web/packages/pracma/")
16173 (synopsis "Practical numerical math functions")
16174 (description "This package provides functions for numerical analysis and
16175 linear algebra, numerical optimization, differential equations, plus some
16176 special functions. It uses Matlab function names where appropriate to simplify
16178 (license license:gpl3+)))
16180 (define-public r-subplex
16187 (uri (cran-uri "subplex" version))
16190 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16191 (build-system r-build-system)
16193 `(("gfortran" ,gfortran)))
16194 (home-page "https://cran.r-project.org/web/packages/subplex")
16195 (synopsis "Unconstrained optimization using the subplex algorithm")
16197 "This package implements the Subplex optimization algorithm.
16198 It solves unconstrained optimization problems using a simplex method on
16199 subspaces. The method is well suited for optimizing objective functions that
16200 are noisy or are discontinuous at the solution.")
16201 (license license:gpl3+)))
16203 (define-public r-txtplot
16210 (uri (cran-uri "txtplot" version))
16213 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16214 (build-system r-build-system)
16215 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16216 (synopsis "Text-based plotting")
16217 (description "This package provides functions to produce rudimentary ASCII
16218 graphics directly in the terminal window. This package provides a basic
16219 plotting function (and equivalents of curve, density, acf and barplot) as well
16220 as a boxplot function.")
16221 (license license:lgpl3+)))
16223 (define-public r-bio3d
16230 (uri (cran-uri "bio3d" version))
16233 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16234 (properties `((upstream-name . "bio3d")))
16235 (build-system r-build-system)
16236 (inputs `(("zlib" ,zlib)))
16237 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16238 (home-page "http://thegrantlab.org/bio3d/")
16239 (synopsis "Biological structure analysis")
16241 "This package provides utilities to process, organize and explore protein
16242 structure, sequence and dynamics data. Features include the ability to read
16243 and write structure, sequence and dynamic trajectory data, perform sequence
16244 and structure database searches, data summaries, atom selection, alignment,
16245 superposition, rigid core identification, clustering, torsion analysis,
16246 distance matrix analysis, structure and sequence conservation analysis, normal
16247 mode analysis, principal component analysis of heterogeneous structure data,
16248 and correlation network analysis from normal mode and molecular dynamics data.
16249 In addition, various utility functions are provided to enable the statistical
16250 and graphical power of the R environment to work with biological sequence and
16252 (license license:gpl2+)))
16254 (define-public r-bios2cor
16256 (name "r-bios2cor")
16261 (uri (cran-uri "Bios2cor" version))
16264 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16265 (properties `((upstream-name . "Bios2cor")))
16266 (build-system r-build-system)
16268 `(("r-bigmemory" ,r-bigmemory)
16269 ("r-bio3d" ,r-bio3d)
16270 ("r-circular" ,r-circular)
16271 ("r-igraph" ,r-igraph)))
16272 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16273 (synopsis "From biological sequences and simulations to correlation analysis")
16275 "This package provides utilities for computation and analysis of
16276 correlation/covariation in multiple sequence alignments and in side chain
16277 motions during molecular dynamics simulations. Features include the
16278 computation of correlation/covariation scores using a variety of scoring
16279 functions between either sequence positions in alignments or side chain
16280 dihedral angles in molecular dynamics simulations and utilities to analyze the
16281 correlation/covariation matrix through a variety of tools including network
16282 representation and principal components analysis. In addition, several
16283 utility functions are based on the R graphical environment to provide friendly
16284 tools for help in data interpretation.")
16285 (license license:gpl2+)))
16287 ;; This package includes minified JavaScript files. When upgrading please
16288 ;; check that there are no new minified JavaScript files.
16289 (define-public r-networkd3
16291 (name "r-networkd3")
16296 (uri (cran-uri "networkD3" version))
16299 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16302 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16304 (properties `((upstream-name . "networkD3")))
16305 (build-system r-build-system)
16307 `(#:modules ((guix build utils)
16308 (guix build r-build-system)
16312 (modify-phases %standard-phases
16313 (add-after 'unpack 'process-javascript
16314 (lambda* (#:key inputs #:allow-other-keys)
16315 (with-directory-excursion "inst/htmlwidgets/lib/"
16319 `((,(assoc-ref inputs "d3.v4.js")
16320 "d3-4.5.0/d3.min.js"))))
16321 (lambda (sources targets)
16322 (for-each (lambda (source target)
16323 (format #t "Processing ~a --> ~a~%"
16325 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16326 (call-with-output-file target
16328 (dump-port minified port)))))
16329 sources targets))))
16332 `(("uglify-js" ,uglify-js)
16333 ;; NOTE: Make sure that this version of d3 is still valid when
16334 ;; upgrading the package.
16338 (uri "https://d3js.org/d3.v4.js")
16341 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16343 `(("r-htmlwidgets" ,r-htmlwidgets)
16344 ("r-igraph" ,r-igraph)
16345 ("r-magrittr" ,r-magrittr)))
16346 (home-page "https://cran.r-project.org/package=networkD3")
16347 (synopsis "D3 JavaScript network graphs from R")
16349 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16351 (license license:gpl3+)))
16353 (define-public r-aasea
16360 (uri (cran-uri "aaSEA" version))
16363 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16364 (properties `((upstream-name . "aaSEA")))
16365 (build-system r-build-system)
16367 `(("r-bios2cor" ,r-bios2cor)
16369 ("r-hmisc" ,r-hmisc)
16370 ("r-magrittr" ,r-magrittr)
16371 ("r-networkd3" ,r-networkd3)
16372 ("r-plotly" ,r-plotly)
16373 ("r-seqinr" ,r-seqinr)
16374 ("r-shiny" ,r-shiny)
16375 ("r-shinydashboard" ,r-shinydashboard)))
16376 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16377 (synopsis "Amino acid substitution effect analyzer")
16379 "Given a protein multiple sequence alignment, it is a daunting task to
16380 assess the effects of substitutions along sequence length. The aaSEA package
16381 is intended to help researchers to rapidly analyze property changes caused by
16382 single, multiple and correlated amino acid substitutions in proteins.")
16383 (license license:gpl3)))
16385 (define-public r-abacus
16392 (uri (cran-uri "ABACUS" version))
16395 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16396 (properties `((upstream-name . "ABACUS")))
16397 (build-system r-build-system)
16399 `(("r-ggplot2" ,r-ggplot2)
16400 ("r-shiny" ,r-shiny)))
16401 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16402 (synopsis "Apps-based activities for communicating and understanding statistics")
16404 "This package provides a set of Shiny apps for effective communication
16405 and understanding in statistics. The current version includes properties of
16406 normal distribution, properties of sampling distribution, one-sample z and t
16407 tests, two samples independent (unpaired) t test and analysis of variance.")
16408 (license license:gpl3)))
16410 (define-public r-abc-rap
16417 (uri (cran-uri "ABC.RAP" version))
16420 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16421 (properties `((upstream-name . "ABC.RAP")))
16422 (build-system r-build-system)
16423 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16424 (synopsis "Array-based CpG region analysis pipeline")
16426 "This package aims to identify candidate genes that are differentially
16427 methylated between cases and controls. It applies Student's t-test and delta
16428 beta analysis to identify candidate genes containing multiple CpG sites.")
16429 (license license:gpl3)))
16431 (define-public r-abcadm
16438 (uri (cran-uri "abcADM" version))
16441 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16442 (properties `((upstream-name . "abcADM")))
16443 (build-system r-build-system)
16446 ("r-rcpp" ,r-rcpp)))
16447 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16448 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16450 "This package provides tools to estimate parameters of accumulated
16451 damage (load duration) models based on failure time data under a Bayesian
16452 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16453 long-term reliability under stochastic load profiles.")
16454 (license license:gpl3)))
16456 (define-public r-rglpk
16463 (uri (cran-uri "Rglpk" version))
16466 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16467 (properties `((upstream-name . "Rglpk")))
16468 (build-system r-build-system)
16470 `(("r-slam" ,r-slam)))
16473 (home-page "https://r-forge.r-project.org/projects/rglp/")
16474 (synopsis "R interface to the GNU Linear Programming Kit")
16476 "This package provides an R interface to the GNU Linear Programming Kit,
16477 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16478 integer linear programming} (MILP) and other related problems.")
16480 (license (list license:gpl2 license:gpl3))))
16482 (define-public r-abcdefba
16484 (name "r-abcdefba")
16489 (uri (cran-uri "abcdeFBA" version))
16492 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16493 (properties `((upstream-name . "abcdeFBA")))
16494 (build-system r-build-system)
16496 `(("r-corrplot" ,r-corrplot)
16497 ("r-lattice" ,r-lattice)
16499 ("r-rglpk" ,r-rglpk)))
16500 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16501 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16503 "This package provides functions for Constraint Based Simulation using
16504 Flux Balance Analysis and informative analysis of the data generated during
16506 (license license:gpl2)))
16508 (define-public r-abcrlda
16515 (uri (cran-uri "abcrlda" version))
16518 "0zjdrbg3zx0znqnh0dvmifs9c12b8vjhbaf3nbwab9xh25nsmg75"))))
16519 (properties `((upstream-name . "abcrlda")))
16520 (build-system r-build-system)
16521 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16522 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16524 "This package offers methods to perform @dfn{asymptotically
16525 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16526 cost-sensitive binary classification. The bias-correction is an estimate of
16527 the bias term added to regularized discriminant analysis that minimizes the
16529 (license license:gpl3)))
16531 (define-public r-abemus
16538 (uri (cran-uri "abemus" version))
16541 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16542 (properties `((upstream-name . "abemus")))
16543 (build-system r-build-system)
16545 `(("r-data-table" ,r-data-table)))
16546 (home-page "https://cran.r-project.org/web/packages/abemus/")
16547 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16549 "This package provides an implementation of @dfn{Adaptive Base Error
16550 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16551 platform-specific genetic knowledge and empirical signal to readily detect and
16552 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16553 cell free DNA} (cfDNA).")
16554 (license license:gpl3)))
16556 ;; This package includes minified JavaScript files. When upgrading please
16557 ;; check that there are no new minified JavaScript files.
16558 (define-public r-rintrojs
16560 (name "r-rintrojs")
16565 (uri (cran-uri "rintrojs" version))
16568 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16569 (properties `((upstream-name . "rintrojs")))
16570 (build-system r-build-system)
16572 `(#:modules ((guix build utils)
16573 (guix build r-build-system)
16577 (modify-phases %standard-phases
16578 (add-after 'unpack 'process-javascript
16579 (lambda* (#:key inputs #:allow-other-keys)
16580 (with-directory-excursion "inst/javascript/introjs/"
16584 `((,(assoc-ref inputs "intro.js")
16586 (lambda (sources targets)
16587 (for-each (lambda (source target)
16588 (format #t "Processing ~a --> ~a~%"
16590 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16591 (call-with-output-file target
16593 (dump-port minified port)))))
16594 sources targets))))
16597 `(("uglify-js" ,uglify-js)
16601 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16604 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16606 `(("r-jsonlite" ,r-jsonlite)
16607 ("r-shiny" ,r-shiny)))
16608 (home-page "https://github.com/carlganz/rintrojs")
16609 (synopsis "Wrapper for the Intro.js library")
16611 "This package provides a wrapper for the @url{http://www.introjs.com,
16612 Intro.js} library. This package makes it easy to include step-by-step
16613 introductions, and clickable hints in a Shiny application. It supports both
16614 static introductions in the UI, and programmatic introductions from the
16616 (license license:agpl3+)))
16618 (define-public r-sysfonts
16620 (name "r-sysfonts")
16625 (uri (cran-uri "sysfonts" version))
16628 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16629 (properties `((upstream-name . "sysfonts")))
16630 (build-system r-build-system)
16632 `(("freetype" ,freetype)
16636 `(("pkg-config" ,pkg-config)))
16637 (home-page "https://github.com/yixuan/sysfonts")
16638 (synopsis "Loading fonts into R")
16640 "This is a package to simplify loading of system fonts and Google Fonts
16641 into R, in order to support other packages.")
16642 (license license:gpl2)))
16644 (define-public r-showtextdb
16646 (name "r-showtextdb")
16651 (uri (cran-uri "showtextdb" version))
16654 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16655 (properties `((upstream-name . "showtextdb")))
16656 (build-system r-build-system)
16658 `(("r-sysfonts" ,r-sysfonts)))
16659 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16660 (synopsis "Font files for the 'showtext' package")
16662 "This package provides font files that can be used by the @code{showtext}
16664 (license license:asl2.0)))
16666 (define-public r-showtext
16668 (name "r-showtext")
16673 (uri (cran-uri "showtext" version))
16676 "0a5gg72bfrc7wm0phj1aflj1wc08kfi81ac32na6ya9s2ivyimw5"))))
16677 (properties `((upstream-name . "showtext")))
16678 (build-system r-build-system)
16680 `(("freetype" ,freetype)
16684 `(("r-showtextdb" ,r-showtextdb)
16685 ("r-sysfonts" ,r-sysfonts)))
16686 (native-inputs `(("pkg-config" ,pkg-config)))
16687 (home-page "https://github.com/yixuan/showtext")
16688 (synopsis "Using fonts more easily in R graphs")
16690 "This package aims to make it easy to use various types of
16691 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16692 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16693 will be converted into polygons or raster images, hence after the plot has
16694 been created, it no longer relies on the font files. No external software
16695 such as Ghostscript is needed to use this package.")
16696 (license license:asl2.0)))
16698 (define-public r-emojifont
16700 (name "r-emojifont")
16705 (uri (cran-uri "emojifont" version))
16708 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16709 (properties `((upstream-name . "emojifont")))
16710 (build-system r-build-system)
16712 `(("r-ggplot2" ,r-ggplot2)
16713 ("r-proto" ,r-proto)
16714 ("r-showtext" ,r-showtext)
16715 ("r-sysfonts" ,r-sysfonts)))
16716 (home-page "https://guangchuangyu.github.io/emojifont")
16717 (synopsis "Emoji and Font Awesome in R graphics")
16719 "This package enables the use of emoji and the Font Awesome glyphs in
16720 both base and ggplot2 graphics.")
16721 (license license:artistic2.0)))
16723 (define-public r-abstractr
16725 (name "r-abstractr")
16730 (uri (cran-uri "abstractr" version))
16733 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16734 (properties `((upstream-name . "abstractr")))
16735 (build-system r-build-system)
16737 `(("r-colourpicker" ,r-colourpicker)
16738 ("r-emojifont" ,r-emojifont)
16739 ("r-ggplot2" ,r-ggplot2)
16740 ("r-gridextra" ,r-gridextra)
16741 ("r-rintrojs" ,r-rintrojs)
16742 ("r-shiny" ,r-shiny)
16743 ("r-shinythemes" ,r-shinythemes)))
16744 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16745 (synopsis "R-Shiny application for creating visual abstracts")
16747 "This package provides an R Shiny application to create visual abstracts
16748 for original research. A variety of user defined options and formatting are
16750 (license license:gpl3)))
16752 (define-public r-abtest
16759 (uri (cran-uri "abtest" version))
16762 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16763 (properties `((upstream-name . "abtest")))
16764 (build-system r-build-system)
16766 `(("r-matrix" ,r-matrix)
16767 ("r-mvtnorm" ,r-mvtnorm)
16768 ("r-plotrix" ,r-plotrix)
16769 ("r-rcolorbrewer" ,r-rcolorbrewer)
16772 ("r-truncnorm" ,r-truncnorm)
16773 ("r-vgam" ,r-vgam)))
16774 (home-page "https://cran.r-project.org/web/packages/abtest/")
16775 (synopsis "Bayesian A/B testing")
16777 "This package provides functions for Bayesian A/B testing including prior
16778 elicitation options based on Kass and Vaidyanathan (1992)
16779 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16780 (license license:gpl2+)))
16782 (define-public r-accept
16789 (uri (cran-uri "accept" version))
16792 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
16793 (properties `((upstream-name . "accept")))
16794 (build-system r-build-system)
16796 `(("r-dplyr" ,r-dplyr)
16797 ("r-extrafont" ,r-extrafont)
16799 ("r-plotly" ,r-plotly)
16800 ("r-stringr" ,r-stringr)
16801 ("r-viridis" ,r-viridis)))
16802 (home-page "https://cran.r-project.org/web/packages/accept/")
16803 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16805 "This package allows clinicians to predict the rate and severity of
16806 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16807 Disease} (COPD) patients, based on the clinical prediction model published in
16808 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16809 (license license:gpl3)))
16811 (define-public r-smpracticals
16813 (name "r-smpracticals")
16818 (uri (cran-uri "SMPracticals" version))
16821 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16822 (properties `((upstream-name . "SMPracticals")))
16823 (build-system r-build-system)
16825 `(("r-ellipse" ,r-ellipse)
16828 ("r-survival" ,r-survival)))
16829 (home-page "http://statwww.epfl.ch/davison/SM/")
16830 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16832 "This package contains the datasets and a few functions for use with the
16833 practicals outlined in Appendix A of the book Statistical Models (Davison,
16834 2003, Cambridge University Press). The practicals themselves can be found at
16835 @url{http://statwww.epfl.ch/davison/SM/}.")
16836 (license license:gpl2+)))
16838 (define-public r-fgui
16845 (uri (cran-uri "fgui" version))
16848 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16849 (properties `((upstream-name . "fgui")))
16850 (build-system r-build-system)
16852 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16853 (synopsis "Create GUI for R functions")
16855 "Rapidly create a GUI for a function you created by automatically
16856 creating widgets for arguments of the function. This package automatically
16857 parses help routines for context-sensitive help to these arguments. The
16858 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16859 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16860 incorporated into the interface for greater customization for the more
16862 ;; Any version of the GPL.
16863 (license (list license:gpl2+ license:gpl3+))))
16865 (define-public r-tcltk2
16872 (uri (cran-uri "tcltk2" version))
16875 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16876 (properties `((upstream-name . "tcltk2")))
16877 (build-system r-build-system)
16881 (home-page "https://www.sciviews.org/SciViews-R")
16882 (synopsis "Tcl/Tk additions")
16884 "This package provides a series of additional Tcl commands and Tk widgets
16885 with style and various functions to supplement the tcltk package")
16886 (license license:lgpl3)))
16888 (define-public r-accrual
16895 (uri (cran-uri "accrual" version))
16898 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16899 (properties `((upstream-name . "accrual")))
16900 (build-system r-build-system)
16902 `(("r-fgui" ,r-fgui)
16903 ("r-smpracticals" ,r-smpracticals)
16904 ("r-tcltk2" ,r-tcltk2)))
16905 (home-page "https://cran.r-project.org/web/packages/accrual/")
16906 (synopsis "Bayesian accrual prediction")
16908 "Subject recruitment for medical research is challenging. Slow patient
16909 accrual leads to delay in research. Accrual monitoring during the process of
16910 recruitment is critical. Researchers need reliable tools to manage the
16911 accrual rate. This package provides an implementation of a Bayesian method
16912 that integrates researcher's experience on previous trials and data from the
16913 current study, providing reliable prediction on accrual rate for clinical
16914 studies. It provides functions for Bayesian accrual prediction which can be
16915 easily used by statisticians and clinical researchers.")
16916 (license license:gpl2)))
16918 (define-public r-accrued
16925 (uri (cran-uri "accrued" version))
16928 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16929 (properties `((upstream-name . "accrued")))
16930 (build-system r-build-system)
16931 (home-page "https://cran.r-project.org/web/packages/accrued/")
16932 (synopsis "Data quality visualization tools for partially accruing data")
16934 "This is a package for visualizing data quality of partially accruing
16936 (license license:gpl3)))
16938 (define-public r-mda
16945 (uri (cran-uri "mda" version))
16948 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16949 (properties `((upstream-name . "mda")))
16950 (build-system r-build-system)
16951 (propagated-inputs `(("r-class" ,r-class)))
16952 (native-inputs `(("gfortran" ,gfortran)))
16953 (home-page "https://cran.r-project.org/web/packages/mda/")
16954 (synopsis "Mixture and flexible discriminant analysis")
16956 "This is a package for mixture and flexible discriminant analysis,
16957 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16958 (license license:gpl2)))
16960 (define-public r-elasticnet
16962 (name "r-elasticnet")
16967 (uri (cran-uri "elasticnet" version))
16970 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16971 (properties `((upstream-name . "elasticnet")))
16972 (build-system r-build-system)
16974 `(("r-lars" ,r-lars)))
16975 (home-page "http://users.stat.umn.edu/~zouxx019/")
16976 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16978 "This package provides functions for fitting the entire solution path of
16979 the Elastic-Net and also provides functions for estimating sparse Principal
16980 Components. The Lasso solution paths can be computed by the same function.")
16981 (license license:gpl2+)))
16983 (define-public r-sparselda
16985 (name "r-sparselda")
16990 (uri (cran-uri "sparseLDA" version))
16993 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16994 (properties `((upstream-name . "sparseLDA")))
16995 (build-system r-build-system)
16997 `(("r-elasticnet" ,r-elasticnet)
17000 (home-page "https://www.imm.dtu.dk/~lkhc/")
17001 (synopsis "Sparse discriminant analysis")
17003 "This package performs sparse linear discriminant analysis for Gaussians
17004 and mixture of Gaussian models.")
17005 (license license:gpl2+)))
17007 (define-public r-accsda
17014 (uri (cran-uri "accSDA" version))
17017 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17018 (properties `((upstream-name . "accSDA")))
17019 (build-system r-build-system)
17021 `(("r-ggplot2" ,r-ggplot2)
17022 ("r-ggthemes" ,r-ggthemes)
17023 ("r-gridextra" ,r-gridextra)
17025 ("r-rarpack" ,r-rarpack)
17026 ("r-sparselda" ,r-sparselda)))
17027 (home-page "https://github.com/gumeo/accSDA/wiki")
17028 (synopsis "Accelerated sparse discriminant analysis")
17030 "This package provides an implementation of sparse linear discriminant
17031 analysis, which is a supervised classification method for multiple classes.
17032 Various novel optimization approaches to this problem are implemented
17033 including @dfn{alternating direction method of multipliers} (ADMM),
17034 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17035 Functions for performing cross validation are also supplied along with basic
17036 prediction and plotting functions. @dfn{Sparse zero variance
17037 discriminant} (SZVD) analysis is also included in the package.")
17038 (license license:gpl2+)))
17040 (define-public r-ace2fastq
17042 (name "r-ace2fastq")
17047 (uri (cran-uri "ace2fastq" version))
17050 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17051 (properties `((upstream-name . "ace2fastq")))
17052 (build-system r-build-system)
17054 `(("r-stringr" ,r-stringr)))
17055 (home-page "https://github.com/c5sire/ace2fastq")
17056 (synopsis "ACE file to FASTQ converter")
17058 "The ACE file format is used in genomics to store contigs from sequencing
17059 machines. This tools converts it into FASTQ format. Both formats contain the
17060 sequence characters and their corresponding quality information. Unlike the
17061 FASTQ file, the ACE file stores the quality values numerically. The
17062 conversion algorithm uses the standard Sanger formula. The package
17063 facilitates insertion into pipelines, and content inspection.")
17064 (license license:gpl3)))
17066 (define-public r-rngwell
17073 (uri (cran-uri "rngWELL" version))
17076 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17077 (properties `((upstream-name . "rngWELL")))
17078 (build-system r-build-system)
17079 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17080 (synopsis "Toolbox for WELL random number generators")
17082 "This is a dedicated package to WELL pseudo random generators, which were
17083 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17084 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17085 (license license:bsd-3)))
17087 (define-public r-randtoolbox
17089 (name "r-randtoolbox")
17094 (uri (cran-uri "randtoolbox" version))
17097 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17098 (properties `((upstream-name . "randtoolbox")))
17099 (build-system r-build-system)
17101 `(("r-rngwell" ,r-rngwell)))
17103 `(("gfortran" ,gfortran)))
17104 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17105 (synopsis "Toolbox for pseudo and quasi random number generation")
17107 "This package provides
17110 @item pseudo random generators, such as general linear
17111 congruential generators, multiple recursive generators and generalized
17112 feedback shift register (SF-Mersenne Twister algorithm and WELL
17115 @item quasi random generators, such as the Torus algorithm, the Sobol
17116 sequence, the Halton sequence (including the Van der Corput sequence), and
17118 @item some generator tests: the gap test, the serial test, the poker test.
17121 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17122 (license license:bsd-3)))
17124 (define-public r-lhs
17131 (uri (cran-uri "lhs" version))
17134 "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
17135 (properties `((upstream-name . "lhs")))
17136 (build-system r-build-system)
17137 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17138 (home-page "https://github.com/bertcarnell/lhs")
17139 (synopsis "Latin Hypercube Samples")
17141 "This package provides a number of methods for creating and augmenting
17142 Latin Hypercube Samples.")
17143 (license license:gpl3)))
17145 (define-public r-acebayes
17147 (name "r-acebayes")
17152 (uri (cran-uri "acebayes" version))
17155 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17156 (properties `((upstream-name . "acebayes")))
17157 (build-system r-build-system)
17159 `(("r-compare" ,r-compare)
17161 ("r-randtoolbox" ,r-randtoolbox)
17163 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17164 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17165 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17167 "Finding an optimal Bayesian experimental design involves maximizing an
17168 objective function given by the expectation of some appropriately chosen
17169 utility function with respect to the joint distribution of unknown
17170 quantities (including responses). This objective function is usually not
17171 available in closed form and the design space can be continuous and of high
17172 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17173 to maximise an approximation to the expectation of the utility function.")
17174 (license license:gpl2)))
17176 (define-public r-acet
17183 (uri (cran-uri "ACEt" version))
17186 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17187 (properties `((upstream-name . "ACEt")))
17188 (build-system r-build-system)
17193 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17194 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17195 (synopsis "Estimating dynamic heritability and twin model comparison")
17197 "This package supports twin models that are able to estimate the dynamic
17198 behaviour of the variance components in the classical twin models with respect
17199 to age using B-splines and P-splines.")
17200 (license license:gpl2+)))
17202 (define-public r-acfmperiod
17204 (name "r-acfmperiod")
17209 (uri (cran-uri "acfMPeriod" version))
17212 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17213 (properties `((upstream-name . "acfMPeriod")))
17214 (build-system r-build-system)
17216 `(("r-mass" ,r-mass)))
17217 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17218 (synopsis "Estimation of the ACF from the M-periodogram")
17220 "This package support non-robust and robust computations of the sample
17221 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17222 univariate and multivariate processes. The methodology consists in reversing
17223 the diagonalization procedure involving the periodogram or the
17224 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17225 ACOVF or the ACF as discussed in Fuller (1995)
17226 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17227 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17228 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17229 (license license:gpl2+)))
17231 (define-public r-gamlss-data
17233 (name "r-gamlss-data")
17238 (uri (cran-uri "gamlss.data" version))
17241 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17242 (properties `((upstream-name . "gamlss.data")))
17243 (build-system r-build-system)
17244 (home-page "http://www.gamlss.org/")
17245 (synopsis "GAMLSS data")
17247 "This package provides data used as examples to demonstrate GAMLSS
17249 ;; Either version of the license
17250 (license (list license:gpl2 license:gpl3))))
17252 (define-public r-gamlss
17259 (uri (cran-uri "gamlss" version))
17262 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17263 (properties `((upstream-name . "gamlss")))
17264 (build-system r-build-system)
17266 `(("r-gamlss-data" ,r-gamlss-data)
17267 ("r-gamlss-dist" ,r-gamlss-dist)
17270 ("r-survival" ,r-survival)))
17271 (home-page "http://www.gamlss.org/")
17272 (synopsis "Generalized additive models for location scale and shape")
17274 "This package provides functions for fitting the generalized additive
17275 models for location scale and shape introduced by Rigby and
17276 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17277 use a distributional regression approach where all the parameters of the
17278 conditional distribution of the response variable are modelled using
17279 explanatory variables.")
17280 ;; Either version of the license
17281 (license (list license:gpl2 license:gpl3))))
17283 (define-public r-acid
17290 (uri (cran-uri "acid" version))
17293 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17294 (properties `((upstream-name . "acid")))
17295 (build-system r-build-system)
17297 `(("r-gamlss" ,r-gamlss)
17298 ("r-gamlss-dist" ,r-gamlss-dist)
17299 ("r-hmisc" ,r-hmisc)))
17300 (home-page "https://cran.r-project.org/web/packages/acid/")
17301 (synopsis "Analysing conditional income distributions")
17303 "This package provides functions for the analysis of income distributions
17304 for subgroups of the population as defined by a set of variables like age,
17305 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17306 distribution as well as functions for moments, inequality measures, entropy
17307 measures and polarisation measures of income distributions. This package thus
17308 aides the analysis of income inequality by offering tools for the exploratory
17309 analysis of income distributions at the disaggregated level.")
17310 (license license:gpl3)))
17312 (define-public r-acm4r
17319 (uri (cran-uri "acm4r" version))
17322 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17323 (properties `((upstream-name . "acm4r")))
17324 (build-system r-build-system)
17325 (propagated-inputs `(("r-mass" ,r-mass)))
17326 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17327 (synopsis "Align-and-count method comparisons of RFLP data")
17329 "This is a package to compare sequence fragment lengths or molecular
17330 weights from pairs of lanes. The number of matching bands in the
17331 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17332 the align-and-count method.")
17333 ;; Any version of the GPL
17334 (license (list license:gpl2+ license:gpl3+))))
17336 (define-public r-filematrix
17338 (name "r-filematrix")
17343 (uri (cran-uri "filematrix" version))
17346 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17347 (properties `((upstream-name . "filematrix")))
17348 (build-system r-build-system)
17349 ;; These inputs are needed for vignettes
17351 `(("r-knitr" ,r-knitr)
17352 ("r-rmarkdown" ,r-rmarkdown)
17353 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17354 (home-page "https://github.com/andreyshabalin/filematrix")
17355 (synopsis "File-backed matrix class with convenient read and write access")
17357 "This package provides an interface for working with large matrices
17358 stored in files, not in computer memory. It supports multiple non-character
17359 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17360 byte real values). Access to parts of the matrix is done by indexing, exactly
17361 as with usual R matrices. It supports very large matrices; the package has
17362 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17363 columns, ad allows for quick addition of extra columns to a filematrix.")
17364 (license license:lgpl3)))
17366 (define-public r-acmeeqtl
17368 (name "r-acmeeqtl")
17373 (uri (cran-uri "ACMEeqtl" version))
17376 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17377 (properties `((upstream-name . "ACMEeqtl")))
17378 (build-system r-build-system)
17380 `(("r-filematrix" ,r-filematrix)))
17381 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17382 (synopsis "Estimation of interpretable eQTL effect sizes")
17384 "This package provides a non-linear model, termed ACME, that reflects a
17385 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17386 With non-linear least-squares algorithm the maximum likelihood parameters can
17387 be estimated. The ACME model provides interpretable effect size estimates and
17388 p-values with well controlled Type-I error.")
17389 (license license:lgpl3)))
17391 (define-public r-acmer
17398 (uri (cran-uri "acmeR" version))
17401 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17402 (properties `((upstream-name . "acmeR")))
17403 (build-system r-build-system)
17404 (propagated-inputs `(("r-foreign" ,r-foreign)))
17405 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17406 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17408 "This package provides an implementation of the ACME estimator, described
17409 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17410 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17411 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17412 as carcasses age; variable bleed-through at successive searches; and interval
17413 mortality estimates. The package provides, based on search data, functions
17414 for estimating the mortality inflation factor in Frequentist and Bayesian
17416 (license license:expat)))
17418 (define-public r-r-huge
17425 (uri (cran-uri "R.huge" version))
17428 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17429 (properties `((upstream-name . "R.huge")))
17430 (build-system r-build-system)
17432 `(("r-r-methodss3" ,r-r-methodss3)
17434 ("r-r-utils" ,r-r-utils)))
17435 (home-page "https://github.com/HenrikBengtsson/R.huge")
17436 (synopsis "Methods for accessing huge amounts of data")
17438 "This is a deprecated package for accessing huge amounts of data.
17439 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17440 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17441 the @code{aroma.affymetrix} package.")
17442 (license license:lgpl2.1+)))
17444 (define-public r-r-filesets
17446 (name "r-r-filesets")
17451 (uri (cran-uri "R.filesets" version))
17454 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17455 (properties `((upstream-name . "R.filesets")))
17456 (build-system r-build-system)
17458 `(("r-digest" ,r-digest)
17459 ("r-r-cache" ,r-r-cache)
17460 ("r-r-methodss3" ,r-r-methodss3)
17462 ("r-r-utils" ,r-r-utils)))
17463 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17464 (synopsis "Easy handling of and access to files")
17466 "This package provides classes and methods to locate, setup, subset,
17467 navigate and iterate file sets, i.e. sets of files located in one or more
17468 directories on the file system. The API is designed such that these classes
17469 can be extended via inheritance to provide a richer API for special file
17470 formats. Moreover, a specific name format is defined such that filenames and
17471 directories can be considered to have full names which consists of a name
17472 followed by comma-separated tags. This adds additional flexibility to
17473 identify file sets and individual files.")
17474 (license license:lgpl2.1+)))
17476 (define-public r-r-devices
17478 (name "r-r-devices")
17483 (uri (cran-uri "R.devices" version))
17486 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17487 (properties `((upstream-name . "R.devices")))
17488 (build-system r-build-system)
17490 `(("r-base64enc" ,r-base64enc)
17491 ("r-r-methodss3" ,r-r-methodss3)
17493 ("r-r-utils" ,r-r-utils)))
17494 (home-page "https://github.com/HenrikBengtsson/R.devices")
17495 (synopsis "Unified handling of graphics devices")
17497 "This package provides functions for creating plots and image files in a
17498 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17499 Default device options as well as scales and aspect ratios are controlled in a
17500 uniform way across all device types. Switching output format requires minimal
17501 changes in code. This package is ideal for large-scale batch processing,
17502 because it will never leave open graphics devices or incomplete image files
17503 behind, even on errors or user interrupts.")
17504 (license license:lgpl2.1+)))
17506 (define-public r-acnr
17513 (uri (cran-uri "acnr" version))
17516 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17517 (properties `((upstream-name . "acnr")))
17518 (build-system r-build-system)
17519 (home-page "https://github.com/mpierrejean/acnr")
17520 (synopsis "Annotated copy-number regions")
17522 "This package provides SNP array data from different types of copy-number
17523 regions. These regions were identified manually by the authors of the package
17524 and may be used to generate realistic data sets with known truth.")
17525 (license license:lgpl2.1+)))
17527 (define-public r-acopula
17534 (uri (cran-uri "acopula" version))
17537 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17538 (properties `((upstream-name . "acopula")))
17539 (build-system r-build-system)
17540 (home-page "https://cran.r-project.org/web/packages/acopula/")
17541 (synopsis "Modelling dependence with multivariate Archimax copulas")
17543 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17544 package provides definitions of several parametric families of generator and
17545 dependence function, computes CDF and PDF, estimates parameters, tests for
17546 goodness of fit, generates random sample and checks copula properties for
17547 custom constructs. In the 2-dimensional case explicit formulas for density
17548 are used, contrary to higher dimensions when all derivatives are linearly
17549 approximated. Several non-archimax families (normal, FGM, Plackett) are
17550 provided as well.")
17551 (license license:gpl2)))
17553 (define-public r-tuner
17560 (uri (cran-uri "tuneR" version))
17563 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17564 (properties `((upstream-name . "tuneR")))
17565 (build-system r-build-system)
17566 (propagated-inputs `(("r-signal" ,r-signal)))
17567 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17568 (synopsis "Analysis of music and speech")
17570 "This is a package for the analysis of music and speech. Analyze music
17571 and speech, extract features like MFCCs, handle wave files and their
17572 representation in various ways, read MP3, read MIDI, perform steps of a
17573 transcription, ...")
17574 ;; Either of these versions.
17575 (license (list license:gpl2 license:gpl3))))
17577 (define-public r-seewave
17584 (uri (cran-uri "seewave" version))
17587 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17588 (properties `((upstream-name . "seewave")))
17589 (build-system r-build-system)
17591 `(("r-tuner" ,r-tuner)))
17592 (home-page "http://rug.mnhn.fr/seewave")
17593 (synopsis "Sound analysis and synthesis")
17595 "This package provides functions for analysing, manipulating, displaying,
17596 editing and synthesizing time waves (particularly sound). This package
17597 processes time analysis (oscillograms and envelopes), spectral content,
17598 resonance quality factor, entropy, cross correlation and autocorrelation,
17599 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17600 and 3D spectrograms and many other analyses.")
17601 (license license:gpl2+)))
17603 (define-public r-acousticndlcoder
17605 (name "r-acousticndlcoder")
17610 (uri (cran-uri "AcousticNDLCodeR" version))
17613 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17615 `((upstream-name . "AcousticNDLCodeR")))
17616 (build-system r-build-system)
17618 `(("r-seewave" ,r-seewave)
17619 ("r-tuner" ,r-tuner)
17621 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17622 (synopsis "Coding sound files for use with NDL")
17624 "Make acoustic cues to use with the R package @code{ndl}.
17625 The package implements functions used in the PLoS ONE paper \"Words from
17626 spontaneous conversational speech can be recognized with human-like accuracy
17627 by an error-driven learning algorithm that discriminates between meanings
17628 straight from smart acoustic features, bypassing the phoneme as recognition
17629 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17630 (license license:gpl2+)))
17632 (define-public r-acp
17639 (uri (cran-uri "acp" version))
17642 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17643 (properties `((upstream-name . "acp")))
17644 (build-system r-build-system)
17646 `(("r-quantmod" ,r-quantmod)
17647 ("r-tseries" ,r-tseries)))
17648 (home-page "https://cran.r-project.org/web/packages/acp/")
17649 (synopsis "Autoregressive conditional Poisson")
17651 "This package supports the analysis of count data exhibiting
17652 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17653 model (ACP(p,q)) proposed by Heinen (2003).")
17654 (license license:gpl2)))
17656 (define-public r-ada
17663 (uri (cran-uri "ada" version))
17666 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17667 (properties `((upstream-name . "ada")))
17668 (build-system r-build-system)
17669 (propagated-inputs `(("r-rpart" ,r-rpart)))
17670 (home-page "https://cran.r-project.org/web/packages/ada/")
17671 (synopsis "Stochastic boosting")
17673 "This package provides a straightforward, well-documented, and broad
17674 boosting routine for classification, ideally suited for small to
17675 moderate-sized data sets. It performs discrete, real, and gentle boost under
17676 both exponential and logistic loss on a given data set.")
17677 ;; Any version of the GPL.
17678 (license (list license:gpl2+ license:gpl3+))))
17680 (define-public r-genalg
17687 (uri (cran-uri "genalg" version))
17690 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17691 (properties `((upstream-name . "genalg")))
17692 (build-system r-build-system)
17693 (home-page "https://github.com/egonw/genalg")
17694 (synopsis "R based genetic algorithm")
17696 "This package provides an R based genetic algorithm for binary and
17697 floating point chromosomes.")
17698 (license license:gpl2)))
17700 (define-public r-kernelfactory
17702 (name "r-kernelfactory")
17707 (uri (cran-uri "kernelFactory" version))
17710 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17711 (properties `((upstream-name . "kernelFactory")))
17712 (build-system r-build-system)
17715 ("r-genalg" ,r-genalg)
17716 ("r-kernlab" ,r-kernlab)
17717 ("r-randomforest" ,r-randomforest)))
17718 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17719 (synopsis "Ensemble of kernel machines")
17721 "Kernel factory is an ensemble method where each base classifier (random
17722 forest) is fit on the kernel matrix of a subset of the training data.")
17723 (license license:gpl2+)))
17725 (define-public r-dummies
17732 (uri (cran-uri "dummies" version))
17735 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17736 (properties `((upstream-name . "dummies")))
17737 (build-system r-build-system)
17738 (home-page "https://decisionpatterns.com")
17739 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17741 "This package lets you expand factors, characters and other eligible
17742 classes into dummy/indicator variables.")
17743 (license license:gpl2+)))
17745 (define-public r-acrm
17752 (uri (cran-uri "aCRM" version))
17755 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17756 (properties `((upstream-name . "aCRM")))
17757 (build-system r-build-system)
17760 ("r-dummies" ,r-dummies)
17761 ("r-kernelfactory" ,r-kernelfactory)
17762 ("r-randomforest" ,r-randomforest)))
17763 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17764 (synopsis "Convenience functions for analytical customer relationship management")
17766 "This package provides convenience functions for data preparation and
17767 modeling often used in @dfn{analytical customer relationship
17768 management} (aCRM).")
17769 (license license:gpl2+)))
17771 (define-public r-treeclust
17773 (name "r-treeclust")
17778 (uri (cran-uri "treeClust" version))
17781 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
17782 (properties `((upstream-name . "treeClust")))
17783 (build-system r-build-system)
17785 `(("r-cluster" ,r-cluster)
17786 ("r-rpart" ,r-rpart)))
17787 (home-page "https://cran.r-project.org/web/packages/treeClust/")
17788 (synopsis "Cluster distances through trees")
17790 "This package provides tools to create a measure of inter-point
17791 dissimilarity useful for clustering mixed data, and, optionally, perform the
17793 (license license:gpl2+)))
17795 (define-public r-acrosstic
17797 (name "r-acrosstic")
17802 (uri (cran-uri "AcrossTic" version))
17805 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
17806 (properties `((upstream-name . "AcrossTic")))
17807 (build-system r-build-system)
17809 `(("r-lpsolve" ,r-lpsolve)
17810 ("r-treeclust" ,r-treeclust)))
17811 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
17812 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
17814 "This is a package for constructing minimum-cost regular spanning
17815 subgraph as part of a non-parametric two-sample test for equality of
17817 (license license:gpl2+)))
17819 (define-public r-acrt
17826 (uri (cran-uri "acrt" version))
17829 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
17830 (properties `((upstream-name . "acrt")))
17831 (build-system r-build-system)
17833 `(("r-rcpp" ,r-rcpp)
17834 ("r-rcppeigen" ,r-rcppeigen)
17835 ("r-sandwich" ,r-sandwich)))
17836 (home-page "https://cran.r-project.org/web/packages/acrt/")
17837 (synopsis "Autocorrelation robust testing")
17839 "This package provides functions for testing affine hypotheses on the
17840 regression coefficient vector in regression models with autocorrelated
17842 (license license:gpl2)))
17844 (define-public r-acs
17851 (uri (cran-uri "acs" version))
17854 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
17855 (properties `((upstream-name . "acs")))
17856 (build-system r-build-system)
17858 `(("r-httr" ,r-httr)
17861 ("r-stringr" ,r-stringr)
17863 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
17864 (synopsis "Work with data from the US Census")
17866 "This package provides a general toolkit for downloading, managing,
17867 analyzing, and presenting data from the
17868 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
17869 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
17870 American Community Survey (ACS). Confidence intervals provided with ACS data
17871 are converted to standard errors to be bundled with estimates in complex
17872 @code{acs} objects. The package provides new methods to conduct standard
17873 operations on @code{acs} objects and present/plot data in statistically
17874 appropriate ways.")
17875 (license license:gpl3)))
17877 (define-public r-acss-data
17879 (name "r-acss-data")
17884 (uri (cran-uri "acss.data" version))
17887 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
17888 (properties `((upstream-name . "acss.data")))
17889 (build-system r-build-system)
17890 (home-page "http://complexitycalculator.com/methodology.html")
17891 (synopsis "Data for algorithmic complexity of short strings")
17893 "This is a data only package providing the algorithmic complexity of
17894 short strings, computed using the coding theorem method. For a given set of
17895 symbols in a string, all possible or a large number of random samples of
17896 Turing machines with a given number of states (e.g., 5) and number of symbols
17897 corresponding to the number of symbols in the strings were simulated until
17898 they reached a halting state or failed to end. This package contains data on
17899 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
17900 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
17901 distribution of the halting states.")
17902 (license license:gpl2+)))
17904 (define-public r-acss
17911 (uri (cran-uri "acss" version))
17914 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
17915 (properties `((upstream-name . "acss")))
17916 (build-system r-build-system)
17918 `(("r-acss-data" ,r-acss-data)
17920 (home-page "http://complexitycalculator.com/methodology.html")
17921 (synopsis "Algorithmic complexity for short strings")
17923 "The main purpose of this package is to provide the algorithmic
17924 complexity for short strings, an approximation of the Kolmogorov Complexity of
17925 a short string using the coding theorem method. While the database containing
17926 the complexity is provided in the data only package @code{acss.data}, this
17927 package provides functions accessing the data such as @code{prob_random}
17928 returning the posterior probability that a given string was produced by a
17929 random process. In addition, two traditional (but problematic) measures of
17930 complexity are also provided: entropy and change complexity.")
17931 (license license:gpl2+)))
17933 (define-public r-acswr
17940 (uri (cran-uri "ACSWR" version))
17943 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
17944 (properties `((upstream-name . "ACSWR")))
17945 (build-system r-build-system)
17947 `(("r-mass" ,r-mass)))
17948 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
17949 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
17951 "This is a companion package for the book \"A Course in Statistics with
17952 R\" (ISBN 978-1-119-15272-9.)")
17953 (license license:gpl2)))
17955 (define-public r-alabama
17958 (version "2015.3-1")
17962 (uri (cran-uri "alabama" version))
17965 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
17966 (properties `((upstream-name . "alabama")))
17967 (build-system r-build-system)
17968 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
17969 (home-page "https://cran.r-project.org/web/packages/alabama/")
17970 (synopsis "Constrained nonlinear optimization")
17972 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
17973 Algorithm; it is used for optimizing smooth nonlinear objective functions with
17974 constraints. Linear or nonlinear equality and inequality constraints are
17976 (license license:gpl2+)))
17978 (define-public r-gdina
17985 (uri (cran-uri "GDINA" version))
17988 "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx"))))
17989 (properties `((upstream-name . "GDINA")))
17990 (build-system r-build-system)
17992 `(("r-alabama" ,r-alabama)
17993 ("r-ggplot2" ,r-ggplot2)
17995 ("r-nloptr" ,r-nloptr)
17996 ("r-numderiv" ,r-numderiv)
17998 ("r-rcpparmadillo" ,r-rcpparmadillo)
17999 ("r-rsolnp" ,r-rsolnp)
18000 ("r-shiny" ,r-shiny)
18001 ("r-shinydashboard" ,r-shinydashboard)))
18002 (home-page "https://github.com/Wenchao-Ma/GDINA")
18003 (synopsis "Generalized DINA model framework")
18005 "This package provides a set of psychometric tools for cognitive
18006 diagnosis modeling based on the generalized deterministic inputs, noisy and
18007 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18008 and its extensions, including the sequential G-DINA model by Ma and de la
18009 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18010 polytomous G-DINA model by Chen and de la Torre
18011 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18012 distribution can be independent, saturated, higher-order, loglinear smoothed
18013 or structured. Q-matrix validation, item and model fit statistics, model
18014 comparison at test and item level and differential item functioning can also
18015 be conducted. A graphical user interface is also provided.")
18016 (license license:gpl3)))
18018 (define-public r-actcd
18025 (uri (cran-uri "ACTCD" version))
18028 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18029 (properties `((upstream-name . "ACTCD")))
18030 (build-system r-build-system)
18032 `(("r-gdina" ,r-gdina)
18033 ("r-r-methodss3" ,r-r-methodss3)))
18035 `(("gfortran" ,gfortran)))
18036 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18037 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18039 "This is a package supporting cluster analysis for cognitive diagnosis
18040 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18041 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18042 sum-scores, cluster analysis techniques can be used to classify examinees into
18043 latent classes based on their attribute patterns. In addition to the
18044 algorithms used to classify data, three labeling approaches are proposed to
18045 label clusters so that examinees' attribute profiles can be obtained.")
18046 (license license:gpl2+)))
18048 (define-public r-ineq
18055 (uri (cran-uri "ineq" version))
18058 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18059 (properties `((upstream-name . "ineq")))
18060 (build-system r-build-system)
18061 (home-page "https://cran.r-project.org/web/packages/ineq/")
18062 (synopsis "Measuring inequality, concentration, and poverty")
18064 "This package provides tools for measuring inequality, concentration, and
18065 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18066 ;; Either of these two versions.
18067 (license (list license:gpl2 license:gpl3))))
18069 (define-public r-actfrag
18076 (uri (cran-uri "ActFrag" version))
18079 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18080 (properties `((upstream-name . "ActFrag")))
18081 (build-system r-build-system)
18083 `(("r-accelerometry" ,r-accelerometry)
18084 ("r-dplyr" ,r-dplyr)
18086 ("r-survival" ,r-survival)
18087 ("r-tidyr" ,r-tidyr)))
18088 (home-page "https://github.com/junruidi/ActFrag")
18089 (synopsis "Activity fragmentation metrics extraction")
18091 "This package provides functions to extract commonly used fragmentation
18092 metrics to quantify time accumulation strategies based on minute level
18093 actigraphy-measured activity counts data.")
18094 (license license:gpl3)))
18096 (define-public r-fda
18099 (version "2.4.8.1")
18103 (uri (cran-uri "fda" version))
18106 "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
18107 (properties `((upstream-name . "fda")))
18108 (build-system r-build-system)
18110 `(("r-matrix" ,r-matrix)))
18111 (home-page "https://www.functionaldata.org")
18112 (synopsis "Functional data analysis")
18114 "These functions were developed to support functional data analysis as
18115 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18116 Analysis. The package includes data sets and script files working many
18118 (license license:gpl2+)))
18120 (define-public r-actigraphy
18122 (name "r-actigraphy")
18127 (uri (cran-uri "Actigraphy" version))
18130 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18131 (properties `((upstream-name . "Actigraphy")))
18132 (build-system r-build-system)
18134 `(("r-fda" ,r-fda)))
18135 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18136 (synopsis "Actigraphy data analysis")
18138 "This package provides tools for functional linear modeling and analysis
18139 of actigraphy data.")
18140 (license license:asl2.0)))
18142 (define-public r-activedriver
18144 (name "r-activedriver")
18149 (uri (cran-uri "ActiveDriver" version))
18152 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18153 (properties `((upstream-name . "ActiveDriver")))
18154 (build-system r-build-system)
18156 `(("r-mass" ,r-mass)))
18157 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18158 (synopsis "Tools for finding cancer driver proteins")
18160 "This package provides a mutation analysis tool that discovers cancer
18161 driver genes with frequent mutations in protein signalling sites such as
18162 post-translational modifications (phosphorylation, ubiquitination, etc). The
18163 Poisson generalized linear regression model identifies genes where cancer
18164 mutations in signalling sites are more frequent than expected from the
18165 sequence of the entire gene. Integration of mutations with signalling
18166 information helps find new driver genes and propose candidate mechanisms to
18168 (license license:gpl2+)))
18170 (define-public r-activitycounts
18172 (name "r-activitycounts")
18177 (uri (cran-uri "activityCounts" version))
18180 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18182 `((upstream-name . "activityCounts")))
18183 (build-system r-build-system)
18185 `(("r-lubridate" ,r-lubridate)
18186 ("r-magrittr" ,r-magrittr)
18187 ("r-seewave" ,r-seewave)
18188 ("r-signal" ,r-signal)
18189 ("r-tibble" ,r-tibble)))
18190 (home-page "https://github.com/walkabillylab/activityCounts")
18191 (synopsis "Generate ActiLife counts")
18193 "ActiLife generates activity counts from data collected by Actigraph
18194 accelerometers. Actigraph is one of the most common research-grade
18195 accelerometers. There is considerable research validating and developing
18196 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18197 counts are proprietary and difficult to implement if researchers use different
18198 accelerometer brands. The code creates ActiLife counts from raw acceleration
18199 data for different accelerometer brands.")
18200 (license license:gpl3)))
18202 (define-public r-activityindex
18204 (name "r-activityindex")
18209 (uri (cran-uri "ActivityIndex" version))
18212 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18213 (properties `((upstream-name . "ActivityIndex")))
18214 (build-system r-build-system)
18216 `(("r-data-table" ,r-data-table)
18217 ("r-matrixstats" ,r-matrixstats)
18218 ("r-r-utils" ,r-r-utils)))
18219 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18220 (synopsis "Activity Index calculation using raw accelerometry data")
18222 "This is a package to read raw accelerometry from GT3X+ accelerometry
18223 data and plain table data to calculate the Activity Index from Bai et
18224 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18225 (license license:gpl3)))
18227 (define-public r-activpal
18229 (name "r-activpal")
18234 (uri (cran-uri "activPAL" version))
18237 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18238 (properties `((upstream-name . "activPAL")))
18239 (build-system r-build-system)
18241 `(("r-devtools" ,r-devtools)
18242 ("r-dplyr" ,r-dplyr)
18243 ("r-ggplot2" ,r-ggplot2)
18244 ("r-lubridate" ,r-lubridate)
18245 ("r-magrittr" ,r-magrittr)
18246 ("r-tidyr" ,r-tidyr)))
18247 (home-page "https://cran.r-project.org/web/packages/activPAL")
18248 (synopsis "Processing and chart generation from activPAL events files")
18250 "This package contains functions to generate pre-defined summary
18251 statistics from activPAL events files. The package also contains functions to
18252 produce informative graphics that visualize physical activity behaviour and
18253 trends. This includes generating graphs that align physical activity
18254 behaviour with additional time based observations described by other data
18255 sets, such as sleep diaries and continuous glucose monitoring data.")
18256 (license license:gpl3)))
18258 (define-public r-activpalprocessing
18260 (name "r-activpalprocessing")
18265 (uri (cran-uri "activpalProcessing" version))
18268 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18270 `((upstream-name . "activpalProcessing")))
18271 (build-system r-build-system)
18273 `(("r-chron" ,r-chron)))
18274 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18275 (synopsis "Process activPAL events files")
18277 "This package performs estimation of physical activity and sedentary
18278 behavior variables from activPAL events files.")
18279 ;; Either version of the GPL.
18280 (license (list license:gpl2 license:gpl3))))
18282 (define-public r-actogrammr
18284 (name "r-actogrammr")
18289 (uri (cran-uri "actogrammr" version))
18292 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18293 (properties `((upstream-name . "actogrammr")))
18294 (build-system r-build-system)
18296 `(("r-dplyr" ,r-dplyr)
18297 ("r-ggplot2" ,r-ggplot2)
18298 ("r-lubridate" ,r-lubridate)
18299 ("r-readr" ,r-readr)
18300 ("r-tidyr" ,r-tidyr)))
18301 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18302 (synopsis "Read in activity data and plot actograms")
18304 "Read in activity measurements from standard file formats used by
18305 circadian rhythm researchers, currently only ClockLab format, and process and
18306 plot the data. The central type of plot is the actogram, as first described
18307 in \"Activity and distribution of certain wild mice in relation to biotic
18308 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18309 (license license:gpl3)))
18311 (define-public r-expint
18318 (uri (cran-uri "expint" version))
18321 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18322 (properties `((upstream-name . "expint")))
18323 (build-system r-build-system)
18324 (home-page "https://gitlab.com/vigou3/expint")
18325 (synopsis "Exponential integral and incomplete Gamma function")
18327 "This package provides the exponential integrals @code{E_1(x)},
18328 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18329 function @code{G(a, x)} defined for negative values of its first argument.
18330 The package also gives easy access to the underlying C routines through an
18331 API; see the package vignette for details.")
18332 (license license:gpl2+)))
18334 (define-public r-actuar
18341 (uri (cran-uri "actuar" version))
18344 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18345 (properties `((upstream-name . "actuar")))
18346 (build-system r-build-system)
18347 (propagated-inputs `(("r-expint" ,r-expint)))
18348 (home-page "https://gitlab.com/vigou3/actuar")
18349 (synopsis "Actuarial functions and heavy tailed distributions")
18351 "This package provides functions and data sets for actuarial science:
18352 modeling of loss distributions; risk theory and ruin theory; simulation of
18353 compound models, discrete mixtures and compound hierarchical models;
18354 credibility theory. It boasts support for many additional probability
18355 distributions to model insurance loss amounts and loss frequency: 19
18356 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18357 distribution; zero-truncated and zero-modified extensions of the standard
18358 discrete distributions. It also supports phase-type distributions commonly
18359 used to compute ruin probabilities.")
18360 (license license:gpl2+)))
18362 (define-public r-bmp
18369 (uri (cran-uri "bmp" version))
18372 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18373 (properties `((upstream-name . "bmp")))
18374 (build-system r-build-system)
18375 (home-page "https://cran.r-project.org/web/packages/bmp/")
18376 (synopsis "Read Bitmap (BMP) images")
18378 "This package provides pure R tools to read BMP format images. It is
18379 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18380 (license license:gpl2+)))
18382 (define-public r-readbitmap
18384 (name "r-readbitmap")
18389 (uri (cran-uri "readbitmap" version))
18392 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18393 (properties `((upstream-name . "readbitmap")))
18394 (build-system r-build-system)
18396 `(("libjpeg" ,libjpeg)
18397 ("libpng" ,libpng)))
18402 ("r-tiff" ,r-tiff)))
18403 (home-page "https://github.com/jefferis/readbitmap")
18404 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18406 "This package provides tools to identify and read BMP, JPEG, PNG, and
18407 TIFF format bitmap images. Identification defaults to the use of the magic
18408 number embedded in the file rather than the file extension.")
18409 (license license:gpl2+)))
18411 (define-public r-imager
18418 (uri (cran-uri "imager" version))
18421 "1d7a49lcna77wyfjf5q1b89jck3p3vnysnkgz4drb0qkpy6hz76b"))))
18422 (properties `((upstream-name . "imager")))
18423 (build-system r-build-system)
18426 ("libtiff" ,libtiff)
18430 `(("r-downloader" ,r-downloader)
18431 ("r-igraph" ,r-igraph)
18433 ("r-magrittr" ,r-magrittr)
18435 ("r-purrr" ,r-purrr)
18437 ("r-readbitmap" ,r-readbitmap)
18438 ("r-stringr" ,r-stringr)))
18439 (native-inputs `(("pkg-config" ,pkg-config)))
18440 (home-page "https://dahtah.github.io/imager/")
18441 (synopsis "Image processing library")
18443 "This is a package for fast image processing for images in up to 4
18444 dimensions (two spatial dimensions, one time/depth dimension, one color
18445 dimension). It provides most traditional image processing tools (filtering,
18446 morphology, transformations, etc.) as well as various functions for easily
18447 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18448 simple, modern C++ library for image processing.")
18449 (license license:lgpl3)))
18451 (define-public r-acuityview
18453 (name "r-acuityview")
18458 (uri (cran-uri "AcuityView" version))
18461 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18462 (properties `((upstream-name . "AcuityView")))
18463 (build-system r-build-system)
18465 `(("r-fftwtools" ,r-fftwtools)
18466 ("r-imager" ,r-imager)
18467 ("r-plotrix" ,r-plotrix)))
18468 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18469 (synopsis "Display scenes as seen by an animal with less acute vision")
18471 "This package provides a simple method for representing a visual scene as
18472 it may be seen by an animal with less acute vision.")
18473 (license license:gpl2+)))
18475 (define-public r-caret
18482 (uri (cran-uri "caret" version))
18485 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
18486 (build-system r-build-system)
18488 `(("r-foreach" ,r-foreach)
18489 ("r-ggplot2" ,r-ggplot2)
18490 ("r-lattice" ,r-lattice)
18491 ("r-modelmetrics" ,r-modelmetrics)
18495 ("r-recipes" ,r-recipes)
18496 ("r-reshape2" ,r-reshape2)
18497 ("r-withr" ,r-withr)))
18499 `(("r-knitr" ,r-knitr)))
18500 (home-page "https://github.com/topepo/caret")
18501 (synopsis "Classification and regression training")
18503 "This package provides miscellaneous functions for training and plotting
18504 classification and regression models.")
18505 (license license:gpl2+)))
18507 (define-public r-adabag
18514 (uri (cran-uri "adabag" version))
18517 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18518 (properties `((upstream-name . "adabag")))
18519 (build-system r-build-system)
18521 `(("r-caret" ,r-caret)
18522 ("r-doparallel" ,r-doparallel)
18523 ("r-foreach" ,r-foreach)
18524 ("r-rpart" ,r-rpart)))
18525 (home-page "https://cran.r-project.org/web/packages/adabag/")
18526 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18528 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18529 Breiman's Bagging algorithm using classification trees as individual
18530 classifiers. Once these classifiers have been trained, they can be used to
18531 predict on new data. Also, cross validation estimation of the error can be
18533 (license license:gpl2+)))
18535 (define-public r-adagio
18542 (uri (cran-uri "adagio" version))
18545 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18546 (properties `((upstream-name . "adagio")))
18547 (build-system r-build-system)
18548 (native-inputs `(("gfortran" ,gfortran)))
18549 (home-page "https://cran.r-project.org/web/packages/adagio/")
18550 (synopsis "Discrete and global optimization routines")
18552 "This package provides methods and algorithms for discrete optimization,
18553 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18554 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18556 (license license:gpl3+)))
18558 (define-public r-univoutl
18560 (name "r-univoutl")
18565 (uri (cran-uri "univOutl" version))
18568 "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
18569 (properties `((upstream-name . "univOutl")))
18570 (build-system r-build-system)
18572 `(("r-hmisc" ,r-hmisc)
18573 ("r-robustbase" ,r-robustbase)))
18574 (home-page "https://github.com/marcellodo/univOutl")
18575 (synopsis "Detection of univariate outliers")
18577 "This package provides well-known outlier detection techniques in the
18578 univariate case. Methods to deal with skewed distribution are included too.
18579 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18580 historical data is implemented as well. When available, survey weights can be
18581 used in outliers detection.")
18582 (license license:gpl2+)))
18584 (define-public r-tolerance
18586 (name "r-tolerance")
18591 (uri (cran-uri "tolerance" version))
18594 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
18595 (properties `((upstream-name . "tolerance")))
18596 (build-system r-build-system)
18598 `(("r-mass" ,r-mass)
18600 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18601 (synopsis "Statistical tolerance intervals and regions")
18603 "This package provides functions for estimating tolerance
18604 limits (intervals) for various univariate distributions (binomial, Cauchy,
18605 discrete Pareto, exponential, two-parameter exponential, extreme value,
18606 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18607 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18608 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18609 nonparametric tolerance intervals, tolerance bands for regression
18610 settings (linear regression, nonlinear regression, nonparametric regression,
18611 and multivariate regression), and analysis of variance tolerance intervals.
18612 Visualizations are also available for most of these settings.")
18613 (license license:gpl2+)))
18615 (define-public r-additivitytests
18617 (name "r-additivitytests")
18622 (uri (cran-uri "additivityTests" version))
18625 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18627 `((upstream-name . "additivityTests")))
18628 (build-system r-build-system)
18629 (home-page "https://github.com/simecek/additivityTests")
18630 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18632 "This package provides an implementation of the Tukey, Mandel,
18633 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18634 (license license:gpl3)))
18636 (define-public r-flexclust
18638 (name "r-flexclust")
18643 (uri (cran-uri "flexclust" version))
18646 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18647 (properties `((upstream-name . "flexclust")))
18648 (build-system r-build-system)
18650 `(("r-class" ,r-class)
18651 ("r-lattice" ,r-lattice)
18652 ("r-modeltools" ,r-modeltools)))
18653 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18654 (synopsis "Flexible cluster algorithms")
18656 "The main function @code{kcca} implements a general framework for
18657 k-centroids cluster analysis supporting arbitrary distance measures and
18658 centroid computation. Further cluster methods include hard competitive
18659 learning, neural gas, and QT clustering. There are numerous visualization
18660 methods for cluster results (neighborhood graphs, convex cluster hulls,
18661 barcharts of centroids, ...), and bootstrap methods for the analysis of
18662 cluster stability.")
18663 (license license:gpl2)))
18665 (define-public r-biclust
18672 (uri (cran-uri "biclust" version))
18675 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
18676 (properties `((upstream-name . "biclust")))
18677 (build-system r-build-system)
18679 `(("r-additivitytests" ,r-additivitytests)
18680 ("r-colorspace" ,r-colorspace)
18681 ("r-flexclust" ,r-flexclust)
18682 ("r-ggplot2" ,r-ggplot2)
18683 ("r-lattice" ,r-lattice)
18685 ("r-tidyr" ,r-tidyr)))
18686 (home-page "https://cran.r-project.org/web/packages/biclust/")
18687 (synopsis "BiCluster algorithms")
18689 "The main function @code{biclust()} provides several algorithms to find
18690 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18691 In addition, the package provides methods for data
18692 preprocessing (normalization and discretization), visualization, and
18693 validation of bicluster solutions.")
18694 (license license:gpl3)))
18696 (define-public r-icge
18703 (uri (cran-uri "ICGE" version))
18706 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18707 (properties `((upstream-name . "ICGE")))
18708 (build-system r-build-system)
18710 `(("r-cluster" ,r-cluster)
18711 ("r-mass" ,r-mass)))
18712 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18713 (synopsis "Cluster estimation and identification of atypical units")
18715 "ICGE is a package that helps to estimate the number of real clusters in
18716 data as well as to identify atypical units. The underlying methods are based
18717 on distances rather than on unit x variables.")
18718 (license license:gpl2+)))
18720 (define-public r-depth
18723 (version "2.1-1.1")
18727 (uri (cran-uri "depth" version))
18730 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18731 (properties `((upstream-name . "depth")))
18732 (build-system r-build-system)
18734 `(("r-abind" ,r-abind)
18735 ("r-circular" ,r-circular)
18738 `(("gfortran" ,gfortran)))
18739 (home-page "https://cran.r-project.org/web/packages/depth/")
18740 (synopsis "Nonparametric depth functions for multivariate analysis")
18742 "This package provides tools for depth functions methodology applied to
18743 multivariate analysis. Besides allowing calculation of depth values and
18744 depth-based location estimators, the package includes functions or drawing
18745 contour plots and perspective plots of depth functions. Euclidian and
18746 spherical depths are supported.")
18747 (license license:gpl2)))
18749 (define-public r-archetypes
18751 (name "r-archetypes")
18752 (version "2.2-0.1")
18756 (uri (cran-uri "archetypes" version))
18759 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18760 (properties `((upstream-name . "archetypes")))
18761 (build-system r-build-system)
18763 `(("r-modeltools" ,r-modeltools)
18764 ("r-nnls" ,r-nnls)))
18765 (home-page "https://cran.r-project.org/web/packages/archetypes")
18766 (synopsis "Archetypal analysis")
18768 "The main function @code{archetypes} implements a framework for
18769 archetypal analysis supporting arbitrary problem solving mechanisms for the
18770 different conceptual parts of the algorithm.")
18771 (license license:gpl2+)))
18773 (define-public r-shapes
18780 (uri (cran-uri "shapes" version))
18783 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
18784 (properties `((upstream-name . "shapes")))
18785 (build-system r-build-system)
18787 `(("r-mass" ,r-mass)
18788 ("r-minpack-lm" ,r-minpack-lm)
18790 ("r-scatterplot3d" ,r-scatterplot3d)))
18791 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
18792 (synopsis "Statistical shape analysis")
18794 "This package provides routines for the statistical analysis of landmark
18795 shapes, including Procrustes analysis, graphical displays, principal
18796 components analysis, permutation and bootstrap tests, thin-plate spline
18797 transformation grids and comparing covariance matrices. See Dryden, I.L. and
18798 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
18799 Edition), John Wiley and Sons.")
18800 (license license:gpl2)))
18802 (define-public r-anthropometry
18804 (name "r-anthropometry")
18809 (uri (cran-uri "Anthropometry" version))
18812 "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
18813 (properties `((upstream-name . "Anthropometry")))
18814 (build-system r-build-system)
18816 `(("r-archetypes" ,r-archetypes)
18817 ("r-biclust" ,r-biclust)
18818 ("r-cluster" ,r-cluster)
18819 ("r-depth" ,r-depth)
18824 ("r-shapes" ,r-shapes)))
18825 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
18826 (synopsis "Statistical methods for anthropometric data")
18828 "This package provides statistical methods especially developed to
18829 analyze anthropometric data. These methods are aimed at providing effective
18830 solutions to some commons problems related to Ergonomics and Anthropometry.
18831 They are based on clustering, the statistical concept of data depth,
18832 statistical shape analysis and archetypal analysis.")
18833 (license license:gpl2+)))
18835 (define-public r-adamethods
18837 (name "r-adamethods")
18842 (uri (cran-uri "adamethods" version))
18845 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
18846 (properties `((upstream-name . "adamethods")))
18847 (build-system r-build-system)
18849 `(("r-anthropometry" ,r-anthropometry)
18850 ("r-archetypes" ,r-archetypes)
18852 ("r-foreach" ,r-foreach)
18854 ("r-tolerance" ,r-tolerance)
18855 ("r-univoutl" ,r-univoutl)))
18856 (home-page "https://cran.r-project.org/web/packages/adamethods/")
18857 (synopsis "Archetypoid algorithms and anomaly detection")
18859 "This package is a collection of several algorithms to obtain
18860 archetypoids with small and large databases and with both classical
18861 multivariate data and functional data (univariate and multivariate). Some of
18862 these algorithms also allow to detect anomalies (outliers).")
18863 (license license:gpl2+)))
18865 (define-public r-idpmisc
18872 (uri (cran-uri "IDPmisc" version))
18875 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
18876 (properties `((upstream-name . "IDPmisc")))
18877 (build-system r-build-system)
18879 `(("r-lattice" ,r-lattice)))
18880 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
18881 (synopsis "Functions for data analyses and visualization")
18883 "This package provides different high-level graphics functions for
18884 displaying large datasets, displaying circular data in a very flexible way,
18885 finding local maxima, brewing color ramps, drawing nice arrows, zooming
18886 2D-plots, creating figures with differently colored margin and plot region.
18887 In addition, the package contains auxiliary functions for data manipulation
18888 like omitting observations with irregular values or selecting data by logical
18889 vectors, which include NAs. Other functions are especially useful in
18890 spectroscopy and analyses of environmental data: robust baseline fitting,
18891 finding peaks in spectra, converting humidity measures.")
18892 (license license:gpl3+)))
18894 (define-public r-qqman
18901 (uri (cran-uri "qqman" version))
18904 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
18905 (properties `((upstream-name . "qqman")))
18906 (build-system r-build-system)
18908 `(("r-calibrate" ,r-calibrate)))
18909 (home-page "https://cran.r-project.org/web/packages/qqman/")
18910 (synopsis "Q-Q and Manhattan plots for GWAS data")
18912 "This package allows you to create Q-Q and Manhattan plots for GWAS data
18913 from PLINK results.")
18914 (license license:gpl3)))
18916 (define-public r-ggplot-multistats
18918 (name "r-ggplot-multistats")
18923 (uri (cran-uri "ggplot.multistats" version))
18926 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
18928 `((upstream-name . "ggplot.multistats")))
18929 (build-system r-build-system)
18931 `(("r-ggplot2" ,r-ggplot2)
18932 ("r-hexbin" ,r-hexbin)
18933 ("r-rlang" ,r-rlang)
18934 ("r-scales" ,r-scales)))
18935 (home-page "https://github.com/flying-sheep/ggplot.multistats")
18936 (synopsis "Multiple summary statistics for binned stats/geometries")
18938 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
18939 which functions similar to its singular form, but allows the use of multiple
18940 statistics per bin. Those statistics can be mapped to multiple bin
18942 (license license:gpl3)))
18944 (define-public r-knn-covertree
18946 (name "r-knn-covertree")
18951 (uri (cran-uri "knn.covertree" version))
18954 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
18955 (properties `((upstream-name . "knn.covertree")))
18956 (build-system r-build-system)
18958 `(("r-matrix" ,r-matrix)
18960 ("r-rcppeigen" ,r-rcppeigen)))
18961 (home-page "https://github.com/flying-sheep/knn.covertree")
18962 (synopsis "Accurate kNN Implementation with multiple distance measures")
18964 "Similarly to the FNN package, this package allows calculation of the k
18965 nearest neighbors (kNN) of a data matrix. The implementation is based on
18966 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
18967 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
18968 (license license:agpl3+)))
18970 (define-public r-poibin
18977 (uri (cran-uri "poibin" version))
18980 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
18981 (properties `((upstream-name . "poibin")))
18982 (build-system r-build-system)
18983 (home-page "https://cran.r-project.org/web/packages/poibin/")
18984 (synopsis "Poisson binomial distribution")
18986 "This package provides an implementation of both the exact and
18987 approximation methods for computing the @dfn{cumulative distribution
18988 function} (CDF) of the Poisson binomial distribution. It also provides the
18989 @dfn{probability mass function} (PMF), quantile function, and random number
18990 generation for the Poisson binomial distribution.")
18991 (license license:gpl2)))
18993 (define-public r-diagram
19000 (uri (cran-uri "diagram" version))
19003 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19004 (properties `((upstream-name . "diagram")))
19005 (build-system r-build-system)
19007 `(("r-shape" ,r-shape)))
19008 (home-page "https://cran.r-project.org/web/packages/diagram/")
19009 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19011 "This package provides tools to visualize simple graphs (networks) based
19012 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19013 electrical networks, etc. It also includes supporting material for the book
19014 \"A practical guide to ecological modelling - using R as a simulation
19015 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19016 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19017 Francesca Mazzia (2012).")
19018 (license license:gpl2+)))
19020 (define-public r-lim
19027 (uri (cran-uri "LIM" version))
19030 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19031 (properties `((upstream-name . "LIM")))
19032 (build-system r-build-system)
19034 `(("r-diagram" ,r-diagram)
19035 ("r-limsolve" ,r-limsolve)))
19036 (home-page "https://cran.r-project.org/web/packages/LIM/")
19037 (synopsis "Linear inverse model examples and solution methods")
19039 "This package provides functions that read and solve linear inverse
19040 problems (food web problems, linear programming problems).")
19041 (license license:gpl2+)))
19043 (define-public r-shinycssloaders
19045 (name "r-shinycssloaders")
19050 (uri (cran-uri "shinycssloaders" version))
19053 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19055 `((upstream-name . "shinycssloaders")))
19056 (build-system r-build-system)
19058 `(("r-digest" ,r-digest)
19060 ("r-shiny" ,r-shiny)))
19061 (home-page "https://github.com/andrewsali/shinycssloaders")
19062 (synopsis "Add CSS loading animations to Shiny outputs")
19064 "This package provides tools to create a lightweight Shiny wrapper for
19065 the css-loaders created by Luke Hass
19066 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19067 automatically show a loader when the output is (re)calculating.")
19068 (license license:gpl3)))
19070 (define-public r-rsvg
19077 (uri (cran-uri "rsvg" version))
19080 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
19081 (properties `((upstream-name . "rsvg")))
19082 (build-system r-build-system)
19084 `(("librsvg" ,librsvg)
19087 `(("pkg-config" ,pkg-config)))
19088 (home-page "https://github.com/jeroen/rsvg#readme")
19089 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19091 "This package allows you to render vector-based SVG images into
19092 high-quality custom-size bitmap arrays using the librsvg2 library. The
19093 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19094 addition, the package can convert images directly to various formats such as
19095 PDF or PostScript.")
19096 (license license:expat)))
19098 (define-public r-influencer
19100 (name "r-influencer")
19105 (uri (cran-uri "influenceR" version))
19108 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19109 (properties `((upstream-name . "influenceR")))
19110 (build-system r-build-system)
19112 `(("r-igraph" ,r-igraph)
19113 ("r-matrix" ,r-matrix)))
19114 (home-page "https://github.com/rcc-uchicago/influenceR")
19115 (synopsis "Tools to quantify structural importance of nodes in a network")
19117 "This package provides functionality to compute various node centrality
19118 measures on networks. Included are functions to compute betweenness
19119 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19120 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19121 algorithm to identify key players, and Valente's bridging metric. The
19122 betweenness, Key Players, and bridging implementations are parallelized with
19124 (license license:gpl2)))
19126 (define-public r-emplik
19129 (version "1.0-4.3")
19133 (uri (cran-uri "emplik" version))
19136 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19137 (properties `((upstream-name . "emplik")))
19138 (build-system r-build-system)
19140 `(("r-quantreg" ,r-quantreg)))
19141 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19142 (synopsis "Empirical likelihood ratio for censored/truncated data")
19144 "This package provides empirical likelihood ratio tests for
19145 means/quantiles/hazards from possibly censored and/or truncated data. It also
19147 (license license:gpl2+)))
19149 (define-public r-imputeyn
19151 (name "r-imputeyn")
19156 (uri (cran-uri "imputeYn" version))
19159 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19160 (properties `((upstream-name . "imputeYn")))
19161 (build-system r-build-system)
19163 `(("r-boot" ,r-boot)
19164 ("r-emplik" ,r-emplik)
19165 ("r-mvtnorm" ,r-mvtnorm)
19166 ("r-quadprog" ,r-quadprog)
19167 ("r-survival" ,r-survival)))
19168 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19169 (synopsis "Impute last largest censored observation under weighted least squares")
19171 "This package allows for the imputation of the last largest censored
19172 observantions. This method brings less bias and more efficient estimates for
19174 (license license:gpl2)))
19176 (define-public r-adapenetclass
19178 (name "r-adapenetclass")
19183 (uri (cran-uri "AdapEnetClass" version))
19186 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19187 (properties `((upstream-name . "AdapEnetClass")))
19188 (build-system r-build-system)
19190 `(("r-glmnet" ,r-glmnet)
19191 ("r-imputeyn" ,r-imputeyn)
19193 ("r-quadprog" ,r-quadprog)))
19194 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19195 (synopsis "Class of adaptive elastic net methods for censored data")
19197 "This package provides methods for variable selection for AFT models.")
19198 (license license:gpl2)))
19200 (define-public r-flock
19207 (uri (cran-uri "flock" version))
19210 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19211 (properties `((upstream-name . "flock")))
19212 (build-system r-build-system)
19213 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19214 (home-page "https://cran.r-project.org/web/packages/flock/")
19215 (synopsis "Process synchronization using file locks")
19217 "This package implements synchronization between R processes (spawned by
19218 using the @code{parallel} package for instance) using file locks. It supports
19219 both exclusive and shared locking.")
19220 (license license:asl2.0)))
19222 (define-public r-archivist
19224 (name "r-archivist")
19229 (uri (cran-uri "archivist" version))
19232 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19233 (properties `((upstream-name . "archivist")))
19234 (build-system r-build-system)
19237 ("r-digest" ,r-digest)
19238 ("r-flock" ,r-flock)
19240 ("r-lubridate" ,r-lubridate)
19241 ("r-magrittr" ,r-magrittr)
19242 ("r-rcurl" ,r-rcurl)
19243 ("r-rsqlite" ,r-rsqlite)))
19244 (home-page "https://pbiecek.github.io/archivist/")
19245 (synopsis "Tools for storing, restoring and searching for R objects")
19247 "Data exploration and modelling is a process in which a lot of data
19248 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19249 statistical models, different versions of data sets and different versions of
19250 results. Archivist helps to store and manage artifacts created in R. It
19251 allows you to store selected artifacts as binary files together with their
19252 metadata and relations. Archivist allows sharing artifacts with others. It
19253 can look for already created artifacts by using its class, name, date of the
19254 creation or other properties. It also makes it easy to restore such
19256 (license license:gpl2)))
19258 (define-public r-versions
19260 (name "r-versions")
19265 (uri (cran-uri "versions" version))
19268 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19269 (properties `((upstream-name . "versions")))
19270 (build-system r-build-system)
19271 (home-page "https://cran.r-project.org/web/packages/versions/")
19272 (synopsis "Query and install specific versions of CRAN packages")
19274 "This package allows you to install specified versions of R packages
19275 hosted on CRAN and provides functions to list available versions and the
19276 versions of currently installed packages.")
19277 (license license:bsd-3)))
19279 (define-public r-adapr
19286 (uri (cran-uri "adapr" version))
19289 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19290 (properties `((upstream-name . "adapr")))
19291 (build-system r-build-system)
19293 `(("r-archivist" ,r-archivist)
19294 ("r-devtools" ,r-devtools)
19295 ("r-digest" ,r-digest)
19296 ("r-doparallel" ,r-doparallel)
19297 ("r-gdata" ,r-gdata)
19298 ("r-ggplot2" ,r-ggplot2)
19299 ("r-git2r" ,r-git2r)
19300 ("r-igraph" ,r-igraph)
19301 ("r-knitr" ,r-knitr)
19302 ("r-plotly" ,r-plotly)
19304 ("r-rmarkdown" ,r-rmarkdown)
19305 ("r-shiny" ,r-shiny)
19306 ("r-shinydashboard" ,r-shinydashboard)
19307 ("r-versions" ,r-versions)))
19308 (home-page "https://cran.r-project.org/web/packages/adapr/")
19309 (synopsis "Implementation of an accountable data analysis process")
19311 "This package tracks reading and writing within R scripts that are
19312 organized into a directed acyclic graph. It contains an interactive Shiny
19313 application @code{adaprApp()}. It uses Git and file hashes to track version
19314 histories of inputs and outputs.")
19315 (license license:lgpl2.0)))
19317 (define-public r-adapsamp
19319 (name "r-adapsamp")
19324 (uri (cran-uri "AdapSamp" version))
19327 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19328 (properties `((upstream-name . "AdapSamp")))
19329 (build-system r-build-system)
19330 (propagated-inputs `(("r-pracma" ,r-pracma)))
19331 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19332 (synopsis "Adaptive sampling algorithms")
19334 "For distributions whose probability density functions are log-concave,
19335 the adaptive rejection sampling algorithm can be used to build envelope
19336 functions for sampling. For others, the modified adaptive rejection sampling
19337 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19338 adaptive slice sampling algorithm can be used. This R package mainly includes
19339 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19340 @code{rASS()}. These functions can realize sampling based on the algorithms
19342 (license license:gpl2)))
19344 (define-public r-adaptalint
19346 (name "r-adaptalint")
19351 (uri (cran-uri "adaptalint" version))
19354 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19355 (properties `((upstream-name . "adaptalint")))
19356 (build-system r-build-system)
19358 `(("r-dplyr" ,r-dplyr)
19359 ("r-lintr" ,r-lintr)
19360 ("r-purrr" ,r-purrr)))
19361 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19362 (synopsis "Check R code style")
19364 "This package provides tools to infer the code style (which style rules
19365 are followed and which ones are not) from one package and use it to check
19366 another. This makes it easier to find and correct the most important problems
19368 (license license:gpl3)))
19370 (define-public r-fracdiff
19372 (name "r-fracdiff")
19377 (uri (cran-uri "fracdiff" version))
19380 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19381 (properties `((upstream-name . "fracdiff")))
19382 (build-system r-build-system)
19383 (home-page "https://github.com/mmaechler/fracdiff")
19385 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19387 "This package provides tools for the maximum likelihood estimation of the
19388 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19389 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19390 (license license:gpl2+)))
19392 (define-public r-forecast
19394 (name "r-forecast")
19399 (uri (cran-uri "forecast" version))
19402 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19403 (properties `((upstream-name . "forecast")))
19404 (build-system r-build-system)
19406 `(("r-colorspace" ,r-colorspace)
19407 ("r-fracdiff" ,r-fracdiff)
19408 ("r-ggplot2" ,r-ggplot2)
19409 ("r-lmtest" ,r-lmtest)
19410 ("r-magrittr" ,r-magrittr)
19413 ("r-rcpparmadillo" ,r-rcpparmadillo)
19414 ("r-timedate" ,r-timedate)
19415 ("r-tseries" ,r-tseries)
19419 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19420 (home-page "https://pkg.robjhyndman.com/forecast/")
19421 (synopsis "Forecasting functions for time series and linear models")
19423 "This package provides methods and tools for displaying and analysing
19424 univariate time series forecasts including exponential smoothing via state
19425 space models and automatic ARIMA modelling.")
19426 (license license:gpl3)))
19428 (define-public r-xmisc
19435 (uri (cran-uri "Xmisc" version))
19438 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
19439 (properties `((upstream-name . "Xmisc")))
19440 (build-system r-build-system)
19441 (home-page "https://cran.r-project.org/package=Xmisc")
19443 "Xiaobei's miscellaneous classes and functions")
19445 "This package provides Xiaobei's miscellaneous classes and functions,
19446 which are useful when developing R packages for @dfn{object oriented
19447 programming} (OOP) using R Reference Class.")
19448 (license license:gpl2+)))
19450 (define-public r-proxyc
19457 (uri (cran-uri "proxyC" version))
19460 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
19461 (properties `((upstream-name . "proxyC")))
19462 (build-system r-build-system)
19464 `(("r-matrix" ,r-matrix)
19466 ("r-rcpparmadillo" ,r-rcpparmadillo)
19467 ("r-rcppparallel" ,r-rcppparallel)))
19468 (home-page "https://cran.r-project.org/package=proxyC")
19469 (synopsis "Compute proximity in large sparse matrices")
19471 "This package provides efficient tools to compute the proximity between
19472 rows or columns of large matrices. Functions are optimised for large sparse
19473 matrices using the Armadillo and Intel TBB libraries. Among several built-in
19474 similarity/distance measures, computation of correlation, cosine similarity
19475 and Euclidean distance is particularly fast.")
19476 (license license:gpl3)))
19478 (define-public r-isocodes
19480 (name "r-isocodes")
19481 (version "2020.03.16")
19485 (uri (cran-uri "ISOcodes" version))
19488 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
19489 (properties `((upstream-name . "ISOcodes")))
19490 (build-system r-build-system)
19491 (home-page "https://cran.r-project.org/package=ISOcodes")
19492 (synopsis "Selected ISO codes")
19494 "This package provides ISO language, territory, currency, script and
19495 character codes. It provides ISO 639 language codes, ISO 3166 territory
19496 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
19497 character codes as well as the UN M.49 area codes.")
19498 (license license:gpl2)))
19500 (define-public r-stopwords
19502 (name "r-stopwords")
19507 (uri (cran-uri "stopwords" version))
19510 "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
19511 (properties `((upstream-name . "stopwords")))
19512 (build-system r-build-system)
19513 (propagated-inputs `(("r-isocodes" ,r-isocodes)))
19514 (home-page "https://github.com/quanteda/stopwords")
19515 (synopsis "Multilingual stopword lists")
19517 "This package provides multiple sources of stopwords, for use in text
19518 analysis and natural language processing.")
19519 (license license:expat)))
19521 (define-public r-spacyr
19528 (uri (cran-uri "spacyr" version))
19531 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
19532 (properties `((upstream-name . "spacyr")))
19533 (build-system r-build-system)
19535 `(("r-data-table" ,r-data-table)
19536 ("r-reticulate" ,r-reticulate)))
19537 (home-page "https://spacyr.quanteda.io")
19538 (synopsis "R wrapper for the spaCy NLP library")
19540 "This package provides an R wrapper to the Python @dfn{natural language
19541 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
19542 (license license:gpl3)))
19544 (define-public r-snowballc
19546 (name "r-snowballc")
19551 (uri (cran-uri "SnowballC" version))
19554 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
19555 (properties `((upstream-name . "SnowballC")))
19556 (build-system r-build-system)
19557 (home-page "https://r-forge.r-project.org/projects/r-temis/")
19558 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
19560 "This package provides an R interface to the C @code{libstemmer} library
19561 that implements Porter's word stemming algorithm for collapsing words to a
19562 common root to aid comparison of vocabulary. Currently supported languages
19563 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
19564 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
19565 (license license:bsd-3)))
19567 (define-public r-quanteda
19569 (name "r-quanteda")
19574 (uri (cran-uri "quanteda" version))
19577 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
19578 (properties `((upstream-name . "quanteda")))
19579 (build-system r-build-system)
19581 `(("r-data-table" ,r-data-table)
19582 ("r-extrafont" ,r-extrafont)
19583 ("r-fastmatch" ,r-fastmatch)
19584 ("r-ggplot2" ,r-ggplot2)
19585 ("r-ggrepel" ,r-ggrepel)
19586 ("r-jsonlite" ,r-jsonlite)
19587 ("r-magrittr" ,r-magrittr)
19588 ("r-matrix" ,r-matrix)
19589 ("r-network" ,r-network)
19590 ("r-proxyc" ,r-proxyc)
19592 ("r-rcpparmadillo" ,r-rcpparmadillo)
19593 ("r-rcppparallel" ,r-rcppparallel)
19595 ("r-snowballc" ,r-snowballc)
19596 ("r-stopwords" ,r-stopwords)
19597 ("r-stringi" ,r-stringi)
19599 ("r-yaml" ,r-yaml)))
19601 `(("r-knitr" ,r-knitr)))
19602 (home-page "https://quanteda.io")
19603 (synopsis "Quantitative analysis of textual data")
19605 "This package provides a fast, flexible, and comprehensive framework for
19606 quantitative text analysis in R. It provides functionality for corpus
19607 management, creating and manipulating tokens and ngrams, exploring keywords in
19608 context, forming and manipulating sparse matrices of documents by features and
19609 feature co-occurrences, analyzing keywords, computing feature similarities and
19610 distances, applying content dictionaries, applying supervised and unsupervised
19611 machine learning, visually representing text and text analyses, and more.")
19612 (license license:gpl3)))
19614 (define-public r-topicmodels
19616 (name "r-topicmodels")
19621 (uri (cran-uri "topicmodels" version))
19624 "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
19625 (properties `((upstream-name . "topicmodels")))
19626 (build-system r-build-system)
19630 `(("r-modeltools" ,r-modeltools)
19633 (home-page "https://cran.r-project.org/package=topicmodels")
19634 (synopsis "Topic models")
19636 "This package provides an interface to the C code for @dfn{Latent
19637 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
19638 David M. Blei and co-authors and the C++ code for fitting LDA models using
19639 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
19640 (license license:gpl2)))
19642 (define-public r-stm
19649 (uri (cran-uri "stm" version))
19652 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
19653 (properties `((upstream-name . "stm")))
19654 (build-system r-build-system)
19656 `(("r-data-table" ,r-data-table)
19657 ("r-glmnet" ,r-glmnet)
19659 ("r-matrix" ,r-matrix)
19660 ("r-matrixstats" ,r-matrixstats)
19661 ("r-quadprog" ,r-quadprog)
19662 ("r-quanteda" ,r-quanteda)
19664 ("r-rcpparmadillo" ,r-rcpparmadillo)
19666 ("r-stringr" ,r-stringr)))
19667 (home-page "http://www.structuraltopicmodel.com/")
19668 (synopsis "Estimation of the Structural Topic Model")
19670 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
19671 topic models with document-level covariates. The package also includes tools
19672 for model selection, visualization, and estimation of topic-covariate
19674 (license license:expat)))
19676 (define-public r-polycor
19683 (uri (cran-uri "polycor" version))
19686 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
19687 (properties `((upstream-name . "polycor")))
19688 (build-system r-build-system)
19690 `(("r-matrix" ,r-matrix)
19691 ("r-mvtnorm" ,r-mvtnorm)))
19692 (home-page "https://r-forge.r-project.org/projects/polycor/")
19693 (synopsis "Polychoric and polyserial correlations")
19695 "This package provides tools to compute polychoric and polyserial
19696 correlations by quick \"two-step\" methods or ML, optionally with standard
19697 errors; tetrachoric and biserial correlations are special cases.")
19698 (license license:gpl2+)))
19700 (define-public r-msm
19707 (uri (cran-uri "msm" version))
19710 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
19711 (properties `((upstream-name . "msm")))
19712 (build-system r-build-system)
19714 `(("r-expm" ,r-expm)
19715 ("r-mvtnorm" ,r-mvtnorm)
19716 ("r-survival" ,r-survival)))
19717 (home-page "https://github.com/chjackson/msm")
19718 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
19720 "This package provides functions for fitting continuous-time Markov and
19721 hidden Markov multi-state models to longitudinal data. It was designed for
19722 processes observed at arbitrary times in continuous time (panel data) but some
19723 other observation schemes are supported. Both Markov transition rates and the
19724 hidden Markov output process can be modelled in terms of covariates, which may
19725 be constant or piecewise-constant in time.")
19726 (license license:gpl2+)))
19728 (define-public r-ltm
19735 (uri (cran-uri "ltm" version))
19738 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
19739 (properties `((upstream-name . "ltm")))
19740 (build-system r-build-system)
19742 `(("r-mass" ,r-mass)
19744 ("r-polycor" ,r-polycor)))
19745 (home-page "https://github.com/drizopoulos/ltm")
19746 (synopsis "Latent trait models under IRT")
19748 "This is a package supporting the analysis of multivariate dichotomous
19749 and polytomous data using latent trait models under the Item Response Theory
19750 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
19751 Three-Parameter, the Graded Response, and the Generalized Partial Credit
19753 (license license:gpl2+)))
19755 (define-public r-mi
19762 (uri (cran-uri "mi" version))
19765 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
19766 (properties `((upstream-name . "mi")))
19767 (build-system r-build-system)
19770 ("r-matrix" ,r-matrix)))
19771 (home-page "http://www.stat.columbia.edu/~gelman/")
19772 (synopsis "Missing data imputation and model checking")
19774 "This package provides functions for data manipulation, imputing missing
19775 values in an approximate Bayesian framework, diagnostics of the models used to
19776 generate the imputations, confidence-building mechanisms to validate some of
19777 the assumptions of the imputation algorithm, and functions to analyze multiply
19778 imputed data sets with the appropriate degree of sampling uncertainty.")
19779 (license license:gpl2+)))
19781 (define-public r-matrixcalc
19783 (name "r-matrixcalc")
19788 (uri (cran-uri "matrixcalc" version))
19791 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
19792 (properties `((upstream-name . "matrixcalc")))
19793 (build-system r-build-system)
19794 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
19795 (synopsis "Collection of functions for matrix calculations")
19797 "This package provides a collection of functions to support matrix
19798 calculations for probability, econometric and numerical analysis. There are
19799 additional functions that are comparable to APL functions which are useful for
19800 actuarial models such as pension mathematics.")
19801 (license license:gpl2+)))
19803 (define-public r-sem
19810 (uri (cran-uri "sem" version))
19813 "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
19814 (properties `((upstream-name . "sem")))
19815 (build-system r-build-system)
19817 `(("r-boot" ,r-boot)
19819 ("r-matrixcalc" ,r-matrixcalc)
19821 (home-page "https://cran.r-project.org/package=sem")
19822 (synopsis "Structural equation models")
19824 "This package provides functions for fitting general linear structural
19825 equation models (with observed and latent variables) using the RAM approach,
19826 and for fitting structural equations in observed-variable models by two-stage
19828 (license license:gpl2+)))
19830 (define-public r-semtools
19832 (name "r-semtools")
19837 (uri (cran-uri "semTools" version))
19840 "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
19841 (properties `((upstream-name . "semTools")))
19842 (build-system r-build-system)
19844 `(("r-lavaan" ,r-lavaan)))
19845 (home-page "https://github.com/simsem/semTools/wiki")
19846 (synopsis "Useful tools for structural equation modeling")
19848 "This package provides useful tools for structural equation modeling.")
19849 (license license:gpl2+)))
19851 (define-public r-regsem
19858 (uri (cran-uri "regsem" version))
19861 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
19862 (properties `((upstream-name . "regsem")))
19863 (build-system r-build-system)
19865 `(("r-lavaan" ,r-lavaan)
19867 ("r-rcpparmadillo" ,r-rcpparmadillo)
19868 ("r-rsolnp" ,r-rsolnp)))
19869 (home-page "https://cran.r-project.org/package=regsem")
19870 (synopsis "Regularized structural equation modeling")
19872 "This package uses both ridge and lasso penalties (and extensions) to
19873 penalize specific parameters in structural equation models. The package
19874 offers additional cost functions, cross validation, and other extensions
19875 beyond traditional structural equation models. It also contains a function to
19876 perform @dfn{exploratory mediation} (XMed).")
19877 (license license:gpl2+)))
19879 (define-public r-stanheaders
19881 (name "r-stanheaders")
19886 (uri (cran-uri "StanHeaders" version))
19889 "0cmk0fzczx7dcywcw1dhm6gfq84qlsx77qrsk4z3bf3dhr4bznam"))))
19890 (properties `((upstream-name . "StanHeaders")))
19891 (build-system r-build-system)
19892 (inputs `(("pandoc" ,ghc-pandoc)))
19894 `(("gfortran" ,gfortran)
19895 ("r-knitr" ,r-knitr))) ; for vignettes
19896 (home-page "https://mc-stan.org/")
19897 (synopsis "C++ header files for Stan")
19899 "The C++ header files of the Stan project are provided by this package.
19900 There is a shared object containing part of the @code{CVODES} library, but it
19901 is not accessible from R. @code{r-stanheaders} is only useful for developers
19902 who want to utilize the @code{LinkingTo} directive of their package's
19903 DESCRIPTION file to build on the Stan library without incurring unnecessary
19906 The Stan project develops a probabilistic programming language that implements
19907 full or approximate Bayesian statistical inference via Markov Chain Monte
19908 Carlo or variational methods and implements (optionally penalized) maximum
19909 likelihood estimation via optimization. The Stan library includes an advanced
19910 automatic differentiation scheme, templated statistical and linear algebra
19911 functions that can handle the automatically differentiable scalar types (and
19912 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
19913 package provides user-facing R functions to parse, compile, test, estimate,
19914 and analyze Stan models.")
19915 (license license:bsd-3)))
19917 (define-public r-rpf
19924 (uri (cran-uri "rpf" version))
19927 "1i2kqd7nx55nn35qnw89xmnqk23x9c8xhkh736c2xg7k2ai84ybl"))))
19928 (properties `((upstream-name . "rpf")))
19929 (build-system r-build-system)
19931 `(("r-lifecycle" ,r-lifecycle)
19932 ("r-mvtnorm" ,r-mvtnorm)
19934 ("r-rcppeigen" ,r-rcppeigen)))
19935 (home-page "https://github.com/jpritikin/rpf")
19936 (synopsis "Response probability functions")
19938 "The purpose of this package is to factor out logic and math common to
19939 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
19940 core support code suitable for more specialized IRT packages to build upon.
19941 Complete access to optimized C functions is made available with
19942 @code{R_RegisterCCallable()}.")
19943 (license license:gpl3+)))
19945 (define-public r-openmx
19952 (uri (cran-uri "OpenMx" version))
19955 "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc"))))
19956 (properties `((upstream-name . "OpenMx")))
19957 (build-system r-build-system)
19960 ("r-digest" ,r-digest)
19962 ("r-matrix" ,r-matrix)
19964 ("r-rcppeigen" ,r-rcppeigen)
19966 ("r-stanheaders" ,r-stanheaders)))
19967 (native-inputs `(("gfortran" ,gfortran)))
19968 (home-page "http://openmx.ssri.psu.edu")
19969 (synopsis "Extended structural equation modelling")
19971 "This package allows for the estimation of a wide variety of advanced
19972 multivariate statistical models. It consists of a library of functions and
19973 optimizers that allow you to quickly and flexibly define an SEM model and
19974 estimate parameters given observed data.")
19975 (license license:asl2.0)))
19977 (define-public r-kutils
19984 (uri (cran-uri "kutils" version))
19987 "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
19988 (properties `((upstream-name . "kutils")))
19989 (build-system r-build-system)
19991 `(("r-foreign" ,r-foreign)
19992 ("r-lavaan" ,r-lavaan)
19993 ("r-openxlsx" ,r-openxlsx)
19995 ("r-runit" ,r-runit)
19996 ("r-xtable" ,r-xtable)))
19997 (home-page "https://cran.r-project.org/package=kutils")
19998 (synopsis "Project management tools")
20000 "This package provides tools for data importation, recoding, and
20001 inspection. There are functions to create new project folders, R code
20002 templates, create uniquely named output directories, and to quickly obtain a
20003 visual summary for each variable in a data frame. The main feature here is
20004 the systematic implementation of the \"variable key\" framework for data
20005 importation and recoding.")
20006 (license license:gpl2)))
20008 (define-public r-rockchalk
20010 (name "r-rockchalk")
20011 (version "1.8.144")
20015 (uri (cran-uri "rockchalk" version))
20018 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20019 (properties `((upstream-name . "rockchalk")))
20020 (build-system r-build-system)
20022 `(("r-cardata" ,r-cardata)
20023 ("r-kutils" ,r-kutils)
20025 ("r-mass" ,r-mass)))
20026 (home-page "https://cran.r-project.org/package=rockchalk")
20027 (synopsis "Regression estimation and presentation")
20029 "This package provides a collection of functions for interpretation and
20030 presentation of regression analysis. These functions are used to produce the
20031 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20032 includes regression diagnostics, regression tables, and plots of interactions
20033 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20034 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20035 fairly comprehensive overview.")
20036 (license license:gpl3+)))
20038 (define-public r-lisreltor
20040 (name "r-lisreltor")
20045 (uri (cran-uri "lisrelToR" version))
20048 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20049 (properties `((upstream-name . "lisrelToR")))
20050 (build-system r-build-system)
20051 (home-page "https://cran.r-project.org/package=lisrelToR")
20052 (synopsis "Import output from LISREL into R")
20054 "This is an unofficial package aimed at automating the import of LISREL
20056 (license license:gpl2)))
20058 (define-public r-bdgraph
20065 (uri (cran-uri "BDgraph" version))
20068 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20069 (properties `((upstream-name . "BDgraph")))
20070 (build-system r-build-system)
20072 `(("r-igraph" ,r-igraph)))
20073 (home-page "https://www.uva.nl/profile/a.mohammadi")
20074 (synopsis "Bayesian structure learning in graphical models")
20076 "This package provides statistical tools for Bayesian structure learning
20077 in undirected graphical models for continuous, discrete, and mixed data. It
20078 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20079 on a continuous-time birth-death process.")
20080 (license license:gpl2+)))
20082 (define-public r-d3network
20084 (name "r-d3network")
20085 (version "0.5.2.1")
20089 (uri (cran-uri "d3Network" version))
20092 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20093 (properties `((upstream-name . "d3Network")))
20094 (build-system r-build-system)
20096 `(("r-plyr" ,r-plyr)
20097 ("r-rjson" ,r-rjson)
20098 ("r-whisker" ,r-whisker)))
20099 (home-page "http://christophergandrud.github.io/d3Network/")
20100 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20102 "This package is intended to make it easy to create D3 JavaScript
20103 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20104 (license license:gpl3+)))
20106 (define-public r-qgraph
20113 (uri (cran-uri "qgraph" version))
20116 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20117 (properties `((upstream-name . "qgraph")))
20118 (build-system r-build-system)
20120 `(("r-abind" ,r-abind)
20121 ("r-bdgraph" ,r-bdgraph)
20122 ("r-colorspace" ,r-colorspace)
20123 ("r-corpcor" ,r-corpcor)
20124 ("r-d3network" ,r-d3network)
20125 ("r-dplyr" ,r-dplyr)
20126 ("r-fdrtool" ,r-fdrtool)
20127 ("r-ggplot2" ,r-ggplot2)
20128 ("r-ggraph" ,r-ggraph)
20129 ("r-glasso" ,r-glasso)
20130 ("r-gtools" ,r-gtools)
20131 ("r-hmisc" ,r-hmisc)
20133 ("r-igraph" ,r-igraph)
20135 ("r-lavaan" ,r-lavaan)
20136 ("r-matrix" ,r-matrix)
20137 ("r-pbapply" ,r-pbapply)
20140 ("r-psych" ,r-psych)
20142 ("r-reshape2" ,r-reshape2)
20143 ("r-tidygraph" ,r-tidygraph)))
20144 (home-page "http://sachaepskamp.com/qgraph/")
20145 (synopsis "Weighted network visualization and analysis")
20147 "This package implements tools for weighted network visualization and
20148 analysis, as well as Gaussian graphical model computation. It contains graph
20149 plotting methods, and tools for psychometric data visualization and graphical
20150 model estimation. See Epskamp et al. (2012)
20151 @url{doi:10.18637/jss.v048.i04}.")
20152 (license license:gpl2)))
20154 (define-public r-semplot
20161 (uri (cran-uri "semPlot" version))
20164 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20165 (properties `((upstream-name . "semPlot")))
20166 (build-system r-build-system)
20168 `(("r-colorspace" ,r-colorspace)
20169 ("r-corpcor" ,r-corpcor)
20170 ("r-igraph" ,r-igraph)
20171 ("r-lavaan" ,r-lavaan)
20172 ("r-lisreltor" ,r-lisreltor)
20173 ("r-openmx" ,r-openmx)
20175 ("r-qgraph" ,r-qgraph)
20176 ("r-regsem" ,r-regsem)
20177 ("r-rockchalk" ,r-rockchalk)
20180 (home-page "https://github.com/SachaEpskamp/semPlot")
20181 (synopsis "Unified visualizations of structural equation models")
20183 "Structural equation modeling (SEM) has a long history of representing
20184 models graphically as path diagrams. The semPlot package for R fills the gap
20185 between advanced, but time-consuming, graphical software and the limited
20186 graphics produced automatically by SEM software. In addition, semPlot offers
20187 more functionality than drawing path diagrams: it can act as a common ground
20188 for importing SEM results into R. Any result usable as input to semPlot can
20189 also be represented in any of the three popular SEM frame-works, as well as
20190 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20191 (license license:gpl2)))
20193 (define-public r-cdm
20200 (uri (cran-uri "CDM" version))
20203 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20204 (properties `((upstream-name . "CDM")))
20205 (build-system r-build-system)
20207 `(("r-mvtnorm" ,r-mvtnorm)
20208 ("r-polycor" ,r-polycor)
20210 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20212 "https://github.com/alexanderrobitzsch/CDM")
20213 (synopsis "Cognitive diagnosis modeling")
20215 "This package provides functions for cognitive diagnosis modeling and
20216 multidimensional item response modeling for dichotomous and polytomous item
20217 responses. It enables the estimation of the DINA and DINO model, the multiple
20218 group (polytomous) GDINA model, the multiple choice DINA model, the general
20219 diagnostic model (GDM), the structured latent class model (SLCA), and
20220 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20221 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20222 estimation and the package structure. For tutorials on how to use the CDM
20223 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20224 well as Ravand and Robitzsch (2015).")
20225 (license license:gpl2+)))
20227 (define-public r-tam
20234 (uri (cran-uri "TAM" version))
20237 "111d7qkxhwh1lfvldyh9d61pdb5vb6x8lr8n9h95ssvw07vjqvk9"))))
20238 (properties `((upstream-name . "TAM")))
20239 (build-system r-build-system)
20243 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20244 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20245 (synopsis "Test analysis modules")
20247 "This package includes tools for marginal maximum likelihood estimation
20248 and joint maximum likelihood estimation for unidimensional and
20249 multidimensional item response models. The package functionality covers the
20250 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20251 multi-faceted Rasch model, nominal item response model, structured latent
20252 class model, mixture distribution IRT models, and located latent class models.
20253 Latent regression models and plausible value imputation are also supported.")
20254 (license license:gpl2+)))
20256 (define-public r-erm
20263 (uri (cran-uri "eRm" version))
20266 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20267 (properties `((upstream-name . "eRm")))
20268 (build-system r-build-system)
20270 `(("r-colorspace" ,r-colorspace)
20271 ("r-lattice" ,r-lattice)
20273 ("r-matrix" ,r-matrix)
20274 ("r-psych" ,r-psych)))
20275 (native-inputs `(("gfortran" ,gfortran)))
20276 (home-page "https://cran.r-project.org/package=eRm")
20277 (synopsis "Extended Rasch modeling")
20279 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20280 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20281 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20282 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20283 data matrix. Additional features are the ML estimation of the person
20284 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20285 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20286 infit and outfit measures, ICC and other plots, automated stepwise item
20287 elimination, and a simulation module for various binary data matrices.")
20288 (license license:gpl3)))
20290 (define-public r-irtoys
20297 (uri (cran-uri "irtoys" version))
20300 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20301 (properties `((upstream-name . "irtoys")))
20302 (build-system r-build-system)
20306 (home-page "https://cran.r-project.org/package=irtoys")
20307 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20309 "This package provides a collection of functions useful in learning and
20310 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20311 programs. It provides basic CTT analysis, a simple common interface to the
20312 estimation of item parameters in IRT models for binary responses with three
20313 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20314 EAP, WLE, plausible values), item and person fit statistics, scaling
20315 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20316 array of parametric and non-parametric (kernel) plots. It estimates and plots
20317 Haberman's interaction model when all items are dichotomously scored.")
20318 (license license:gpl2+)))
20320 (define-public r-iheatmapr
20322 (name "r-iheatmapr")
20327 (uri (cran-uri "iheatmapr" version))
20330 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20331 (properties `((upstream-name . "iheatmapr")))
20332 (build-system r-build-system)
20334 `(("r-fastcluster" ,r-fastcluster)
20335 ("r-ggdendro" ,r-ggdendro)
20336 ("r-htmlwidgets" ,r-htmlwidgets)
20337 ("r-jsonlite" ,r-jsonlite)
20338 ("r-knitr" ,r-knitr)
20339 ("r-magrittr" ,r-magrittr)
20341 ("r-rcolorbrewer" ,r-rcolorbrewer)
20342 ("r-s4vectors" ,r-s4vectors)
20343 ("r-scales" ,r-scales)))
20344 (home-page "https://docs.ropensci.org/iheatmapr")
20345 (synopsis "Interactive, Complex Heatmaps")
20347 "iheatmapr is an R package for building complex, interactive heatmaps
20348 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20349 subplots along the rows or columns of the main heatmap add more information
20350 about each row or column. For example, a one column additional heatmap may
20351 indicate what group a particular row or column belongs to. Complex heatmaps
20352 may also include multiple side by side heatmaps which show different types of
20353 data for the same conditions. Interactivity can improve complex heatmaps by
20354 providing tooltips with information about each cell and enabling zooming into
20355 interesting features. iheatmapr uses the plotly library for interactivity.")
20356 (license license:expat)))
20358 (define-public r-packrat
20365 (uri (cran-uri "packrat" version))
20368 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20369 (properties `((upstream-name . "packrat")))
20370 (build-system r-build-system)
20371 (home-page "https://github.com/rstudio/packrat/")
20372 (synopsis "Dependency management R projects")
20374 "This package provides a dependency manager for R projects that allows
20375 you to manage the R packages your project depends on in an isolated, portable,
20376 and reproducible way.")
20377 (license license:gpl2)))
20379 (define-public r-rsconnect
20381 (name "r-rsconnect")
20386 (uri (cran-uri "rsconnect" version))
20389 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20390 (properties `((upstream-name . "rsconnect")))
20391 (build-system r-build-system)
20393 `(("r-curl" ,r-curl)
20394 ("r-digest" ,r-digest)
20395 ("r-jsonlite" ,r-jsonlite)
20396 ("r-openssl" ,r-openssl)
20397 ("r-packrat" ,r-packrat)
20398 ("r-rstudioapi" ,r-rstudioapi)
20399 ("r-yaml" ,r-yaml)))
20400 (home-page "https://github.com/rstudio/rsconnect")
20401 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20403 "This package provides a programmatic deployment interface for RPubs,
20404 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20405 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20406 (license license:gpl2)))
20408 ;; This package includes minified JavaScript files. When upgrading please
20409 ;; check that there are no new minified JavaScript files.
20410 (define-public r-dygraphs
20412 (name "r-dygraphs")
20413 (version "1.1.1.6")
20417 (uri (cran-uri "dygraphs" version))
20420 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20421 (properties `((upstream-name . "dygraphs")))
20422 (build-system r-build-system)
20424 `(#:modules ((guix build utils)
20425 (guix build r-build-system)
20429 (modify-phases %standard-phases
20430 (add-after 'unpack 'process-javascript
20431 (lambda* (#:key inputs #:allow-other-keys)
20432 (with-directory-excursion "inst/htmlwidgets/lib/"
20436 `(("dygraphs/dygraph-combined-dev.js"
20437 "dygraph-combined.js")
20438 (,(assoc-ref inputs "js-jquery")
20439 "jquery/jquery.min.js")
20440 (,(assoc-ref inputs "js-fquarter")
20441 "fquarter/moment-fquarter.min.js"))))
20442 (lambda (sources targets)
20443 (for-each (lambda (source target)
20444 (format #t "Processing ~a --> ~a~%"
20446 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
20447 (call-with-output-file target
20449 (dump-port minified port)))))
20450 sources targets))))
20453 `(("uglify-js" ,uglify-js)
20454 ;; They actually use version 1.11.1, but this more recent version
20455 ;; should be just fine.
20459 (uri "https://code.jquery.com/jquery-1.12.4.js")
20462 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
20466 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
20467 "moment-fquarter/1.0.1/moment-fquarter.js"))
20470 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
20472 `(("r-htmltools" ,r-htmltools)
20473 ("r-htmlwidgets" ,r-htmlwidgets)
20474 ("r-magrittr" ,r-magrittr)
20477 (home-page "https://github.com/rstudio/dygraphs")
20478 (synopsis "Interface to Dygraphs interactive time series charting library")
20480 "This package provides an R interface to the dygraphs JavaScript charting
20481 library (a copy of which is included in the package). It provides rich
20482 facilities for charting time-series data in R, including highly configurable
20483 series- and axis-display and interactive features like zoom/pan and
20484 series/point highlighting.")
20485 (license license:expat)))
20487 (define-public r-shinystan
20489 (name "r-shinystan")
20494 (uri (cran-uri "shinystan" version))
20497 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
20498 (properties `((upstream-name . "shinystan")))
20499 (build-system r-build-system)
20501 `(("r-bayesplot" ,r-bayesplot)
20502 ("r-colourpicker" ,r-colourpicker)
20504 ("r-dygraphs" ,r-dygraphs)
20505 ("r-ggplot2" ,r-ggplot2)
20506 ("r-gridextra" ,r-gridextra)
20507 ("r-gtools" ,r-gtools)
20508 ("r-markdown" ,r-markdown)
20509 ("r-reshape2" ,r-reshape2)
20510 ("r-rsconnect" ,r-rsconnect)
20511 ("r-rstan" ,r-rstan)
20512 ("r-shiny" ,r-shiny)
20513 ("r-shinyjs" ,r-shinyjs)
20514 ("r-shinythemes" ,r-shinythemes)
20515 ("r-threejs" ,r-threejs)
20516 ("r-xtable" ,r-xtable)
20518 (home-page "https://mc-stan.org/")
20519 (synopsis "Interactive visual and numerical analysis for Bayesian models")
20521 "This package provides a graphical user interface for interactive
20522 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
20523 for analyzing a posterior sample. The interface is powered by the Shiny web
20524 application framework and works with the output of MCMC programs written in
20525 any programming language (and has extended functionality for Stan models fit
20526 using the @code{rstan} and @code{rstanarm} packages).")
20527 (license license:gpl3+)))
20529 (define-public r-rstantools
20531 (name "r-rstantools")
20536 (uri (cran-uri "rstantools" version))
20539 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
20540 (properties `((upstream-name . "rstantools")))
20541 (build-system r-build-system)
20542 (inputs `(("pandoc" ,ghc-pandoc)))
20544 `(("r-desc" ,r-desc)
20545 ("r-rcpp" ,r-rcpp)))
20546 (home-page "https://mc-stan.org/rstantools/")
20547 (synopsis "Tools for developing R packages interfacing with Stan")
20549 "This package provides various tools for developers of R packages
20550 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
20551 up the required package structure, S3 generics and default methods to unify
20552 function naming across Stan-based R packages, and vignettes with
20553 recommendations for developers.")
20554 (license license:gpl3+)))
20556 (define-public r-loo
20563 (uri (cran-uri "loo" version))
20566 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
20567 (properties `((upstream-name . "loo")))
20568 (build-system r-build-system)
20570 `(("pandoc" ,ghc-pandoc)
20571 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20573 `(("r-checkmate" ,r-checkmate)
20574 ("r-matrixstats" ,r-matrixstats)))
20575 (home-page "https://mc-stan.org/loo/")
20576 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
20578 "This package provides an implementation of efficient approximate
20579 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
20580 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
20581 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
20582 procedure for regularizing importance weights. As a byproduct of the
20583 calculations, we also obtain approximate standard errors for estimated
20584 predictive errors and for the comparison of predictive errors between models.
20585 The package also provides methods for using stacking and other model weighting
20586 techniques to average Bayesian predictive distributions.")
20587 (license license:gpl3+)))
20589 (define-public r-rstan
20596 (uri (cran-uri "rstan" version))
20599 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
20600 (properties `((upstream-name . "rstan")))
20601 (build-system r-build-system)
20604 (modify-phases %standard-phases
20605 (add-before 'install 'set-timezone
20606 ;; This package is picky about timezones.
20607 (lambda* (#:key inputs #:allow-other-keys)
20608 (setenv "TZ" "UTC+1")
20610 (string-append (assoc-ref inputs "tzdata")
20611 "/share/zoneinfo"))
20614 `(("tzdata" ,tzdata)
20615 ("pandoc" ,ghc-pandoc)))
20618 ("r-ggplot2" ,r-ggplot2)
20619 ("r-gridextra" ,r-gridextra)
20620 ("r-inline" ,r-inline)
20622 ("r-pkgbuild" ,r-pkgbuild)
20624 ("r-rcppeigen" ,r-rcppeigen)
20625 ("r-stanheaders" ,r-stanheaders)))
20626 (home-page "https://discourse.mc-stan.org/")
20627 (synopsis "R interface to Stan")
20629 "User-facing R functions are provided to parse, compile, test, estimate,
20630 and analyze Stan models by accessing the header-only Stan library provided by
20631 the StanHeaders package. The Stan project develops a probabilistic
20632 programming language that implements full Bayesian statistical inference via
20633 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
20634 approximation, and (optionally penalized) maximum likelihood estimation via
20635 optimization. In all three cases, automatic differentiation is used to
20636 quickly and accurately evaluate gradients without burdening the user with the
20637 need to derive the partial derivatives.")
20638 (license license:gpl3+)))
20640 (define-public r-rstanarm
20642 (name "r-rstanarm")
20647 (uri (cran-uri "rstanarm" version))
20650 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
20651 (properties `((upstream-name . "rstanarm")))
20652 (build-system r-build-system)
20654 `(("pandoc" ,ghc-pandoc)
20655 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20657 `(("r-bayesplot" ,r-bayesplot)
20659 ("r-ggplot2" ,r-ggplot2)
20662 ("r-matrix" ,r-matrix)
20665 ("r-rcppeigen" ,r-rcppeigen)
20666 ("r-rcppparallel" ,r-rcppparallel)
20667 ("r-rstan" ,r-rstan)
20668 ("r-rstantools" ,r-rstantools)
20669 ("r-shinystan" ,r-shinystan)
20670 ("r-stanheaders" ,r-stanheaders)
20671 ("r-survival" ,r-survival)))
20672 (home-page "https://mc-stan.org/rstanarm/")
20673 (synopsis "Bayesian applied regression modeling via Stan")
20675 "This package estimates previously compiled regression models using the
20676 @code{rstan} package, which provides the R interface to the Stan C++ library
20677 for Bayesian estimation. Users specify models via the customary R syntax with
20678 a formula and @code{data.frame} plus some additional arguments for priors.")
20679 (license license:gpl3+)))
20681 (define-public r-kendall
20688 (uri (cran-uri "Kendall" version))
20691 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
20692 (properties `((upstream-name . "Kendall")))
20693 (build-system r-build-system)
20695 `(("r-boot" ,r-boot)))
20697 `(("gfortran" ,gfortran)))
20698 (home-page "https://cran.r-project.org/web/packages/Kendall/")
20699 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
20701 "This package computes the Kendall rank correlation and Mann-Kendall
20703 (license license:gpl2+)))
20705 (define-public r-zyp
20708 (version "0.10-1.1")
20712 (uri (cran-uri "zyp" version))
20715 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
20716 (properties `((upstream-name . "zyp")))
20717 (build-system r-build-system)
20719 `(("r-kendall" ,r-kendall)))
20720 (home-page "https://cran.r-project.org/web/packages/zyp/")
20721 (synopsis "Zhang + Yue-Pilon Trends Package")
20723 "This package contains an efficient implementation of Sen's slope
20724 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
20725 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
20727 (license license:lgpl2.1)))
20729 (define-public r-zvcv
20736 (uri (cran-uri "ZVCV" version))
20739 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
20740 (properties `((upstream-name . "ZVCV")))
20741 (build-system r-build-system)
20743 `(("r-abind" ,r-abind)
20744 ("r-glmnet" ,r-glmnet)
20745 ("r-mvtnorm" ,r-mvtnorm)
20746 ("r-partitions" ,r-partitions)
20748 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20749 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
20750 (synopsis "Zero-Variance Control Variates")
20752 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
20753 to reduce the variance of Monte Carlo estimators of expectations using the
20754 derivatives of the log target. Once the derivatives are available, the only
20755 additional computational effort is in solving a linear regression problem.
20756 This method has been extended to higher dimensions using regularisation. This
20757 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
20758 samples, derivatives and function evaluations are available. Additional
20759 functions for applying ZV-CV to two estimators for the normalising constant of
20760 the posterior distribution in Bayesian statistics are also supplied.")
20761 (license license:gpl2+)))
20763 (define-public r-ztype
20770 (uri (cran-uri "ztype" version))
20773 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
20774 (properties `((upstream-name . "ztype")))
20775 (build-system r-build-system)
20777 `(("r-assertthat" ,r-assertthat)
20778 ("r-dplyr" ,r-dplyr)
20779 ("r-ggplot2" ,r-ggplot2)
20780 ("r-lubridate" ,r-lubridate)
20781 ("r-magrittr" ,r-magrittr)
20782 ("r-rvest" ,r-rvest)
20783 ("r-stringr" ,r-stringr)))
20784 (home-page "https://cran.r-project.org/web/packages/ztype/")
20785 (synopsis "Run a Ztype game loaded with R functions")
20787 "How fast can you type R functions on your keyboard? Find out by running
20788 a @code{zty.pe} game: export R functions as instructions to type to destroy
20789 opponents' vessels.")
20790 (license license:gpl3)))
20792 (define-public r-zseq
20799 (uri (cran-uri "Zseq" version))
20802 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
20803 (properties `((upstream-name . "Zseq")))
20804 (build-system r-build-system)
20806 `(("r-gmp" ,r-gmp)))
20807 (home-page "https://cran.r-project.org/web/packages/Zseq/")
20808 (synopsis "Integer sequence generator")
20810 "This package generates well-known integer sequences. The @code{gmp}
20811 package is adopted for computing with arbitrarily large numbers. Every
20812 function has a hyperlink to its corresponding item in the @dfn{On-Line
20813 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
20814 (license license:gpl3+)))
20816 (define-public r-isoband
20823 (uri (cran-uri "isoband" version))
20826 "1r023s73qypnvpx18znr9ymylr022m90v65mz2jasn0a1kjrfcbq"))))
20827 (properties `((upstream-name . "isoband")))
20828 (build-system r-build-system)
20830 `(("r-rcpp" ,r-rcpp)
20831 ("r-testthat" ,r-testthat)))
20832 (home-page "https://github.com/wilkelab/isoband")
20833 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
20835 "This package provides a fast C++ implementation to generate contour
20836 lines (isolines) and contour polygons (isobands) from regularly spaced grids
20837 containing elevation data.")
20838 (license license:expat)))
20840 (define-public r-ppcor
20847 (uri (cran-uri "ppcor" version))
20850 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
20851 (properties `((upstream-name . "ppcor")))
20852 (build-system r-build-system)
20854 `(("r-mass" ,r-mass)))
20855 (home-page "https://cran.r-project.org/web/packages/ppcor/")
20856 (synopsis "Partial and semi-partial correlation")
20858 "This package provides users not only with a function to readily
20859 calculate the higher-order partial and semi-partial correlations but also with
20860 statistics and p-values of the correlation coefficients.")
20861 (license license:gpl2)))
20863 (define-public r-hrbrthemes
20865 (name "r-hrbrthemes")
20870 (uri (cran-uri "hrbrthemes" version))
20872 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
20873 (properties `((upstream-name . "hrbrthemes")))
20874 (build-system r-build-system)
20876 `(("r-extrafont" ,r-extrafont)
20877 ("r-gdtools" ,r-gdtools)
20878 ("r-ggplot2" ,r-ggplot2)
20879 ("r-htmltools" ,r-htmltools)
20880 ("r-knitr" ,r-knitr)
20881 ("r-magrittr" ,r-magrittr)
20882 ("r-rmarkdown" ,r-rmarkdown)
20883 ("r-scales" ,r-scales)))
20885 `(("r-knitr" ,r-knitr)))
20886 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
20887 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
20889 "This package provides a compilation of extra @code{ggplot2} themes,
20890 scales and utilities, including a spell check function for plot label fields
20891 and an overall emphasis on typography.")
20892 (license license:expat)))
20894 (define-public r-crochet
20901 (uri (cran-uri "crochet" version))
20904 "1cbv79nyycxk6f8ldcsnn2pvgxqlnrj0qs19nhafnq2clxy863k6"))))
20905 (build-system r-build-system)
20906 (home-page "https://github.com/agrueneberg/crochet")
20907 (synopsis "Implementation Helper for Matrix-Like Types")
20909 "Functions to help implement the extraction / subsetting / indexing
20910 function @code{[} and replacement function @code{[<-} of custom matrix-like
20911 types (based on S3, S4, etc.), modeled as closely to the base matrix class
20912 as possible (with tests to prove it).")
20913 (license license:expat)))
20915 (define-public r-boa
20918 (version "1.1.8-2")
20922 (uri (cran-uri "boa" version))
20925 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
20926 (properties `((upstream-name . "boa")))
20927 (build-system r-build-system)
20928 (home-page "http://www.jstatsoft.org/v21/i11")
20929 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
20931 "This package provides a menu-driven program and library of functions for
20932 carrying out convergence diagnostics and statistical and graphical analysis of
20933 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
20934 (license license:gpl2+)))
20936 (define-public r-httpcode
20938 (name "r-httpcode")
20942 (uri (cran-uri "httpcode" version))
20945 "06k853ihwzkcx4z3jzazpb03p91frqkwz18jy4fwr8j2nwyqbhgv"))))
20946 (build-system r-build-system)
20947 (home-page "https://github.com/sckott/httpcode")
20948 (synopsis "HTTP status code helper")
20949 (description "@code{httpcode} provides functionality for finding and
20950 explaining the meaning of @code{HTTP} status codes. Functions are included for
20951 searching for codes by full or partial number, by message, and to get
20952 appropriate dog and cat images for many status codes.")
20953 (license license:expat)))
20955 (define-public r-latex2exp
20957 (name "r-latex2exp")
20961 (uri (cran-uri "latex2exp" version))
20964 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
20965 (build-system r-build-system)
20967 `(("r-stringr" ,r-stringr)
20968 ("r-magrittr", r-magrittr)))
20969 (home-page "https://github.com/stefano-meschiari/latex2exp/")
20970 (synopsis "Use LaTeX expressions in plots")
20971 (description "@code{latex2exp} parses and converts LaTeX math formulas to
20972 R's plotmath expressions, used to enter mathematical formulas and symbols to be
20973 rendered as text, axis labels, etc. throughout R's plotting system.")
20974 (license license:expat)))
20976 (define-public r-oai
20982 (uri (cran-uri "oai" version))
20985 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
20986 (build-system r-build-system)
20988 `(("r-xml2" ,r-xml2)
20991 ("r-stringr" ,r-stringr)
20992 ("r-tibble" ,r-tibble)))
20993 (home-page "https://github.com/ropensci/oai/")
20994 (synopsis "General purpose OAI-PMH services client")
20995 (description "@code{oai} provides a general purpose client to work with
20996 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
20997 service. Functions are provided to work with the OAI-PMH verbs:
20998 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
20999 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21000 (license license:expat)))
21002 (define-public r-argon2
21009 (uri (cran-uri "argon2" version))
21012 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21013 (properties `((upstream-name . "argon2")))
21014 (build-system r-build-system)
21015 (home-page "https://github.com/wrathematics/argon2")
21016 (synopsis "Secure password hashing based on the argon2 algorithm")
21018 "This package provides utilities for secure password hashing via the
21019 argon2 algorithm.")
21020 (license license:bsd-2)))
21022 (define-public r-getpass
21029 (uri (cran-uri "getPass" version))
21032 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21033 (properties `((upstream-name . "getPass")))
21034 (build-system r-build-system)
21036 `(("r-rstudioapi" ,r-rstudioapi)))
21037 (home-page "https://github.com/wrathematics/getPass")
21038 (synopsis "Masked user input")
21040 "This package provides a micro-package for reading \"passwords\", i.e.
21041 reading user input with masking, so that the input is not displayed as it is
21042 typed. Currently, RStudio, the command line (every OS), and any platform
21043 where tcltk is present are supported.")
21044 (license license:bsd-2)))
21046 (define-public r-remoter
21053 (uri (cran-uri "remoter" version))
21056 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21057 (properties `((upstream-name . "remoter")))
21058 (build-system r-build-system)
21060 `(("r-argon2" ,r-argon2)
21061 ("r-getpass" ,r-getpass)
21062 ("r-pbdzmq" ,r-pbdzmq)
21064 (home-page "https://github.com/RBigData/remoter")
21065 (synopsis "Control a remote R session from a local one")
21067 "This package provides a set of utilities for client/server computing
21068 with R, controlling a remote R session (the server) from a local one (the
21070 (license license:bsd-2)))
21072 (define-public r-asd
21079 (uri (cran-uri "asd" version))
21082 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21083 (properties `((upstream-name . "asd")))
21084 (build-system r-build-system)
21086 `(("r-mvtnorm" ,r-mvtnorm)))
21087 (home-page "https://cran.r-project.org/web/packages/asd")
21088 (synopsis "Simulations for Adaptive Seamless Designs")
21090 "This package provdes means to run simulations for adaptive seamless
21091 designs with and without early outcomes for treatment selection and
21092 subpopulation type designs.")
21093 (license license:gpl3)))