1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 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 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 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>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages cran)
38 #:use-module ((guix licenses) #:prefix license:)
39 #:use-module (guix packages)
40 #:use-module (guix download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system r)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages c)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages databases)
51 #:use-module (gnu packages fontutils)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages geo)
54 #:use-module (gnu packages ghostscript)
55 #:use-module (gnu packages gl)
56 #:use-module (gnu packages gnome)
57 #:use-module (gnu packages graph)
58 #:use-module (gnu packages gtk)
59 #:use-module (gnu packages haskell-xyz)
60 #:use-module (gnu packages icu4c)
61 #:use-module (gnu packages image)
62 #:use-module (gnu packages imagemagick)
63 #:use-module (gnu packages java)
64 #:use-module (gnu packages javascript)
65 #:use-module (gnu packages machine-learning)
66 #:use-module (gnu packages maths)
67 #:use-module (gnu packages mpi)
68 #:use-module (gnu packages multiprecision)
69 #:use-module (gnu packages networking)
70 #:use-module (gnu packages pcre)
71 #:use-module (gnu packages perl)
72 #:use-module (gnu packages pkg-config)
73 #:use-module (gnu packages python)
74 #:use-module (gnu packages python-xyz)
75 #:use-module (gnu packages statistics)
76 #:use-module (gnu packages tcl)
77 #:use-module (gnu packages tls)
78 #:use-module (gnu packages web)
79 #:use-module (gnu packages xorg))
81 (define-public r-clipr
88 (uri (cran-uri "clipr" version))
91 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
92 (build-system r-build-system)
93 (home-page "https://github.com/mdlincoln/clipr")
94 (synopsis "Read and write from the system clipboard")
96 "This package provides simple utility functions to read from and write to
97 the system clipboards.")
98 (license license:gpl3)))
100 (define-public r-scales
107 (uri (cran-uri "scales" version))
109 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
110 (build-system r-build-system)
112 `(("r-farver" ,r-farver)
113 ("r-labeling" ,r-labeling)
114 ("r-lifecycle" ,r-lifecycle)
115 ("r-munsell" ,r-munsell)
116 ("r-rcolorbrewer" ,r-rcolorbrewer)
118 ("r-viridislite" ,r-viridislite)))
119 (home-page "https://github.com/hadley/scales")
120 (synopsis "Scale functions for visualization")
122 "This package provides graphical scales that map data to aesthetics, and
123 provides methods for automatically determining breaks and labels for axes and
125 (license license:expat)))
127 (define-public r-pheatmap
134 (uri (cran-uri "pheatmap" version))
137 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
138 (build-system r-build-system)
140 `(("r-gtable" ,r-gtable)
141 ("r-rcolorbrewer" ,r-rcolorbrewer)
142 ("r-scales" ,r-scales)))
143 (home-page "https://cran.r-project.org/web/packages/pheatmap")
144 (synopsis "Pretty heatmaps")
146 "This package provides an implementation of heatmaps that offers more
147 control over dimensions and appearance.")
148 (license license:gpl2+)))
150 (define-public r-ellipsis
157 (uri (cran-uri "ellipsis" version))
160 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
161 (build-system r-build-system)
163 `(("r-rlang" ,r-rlang)))
164 (home-page "https://github.com/hadley/ellipsis")
165 (synopsis "Tools for working with additional arguments")
167 "In S3 generics, it's useful to take @code{...} so that methods can have
168 additional arguments. But this flexibility comes at a cost: misspelled
169 arguments will be silently ignored. The @code{ellipsis} package is an
170 experiment that allows a generic to warn if any arguments passed in @code{...}
172 (license license:gpl3)))
181 (uri (cran-uri "grr" version))
184 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
185 (build-system r-build-system)
186 (home-page "https://cran.r-project.org/web/packages/grr")
187 (synopsis "Alternative implementations of base R functions")
189 "This package provides alternative implementations of some base R
190 functions, including @code{sort}, @code{order}, and @code{match}. The
191 functions are simplified but can be faster or have other advantages.")
192 (license license:gpl3)))
194 (define-public r-matrix-utils
196 (name "r-matrix-utils")
201 (uri (cran-uri "Matrix.utils" version))
204 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
205 (properties `((upstream-name . "Matrix.utils")))
206 (build-system r-build-system)
209 ("r-matrix" ,r-matrix)))
210 (home-page "https://github.com/cvarrichio/Matrix.utils")
212 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
214 "This package implements data manipulation methods such as @code{cast},
215 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
217 (license license:gpl3)))
226 (uri (cran-uri "sys" version))
229 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
230 (build-system r-build-system)
231 (home-page "https://github.com/jeroen/sys")
232 (synopsis "Powerful and reliable tools for running system commands in R")
234 "This package provides drop-in replacements for the base @code{system2()}
235 function with fine control and consistent behavior across platforms. It
236 supports clean interruption, timeout, background tasks, and streaming STDIN /
237 STDOUT / STDERR over binary or text connections. The package also provides
238 functions for evaluating expressions inside a temporary fork. Such
239 evaluations have no side effects on the main R process, and support reliable
240 interrupts and timeouts. This provides the basis for a sandboxing
242 (license license:expat)))
244 (define-public r-askpass
251 (uri (cran-uri "askpass" version))
254 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
255 (build-system r-build-system)
256 (propagated-inputs `(("r-sys" ,r-sys)))
257 (home-page "https://github.com/jeroen/askpass")
258 (synopsis "Safe password entry for R")
260 "This package provides cross-platform utilities for prompting the user
261 for credentials or a passphrase, for example to authenticate with a server or
262 read a protected key.")
263 (license license:expat)))
265 (define-public r-vegan
272 (uri (cran-uri "vegan" version))
275 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
276 (build-system r-build-system)
278 `(("gfortran" ,gfortran)))
280 `(("r-cluster" ,r-cluster)
281 ("r-knitr" ,r-knitr) ; needed for vignettes
282 ("r-lattice" ,r-lattice)
285 ("r-permute" ,r-permute)))
286 (home-page "https://cran.r-project.org/web/packages/vegan")
287 (synopsis "Functions for community ecology")
289 "The vegan package provides tools for descriptive community ecology. It
290 has most basic functions of diversity analysis, community ordination and
291 dissimilarity analysis. Most of its multivariate tools can be used for other
292 data types as well.")
293 (license license:gpl2+)))
295 (define-public r-tidyverse
302 (uri (cran-uri "tidyverse" version))
305 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
306 (build-system r-build-system)
308 `(("r-broom" ,r-broom)
310 ("r-crayon" ,r-crayon)
311 ("r-dbplyr" ,r-dbplyr)
313 ("r-forcats" ,r-forcats)
314 ("r-ggplot2" ,r-ggplot2)
318 ("r-jsonlite" ,r-jsonlite)
319 ("r-lubridate" ,r-lubridate)
320 ("r-magrittr" ,r-magrittr)
321 ("r-modelr" ,r-modelr)
322 ("r-pillar" ,r-pillar)
325 ("r-readxl" ,r-readxl)
326 ("r-reprex" ,r-reprex)
328 ("r-rstudioapi" ,r-rstudioapi)
330 ("r-stringr" ,r-stringr)
331 ("r-tibble" ,r-tibble)
334 (home-page "https://tidyverse.tidyverse.org")
335 (synopsis "Install and load packages from the \"Tidyverse\"")
337 "The @code{tidyverse} is a set of packages that work in harmony because
338 they share common data representations and API design. This package is
339 designed to make it easy to install and load multiple tidyverse packages in a
341 (license license:gpl3)))
343 (define-public r-rvest
350 (uri (cran-uri "rvest" version))
352 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
353 (build-system r-build-system)
356 ("r-magrittr" ,r-magrittr)
357 ("r-selectr" ,r-selectr)
359 (home-page "https://github.com/hadley/rvest")
360 (synopsis "Simple web scraping for R")
362 "@code{r-rvest} helps you scrape information from web pages. It is
363 designed to work with @code{magrittr} to make it easy to express common web
364 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
365 (license license:gpl3)))
367 (define-public r-selectr
374 (uri (cran-uri "selectr" version))
376 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
377 (build-system r-build-system)
379 `(("r-stringr" ,r-stringr)
381 (home-page "https://sjp.co.nz/projects/selectr/")
382 (synopsis "Translate CSS selectors to XPath expressions")
384 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
385 expression. This allows you to use CSS selectors when working with the XML
386 package as it can only evaluate XPath expressions. Also provided are
387 convenience functions useful for using CSS selectors on XML nodes. This
388 package is a port of the Python package @code{cssselect}.")
389 (license license:bsd-3)))
391 (define-public r-reprex
398 (uri (cran-uri "reprex" version))
401 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
402 (build-system r-build-system)
404 `(("r-callr" ,r-callr)
408 ("r-rmarkdown" ,r-rmarkdown)
409 ("r-whisker" ,r-whisker)
410 ("r-withr" ,r-withr)))
411 (home-page "https://github.com/tidyverse/reprex")
412 (synopsis "Prepare reproducible R code examples for sharing")
414 "This package provides a convenience wrapper that uses the
415 @code{rmarkdown} package to render small snippets of code to target formats
416 that include both code and output. The goal is to encourage the sharing of
417 small, reproducible, and runnable examples on code-oriented websites or email.
418 @code{reprex} also extracts clean, runnable R code from various common formats,
419 such as copy/paste from an R session.")
420 (license license:expat)))
422 (define-public r-callr
429 (uri (cran-uri "callr" version))
432 "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr"))))
433 (build-system r-build-system)
436 ("r-processx" ,r-processx)))
437 (home-page "https://github.com/r-lib/callr#readme")
438 (synopsis "Call R from R")
440 "It is sometimes useful to perform a computation in a separate R process,
441 without affecting the current R process at all. This package does exactly
443 (license license:expat)))
445 (define-public r-readxl
452 (uri (cran-uri "readxl" version))
455 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
456 (build-system r-build-system)
458 `(("r-cellranger" ,r-cellranger)
459 ("r-progress" ,r-progress)
461 ("r-tibble" ,r-tibble)))
462 (home-page "https://readxl.tidyverse.org")
463 (synopsis "Read Excel files")
465 "This package lets you import Excel files into R. It supports
466 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
467 the embedded @code{RapidXML} C++ library.")
468 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
469 ;; 'rapidxml' which is Boost.
470 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
472 (define-public r-modelr
479 (uri (cran-uri "modelr" version))
482 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
483 (build-system r-build-system)
485 `(("r-broom" ,r-broom)
487 ("r-magrittr" ,r-magrittr)
490 ("r-tibble" ,r-tibble)
491 ("r-tidyr" ,r-tidyr)))
492 (home-page "https://github.com/tidyverse/modelr")
493 (synopsis "Helper functions for modelling in pipelines")
495 "Functions for modelling that help you seamlessly integrate modelling
496 into a pipeline of data manipulation and visualisation.")
497 (license license:gpl3)))
499 (define-public r-httpuv
505 (uri (cran-uri "httpuv" version))
508 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
509 (build-system r-build-system)
513 ("r-promises" ,r-promises)
516 (home-page "https://github.com/rstudio/httpuv")
517 (synopsis "HTTP and WebSocket server library for R")
519 "The httpuv package provides low-level socket and protocol support for
520 handling HTTP and WebSocket requests directly from within R. It is primarily
521 intended as a building block for other packages, rather than making it
522 particularly easy to create complete web applications using httpuv alone.")
523 ;; This package includes third-party code that was originally released
524 ;; under various non-copyleft licenses. Full licensing information can be
525 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
526 (license license:gpl3+)))
528 (define-public r-jsonlite
534 (uri (cran-uri "jsonlite" version))
537 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
538 (build-system r-build-system)
539 (home-page "http://arxiv.org/abs/1403.2805")
540 (synopsis "Robust, high performance JSON parser and generator for R")
542 "The jsonlite package provides a fast JSON parser and generator optimized
543 for statistical data and the web. It offers flexible, robust, high
544 performance tools for working with JSON in R and is particularly powerful for
545 building pipelines and interacting with a web API. In addition to converting
546 JSON data from/to R objects, jsonlite contains functions to stream, validate,
547 and prettify JSON data. The unit tests included with the package verify that
548 all edge cases are encoded and decoded consistently for use with dynamic data
549 in systems and applications.")
550 (license license:expat)))
552 (define-public r-servr
558 (uri (cran-uri "servr" version))
561 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
562 (build-system r-build-system)
564 `(("r-httpuv" ,r-httpuv)
565 ("r-jsonlite" ,r-jsonlite)
568 (home-page "https://github.com/yihui/servr")
569 (synopsis "Simple HTTP server to serve static files or dynamic documents")
571 "Servr provides an HTTP server in R to serve static files, or dynamic
572 documents that can be converted to HTML files (e.g., R Markdown) under a given
574 (license license:expat)))
576 (define-public r-htmltools
582 (uri (cran-uri "htmltools" version))
585 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
586 (build-system r-build-system)
588 `(("r-digest" ,r-digest)
590 ("r-rlang" ,r-rlang)))
591 (home-page "https://cran.r-project.org/web/packages/htmltools")
592 (synopsis "R tools for HTML")
594 "This package provides tools for HTML generation and output in R.")
595 (license license:expat)))
597 (define-public r-htmlwidgets
599 (name "r-htmlwidgets")
603 (uri (cran-uri "htmlwidgets" version))
606 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
607 (build-system r-build-system)
609 `(("r-htmltools" ,r-htmltools)
610 ("r-jsonlite" ,r-jsonlite)
612 (home-page "https://github.com/ramnathv/htmlwidgets")
613 (synopsis "HTML Widgets for R")
615 "HTML widgets is a framework for creating HTML widgets that render in
616 various contexts including the R console, R Markdown documents, and Shiny web
618 (license license:expat)))
620 (define-public r-htmltable
627 (uri (cran-uri "htmlTable" version))
630 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
631 (properties `((upstream-name . "htmlTable")))
632 (build-system r-build-system)
634 `(("r-checkmate" ,r-checkmate)
635 ("r-htmltools" ,r-htmltools)
636 ("r-htmlwidgets" ,r-htmlwidgets)
638 ("r-magrittr" ,r-magrittr)
639 ("r-rstudioapi" ,r-rstudioapi)
640 ("r-stringr" ,r-stringr)))
641 (home-page "http://gforge.se/packages/")
642 (synopsis "Advanced tables for Markdown/HTML")
644 "This package provides functions to build tables with advanced layout
645 elements such as row spanners, column spanners, table spanners, zebra
646 striping, and more. While allowing advanced layout, the underlying
647 CSS-structure is simple in order to maximize compatibility with word
648 processors such as LibreOffice. The package also contains a few text
649 formatting functions that help outputting text compatible with HTML or
651 (license license:gpl3+)))
653 (define-public r-curl
659 (uri (cran-uri "curl" version))
662 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
663 (build-system r-build-system)
666 (modify-phases %standard-phases
667 ;; The environment variable CURL_CA_BUNDLE is only respected when
668 ;; running Windows, so we disable the platform checks.
669 ;; This can be removed once the libcurl has been patched.
670 (add-after 'unpack 'allow-CURL_CA_BUNDLE
672 (substitute* "R/onload.R"
673 (("if \\(!grepl\\(\"mingw\".*")
675 (substitute* "src/handle.c"
676 (("#ifdef _WIN32") "#if 1"))
682 `(("pkg-config" ,pkg-config)))
683 (home-page "https://github.com/jeroenooms/curl")
684 (synopsis "HTTP client for R")
686 "The @code{curl()} and @code{curl_download()} functions provide highly
687 configurable drop-in replacements for base @code{url()} and
688 @code{download.file()} with better performance, support for encryption, gzip
689 compression, authentication, and other @code{libcurl} goodies. The core of
690 the package implements a framework for performing fully customized requests
691 where data can be processed either in memory, on disk, or streaming via the
692 callback or connection interfaces.")
693 (license license:expat)))
695 (define-public r-hwriter
702 (uri (cran-uri "hwriter" version))
705 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
706 (build-system r-build-system)
707 (home-page "https://cran.r-project.org/web/packages/hwriter")
708 (synopsis "Output R objects in HTML format")
710 "This package provides easy-to-use and versatile functions to output R
711 objects in HTML format.")
712 (license license:lgpl2.1+)))
714 (define-public r-rjson
721 (uri (cran-uri "rjson" version))
724 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
725 (build-system r-build-system)
726 (home-page "https://cran.r-project.org/web/packages/rjson")
727 (synopsis "JSON library for R")
729 "This package provides functions to convert R objects into JSON objects
731 (license license:gpl2+)))
733 (define-public r-fastmap
740 (uri (cran-uri "fastmap" version))
743 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
744 (properties `((upstream-name . "fastmap")))
745 (build-system r-build-system)
746 (home-page "https://r-lib.github.io/fastmap/")
747 (synopsis "Fast implementation of a key-value store")
749 "This package provides a fast implementation of a key-value store.
750 Environments are commonly used as key-value stores, but every time a new key
751 is used, it is added to R's global symbol table, causing a small amount of
752 memory leakage. This can be problematic in cases where many different keys
753 are used. Fastmap avoids this memory leak issue by implementing the map using
754 data structures in C++.")
755 (license license:expat)))
757 (define-public r-shiny
765 (url "https://github.com/rstudio/shiny.git")
766 (commit (string-append "v" version))))
767 (file-name (git-file-name name version))
770 "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
771 (build-system r-build-system)
773 `(#:modules ((guix build r-build-system)
774 (guix build minify-build-system)
777 #:imported-modules (,@%r-build-system-modules
778 (guix build minify-build-system))
780 (modify-phases (@ (guix build r-build-system) %standard-phases)
781 (add-after 'unpack 'replace-bundled-minified-JavaScript
782 (lambda* (#:key inputs #:allow-other-keys)
783 (let ((replace-file (lambda (old new)
784 (format #t "replacing ~a with ~a\n" old new)
787 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
788 ;; contain just data. They are not minified code, so we don't
790 (with-directory-excursion "inst/www/shared"
791 (replace-file "bootstrap/shim/respond.min.js"
792 (string-append (assoc-ref inputs "js-respond")
793 "/share/javascript/respond.min.js"))
794 (replace-file "bootstrap/shim/html5shiv.min.js"
795 (string-append (assoc-ref inputs "js-html5shiv")
796 "/share/javascript/html5shiv.min.js"))
797 (replace-file "json2-min.js"
798 (string-append (assoc-ref inputs "js-json2")
799 "/share/javascript/json2-min.js"))
800 (replace-file "strftime/strftime-min.js"
801 (string-append (assoc-ref inputs "js-strftime")
802 "/share/javascript/strftime.min.js"))
803 (replace-file "highlight/highlight.pack.js"
804 (string-append (assoc-ref inputs "js-highlight")
805 "/share/javascript/highlight.min.js"))
806 (replace-file "datatables/js/jquery.dataTables.min.js"
807 (string-append (assoc-ref inputs "js-datatables")
808 "/share/javascript/jquery.dataTables.min.js"))
809 (replace-file "selectize/js/selectize.min.js"
810 (string-append (assoc-ref inputs "js-selectize")
811 "/share/javascript/selectize.min.js"))
812 (replace-file "selectize/js/es5-shim.min.js"
813 (string-append (assoc-ref inputs "js-es5-shim")
814 "/share/javascript/es5-shim.min.js"))
815 (for-each (match-lambda
818 (minify source #:target target)))
819 '(("jqueryui/jquery-ui.js" .
820 "jqueryui/jquery-ui.min.js")
821 ("datepicker/js/bootstrap-datepicker.js" .
822 "datepicker/js/bootstrap-datepicker.min.js")
823 ("ionrangeslider/js/ion.rangeSlider.js" .
824 "ionrangeslider/js/ion.rangeSlider.min.js")
825 ("bootstrap/js/bootstrap.js" .
826 "bootstrap/js/bootstrap.min.js")
831 ("legacy/jquery.js" .
832 "legacy/jquery.min.js")
833 ("showdown/src/showdown.js" .
834 "showdown/compressed/showdown.js")))))
837 `(("r-crayon" ,r-crayon)
838 ("r-fastmap" ,r-fastmap)
839 ("r-httpuv" ,r-httpuv)
841 ("r-jsonlite" ,r-jsonlite)
842 ("r-xtable" ,r-xtable)
843 ("r-digest" ,r-digest)
844 ("r-htmltools" ,r-htmltools)
846 ("r-sourcetools" ,r-sourcetools)))
848 `(("js-datatables" ,js-datatables)
849 ("js-html5shiv" ,js-html5shiv)
850 ("js-json2" ,js-json2)
851 ("js-respond" ,js-respond)
852 ("js-selectize" ,js-selectize)
853 ("js-strftime" ,js-strftime)
854 ("js-highlight" ,js-highlight)
855 ("js-es5-shim" ,js-es5-shim)))
857 `(("uglify-js" ,uglify-js)))
858 (home-page "http://shiny.rstudio.com")
859 (synopsis "Easy interactive web applications with R")
861 "Makes it incredibly easy to build interactive web applications
862 with R. Automatic \"reactive\" binding between inputs and outputs and
863 extensive prebuilt widgets make it possible to build beautiful,
864 responsive, and powerful applications with minimal effort.")
865 (license license:artistic2.0)))
867 ;; This package includes minified JavaScript files. When upgrading please
868 ;; check that there are no new minified JavaScript files.
869 (define-public r-shinytree
876 (uri (cran-uri "shinyTree" version))
879 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
880 (modules '((guix build utils)))
883 ;; Delete minified JavaScript
884 (for-each delete-file
885 '("inst/www/jsTree-3.3.7/libs/require.js"
886 "inst/www/jsTree-3.3.7/libs/jquery.js"
887 "inst/www/jsTree-3.3.7/jstree.min.js"))
889 (properties `((upstream-name . "shinyTree")))
890 (build-system r-build-system)
892 `(#:modules ((guix build utils)
893 (guix build r-build-system)
897 (modify-phases %standard-phases
898 (add-after 'unpack 'replace-minified-javascript
899 (lambda* (#:key inputs #:allow-other-keys)
900 (with-directory-excursion "inst/www/jsTree-3.3.7/"
901 (symlink (string-append (assoc-ref inputs "js-requirejs")
902 "/share/javascript/require.min.js")
907 `((,(assoc-ref inputs "js-jquery")
911 (lambda (sources targets)
912 (for-each (lambda (source target)
913 (format #t "Processing ~a --> ~a~%"
915 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
916 (call-with-output-file target
918 (dump-port minified port)))))
922 `(("r-htmlwidgets" ,r-htmlwidgets)
923 ("r-jsonlite" ,r-jsonlite)
924 ("r-promises" ,r-promises)
926 ("r-stringr" ,r-stringr)))
928 `(("js-requirejs" ,js-requirejs)))
930 `(("uglify-js" ,uglify-js)
934 (uri "https://code.jquery.com/jquery-3.3.1.js")
937 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
938 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
939 (synopsis "jsTree bindings for Shiny")
941 "This package exposes R bindings to jsTree, a JavaScript library that
942 supports interactive trees, to enable rich, editable trees in Shiny.")
943 (license license:expat)))
945 (define-public r-shinydashboard
947 (name "r-shinydashboard")
951 (uri (cran-uri "shinydashboard" version))
954 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
955 (build-system r-build-system)
956 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
957 ;; Regenerate it from the included sources.
959 `(#:modules ((guix build utils)
960 (guix build r-build-system)
963 (modify-phases %standard-phases
964 (add-after 'unpack 'generate-minified-javascript
966 (with-directory-excursion "inst/AdminLTE"
967 (delete-file "app.min.js")
968 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
969 (call-with-output-file "app.min.js"
971 (dump-port minified port))))))))))
973 `(("r-htmltools" ,r-htmltools)
974 ("r-promises" ,r-promises)
975 ("r-shiny" ,r-shiny)))
977 `(("uglify-js" ,uglify-js)))
978 (home-page "http://rstudio.github.io/shinydashboard/")
979 (synopsis "Create dashboards with shiny")
980 (description "This package provides an extension to the Shiny web
981 application framework for R, making it easy to create attractive dashboards.")
982 ;; This package includes software that was released under the Expat
983 ;; license, but the whole package is released under GPL version 2 or
985 (license license:gpl2+)))
987 (define-public r-shinyfiles
989 (name "r-shinyfiles")
994 (uri (cran-uri "shinyFiles" version))
996 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
997 (properties `((upstream-name . "shinyFiles")))
998 (build-system r-build-system)
1001 ("r-htmltools" ,r-htmltools)
1002 ("r-jsonlite" ,r-jsonlite)
1003 ("r-shiny" ,r-shiny)
1004 ("r-tibble" ,r-tibble)))
1005 (home-page "https://github.com/thomasp85/shinyFiles")
1006 (synopsis "Server-side file system viewer for Shiny")
1008 "This package provides functionality for client-side navigation of the
1009 server side file system in shiny apps. In case the app is running locally
1010 this gives the user direct access to the file system without the need to
1011 \"download\" files to a temporary location. Both file and folder selection as
1012 well as file saving is available.")
1013 (license license:gpl2+)))
1015 (define-public r-shinythemes
1017 (name "r-shinythemes")
1022 (uri (cran-uri "shinythemes" version))
1025 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1026 (properties `((upstream-name . "shinythemes")))
1027 (build-system r-build-system)
1028 (propagated-inputs `(("r-shiny" ,r-shiny)))
1029 (home-page "http://rstudio.github.io/shinythemes/")
1030 (synopsis "Themes for Shiny")
1032 "This package provides themes for use with Shiny. It includes several
1033 Bootstrap themes, which are packaged for use with Shiny applications.")
1034 ;; The package is released under version 3 of the GPL, but it includes
1035 ;; source files that are covered by the Expat license. It also includes
1036 ;; fonts under SIL or the ASL.
1037 (license (list license:gpl3 license:expat
1038 license:silofl1.1 license:asl2.0))))
1040 ;; The package sources include minified variants of d3.js and non-minified
1041 ;; source code of d3-jetpack.
1042 (define-public r-d3r
1049 (uri (cran-uri "d3r" version))
1052 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1053 (build-system r-build-system)
1055 `(#:modules ((guix build utils)
1056 (guix build r-build-system)
1060 (modify-phases %standard-phases
1061 (add-after 'unpack 'process-javascript
1062 (lambda* (#:key inputs #:allow-other-keys)
1063 (with-directory-excursion "inst/www/d3/"
1067 `((,(assoc-ref inputs "d3.v3.js")
1068 "v3/dist/d3.min.js")
1069 (,(assoc-ref inputs "d3.v4.js")
1070 "v4/dist/d3.min.js")
1071 (,(assoc-ref inputs "d3.v5.js")
1072 "v5/dist/d3.min.js"))))
1073 (lambda (sources targets)
1074 (for-each (lambda (source target)
1075 (format #t "Processing ~a --> ~a~%"
1077 (delete-file target)
1078 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1079 (call-with-output-file target
1081 (dump-port minified port)))))
1085 `(("r-dplyr" ,r-dplyr)
1086 ("r-htmltools" ,r-htmltools)
1087 ("r-tidyr" ,r-tidyr)))
1089 `(("uglify-js" ,uglify-js)
1093 (uri "https://d3js.org/d3.v3.js")
1096 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1100 (uri "https://d3js.org/d3.v4.js")
1103 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1107 (uri "https://d3js.org/d3.v5.js")
1110 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1111 (home-page "https://github.com/timelyportfolio/d3r")
1112 (synopsis "d3.js utilities for R")
1114 "This package provides a suite of functions to help ease the use of the
1115 d3.js visualization library in R. These helpers include
1116 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1117 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1118 R objects into the JSON format that the d3.js library expects.")
1119 (license license:bsd-3)))
1121 ;; We use the latest commit here because the last release was in 2016 while
1122 ;; the latest commit was in 2018.
1123 (define-public r-sankeyd3
1124 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1128 (version (git-version "0.3.2" revision commit))
1133 (url "https://github.com/fbreitwieser/sankeyD3.git")
1135 (file-name (git-file-name name version))
1138 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1139 (build-system r-build-system)
1142 ("r-htmlwidgets" ,r-htmlwidgets)
1143 ("r-shiny" ,r-shiny)
1144 ("r-magrittr" ,r-magrittr)))
1145 (home-page "https://github.com/fbreitwieser/sankeyD3")
1146 (synopsis "Sankey network graphs from R")
1148 "This package provides an R library to generate Sankey network graphs
1149 in R and Shiny via the D3 visualization library.")
1150 ;; The R code is licensed under GPLv3+. It includes the non-minified
1151 ;; JavaScript source code of d3-sankey, which is released under the
1152 ;; 3-clause BSD license.
1153 (license (list license:gpl3+ license:bsd-3)))))
1155 (define-public r-crosstalk
1157 (name "r-crosstalk")
1162 (uri (cran-uri "crosstalk" version))
1165 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1166 (build-system r-build-system)
1168 `(("r-ggplot2" ,r-ggplot2)
1169 ("r-htmltools" ,r-htmltools)
1170 ("r-jsonlite" ,r-jsonlite)
1171 ("r-lazyeval" ,r-lazyeval)
1173 ("r-shiny" ,r-shiny)))
1174 (home-page "https://rstudio.github.io/crosstalk/")
1175 (synopsis "Inter-widget interactivity for HTML widgets")
1177 "This package provides building blocks for allowing HTML widgets to
1178 communicate with each other, with Shiny or without (i.e. static @code{.html}
1179 files). It currently supports linked brushing and filtering.")
1180 (license license:expat)))
1182 (define-public r-rook
1189 (uri (cran-uri "Rook" version))
1192 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1193 (properties `((upstream-name . "Rook")))
1194 (build-system r-build-system)
1195 (propagated-inputs `(("r-brew" ,r-brew)))
1196 (home-page "https://cran.r-project.org/web/packages/Rook")
1197 (synopsis "Web server interface for R")
1199 "This package contains the Rook specification and convenience software
1200 for building and running Rook applications. A Rook application is an R
1201 reference class object that implements a @code{call} method or an R closure
1202 that takes exactly one argument, an environment, and returns a list with three
1203 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1204 (license license:gpl2)))
1206 (define-public r-miniui
1213 (uri (cran-uri "miniUI" version))
1216 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1217 (properties `((upstream-name . "miniUI")))
1218 (build-system r-build-system)
1220 `(("r-htmltools" ,r-htmltools)
1221 ("r-shiny" ,r-shiny)))
1222 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1223 (synopsis "Shiny UI widgets for small screens")
1225 "This package provides UI widget and layout functions for writing Shiny apps that
1226 work well on small screens.")
1227 (license license:gpl3)))
1229 (define-public r-feather
1236 (uri (cran-uri "feather" version))
1239 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1240 (build-system r-build-system)
1244 ("r-tibble" ,r-tibble)))
1245 (home-page "https://github.com/wesm/feather")
1246 (synopsis "R Bindings to the Feather API")
1247 (description "Read and write feather files, a lightweight binary columnar
1248 data store designed for maximum speed.")
1249 (license license:asl2.0)))
1251 (define-public r-maps
1258 (uri (cran-uri "maps" version))
1261 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1262 (build-system r-build-system)
1263 (home-page "https://cran.r-project.org/web/packages/maps")
1264 (synopsis "Draw geographical maps")
1265 (description "This package provides an R module for display of maps.
1266 Projection code and larger maps are in separate packages (@code{mapproj} and
1268 (license license:gpl2)))
1270 (define-public r-mapproj
1277 (uri (cran-uri "mapproj" version))
1280 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1281 (build-system r-build-system)
1282 (propagated-inputs `(("r-maps" ,r-maps)))
1283 (home-page "https://cran.r-project.org/web/packages/mapproj")
1284 (synopsis "Map projection in R")
1285 (description "This package converts latitude/longitude into projected
1287 (license (list license:gpl2 ; The R interface
1288 (license:non-copyleft ; The C code
1289 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1290 "Lucent Public License Version 1.02")))))
1292 (define-public r-rgooglemaps
1294 (name "r-rgooglemaps")
1299 (uri (cran-uri "RgoogleMaps" version))
1302 "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7"))))
1303 (properties `((upstream-name . "RgoogleMaps")))
1304 (build-system r-build-system)
1305 (propagated-inputs `(("r-png" ,r-png)))
1306 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1307 (synopsis "Use Google Maps in R")
1308 (description "This package serves two purposes:
1310 @item Provide a comfortable R interface to query the Google server for static
1312 @item Use the map as a background image to overlay plots within R. This
1313 requires proper coordinate scaling.
1315 (license license:gpl2+)))
1317 (define-public r-geosphere
1319 (name "r-geosphere")
1324 (uri (cran-uri "geosphere" version))
1327 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1328 (build-system r-build-system)
1329 (propagated-inputs `(("r-sp" ,r-sp)))
1330 (home-page "https://cran.r-project.org/web/packages/geosphere")
1331 (synopsis "Spherical trigonometry")
1332 (description "This package computes spherical trigonometry for geographic
1333 applications. That is, compute distances and related measures for angular
1334 (longitude/latitude) locations.")
1335 (license license:gpl3+)))
1337 (define-public r-jpeg
1344 (uri (cran-uri "jpeg" version))
1347 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1348 (build-system r-build-system)
1349 (inputs `(("libjpeg" ,libjpeg)))
1350 (home-page "http://www.rforge.net/jpeg/")
1351 (synopsis "Read and write JPEG images with R")
1352 (description "This package provides a way to read, write and display
1353 bitmap images stored in the JPEG format with R. It can read and write both
1354 files and in-memory raw vectors.")
1355 (license license:gpl2+)))
1357 (define-public r-ggmap
1364 (uri (cran-uri "ggmap" version))
1367 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1368 (build-system r-build-system)
1370 `(("r-bitops" ,r-bitops)
1371 ("r-digest" ,r-digest)
1372 ("r-dplyr" ,r-dplyr)
1373 ("r-ggplot2" ,r-ggplot2)
1377 ("r-magrittr" ,r-magrittr)
1380 ("r-purrr" ,r-purrr)
1381 ("r-rgooglemaps" ,r-rgooglemaps)
1382 ("r-rjson" ,r-rjson)
1383 ("r-scales" ,r-scales)
1384 ("r-stringr" ,r-stringr)
1385 ("r-tibble" ,r-tibble)
1386 ("r-tidyr" ,r-tidyr)))
1387 (home-page "https://github.com/dkahle/ggmap")
1388 (synopsis "Spatial visualization with ggplot2")
1389 (description "This package provides a collection of functions to visualize
1390 spatial data and models on top of static maps from various online sources (e.g
1391 Google Maps and Stamen Maps). It includes tools common to those tasks,
1392 including functions for geolocation and routing.")
1393 (license license:gpl2)))
1395 (define-public r-haven
1402 (uri (cran-uri "haven" version))
1405 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1406 (build-system r-build-system)
1410 `(("r-forcats" ,r-forcats)
1413 ("r-rlang" ,r-rlang)
1414 ("r-readr" ,r-readr)
1415 ("r-tibble" ,r-tibble)
1416 ("r-tidyselect" ,r-tidyselect)))
1417 (home-page "https://haven.tidyverse.org")
1418 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1420 "This package lets you mport foreign statistical formats into R via the
1421 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1422 (license license:expat)))
1424 (define-public r-amap
1430 (uri (cran-uri "amap" version))
1433 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1434 (build-system r-build-system)
1436 `(("gfortran" ,gfortran)))
1437 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1438 (synopsis "Another multidimensional analysis package")
1439 (description "This package provides tools for clustering and principal
1440 component analysis (with robust methods, and parallelized functions).")
1441 (license license:gpl2+)))
1443 (define-public r-ape
1450 (uri (cran-uri "ape" version))
1453 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1454 (build-system r-build-system)
1456 `(("r-lattice" ,r-lattice)
1458 ("r-rcpp" ,r-rcpp)))
1459 (home-page "http://ape-package.ird.fr/")
1460 (synopsis "Analyses of phylogenetics and evolution")
1462 "This package provides functions for reading, writing, plotting, and
1463 manipulating phylogenetic trees, analyses of comparative data in a
1464 phylogenetic framework, ancestral character analyses, analyses of
1465 diversification and macroevolution, computing distances from DNA sequences,
1466 and several other tools.")
1467 (license license:gpl2+)))
1469 (define-public r-abbyyr
1476 (uri (cran-uri "abbyyR" version))
1479 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1480 (properties `((upstream-name . "abbyyR")))
1481 (build-system r-build-system)
1483 `(("r-curl" ,r-curl)
1486 ("r-progress" ,r-progress)
1487 ("r-readr" ,r-readr)
1489 (home-page "https://github.com/soodoku/abbyyR")
1490 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1492 "This package provides tools to get text from images of text using Abbyy
1493 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1494 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1495 passports and get the results in a variety of formats including plain text and
1496 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1497 (license license:expat)))
1499 (define-public r-colorspace
1501 (name "r-colorspace")
1506 (uri (cran-uri "colorspace" version))
1508 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1509 (build-system r-build-system)
1510 (home-page "https://cran.r-project.org/web/packages/colorspace")
1511 (synopsis "Color space manipulation")
1513 "This package carries out a mapping between assorted color spaces
1514 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1515 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1516 colors are provided.")
1517 (license license:bsd-3)))
1519 (define-public r-glue
1526 (uri (cran-uri "glue" version))
1529 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1530 (build-system r-build-system)
1531 (home-page "https://github.com/tidyverse/glue")
1532 (synopsis "Interpreted string literals")
1534 "This package provides an implementation of interpreted string literals,
1535 inspired by Python's Literal String Interpolation (PEP-0498) and
1536 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1537 (license license:expat)))
1539 (define-public r-pastecs
1545 (uri (cran-uri "pastecs" version))
1548 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1549 (build-system r-build-system)
1551 `(("r-boot" ,r-boot)))
1552 (home-page "http://www.sciviews.org/pastecs")
1553 (synopsis "Analysis of space-time ecological series")
1555 "This package provides functions for regulation, decomposition and analysis
1556 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1557 initiative to bring PASSTEC 2000 functionalities to R.")
1558 (license license:gpl2+)))
1560 (define-public r-plogr
1567 (uri (cran-uri "plogr" version))
1570 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1571 (build-system r-build-system)
1572 (home-page "https://github.com/krlmlr/plogr")
1573 (synopsis "R bindings for the plog C++ logging library")
1575 "This package provides the header files for a stripped-down version of
1576 the plog header-only C++ logging library, and a method to log to R's standard
1578 (license license:expat)))
1580 (define-public r-pls
1587 (uri (cran-uri "pls" version))
1589 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1590 (build-system r-build-system)
1591 (home-page "http://mevik.net/work/software/pls.html")
1592 (synopsis "Partial Least Squares and Principal Component Regression")
1594 "The pls package implements multivariate regression methods: Partial Least
1595 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1596 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1599 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1600 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1601 @item multi-response models (or @dfn{PLS2})
1602 @item flexible cross-validation
1603 @item Jackknife variance estimates of regression coefficients
1604 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1605 (R)MSEP, R², and correlation loadings
1606 @item formula interface, modelled after @code{lm()}, with methods for predict,
1607 print, summary, plot, update, etc.
1608 @item extraction functions for coefficients, scores, and loadings
1609 @item MSEP, RMSEP, and R² estimates
1610 @item multiplicative scatter correction (@dfn{MSC})
1612 (license license:gpl2)))
1621 (uri (cran-uri "ps" version))
1623 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1624 (build-system r-build-system)
1625 (home-page "http://ps.r-lib.org")
1626 (synopsis "List, query, and manipulate system processes")
1628 "The ps package implements an API to list, query, and manipulate system
1629 processes. Most of its code is based on the @code{psutil} Python package.")
1630 (license license:bsd-3)))
1632 (define-public r-pkgbuild
1639 (uri (cran-uri "pkgbuild" version))
1641 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1642 (build-system r-build-system)
1644 `(("r-callr" ,r-callr)
1646 ("r-crayon" ,r-crayon)
1648 ("r-prettyunits" ,r-prettyunits)
1650 ("r-rprojroot" ,r-rprojroot)
1651 ("r-withr" ,r-withr)))
1652 (home-page "https://github.com/r-pkgs/pkgbuild")
1653 (synopsis "Find tools needed to build R packages")
1655 "This package provides functions used to build R packages. It locates
1656 compilers needed to build R packages on various platforms and ensures the PATH
1657 is configured appropriately so R can use them.")
1658 (license license:gpl3)))
1660 (define-public r-pkgload
1667 (uri (cran-uri "pkgload" version))
1670 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1671 (build-system r-build-system)
1673 `(("r-desc" ,r-desc)
1674 ("r-pkgbuild" ,r-pkgbuild)
1675 ("r-rlang" ,r-rlang)
1676 ("r-rprojroot" ,r-rprojroot)
1677 ("r-rstudioapi" ,r-rstudioapi)
1678 ("r-withr" ,r-withr)))
1679 (home-page "https://github.com/r-lib/pkgload")
1680 (synopsis "Simulate package installation and attach")
1682 "This package simulates the process of installing a package and then
1683 attaching it. This is a key part of the @code{devtools} package as it allows
1684 you to rapidly iterate while developing a package.")
1685 (license license:gpl3)))
1687 (define-public r-rcpp
1694 (uri (cran-uri "Rcpp" version))
1696 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1697 (build-system r-build-system)
1699 `(("r-knitr" ,r-knitr))) ; for vignettes
1700 (home-page "http://www.rcpp.org")
1701 (synopsis "Seamless R and C++ integration")
1703 "The Rcpp package provides R functions as well as C++ classes which offer
1704 a seamless integration of R and C++. Many R data types and objects can be
1705 mapped back and forth to C++ equivalents which facilitates both writing of new
1706 code as well as easier integration of third-party libraries. Documentation
1707 about Rcpp is provided by several vignettes included in this package, via the
1708 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1709 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1710 @code{citation(\"Rcpp\")} for details on these last two.")
1711 (license license:gpl2+)))
1713 (define-public r-bindr
1720 (uri (cran-uri "bindr" version))
1723 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1724 (build-system r-build-system)
1725 (home-page "https://github.com/krlmlr/bindr")
1726 (synopsis "Parametrized active bindings")
1728 "This package provides a simple interface for creating active bindings
1729 where the bound function accepts additional arguments.")
1730 (license license:expat)))
1732 (define-public r-bindrcpp
1739 (uri (cran-uri "bindrcpp" version))
1742 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1743 (build-system r-build-system)
1745 `(("r-bindr" ,r-bindr)
1746 ("r-plogr" ,r-plogr)
1747 ("r-rcpp" ,r-rcpp)))
1748 (home-page "https://github.com/krlmlr/bindrcpp")
1749 (synopsis "Rcpp interface to active bindings")
1751 "This package provides an easy way to fill an environment with active
1752 bindings that call a C++ function.")
1753 (license license:expat)))
1755 (define-public r-auc
1762 (uri (cran-uri "AUC" version))
1765 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1766 (properties `((upstream-name . "AUC")))
1767 (build-system r-build-system)
1768 (home-page "https://cran.r-project.org/web/packages/AUC")
1769 (synopsis "Compute the area under the curve of selected measures")
1771 "This package includes functions to compute the area under the curve of
1772 selected measures: the area under the sensitivity curve (AUSEC), the area
1773 under the specificity curve (AUSPC), the area under the accuracy
1774 curve (AUACC), and the area under the receiver operating characteristic
1775 curve (AUROC). The curves can also be visualized. Support for partial areas
1777 (license license:gpl2+)))
1779 (define-public r-calibrate
1781 (name "r-calibrate")
1786 (uri (cran-uri "calibrate" version))
1788 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1789 (build-system r-build-system)
1791 `(("r-mass" ,r-mass)))
1792 (home-page "https://cran.r-project.org/web/packages/calibrate")
1793 (synopsis "Calibration of scatterplot and biplot axes")
1795 "This is a package for drawing calibrated scales with tick marks
1796 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1797 (license license:gpl2)))
1799 (define-public r-shape
1806 (uri (cran-uri "shape" version))
1809 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1810 (build-system r-build-system)
1811 (home-page "https://cran.r-project.org/web/packages/shape")
1812 (synopsis "Functions for plotting graphical shapes")
1814 "This package provides functions for plotting graphical shapes such as
1815 ellipses, circles, cylinders, arrows, ...")
1816 (license license:gpl3+)))
1818 (define-public r-globaloptions
1820 (name "r-globaloptions")
1825 (uri (cran-uri "GlobalOptions" version))
1827 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1828 (properties `((upstream-name . "GlobalOptions")))
1829 (build-system r-build-system)
1830 (home-page "https://github.com/jokergoo/GlobalOptions")
1831 (synopsis "Generate functions to get or set global options")
1833 "This package provides more controls on the option values such as
1834 validation and filtering on the values, making options invisible or private.")
1835 (license license:gpl2+)))
1837 (define-public r-circlize
1844 (uri (cran-uri "circlize" version))
1847 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1848 (build-system r-build-system)
1850 `(("r-colorspace" ,r-colorspace)
1851 ("r-globaloptions" ,r-globaloptions)
1852 ("r-shape" ,r-shape)))
1853 (home-page "https://github.com/jokergoo/circlize")
1854 (synopsis "Circular visualization")
1856 "Circular layout is an efficient way to visualise huge amounts of
1857 information. This package provides an implementation of circular layout
1858 generation in R as well as an enhancement of available software. Its
1859 flexibility is based on the usage of low-level graphics functions such that
1860 self-defined high-level graphics can be easily implemented by users for
1861 specific purposes. Together with the seamless connection between the powerful
1862 computational and visual environment in R, it gives users more convenience and
1863 freedom to design figures for better understanding complex patterns behind
1864 multi-dimensional data.")
1865 (license license:gpl2+)))
1867 (define-public r-powerlaw
1874 (uri (cran-uri "poweRlaw" version))
1877 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1878 (properties `((upstream-name . "poweRlaw")))
1879 (build-system r-build-system)
1881 `(("r-vgam" ,r-vgam)))
1882 (home-page "https://github.com/csgillespie/poweRlaw")
1883 (synopsis "Tools for the analysis of heavy tailed distributions")
1885 "This package provides an implementation of maximum likelihood estimators
1886 for a variety of heavy tailed distributions, including both the discrete and
1887 continuous power law distributions. Additionally, a goodness-of-fit based
1888 approach is used to estimate the lower cut-off for the scaling region.")
1889 ;; Any of these GPL versions.
1890 (license (list license:gpl2 license:gpl3))))
1892 (define-public r-compare
1899 (uri (cran-uri "compare" version))
1902 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1903 (build-system r-build-system)
1904 (home-page "https://cran.r-project.org/web/packages/compare")
1905 (synopsis "Comparing objects for differences")
1907 "This package provides functions to compare a model object to a
1908 comparison object. If the objects are not identical, the functions can be
1909 instructed to explore various modifications of the objects (e.g., sorting
1910 rows, dropping names) to see if the modified versions are identical.")
1911 (license license:gpl2+)))
1913 (define-public r-dendextend
1915 (name "r-dendextend")
1920 (uri (cran-uri "dendextend" version))
1923 "1iclvd9cyckd4djpa87ynm05fk6zl4b4m735za1w4irimc130m3r"))))
1924 (build-system r-build-system)
1926 `(("r-ggplot2" ,r-ggplot2)
1927 ("r-magrittr" ,r-magrittr)
1928 ("r-viridis" ,r-viridis)))
1929 (home-page "https://cran.r-project.org/web/packages/dendextend")
1930 (synopsis "Extending 'dendrogram' functionality in R")
1932 "This package offers a set of functions for extending @code{dendrogram}
1933 objects in R, letting you visualize and compare trees of hierarchical
1934 clusterings. You can adjust a tree's graphical parameters (the color, size,
1935 type, etc of its branches, nodes and labels) and visually and statistically
1936 compare different dendrograms to one another.")
1937 ;; Any of these versions
1938 (license (list license:gpl2 license:gpl3))))
1940 (define-public r-getoptlong
1942 (name "r-getoptlong")
1947 (uri (cran-uri "GetoptLong" version))
1950 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1951 (properties `((upstream-name . "GetoptLong")))
1952 (build-system r-build-system)
1956 `(("r-globaloptions" ,r-globaloptions)
1957 ("r-rjson" ,r-rjson)))
1958 (home-page "https://github.com/jokergoo/GetoptLong")
1959 (synopsis "Parsing command-line arguments and variable interpolation")
1961 "This is yet another command-line argument parser which wraps the
1962 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1963 use in R. It also provides a simple way for variable interpolation in R.")
1964 (license license:gpl2+)))
1966 (define-public r-fastmatch
1968 (name "r-fastmatch")
1973 (uri (cran-uri "fastmatch" version))
1976 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1977 (build-system r-build-system)
1978 (home-page "http://www.rforge.net/fastmatch")
1979 (synopsis "Fast match function")
1981 "This package provides a fast @code{match} replacement for cases that
1982 require repeated look-ups. It is slightly faster that R's built-in
1983 @code{match} function on first match against a table, but extremely fast on
1984 any subsequent lookup as it keeps the hash table in memory.")
1985 (license license:gpl2)))
1994 (uri (cran-uri "ff" version))
1997 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1998 (build-system r-build-system)
1999 (propagated-inputs `(("r-bit" ,r-bit)))
2000 (home-page "http://ff.r-forge.r-project.org/")
2001 (synopsis "Memory-efficient storage of large data on disk and access functions")
2003 "This package provides data structures that are stored on disk but
2004 behave (almost) as if they were in RAM by transparently mapping only a section
2006 ;; error Architecture not supported.
2007 (supported-systems (delete "aarch64-linux" %supported-systems))
2008 (license license:gpl2)))
2010 (define-public r-ffbase
2017 (uri (cran-uri "ffbase" version))
2020 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
2021 (build-system r-build-system)
2024 ("r-fastmatch" ,r-fastmatch)
2026 (home-page "http://github.com/edwindj/ffbase")
2027 (synopsis "Basic statistical functions for package 'ff'")
2029 "This package extends the out of memory vectors of @code{ff} with
2030 statistical functions and other utilities to ease their usage.")
2031 (license license:gpl3)))
2033 (define-public r-prettyunits
2035 (name "r-prettyunits")
2040 (uri (cran-uri "prettyunits" version))
2043 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
2044 (build-system r-build-system)
2046 `(("r-assertthat" ,r-assertthat)
2047 ("r-magrittr" ,r-magrittr)))
2048 (home-page "https://github.com/gaborcsardi/prettyunits")
2049 (synopsis "Pretty, human readable formatting of quantities")
2051 "This package provides tools for pretty, human readable formatting of
2053 (license license:expat)))
2055 (define-public r-reshape
2062 (uri (cran-uri "reshape" version))
2065 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2066 (build-system r-build-system)
2068 `(("r-plyr" ,r-plyr)
2069 ("r-rcpp" ,r-rcpp)))
2070 (home-page "http://had.co.nz/reshape")
2071 (synopsis "Flexibly reshape data")
2073 "Flexibly restructure and aggregate data using just two functions:
2074 @code{melt} and @code{cast}. This package provides them.")
2075 (license license:expat)))
2077 (define-public r-progress
2084 (uri (cran-uri "progress" version))
2087 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2088 (build-system r-build-system)
2090 `(("r-crayon" ,r-crayon)
2092 ("r-prettyunits" ,r-prettyunits)
2094 (home-page "https://github.com/gaborcsardi/progress")
2095 (synopsis "Terminal progress bars")
2097 "This package provides configurable progress bars. They may include
2098 percentage, elapsed time, and/or the estimated completion time. They work in
2099 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2100 package also provides a C++ API, that works with or without Rcpp.")
2101 (license license:expat)))
2103 (define-public r-ggally
2110 (uri (cran-uri "GGally" version))
2113 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2114 (properties `((upstream-name . "GGally")))
2115 (build-system r-build-system)
2117 `(("libressl" ,libressl)))
2119 `(("r-ggplot2" ,r-ggplot2)
2120 ("r-gtable" ,r-gtable)
2122 ("r-progress" ,r-progress)
2123 ("r-rcolorbrewer" ,r-rcolorbrewer)
2124 ("r-reshape" ,r-reshape)
2125 ("r-rlang" ,r-rlang)))
2126 (home-page "https://ggobi.github.io/ggally")
2127 (synopsis "Extension to ggplot2")
2129 "The R package ggplot2 is a plotting system based on the grammar of
2130 graphics. GGally extends ggplot2 by adding several functions to reduce the
2131 complexity of combining geometric objects with transformed data. Some of
2132 these functions include a pairwise plot matrix, a two group pairwise plot
2133 matrix, a parallel coordinates plot, a survival plot, and several functions to
2135 (license license:gpl2+)))
2137 (define-public r-proxy
2144 (uri (cran-uri "proxy" version))
2147 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2148 (build-system r-build-system)
2149 (home-page "https://cran.r-project.org/web/packages/proxy")
2150 (synopsis "Distance and similarity measures")
2152 "This package provides an extensible framework for the efficient
2153 calculation of auto- and cross-proximities, along with implementations of the
2154 most popular ones.")
2155 (license license:gpl2)))
2164 (uri (cran-uri "sp" version))
2166 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2167 (build-system r-build-system)
2169 `(("r-lattice" ,r-lattice)))
2170 (home-page "https://cran.r-project.org/web/packages/sp")
2171 (synopsis "Classes and methods for spatial data")
2173 "This package provides classes and methods for spatial data; the classes
2174 document where the spatial location information resides, for 2D or 3D data.
2175 Utility functions are provided, e.g. for plotting data as maps, spatial
2176 selection, as well as methods for retrieving coordinates, for subsetting,
2177 print, summary, etc.")
2178 (license license:gpl2+)))
2180 (define-public r-rmtstat
2187 (uri (cran-uri "RMTstat" version))
2190 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2191 (properties `((upstream-name . "RMTstat")))
2192 (build-system r-build-system)
2193 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2194 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2196 "This package provides functions for working with the Tracy-Widom laws
2197 and other distributions related to the eigenvalues of large Wishart
2199 (license license:bsd-3)))
2201 (define-public r-rmpi
2207 (uri (cran-uri "Rmpi" version))
2210 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2211 (properties `((upstream-name . "Rmpi")))
2212 (build-system r-build-system)
2214 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2215 #:phases (modify-phases %standard-phases
2216 (add-before 'install 'mpi-setup
2219 `(("openmpi" ,openmpi)))
2221 `(("pkg-config" ,pkg-config)))
2222 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2223 (synopsis "R interface to message-passing interface (MPI)")
2225 "This package provides an interface (wrapper) to MPI APIs. It also
2226 provides an interactive R manager and worker environment.")
2227 (license license:gpl2+)))
2229 (define-public r-lmoments
2236 (uri (cran-uri "Lmoments" version))
2239 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2240 (properties `((upstream-name . "Lmoments")))
2241 (build-system r-build-system)
2243 `(("r-rcpp" ,r-rcpp)
2244 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2245 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2246 (synopsis "L-moments and quantile mixtures")
2248 "This package contains functions to estimate L-moments and trimmed
2249 L-moments from the data. It also contains functions to estimate the
2250 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2251 quantile mixture from L-moments and trimmed L-moments.")
2252 (license license:gpl2)))
2254 (define-public r-distillery
2256 (name "r-distillery")
2261 (uri (cran-uri "distillery" version))
2264 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2265 (build-system r-build-system)
2266 (home-page "http://www.ral.ucar.edu/staff/ericg")
2267 (synopsis "Functions for confidence intervals and object information")
2269 "This package provides some very simple method functions for confidence
2270 interval calculation and to distill pertinent information from a potentially
2271 complex object; primarily used in common with the packages extRemes and
2273 (license license:gpl2+)))
2275 (define-public r-extremes
2282 (uri (cran-uri "extRemes" version))
2285 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2286 (properties `((upstream-name . "extRemes")))
2287 (build-system r-build-system)
2289 `(("r-distillery" ,r-distillery)
2290 ("r-lmoments" ,r-lmoments)))
2291 (home-page "http://www.assessment.ucar.edu/toolkit/")
2292 (synopsis "Extreme value analysis")
2294 "ExtRemes is a suite of functions for carrying out analyses on the
2295 extreme values of a process of interest; be they block maxima over long blocks
2296 or excesses over a high threshold.")
2297 (license license:gpl2+)))
2299 (define-public r-lmtest
2306 (uri (cran-uri "lmtest" version))
2309 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2310 (build-system r-build-system)
2312 `(("r-zoo" ,r-zoo)))
2314 `(("gfortran" ,gfortran)))
2315 (home-page "https://cran.r-project.org/web/packages/lmtest")
2316 (synopsis "Testing linear regression models")
2318 "This package provides a collection of tests, data sets, and examples for
2319 diagnostic checking in linear regression models. Furthermore, some generic
2320 tools for inference in parametric models are provided.")
2321 ;; Either version is okay
2322 (license (list license:gpl2 license:gpl3))))
2324 (define-public r-idr
2330 (uri (cran-uri "idr" version))
2333 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2334 (build-system r-build-system)
2335 (home-page "https://cran.r-project.org/web/packages/idr/")
2336 (synopsis "Irreproducible discovery rate")
2338 "This is a package for estimating the copula mixture model and plotting
2339 correspondence curves in \"Measuring reproducibility of high-throughput
2340 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2341 by Li, Brown, Huang, and Bickel")
2342 (license license:gpl2+)))
2344 (define-public r-inline
2350 (uri (cran-uri "inline" version))
2353 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2354 (build-system r-build-system)
2355 (home-page "https://cran.r-project.org/web/packages/inline")
2356 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2358 "This package provides functionality to dynamically define R functions
2359 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2360 @code{.Call} calling conventions.")
2361 ;; Any version of the LGPL.
2362 (license license:lgpl3+)))
2364 (define-public r-bdsmatrix
2366 (name "r-bdsmatrix")
2371 (uri (cran-uri "bdsmatrix" version))
2374 "17ddvz4gnih7rx0lr1gzk280xyh6x796cf2x794dvplpiiq83skh"))))
2375 (properties `((upstream-name . "bdsmatrix")))
2376 (build-system r-build-system)
2377 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2378 (synopsis "Routines for block diagonal symmetric matrices")
2380 "This package provides procedures to work with block diagonal symmetric
2381 matrices, a special case of sparse matrices.")
2382 (license license:lgpl2.0)))
2384 (define-public r-bbmle
2391 (uri (cran-uri "bbmle" version))
2394 "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4"))))
2395 (build-system r-build-system)
2397 `(("r-bdsmatrix" ,r-bdsmatrix)
2398 ("r-lattice" ,r-lattice)
2400 ("r-matrix" ,r-matrix)
2401 ("r-mvtnorm" ,r-mvtnorm)
2402 ("r-numderiv" ,r-numderiv)))
2403 (home-page "https://cran.r-project.org/web/packages/bbmle")
2404 (synopsis "Tools for General Maximum Likelihood Estimation")
2406 "This package provides methods and functions for fitting maximum
2407 likelihood models in R. This package modifies and extends the @code{mle}
2408 classes in the @code{stats4} package.")
2409 ;; Any version of the GPL
2410 (license license:gpl2+)))
2412 (define-public r-emdbook
2419 (uri (cran-uri "emdbook" version))
2422 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2423 (build-system r-build-system)
2425 `(("r-bbmle" ,r-bbmle)
2427 ("r-lattice" ,r-lattice)
2430 ("r-rcpp" ,r-rcpp)))
2431 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2432 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2434 "This package provides auxiliary functions and data sets for \"Ecological
2435 Models and Data\", a book presenting maximum likelihood estimation and related
2436 topics for ecologists (ISBN 978-0-691-12522-0).")
2438 (license (list license:gpl2 license:gpl3))))
2440 (define-public r-lpsolve
2443 (version "5.6.13.3")
2447 (uri (cran-uri "lpSolve" version))
2450 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2451 (properties `((upstream-name . "lpSolve")))
2452 (build-system r-build-system)
2453 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2454 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2456 "Lp_solve is software for solving linear, integer and mixed integer
2457 programs. This implementation supplies a \"wrapper\" function in C and some R
2458 functions that solve general linear/integer problems, assignment problems, and
2459 transportation problems.")
2460 (license license:lgpl2.0)))
2462 (define-public r-limsolve
2469 (uri (cran-uri "limSolve" version))
2472 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2473 (properties `((upstream-name . "limSolve")))
2474 (build-system r-build-system)
2476 `(("r-lpsolve" ,r-lpsolve)
2478 ("r-quadprog" ,r-quadprog)))
2479 (native-inputs `(("gfortran" ,gfortran)))
2480 (home-page "https://cran.r-project.org/web/packages/limSolve")
2481 (synopsis "Solving linear inverse models")
2483 "This package provides functions that:
2486 @item find the minimum/maximum of a linear or quadratic function,
2487 @item sample an underdetermined or overdetermined system,
2488 @item solve a linear system Ax=B for the unknown x.
2491 It includes banded and tridiagonal linear systems. The package calls Fortran
2492 functions from LINPACK.")
2494 (license (list license:gpl2+ license:gpl3+))))
2496 (define-public r-fitdistrplus
2498 (name "r-fitdistrplus")
2503 (uri (cran-uri "fitdistrplus" version))
2506 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2507 (build-system r-build-system)
2509 `(("r-mass" ,r-mass)
2510 ("r-npsurv" ,r-npsurv)
2511 ("r-survival" ,r-survival)))
2512 (home-page "http://riskassessment.r-forge.r-project.org")
2513 (synopsis "Fitting a parametric distribution from data")
2515 "This package extends the @code{fitdistr} function of the MASS package
2516 with several functions to help the fit of a parametric distribution to
2517 non-censored or censored data. Censored data may contain left-censored,
2518 right-censored and interval-censored values, with several lower and upper
2519 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2520 provides moment matching (MME), quantile matching (QME) and maximum
2521 goodness-of-fit estimation (MGE) methods (available only for non-censored
2522 data). Weighted versions of MLE, MME and QME are available.")
2523 (license license:gpl2+)))
2525 (define-public r-energy
2532 (uri (cran-uri "energy" version))
2535 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2536 (build-system r-build-system)
2538 `(("r-boot" ,r-boot)
2539 ("r-rcpp" ,r-rcpp)))
2540 (home-page "https://cran.r-project.org/web/packages/energy")
2541 (synopsis "Multivariate inference via the energy of data")
2543 "This package provides e-statistics (energy) tests and statistics for
2544 multivariate and univariate inference, including distance correlation,
2545 one-sample, two-sample, and multi-sample tests for comparing multivariate
2546 distributions, are implemented. Measuring and testing multivariate
2547 independence based on distance correlation, partial distance correlation,
2548 multivariate goodness-of-fit tests, clustering based on energy distance,
2549 testing for multivariate normality, distance components (disco) for
2550 non-parametric analysis of structured data, and other energy
2551 statistics/methods are implemented.")
2552 (license license:gpl2+)))
2554 (define-public r-suppdists
2556 (name "r-suppdists")
2561 (uri (cran-uri "SuppDists" version))
2564 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2565 (properties `((upstream-name . "SuppDists")))
2566 (build-system r-build-system)
2567 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2568 (synopsis "Supplementary distributions")
2570 "This package provides ten distributions supplementing those built into
2571 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2572 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2573 coefficient, Johnson distributions, normal scores and generalized
2574 hypergeometric distributions. In addition two random number generators of
2575 George Marsaglia are included.")
2576 (license license:gpl2+)))
2578 (define-public r-ksamples
2585 (uri (cran-uri "kSamples" version))
2588 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2589 (properties `((upstream-name . "kSamples")))
2590 (build-system r-build-system)
2592 `(("r-suppdists" ,r-suppdists)))
2593 (home-page "https://cran.r-project.org/web/packages/kSamples")
2594 (synopsis "K-Sample rank tests and their combinations")
2596 "This package provides tools to compares k samples using the
2597 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2598 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2599 test. It computes asymptotic, simulated or (limited) exact P-values, all
2600 valid under randomization, with or without ties, or conditionally under random
2601 sampling from populations, given the observed tie pattern. Except for Steel's
2602 test and the JT test it also combines these tests across several blocks of
2604 (license license:gpl2+)))
2606 (define-public r-cvst
2613 (uri (cran-uri "CVST" version))
2616 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2617 (properties `((upstream-name . "CVST")))
2618 (build-system r-build-system)
2620 `(("r-kernlab" ,r-kernlab)
2621 ("r-matrix" ,r-matrix)))
2622 (home-page "https://cran.r-project.org/web/packages/CVST")
2623 (synopsis "Fast cross-validation via sequential testing")
2625 "This package implements the fast cross-validation via sequential
2626 testing (CVST) procedure. CVST is an improved cross-validation procedure
2627 which uses non-parametric testing coupled with sequential analysis to
2628 determine the best parameter set on linearly increasing subsets of the data.
2629 Additionally to the CVST the package contains an implementation of the
2630 ordinary k-fold cross-validation with a flexible and powerful set of helper
2631 objects and methods to handle the overall model selection process. The
2632 implementations of the Cochran's Q test with permutations and the sequential
2633 testing framework of Wald are generic and can therefore also be used in other
2635 (license license:gpl2+)))
2637 (define-public r-squarem
2640 (version "2017.10-1")
2644 (uri (cran-uri "SQUAREM" version))
2647 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2648 (properties `((upstream-name . "SQUAREM")))
2649 (build-system r-build-system)
2650 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2651 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2653 "This package provides algorithms for accelerating the convergence of
2654 slow, monotone sequences from smooth, contraction mapping such as the EM
2655 algorithm. It can be used to accelerate any smooth, linearly convergent
2656 acceleration scheme. A tutorial style introduction to this package is
2657 available in a vignette.")
2658 (license license:gpl2+)))
2660 (define-public r-lava
2667 (uri (cran-uri "lava" version))
2670 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2671 (build-system r-build-system)
2673 `(("r-numderiv" ,r-numderiv)
2674 ("r-squarem" ,r-squarem)
2675 ("r-survival" ,r-survival)))
2676 (home-page "https://github.com/kkholst/lava")
2677 (synopsis "Latent variable models")
2679 "This package provides tools for the estimation and simulation of latent
2681 (license license:gpl3)))
2683 (define-public r-drr
2690 (uri (cran-uri "DRR" version))
2693 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2694 (properties `((upstream-name . "DRR")))
2695 (build-system r-build-system)
2697 `(("r-cvst" ,r-cvst)
2698 ("r-kernlab" ,r-kernlab)
2699 ("r-matrix" ,r-matrix)))
2700 (home-page "https://cran.r-project.org/web/packages/DRR")
2701 (synopsis "Dimensionality reduction via regression")
2703 "This package provides an implementation of dimensionality reduction via
2704 regression using Kernel Ridge Regression.")
2705 (license license:gpl3)))
2707 (define-public r-prodlim
2710 (version "2019.11.13")
2714 (uri (cran-uri "prodlim" version))
2717 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2718 (build-system r-build-system)
2720 `(("r-kernsmooth" ,r-kernsmooth)
2723 ("r-survival" ,r-survival)))
2724 (home-page "https://cran.r-project.org/web/packages/prodlim")
2725 (synopsis "Product-limit estimation for censored event history analysis")
2727 "This package provides a fast and user-friendly implementation of
2728 nonparametric estimators for censored event history (survival) analysis with
2729 the Kaplan-Meier and Aalen-Johansen methods.")
2730 (license license:gpl2+)))
2732 (define-public r-dimred
2739 (uri (cran-uri "dimRed" version))
2742 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2743 (properties `((upstream-name . "dimRed")))
2744 (build-system r-build-system)
2747 ("r-magrittr" ,r-magrittr)))
2748 (home-page "https://github.com/gdkrmr/dimRed")
2749 (synopsis "Framework for dimensionality reduction")
2751 "This package provides a collection of dimensionality reduction
2752 techniques from R packages and provides a common interface for calling the
2754 (license license:gpl3)))
2756 (define-public r-timedate
2759 (version "3043.102")
2763 (uri (cran-uri "timeDate" version))
2766 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2767 (properties `((upstream-name . "timeDate")))
2768 (build-system r-build-system)
2769 (home-page "https://www.rmetrics.org")
2770 (synopsis "Chronological and calendar objects")
2772 "This package provides an environment for teaching \"Financial
2773 Engineering and Computational Finance\" and for managing chronological and
2775 (license license:gpl2+)))
2777 (define-public r-magic
2784 (uri (cran-uri "magic" version))
2787 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2788 (build-system r-build-system)
2790 `(("r-abind" ,r-abind)))
2791 (home-page "https://github.com/RobinHankin/magic.git")
2792 (synopsis "Create and investigate magic squares")
2794 "This package provides a collection of efficient, vectorized algorithms
2795 for the creation and investigation of magic squares and hypercubes, including
2796 a variety of functions for the manipulation and analysis of arbitrarily
2797 dimensioned arrays.")
2798 (license license:gpl2)))
2800 (define-public r-rmysql
2807 (uri (cran-uri "RMySQL" version))
2810 "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4"))))
2811 (properties `((upstream-name . "RMySQL")))
2812 (build-system r-build-system)
2814 `(("mariadb" ,mariadb "lib")
2815 ("mariadb-dev" ,mariadb "dev")
2818 `(("r-dbi" ,r-dbi)))
2819 (home-page "https://github.com/r-dbi/RMySQL")
2820 (synopsis "Database interface and MySQL driver for R")
2822 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2823 package contains an old implementation based on legacy code from S-PLUS which
2824 is being phased out. A modern MySQL client based on Rcpp is available from
2825 the RMariaDB package.")
2826 (license license:gpl2)))
2828 (define-public r-rpostgresql
2830 (name "r-rpostgresql")
2835 (uri (cran-uri "RPostgreSQL" version))
2838 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2839 (properties `((upstream-name . "RPostgreSQL")))
2840 (build-system r-build-system)
2842 `(("postgresql" ,postgresql)))
2844 `(("r-dbi" ,r-dbi)))
2845 (home-page "https://github.com/tomoakin/RPostgreSQL")
2846 (synopsis "R interface to the PostgreSQL database system")
2848 "This package provides a Database Interface (DBI) compliant driver for R
2849 to access PostgreSQL database systems.")
2850 ;; The whole package is released under GPL version 2. It includes code
2851 ;; under the PostgreSQL license.
2852 (license license:gpl2)))
2854 (define-public r-linprog
2861 (uri (cran-uri "linprog" version))
2864 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2865 (build-system r-build-system)
2866 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2867 (home-page "http://linprog.r-forge.r-project.org/")
2868 (synopsis "Linear programming and optimization")
2870 "This package can be used to solve Linear Programming / Linear
2871 Optimization problems by using the simplex algorithm.")
2872 (license license:gpl2+)))
2874 (define-public r-geometry
2881 (uri (cran-uri "geometry" version))
2884 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2885 (build-system r-build-system)
2887 `(("r-magic" ,r-magic)
2888 ("r-linprog" ,r-linprog)
2889 ("r-lpsolve" ,r-lpsolve)
2891 ("r-rcppprogress" ,r-rcppprogress)))
2892 (home-page "http://geometry.r-forge.r-project.org/")
2893 (synopsis "Mesh generation and surface tesselation")
2895 "This package makes the qhull library available in R, in a similar manner
2896 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2897 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2898 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2899 and higher dimensions. It implements the Quickhull algorithm for computing
2900 the convex hull. Qhull does not support constrained Delaunay triangulations,
2901 or mesh generation of non-convex objects, but the package does include some R
2902 functions that allow for this. Currently the package only gives access to
2903 Delaunay triangulation and convex hull computation.")
2904 ;; The Qhull sources are included and are distributed under a custom
2905 ;; non-copyleft license. The R sources are released under GPL version 2.
2906 (license (list license:gpl2
2907 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2909 (define-public r-ddalpha
2916 (uri (cran-uri "ddalpha" version))
2919 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2920 (build-system r-build-system)
2923 ("r-class" ,r-class)
2924 ("r-geometry" ,r-geometry)
2927 ("r-robustbase" ,r-robustbase)
2928 ("r-sfsmisc" ,r-sfsmisc)))
2930 `(("gfortran" ,gfortran)))
2931 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2932 (synopsis "Depth-Based classification and calculation of data depth")
2934 "This package contains procedures for depth-based supervised learning,
2935 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2936 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2937 statistical depth function to a compact low-dimensional space, where the final
2938 classification is done. It also offers an extension to functional data and
2939 routines for calculating certain notions of statistical depth functions. 50
2940 multivariate and 5 functional classification problems are included.")
2941 (license license:gpl2)))
2943 (define-public r-gower
2950 (uri (cran-uri "gower" version))
2953 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2954 (build-system r-build-system)
2955 (home-page "https://github.com/markvanderloo/gower")
2956 (synopsis "Gower's distance")
2958 "This package provides tools to compute Gower's distance (or similarity)
2959 coefficient between records, and to compute the top-n matches between records.
2960 Core algorithms are executed in parallel on systems supporting OpenMP.")
2961 (license license:gpl3)))
2963 (define-public r-rcpproll
2970 (uri (cran-uri "RcppRoll" version))
2973 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2974 (properties `((upstream-name . "RcppRoll")))
2975 (build-system r-build-system)
2977 `(("r-rcpp" ,r-rcpp)))
2978 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2979 (synopsis "Efficient rolling and windowed operations")
2981 "This package provides fast and efficient routines for common rolling /
2982 windowed operations. Routines for the efficient computation of windowed mean,
2983 median, sum, product, minimum, maximum, standard deviation and variance are
2985 (license license:gpl2+)))
2987 (define-public r-ipred
2994 (uri (cran-uri "ipred" version))
2997 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2998 (build-system r-build-system)
3000 `(("r-class" ,r-class)
3003 ("r-prodlim" ,r-prodlim)
3004 ("r-rpart" ,r-rpart)
3005 ("r-survival" ,r-survival)))
3006 (home-page "https://cran.r-project.org/web/packages/ipred")
3007 (synopsis "Improved predictors")
3009 "This package provides improved predictive models by indirect
3010 classification and bagging for classification, regression and survival
3011 problems as well as resampling based estimators of prediction error.")
3012 (license license:gpl2+)))
3014 (define-public r-psych
3021 (uri (cran-uri "psych" version))
3024 "13r7fyjsl93m121awnwfhya8a0lw0l2byn60yqdbf9gp3lmb9ny0"))))
3025 (build-system r-build-system)
3027 `(("r-foreign" ,r-foreign)
3028 ("r-lattice" ,r-lattice)
3029 ("r-mnormt" ,r-mnormt)
3030 ("r-nlme" ,r-nlme)))
3031 (home-page "https://cran.r-project.org/web/packages/psych/")
3032 (synopsis "Procedures for psychological, psychometric, and personality research")
3034 "This package provides a general purpose toolbox for personality,
3035 psychometric theory and experimental psychology. Functions are primarily for
3036 multivariate analysis and scale construction using factor analysis, principal
3037 component analysis, cluster analysis and reliability analysis, although others
3038 provide basic descriptive statistics. Item Response Theory is done using
3039 factor analysis of tetrachoric and polychoric correlations. Functions for
3040 analyzing data at multiple levels include within and between group statistics,
3041 including correlations and factor analysis. Functions for simulating and
3042 testing particular item and test structures are included. Several functions
3043 serve as a useful front end for structural equation modeling. Graphical
3044 displays of path diagrams, factor analysis and structural equation models are
3045 created using basic graphics.")
3046 (license license:gpl2+)))
3048 (define-public r-generics
3055 (uri (cran-uri "generics" version))
3058 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3059 (build-system r-build-system)
3060 (home-page "https://github.com/r-lib/generics")
3061 (synopsis "Common S3 generics not provided by base R methods")
3063 "In order to reduce potential package dependencies and conflicts,
3064 generics provides a number of commonly used S3 generics that are not provided
3065 by base R methods related to model fitting.")
3066 (license license:gpl2)))
3068 (define-public r-broom
3075 (uri (cran-uri "broom" version))
3078 "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d"))))
3079 (build-system r-build-system)
3081 `(("r-backports" ,r-backports)
3082 ("r-dplyr" ,r-dplyr)
3083 ("r-generics" ,r-generics)
3085 ("r-purrr" ,r-purrr)
3086 ("r-reshape2" ,r-reshape2)
3087 ("r-stringr" ,r-stringr)
3088 ("r-tibble" ,r-tibble)
3089 ("r-tidyr" ,r-tidyr)))
3090 (home-page "https://github.com/tidyverse/broom")
3091 (synopsis "Convert statistical analysis objects into tidy data frames")
3093 "This package provides tools to convert statistical analysis objects from
3094 R into tidy data frames, so that they can more easily be combined, reshaped
3095 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3096 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3097 summarizes a model's statistical findings such as coefficients of a
3098 regression; @code{augment}, which adds columns to the original data such as
3099 predictions, residuals and cluster assignments; and @code{glance}, which
3100 provides a one-row summary of model-level statistics.")
3101 (license license:expat)))
3103 (define-public r-recipes
3110 (uri (cran-uri "recipes" version))
3113 "1n32qc2a3n9cykm8dv9qcr77kdhqfsjiqf6kgfk9s0lnpx2zaldm"))))
3114 (build-system r-build-system)
3116 `(("r-dplyr" ,r-dplyr)
3117 ("r-generics" ,r-generics)
3119 ("r-gower" ,r-gower)
3120 ("r-ipred" ,r-ipred)
3121 ("r-lubridate" ,r-lubridate)
3122 ("r-magrittr" ,r-magrittr)
3123 ("r-matrix" ,r-matrix)
3124 ("r-purrr" ,r-purrr)
3125 ("r-rlang" ,r-rlang)
3126 ("r-tibble" ,r-tibble)
3127 ("r-tidyr" ,r-tidyr)
3128 ("r-tidyselect" ,r-tidyselect)
3129 ("r-timedate" ,r-timedate)
3130 ("r-withr" ,r-withr)))
3131 (home-page "https://github.com/topepo/recipes")
3132 (synopsis "Preprocessing tools to create design matrices")
3134 "Recipes is an extensible framework to create and preprocess design
3135 matrices. Recipes consist of one or more data manipulation and analysis
3136 \"steps\". Statistical parameters for the steps can be estimated from an
3137 initial data set and then applied to other data sets. The resulting design
3138 matrices can then be used as inputs into statistical or machine learning
3140 (license license:gpl2)))
3142 (define-public r-pdist
3149 (uri (cran-uri "pdist" version))
3152 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3153 (build-system r-build-system)
3154 (home-page "https://github.com/jeffwong/pdist")
3155 (synopsis "Partitioned distance function")
3157 "Pdist computes the euclidean distance between rows of a matrix X and
3158 rows of another matrix Y. Previously, this could be done by binding the two
3159 matrices together and calling @code{dist}, but this creates unnecessary
3160 computation by computing the distances between a row of X and another row of
3161 X, and likewise for Y. Pdist strictly computes distances across the two
3162 matrices, not within the same matrix, making computations significantly faster
3163 for certain use cases.")
3164 (license license:gpl3+)))
3166 (define-public r-ggrepel
3173 (uri (cran-uri "ggrepel" version))
3176 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3177 (build-system r-build-system)
3179 `(("r-ggplot2" ,r-ggplot2)
3181 ("r-scales" ,r-scales)))
3182 (home-page "http://github.com/slowkow/ggrepel")
3183 (synopsis "Repulsive text and label geometries for ggplot2")
3185 "This package provides text and label geometries for ggplot2 that help to
3186 avoid overlapping text labels. Labels repel away from each other and away
3187 from the data points.")
3188 (license license:gpl3)))
3190 (define-public r-corrplot
3197 (uri (cran-uri "corrplot" version))
3200 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3201 (build-system r-build-system)
3202 (home-page "https://github.com/taiyun/corrplot")
3203 (synopsis "Visualization of a correlation matrix")
3205 "This package provides a graphical display of a correlation matrix or
3206 general matrix. It also contains some algorithms to do matrix reordering. In
3207 addition, corrplot is good at details, including choosing color, text labels,
3208 color labels, layout, etc.")
3209 ;; Any version of the GPL
3210 (license license:gpl2+)))
3212 (define-public r-stringdist
3214 (name "r-stringdist")
3219 (uri (cran-uri "stringdist" version))
3221 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3222 (build-system r-build-system)
3223 (home-page "https://github.com/markvanderloo/stringdist")
3224 (synopsis "Approximate string matching and string distance functions")
3226 "This package implements an approximate string matching version of R's
3227 native @code{match} function. It can calculate various string distances based
3228 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3229 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3230 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3231 can be computed between character vectors while taking proper care of encoding
3232 or between integer vectors representing generic sequences.")
3233 (license license:gpl3+)))
3235 (define-public r-ucminf
3242 (uri (cran-uri "ucminf" version))
3245 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3246 (build-system r-build-system)
3247 (native-inputs `(("gfortran" ,gfortran)))
3248 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3249 (synopsis "General-purpose unconstrained non-linear optimization")
3251 "This package provides an implementation of an algorithm for
3252 general-purpose unconstrained non-linear optimization. The algorithm is of
3253 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3254 search with a trust region type monitoring of the input to the line search
3255 algorithm. The interface of @code{ucminf} is designed for easy interchange
3256 with the package @code{optim}.")
3257 (license license:gpl2+)))
3259 (define-public r-ordinal
3262 (version "2019.12-10")
3266 (uri (cran-uri "ordinal" version))
3269 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3270 (build-system r-build-system)
3272 `(("r-mass" ,r-mass)
3273 ("r-matrix" ,r-matrix)
3274 ("r-numderiv" ,r-numderiv)
3275 ("r-ucminf" ,r-ucminf)))
3276 (home-page "https://github.com/runehaubo/ordinal")
3277 (synopsis "Regression models for ordinal data")
3279 "This package provides an implementation of cumulative link (mixed)
3280 models also known as ordered regression models, proportional odds models,
3281 proportional hazards models for grouped survival times and ordered models.
3282 Estimation is via maximum likelihood and mixed models are fitted with the
3283 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3284 (license license:gpl2+)))
3286 (define-public r-jomo
3293 (uri (cran-uri "jomo" version))
3296 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3297 (build-system r-build-system)
3299 `(("r-lme4" ,r-lme4)
3301 ("r-ordinal" ,r-ordinal)
3302 ("r-survival" ,r-survival)))
3303 (home-page "https://cran.r-project.org/web/packages/jomo/")
3304 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3306 "Similarly to Schafer's package pan, jomo is a package for multilevel
3307 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3308 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3309 possibility of handling binary and categorical data through latent normal
3310 variables, the option to use cluster-specific covariance matrices and to
3311 impute compatibly with the substantive model.")
3312 (license license:gpl2)))
3314 (define-public r-pan
3321 (uri (cran-uri "pan" version))
3324 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3325 (build-system r-build-system)
3326 (native-inputs `(("gfortran" ,gfortran)))
3327 (home-page "https://cran.r-project.org/web/packages/pan/")
3328 (synopsis "Multiple imputation for multivariate panel or clustered data")
3330 "This package implements multiple imputation for multivariate panel or
3332 (license license:gpl3)))
3334 (define-public r-mitml
3341 (uri (cran-uri "mitml" version))
3344 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3345 (build-system r-build-system)
3347 `(("r-haven" ,r-haven)
3350 (home-page "https://cran.r-project.org/web/packages/mitml/")
3351 (synopsis "Tools for multiple imputation in multilevel modeling")
3353 "This package provides tools for multiple imputation of missing data in
3354 multilevel modeling. It includes a user-friendly interface to the packages
3355 pan and jomo, and several functions for visualization, data management and the
3356 analysis of multiply imputed data sets.")
3357 (license license:gpl2+)))
3359 (define-public r-mice
3366 (uri (cran-uri "mice" version))
3369 "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf"))))
3370 (build-system r-build-system)
3372 `(("r-broom" ,r-broom)
3373 ("r-dplyr" ,r-dplyr)
3374 ("r-lattice" ,r-lattice)
3376 ("r-mitml" ,r-mitml)
3379 ("r-rlang" ,r-rlang)
3380 ("r-rpart" ,r-rpart)
3381 ("r-survival" ,r-survival)))
3382 (home-page "https://cran.r-project.org/web/packages/mice/")
3383 (synopsis "Multivariate imputation by chained equations")
3385 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3386 implemented by the MICE algorithm as described in @url{Van Buuren and
3387 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3388 variable has its own imputation model. Built-in imputation models are
3389 provided for continuous data (predictive mean matching, normal), binary
3390 data (logistic regression), unordered categorical data (polytomous logistic
3391 regression) and ordered categorical data (proportional odds). MICE can also
3392 impute continuous two-level data (normal model, pan, second-level variables).
3393 Passive imputation can be used to maintain consistency between variables.
3394 Various diagnostic plots are available to inspect the quality of the
3396 ;; Any of these two versions.
3397 (license (list license:gpl2 license:gpl3))))
3399 (define-public r-truncnorm
3401 (name "r-truncnorm")
3406 (uri (cran-uri "truncnorm" version))
3409 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3410 (build-system r-build-system)
3411 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3412 (synopsis "Truncated normal distribution")
3413 (description "This package provides functions for the truncated normal
3414 distribution with mean equal to @code{mean} and standard deviation equal to
3415 @code{sd}. It includes density, distribution, quantile, and expected value
3416 functions, as well as a random generation function.")
3417 (license license:gpl2)))
3419 (define-public r-rsolnp
3426 (uri (cran-uri "Rsolnp" version))
3429 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3430 (properties `((upstream-name . "Rsolnp")))
3431 (build-system r-build-system)
3433 `(("r-truncnorm" ,r-truncnorm)))
3434 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3435 (synopsis "General non-linear optimization")
3436 (description "The Rsolnp package implements a general non-linear augmented
3437 Lagrange multiplier method solver, a @dfn{sequential quadratic
3438 programming} (SQP) based solver).")
3439 ;; Any version of the GPL.
3440 (license license:gpl2+)))
3442 (define-public r-hardyweinberg
3444 (name "r-hardyweinberg")
3449 (uri (cran-uri "HardyWeinberg" version))
3452 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3453 (properties `((upstream-name . "HardyWeinberg")))
3454 (build-system r-build-system)
3456 `(("r-mice" ,r-mice)
3458 ("r-rsolnp" ,r-rsolnp)))
3459 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3460 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3462 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3463 diallelic genetic marker data. All classical tests (chi-square, exact,
3464 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3465 included in the package, as well as functions for power computation and for
3466 the simulation of marker data under equilibrium and disequilibrium. Routines
3467 for dealing with markers on the X-chromosome are included. Functions for
3468 testing equilibrium in the presence of missing data by using multiple
3469 imputation are also provided. Implements several graphics for exploring the
3470 equilibrium status of a large set of diallelic markers: ternary plots with
3471 acceptance regions, log-ratio plots and Q-Q plots.")
3472 (license license:gpl2+)))
3481 (uri (cran-uri "sm" version))
3484 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3485 (build-system r-build-system)
3486 (native-inputs `(("gfortran" ,gfortran)))
3487 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3488 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3490 "This is software accompanying the book 'Applied Smoothing Techniques for
3491 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3492 University Press. It provides smoothing methods for nonparametric regression
3493 and density estimation")
3494 (license license:gpl2+)))
3496 (define-public r-venndiagram
3498 (name "r-venndiagram")
3502 (uri (cran-uri "VennDiagram" version))
3505 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3506 (properties `((upstream-name . "VennDiagram")))
3507 (build-system r-build-system)
3509 `(("r-futile-logger" ,r-futile-logger)))
3510 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3511 (synopsis "Generate High-Resolution Venn and Euler Plots")
3513 "This package provides a set of functions to generate high-resolution
3514 Venn and Euler plots. It includes handling for several special cases,
3515 including two-case scaling, and extensive customization of plot shape and
3517 (license license:gpl2+)))
3519 (define-public r-vioplot
3526 (uri (cran-uri "vioplot" version))
3529 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3530 (build-system r-build-system)
3534 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3535 (synopsis "Violin plot")
3537 "This package provides a violin plot, which is a combination of a box
3538 plot and a kernel density plot.")
3539 (license license:bsd-3)))
3541 (define-public r-rsofia
3547 ;; This package has been removed from CRAN, so we can
3548 ;; only fetch it from the archives.
3549 (uri (string-append "https://cran.r-project.org/src/"
3550 "contrib/Archive/RSofia/RSofia_"
3554 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3555 (properties `((upstream-name . "RSofia")))
3556 (build-system r-build-system)
3558 `(("r-rcpp" ,r-rcpp)))
3559 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3560 (synopsis "Port of sofia-ml to R")
3561 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3562 suite of fast incremental algorithms for machine learning that can be used for
3563 training models for classification or ranking.")
3564 (license license:asl2.0)))
3566 (define-public r-xts
3573 (uri (cran-uri "xts" version))
3576 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3577 (build-system r-build-system)
3578 (propagated-inputs `(("r-zoo" ,r-zoo)))
3579 (home-page "https://github.com/joshuaulrich/xts")
3580 (synopsis "Extensible time series")
3582 "This package provides for uniform handling of R's different time-based
3583 data classes by extending @code{zoo}, maximizing native format information
3584 preservation and allowing for user-level customization and extension, while
3585 simplifying cross-class interoperability.")
3586 (license license:gpl2+)))
3588 (define-public r-performanceanalytics
3590 (name "r-performanceanalytics")
3595 (uri (cran-uri "PerformanceAnalytics" version))
3598 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3600 `((upstream-name . "PerformanceAnalytics")))
3601 (build-system r-build-system)
3603 `(("r-quadprog" ,r-quadprog)
3606 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3607 (synopsis "Econometric tools for performance and risk analysis")
3608 (description "This is a collection of econometric functions for
3609 performance and risk analysis. This package aims to aid practitioners and
3610 researchers in utilizing the latest research in analysis of non-normal return
3611 streams. In general, it is most tested on return (rather than price) data on
3612 a regular scale, but most functions will work with irregular return data as
3613 well, and increasing numbers of functions will work with P&L or price data
3615 ;; Either version may be picked.
3616 (license (list license:gpl2 license:gpl3))))
3618 (define-public r-laeken
3625 (uri (cran-uri "laeken" version))
3628 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3629 (build-system r-build-system)
3631 `(("r-boot" ,r-boot)
3632 ("r-mass" ,r-mass)))
3633 (home-page "https://cran.r-project.org/web/packages/laeken/")
3634 (synopsis "Estimation of indicators on social exclusion and poverty")
3635 (description "This package provides tools for the estimation of indicators
3636 on social exclusion and poverty, as well as an implementation of Pareto tail
3637 modeling for empirical income distributions.")
3638 (license license:gpl2+)))
3640 (define-public r-vcd
3647 (uri (cran-uri "vcd" version))
3650 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3651 (build-system r-build-system)
3653 `(("r-colorspace" ,r-colorspace)
3654 ("r-lmtest" ,r-lmtest)
3655 ("r-mass" ,r-mass)))
3656 (home-page "https://cran.r-project.org/web/packages/vcd/")
3657 (synopsis "Visualizing categorical data")
3658 (description "This package provides visualization techniques, data sets,
3659 summary and inference procedures aimed particularly at categorical data.
3660 Special emphasis is given to highly extensible grid graphics. The package was
3661 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3662 Friendly and is now the main support package for a new book, \"Discrete Data
3663 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3664 (license license:gpl2)))
3666 (define-public r-ica
3673 (uri (cran-uri "ica" version))
3676 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3677 (build-system r-build-system)
3678 (home-page "https://cran.r-project.org/web/packages/ica/")
3679 (synopsis "Independent component analysis")
3680 (description "This package provides tools for @dfn{Independent Component
3681 Analysis} (ICA) using various algorithms: FastICA,
3682 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3683 of Eigenmatrices} (JADE).")
3684 (license license:gpl2+)))
3686 (define-public r-dtw
3693 (uri (cran-uri "dtw" version))
3696 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3697 (build-system r-build-system)
3698 (propagated-inputs `(("r-proxy" ,r-proxy)))
3699 (home-page "http://dtw.r-forge.r-project.org/")
3700 (synopsis "Dynamic Time Warping Algorithms")
3701 (description "This package provides a comprehensive implementation of
3702 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3703 optimal (least cumulative distance) alignment between points of two time
3704 series. Common DTW variants covered include local (slope) and global (window)
3705 constraints, subsequence matches, arbitrary distance definitions,
3706 normalizations, minimum variance matching, and so on.")
3707 (license license:gpl2+)))
3709 (define-public r-sdmtools
3712 (version "1.1-221.2")
3716 (uri (cran-uri "SDMTools" version))
3719 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3720 (properties `((upstream-name . "SDMTools")))
3721 (build-system r-build-system)
3722 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3723 (home-page "http://www.rforge.net/SDMTools/")
3724 (synopsis "Species distribution modelling tools")
3725 (description "This package provides a set of tools for post processing
3726 the outcomes of species distribution modeling exercises. It includes novel
3727 methods for comparing models and tracking changes in distributions through
3728 time. It further includes methods for visualizing outcomes, selecting
3729 thresholds, calculating measures of accuracy and landscape fragmentation
3731 (license license:gpl3+)))
3733 (define-public r-scatterplot3d
3735 (name "r-scatterplot3d")
3740 (uri (cran-uri "scatterplot3d" version))
3743 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3744 (build-system r-build-system)
3745 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3746 (synopsis "3D scatter plot")
3747 (description "This package provides an implementation of scatter plots for
3748 plotting. a three dimensional point cloud.")
3749 (license license:gpl2)))
3751 (define-public r-ggridges
3758 (uri (cran-uri "ggridges" version))
3761 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3762 (build-system r-build-system)
3764 `(("r-ggplot2" ,r-ggplot2)
3766 ("r-scales" ,r-scales)
3767 ("r-withr" ,r-withr)))
3768 (home-page "https://github.com/clauswilke/ggridges")
3769 (synopsis "Ridgeline plots in ggplot2")
3771 "Ridgeline plots provide a convenient way of visualizing changes in
3772 distributions over time or space. This package enables the creation of such
3773 plots in @code{ggplot2}.")
3774 (license license:gpl2)))
3776 (define-public r-ggjoy
3783 (uri (cran-uri "ggjoy" version))
3786 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3787 (build-system r-build-system)
3789 `(("r-ggplot2" ,r-ggplot2)
3790 ("r-ggridges" ,r-ggridges)))
3791 (home-page "https://github.com/clauswilke/ggjoy")
3792 (synopsis "Joyplots in ggplot2")
3793 (description "Joyplots provide a convenient way of visualizing changes in
3794 distributions over time or space. This package enables the creation of such
3795 plots in @code{ggplot2}.")
3796 (license license:gpl2)))
3798 (define-public r-cli
3805 (uri (cran-uri "cli" version))
3808 "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki"))))
3809 (build-system r-build-system)
3811 `(("r-assertthat" ,r-assertthat)
3812 ("r-crayon" ,r-crayon)
3813 ("r-fansi" ,r-fansi)
3814 ("r-glue" ,r-glue)))
3815 (home-page "https://github.com/r-lib/cli#readme")
3816 (synopsis "Helpers for developing command line interfaces")
3817 (description "This package provides a suite of tools designed to build
3818 attractive command line interfaces (CLIs). It includes tools for drawing
3819 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3820 (license license:expat)))
3822 (define-public r-argparser
3824 (name "r-argparser")
3829 (uri (cran-uri "argparser" version))
3832 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3833 (build-system r-build-system)
3834 (home-page "https://bitbucket.org/djhshih/argparser")
3835 (synopsis "Command-line argument parser")
3837 "This package provides a cross-platform command-line argument parser
3838 written purely in R with no external dependencies. It is useful with the
3839 Rscript front-end and facilitates turning an R script into an executable
3841 (license license:gpl3+)))
3843 (define-public r-debugme
3850 (uri (cran-uri "debugme" version))
3853 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3854 (build-system r-build-system)
3855 (propagated-inputs `(("r-crayon" ,r-crayon)))
3856 (home-page "https://github.com/r-lib/debugme#readme")
3857 (synopsis "Debug R packages")
3859 "This package allows the user to specify debug messages as special string
3860 constants, and control debugging of packages via environment variables.")
3861 (license license:expat)))
3863 (define-public r-processx
3870 (uri (cran-uri "processx" version))
3873 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3874 (build-system r-build-system)
3878 (home-page "https://github.com/r-lib/processx3")
3879 (synopsis "Execute and control system processes")
3881 "This package provides portable tools to run system processes in the
3882 background. It can check if a background process is running; wait on a
3883 background process to finish; get the exit status of finished processes; kill
3884 background processes and their children; restart processes. It can read the
3885 standard output and error of the processes, using non-blocking connections.
3886 @code{processx} can poll a process for standard output or error, with a
3887 timeout. It can also poll several processes at once.")
3888 (license license:expat)))
3890 (define-public r-tsp
3897 (uri (cran-uri "TSP" version))
3900 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3901 (properties `((upstream-name . "TSP")))
3902 (build-system r-build-system)
3903 (propagated-inputs `(("r-foreach" ,r-foreach)))
3904 (home-page "https://cran.r-project.org/web/packages/TSP/")
3905 (synopsis "Traveling salesperson problem (TSP)")
3906 (description "This package provides basic infrastructure and some
3907 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3908 traveling salesman problem).")
3909 (license license:gpl3)))
3911 (define-public r-qap
3918 (uri (cran-uri "qap" version))
3921 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3922 (build-system r-build-system)
3923 (native-inputs `(("gfortran" ,gfortran)))
3924 (home-page "https://cran.r-project.org/web/packages/qap/")
3925 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3926 (description "This package implements heuristics for the @dfn{quadratic
3927 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3929 (license license:gpl3)))
3931 (define-public r-gclus
3938 (uri (cran-uri "gclus" version))
3941 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3942 (build-system r-build-system)
3943 (propagated-inputs `(("r-cluster" ,r-cluster)))
3944 (home-page "https://cran.r-project.org/web/packages/gclus/")
3945 (synopsis "Clustering graphics")
3946 (description "This package orders panels in scatterplot matrices and
3947 parallel coordinate displays by some merit index. It contains various indices
3948 of merit, ordering functions, and enhanced versions of @code{pairs} and
3949 @code{parcoord} which color panels according to their merit level.")
3950 (license license:gpl2+)))
3952 (define-public r-webshot
3959 (uri (cran-uri "webshot" version))
3962 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3963 (build-system r-build-system)
3965 `(("r-callr" ,r-callr)
3966 ("r-jsonlite" ,r-jsonlite)
3967 ("r-magrittr" ,r-magrittr)))
3968 (home-page "https://github.com/wch/webshot/")
3969 (synopsis "Take screenshots of web pages")
3971 "Webshot makes it easy to take screenshots of web pages from within R.
3972 It can also run Shiny applications locally and take screenshots of the
3973 application; and it can render and screenshot static as well as interactive R
3974 Markdown documents.")
3975 (license license:gpl2)))
3977 (define-public r-seriation
3979 (name "r-seriation")
3984 (uri (cran-uri "seriation" version))
3987 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3988 (build-system r-build-system)
3990 `(("r-cluster" ,r-cluster)
3991 ("r-colorspace" ,r-colorspace)
3992 ("r-dendextend" ,r-dendextend)
3993 ("r-gclus" ,r-gclus)
3994 ("r-gplots" ,r-gplots)
3997 ("r-registry" ,r-registry)
3999 (native-inputs `(("gfortran" ,gfortran)))
4000 (home-page "http://s2.smu.edu/IDA/seriation/")
4001 (synopsis "Infrastructure for ordering objects using seriation")
4003 "This package provides infrastructure for seriation with an
4004 implementation of several seriation/sequencing techniques to reorder matrices,
4005 dissimilarity matrices, and dendrograms. It also provides (optimally)
4006 reordered heatmaps, color images and clustering visualizations like
4007 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4009 (license license:gpl3)))
4011 (define-public r-xfun
4018 (uri (cran-uri "xfun" version))
4020 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
4021 (build-system r-build-system)
4022 (home-page "https://github.com/yihui/xfun")
4023 (synopsis "Miscellaneous functions")
4025 "This package provides miscellaneous functions commonly used in other
4026 packages maintained by Yihui Xie.")
4027 (license license:expat)))
4029 (define-public r-utf8
4036 (uri (cran-uri "utf8" version))
4039 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4040 (build-system r-build-system)
4041 (home-page "https://github.com/patperry/r-utf8")
4042 (synopsis "Unicode text processing")
4044 "This package provides tools to process and print UTF-8 encoded
4045 international text (Unicode). Input, validate, normalize, encode, format, and
4047 (license license:asl2.0)))
4049 (define-public r-zeallot
4056 (uri (cran-uri "zeallot" version))
4059 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4060 (build-system r-build-system)
4061 (home-page "https://github.com/nteetor/zeallot")
4062 (synopsis "Multiple, unpacking, and destructuring assignment")
4064 "This package provides a @code{%<-%} operator to perform multiple,
4065 unpacking, and destructuring assignment in R. The operator unpacks the
4066 right-hand side of an assignment into multiple values and assigns these values
4067 to variables on the left-hand side of the assignment.")
4068 (license license:expat)))
4070 (define-public r-vctrs
4077 (uri (cran-uri "vctrs" version))
4080 "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0"))))
4081 (build-system r-build-system)
4083 `(("r-backports" ,r-backports)
4084 ("r-digest" ,r-digest)
4085 ("r-ellipsis" ,r-ellipsis)
4087 ("r-rlang" ,r-rlang)
4088 ("r-zeallot" ,r-zeallot)))
4089 (home-page "https://github.com/r-lib/vctrs")
4090 (synopsis "Vector helpers")
4092 "There are three main goals to the @code{vctrs} package:
4095 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4096 @code{length()} and @code{class()}. These definitions are paired with a
4097 framework for type-coercion and size-recycling.
4098 @item To define type- and size-stability as desirable function properties, use
4099 them to analyse existing base function, and to propose better alternatives.
4100 This work has been particularly motivated by thinking about the ideal
4101 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4102 @item To provide a new @code{vctr} base class that makes it easy to create new
4103 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4104 a few new @code{vctrs} generics, making implementation considerably simpler
4107 (license license:gpl3)))
4109 (define-public r-pillar
4116 (uri (cran-uri "pillar" version))
4119 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4120 (build-system r-build-system)
4123 ("r-crayon" ,r-crayon)
4124 ("r-fansi" ,r-fansi)
4125 ("r-rlang" ,r-rlang)
4127 ("r-vctrs" ,r-vctrs)))
4128 (home-page "https://github.com/r-lib/pillar")
4129 (synopsis "Coloured formatting for columns")
4131 "This package provides a @code{pillar} generic designed for formatting
4132 columns of data using the full range of colours provided by modern
4134 (license license:gpl3)))
4136 (define-public r-uuid
4143 (uri (cran-uri "uuid" version))
4146 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4147 (build-system r-build-system)
4148 (home-page "http://www.rforge.net/uuid")
4149 (synopsis "Tools for generating and handling of UUIDs")
4151 "This package provides tools for generating and handling of
4152 @dfn{Universally Unique Identifiers} (UUIDs).")
4153 (license license:expat)))
4155 (define-public r-tinytex
4162 (uri (cran-uri "tinytex" version))
4165 "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr"))))
4166 (build-system r-build-system)
4168 `(("r-xfun" ,r-xfun)))
4169 (home-page "https://github.com/yihui/tinytex")
4170 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4172 "This package provides helper functions to install and maintain the LaTeX
4173 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4174 easy-to-maintain version of TeX Live. This package also contains helper
4175 functions to compile LaTeX documents, and install missing LaTeX packages
4177 (license license:expat)))
4179 (define-public r-network
4186 (uri (cran-uri "network" version))
4189 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4190 (build-system r-build-system)
4192 `(("r-magrittr" ,r-magrittr)
4193 ("r-tibble" ,r-tibble)))
4194 (home-page "https://statnet.org/")
4195 (synopsis "Classes for relational data")
4197 "This package provides tools to create and modify network objects. The
4198 @code{network} class can represent a range of relational data types, and
4199 supports arbitrary vertex/edge/graph attributes.")
4200 (license license:gpl2+)))
4202 (define-public r-statnet-common
4204 (name "r-statnet-common")
4209 (uri (cran-uri "statnet.common" version))
4212 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4214 `((upstream-name . "statnet.common")))
4215 (build-system r-build-system)
4217 `(("r-coda" ,r-coda)))
4218 (home-page "https://statnet.org")
4219 (synopsis "R scripts and utilities used by the Statnet software")
4220 (description "This package provides non-statistical utilities used by the
4221 software developed by the Statnet Project.")
4222 (license license:gpl3)))
4224 (define-public r-statcheck
4226 (name "r-statcheck")
4231 (uri (cran-uri "statcheck" version))
4234 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4235 (build-system r-build-system)
4237 `(("r-ggplot2" ,r-ggplot2)
4239 ("r-rmarkdown" ,r-rmarkdown)))
4240 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4241 (synopsis "Extract statistics from articles and recompute p-values")
4242 (description "This package can automatically extract statistical
4243 null-hypothesis significant testing (NHST) results from articles and recompute
4244 the p-values based on the reported test statistic and degrees of freedom to
4245 detect possible inconsistencies.")
4246 (license license:gpl2)))
4248 (define-public r-sna
4255 (uri (cran-uri "sna" version))
4258 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4259 (build-system r-build-system)
4261 `(("r-network" ,r-network)
4262 ("r-statnet-common" ,r-statnet-common)))
4263 (home-page "https://statnet.org")
4264 (synopsis "Tools for social network analysis")
4266 "This package provides a range of tools for social network analysis,
4267 including node and graph-level indices, structural distance and covariance
4268 methods, structural equivalence detection, network regression, random graph
4269 generation, and 2D/3D network visualization.")
4270 (license license:gpl2+)))
4272 (define-public r-tfisher
4279 (uri (cran-uri "TFisher" version))
4282 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4283 (properties `((upstream-name . "TFisher")))
4284 (build-system r-build-system)
4286 `(("r-matrix" ,r-matrix)
4287 ("r-mvtnorm" ,r-mvtnorm)
4289 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4290 (synopsis "Optimal thresholding Fisher's p-value combination method")
4292 "This package provides the @dfn{cumulative distribution function} (CDF),
4293 quantile, and statistical power calculator for a collection of thresholding
4294 Fisher's p-value combination methods, including Fisher's p-value combination
4295 method, truncated product method and, in particular, soft-thresholding
4296 Fisher's p-value combination method which is proven to be optimal in some
4297 context of signal detection. The p-value calculator for the omnibus version
4298 of these tests are also included.")
4299 (license license:gpl2)))
4301 (define-public r-ttr
4308 (uri (cran-uri "TTR" version))
4311 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4312 (properties `((upstream-name . "TTR")))
4313 (build-system r-build-system)
4315 `(("r-curl" ,r-curl)
4318 (home-page "https://github.com/joshuaulrich/TTR")
4319 (synopsis "Technical trading rules")
4321 "This package provides functions and data to construct technical trading
4323 (license license:gpl2)))
4325 (define-public r-leaps
4332 (uri (cran-uri "leaps" version))
4335 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4336 (build-system r-build-system)
4337 (native-inputs `(("gfortran" ,gfortran)))
4338 (home-page "https://cran.r-project.org/web/packages/leaps/")
4339 (synopsis "Regression subset selection")
4341 "This package provides tools for regression subset selection, including
4342 exhaustive search.")
4343 (license license:gpl2+)))
4345 (define-public r-splus2r
4352 (uri (cran-uri "splus2R" version))
4355 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4356 (properties `((upstream-name . "splus2R")))
4357 (build-system r-build-system)
4358 (native-inputs `(("gfortran" ,gfortran)))
4359 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4360 (synopsis "Supplemental S-PLUS functionality in R")
4362 "Currently there are many functions in S-PLUS that are missing in R. To
4363 facilitate the conversion of S-PLUS packages to R packages, this package
4364 provides some missing S-PLUS functionality in R.")
4365 (license license:gpl2)))
4367 (define-public r-ifultools
4369 (name "r-ifultools")
4374 (uri (cran-uri "ifultools" version))
4377 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4378 (build-system r-build-system)
4380 `(("r-mass" ,r-mass)
4381 ("r-splus2r" ,r-splus2r)))
4382 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4383 (synopsis "Insightful research tools")
4384 (description "This package provides C code used by the wmtsa, fractal, and
4386 (license license:gpl2)))
4388 (define-public r-sapa
4395 (uri (cran-uri "sapa" version))
4398 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4399 (build-system r-build-system)
4401 `(("r-ifultools" ,r-ifultools)
4402 ("r-splus2r" ,r-splus2r)))
4403 (home-page "https://cran.r-project.org/web/packages/sapa/")
4404 (synopsis "Spectral analysis for physical applications")
4405 (description "This package provides software for the book Spectral
4406 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4407 Cambridge University Press, 1993.")
4408 (license license:gpl2)))
4410 (define-public r-aggregation
4412 (name "r-aggregation")
4417 (uri (cran-uri "aggregation" version))
4420 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4421 (build-system r-build-system)
4422 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4423 (synopsis "Methods for p-value aggregation")
4425 "This package contains functionality for performing the following methods
4426 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4427 Fisher's method), and Sidak correction.")
4428 (license license:gpl3)))
4430 (define-public r-quantmod
4437 (uri (cran-uri "quantmod" version))
4440 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4441 (build-system r-build-system)
4443 `(("r-curl" ,r-curl)
4447 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4448 (synopsis "Quantitative financial modelling framework")
4449 (description "This package provides a quantitative financial modelling
4450 framework to allow users to specify, build, trade, and analyse quantitative
4451 financial trading strategies.")
4452 (license license:gpl3)))
4454 (define-public r-tseries
4461 (uri (cran-uri "tseries" version))
4464 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4465 (build-system r-build-system)
4467 `(("r-quadprog" ,r-quadprog)
4468 ("r-quantmod" ,r-quantmod)
4471 `(("gfortran" ,gfortran)))
4472 (home-page "https://cran.r-project.org/web/packages/tseries/")
4473 (synopsis "Time series analysis and computational finance")
4475 "This package provides functions relating to time series analysis and
4476 computational finance.")
4477 (license license:gpl2)))
4479 (define-public r-wmtsa
4486 (uri (cran-uri "wmtsa" version))
4489 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4490 (build-system r-build-system)
4492 `(("r-ifultools" ,r-ifultools)
4494 ("r-splus2r" ,r-splus2r)))
4495 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4496 (synopsis "Wavelet methods for time series analysis")
4498 "This package provides software to accompany the book \"Wavelet Methods
4499 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4500 University Press, 2000.")
4501 (license license:gpl2)))
4503 (define-public r-tsa
4510 (uri (cran-uri "TSA" version))
4513 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4514 (properties `((upstream-name . "TSA")))
4515 (build-system r-build-system)
4517 `(("r-leaps" ,r-leaps)
4518 ("r-locfit" ,r-locfit)
4519 ("r-mgcv" ,r-mgcv)))
4520 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4521 (synopsis "Time series analysis")
4523 "This package contains R functions and datasets detailed in the book
4524 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4525 Cryer and Kung-Sik Chan.")
4526 (license license:gpl2+)))
4528 (define-public r-extradistr
4530 (name "r-extradistr")
4535 (uri (cran-uri "extraDistr" version))
4538 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4539 (properties `((upstream-name . "extraDistr")))
4540 (build-system r-build-system)
4542 `(("r-rcpp" ,r-rcpp)))
4543 (home-page "https://github.com/twolodzko/extraDistr")
4544 (synopsis "Additional univariate and multivariate distributions")
4546 "This package implements density, distribution functions, quantile
4547 functions and random generation functions for a large number of univariate and
4548 multivariate distributions.")
4549 (license license:gpl2)))
4551 (define-public r-fractal
4558 (uri (cran-uri "fractal" version))
4561 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4562 (build-system r-build-system)
4564 `(("r-ifultools" ,r-ifultools)
4567 ("r-scatterplot3d" ,r-scatterplot3d)
4568 ("r-splus2r" ,r-splus2r)
4569 ("r-wmtsa" ,r-wmtsa)))
4570 (home-page "https://cran.r-project.org/web/packages/fractal/")
4571 (synopsis "Fractal time series modeling and analysis")
4573 "This package provides tools for stochastic fractal and deterministic
4574 chaotic time series analysis.")
4575 (license license:gpl2)))
4577 (define-public r-urca
4584 (uri (cran-uri "urca" version))
4587 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4588 (build-system r-build-system)
4589 (propagated-inputs `(("r-nlme" ,r-nlme)))
4590 (native-inputs `(("gfortran" ,gfortran)))
4591 (home-page "https://cran.r-project.org/web/packages/urca/")
4592 (synopsis "Unit root and cointegration tests for time series data")
4594 "This package provides unit root and cointegration tests encountered in
4595 applied econometric analysis.")
4596 (license license:gpl2+)))
4598 (define-public r-cubature
4605 (uri (cran-uri "cubature" version))
4608 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4609 (build-system r-build-system)
4611 `(("r-rcpp" ,r-rcpp)))
4612 (home-page "https://github.com/bnaras/cubature")
4613 (synopsis "Adaptive multivariate integration over hypercubes")
4615 "This package is an R wrapper around the cubature C library for adaptive
4616 multivariate integration over hypercubes. This version provides both
4617 @code{hcubature} and @code{pcubature} routines in addition to a vector
4619 ;; The included cubature C library is released under GPLv2+, but the
4620 ;; wrapper declares the license to be GPLv3+.
4621 (license (list license:gpl2+ license:gpl3+))))
4623 (define-public r-trend
4630 (uri (cran-uri "trend" version))
4633 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4634 (build-system r-build-system)
4636 `(("r-extradistr" ,r-extradistr)))
4638 `(("gfortran" ,gfortran)))
4639 (home-page "https://cran.r-project.org/web/packages/trend/")
4640 (synopsis "Non-parametric trend tests and change-point detection")
4642 "The analysis of environmental data often requires the detection of
4643 trends and change-points. This package includes tests for trend
4644 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4645 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4646 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4647 correlation trend test), change-point detection (Lanzante's test procedures,
4648 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4649 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4650 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4651 sample Robust Rank-Order Distributional Test.")
4652 (license license:gpl3)))
4654 (define-public r-expm
4661 (uri (cran-uri "expm" version))
4664 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4665 (build-system r-build-system)
4666 (propagated-inputs `(("r-matrix" ,r-matrix)))
4667 (native-inputs `(("gfortran" ,gfortran)))
4668 (home-page "https://r-forge.r-project.org/projects/expm/")
4669 (synopsis "Tools for matrix exponentials and related quantities")
4671 "This package provides tools for the computation of the matrix
4672 exponential, logarithm, square root, and related quantities.")
4673 (license license:gpl2+)))
4675 (define-public r-complexplus
4677 (name "r-complexplus")
4682 (uri (cran-uri "complexplus" version))
4685 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4686 (build-system r-build-system)
4688 `(("r-expm" ,r-expm)
4689 ("r-matrix" ,r-matrix)))
4690 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4691 (synopsis "Functions of complex or real variables")
4693 "This package extends several functions to the complex domain, including
4694 the matrix exponential and logarithm, and the determinant.")
4695 (license license:gpl2)))
4697 (define-public r-phontools
4699 (name "r-phontools")
4704 (uri (cran-uri "phonTools" version))
4707 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4708 (properties `((upstream-name . "phonTools")))
4709 (build-system r-build-system)
4710 (home-page "http://www.santiagobarreda.com/rscripts.html")
4711 (synopsis "Tools for phonetic and acoustic analyses")
4713 "This package contains tools for the organization, display, and analysis
4714 of the sorts of data frequently encountered in phonetics research and
4715 experimentation, including the easy creation of IPA vowel plots, and the
4716 creation and manipulation of WAVE audio files.")
4717 (license license:bsd-2)))
4726 (uri (cran-uri "np" version))
4729 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4730 (build-system r-build-system)
4732 `(("r-boot" ,r-boot)
4733 ("r-cubature" ,r-cubature)
4734 ("r-quadprog" ,r-quadprog)
4735 ("r-quantreg" ,r-quantreg)))
4736 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4737 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4738 (description "This package provides non-parametric (and semi-parametric)
4739 kernel methods that seamlessly handle a mix of continuous, unordered, and
4740 ordered factor data types.")
4741 ;; Any version of the GPL.
4742 (license license:gpl3+)))
4744 (define-public r-powerplus
4746 (name "r-powerplus")
4751 (uri (cran-uri "powerplus" version))
4754 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4755 (build-system r-build-system)
4757 `(("r-complexplus" ,r-complexplus)
4760 ("r-matrix" ,r-matrix)
4761 ("r-phontools" ,r-phontools)))
4762 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4763 (synopsis "Exponentiation operations")
4765 "This package provides tools for the computation of matrix and scalar
4767 (license license:gpl2)))
4769 (define-public r-egg
4776 (uri (cran-uri "egg" version))
4779 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4780 (properties `((upstream-name . "egg")))
4781 (build-system r-build-system)
4783 `(("r-ggplot2" ,r-ggplot2)
4784 ("r-gridextra" ,r-gridextra)
4785 ("r-gtable" ,r-gtable)))
4786 (home-page "https://cran.r-project.org/web/packages/egg")
4787 (synopsis "Extensions for ggplot2")
4789 "This package provides miscellaneous functions to help customize ggplot2
4790 objects. High-level functions are provided to post-process ggplot2 layouts
4791 and allow alignment between plot panels, as well as setting panel sizes to
4792 fixed values. Other functions include a custom @code{geom}, and helper
4793 functions to enforce symmetric scales or add tags to facetted plots.")
4794 (license license:gpl3)))
4796 (define-public r-heatmaply
4798 (name "r-heatmaply")
4803 (uri (cran-uri "heatmaply" version))
4806 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4807 (build-system r-build-system)
4809 `(("r-assertthat" ,r-assertthat)
4810 ("r-colorspace" ,r-colorspace)
4811 ("r-dendextend" ,r-dendextend)
4813 ("r-ggplot2" ,r-ggplot2)
4814 ("r-htmlwidgets" ,r-htmlwidgets)
4815 ("r-magrittr" ,r-magrittr)
4816 ("r-plotly" ,r-plotly)
4817 ("r-rcolorbrewer" ,r-rcolorbrewer)
4818 ("r-reshape2" ,r-reshape2)
4819 ("r-scales" ,r-scales)
4820 ("r-seriation" ,r-seriation)
4821 ("r-viridis" ,r-viridis)
4822 ("r-webshot" ,r-webshot)))
4823 (home-page "https://cran.r-project.org/package=heatmaply")
4824 (synopsis "Interactive cluster heat maps using plotly")
4826 "This package enables you to create interactive cluster heatmaps that can
4827 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4828 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4829 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4830 a popular graphical method for visualizing high-dimensional data, in which a
4831 table of numbers is encoded as a grid of colored cells. The rows and columns
4832 of the matrix are ordered to highlight patterns and are often accompanied by
4834 ;; Either version of the license.
4835 (license (list license:gpl2 license:gpl3))))
4844 (uri (cran-uri "h5" version))
4847 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4848 (build-system r-build-system)
4853 `(("which" ,which)))
4855 `(("r-rcpp" ,r-rcpp)))
4856 (home-page "https://github.com/mannau/h5")
4857 (synopsis "Interface to the HDF5 Library")
4859 "This package provides an S4 interface to the HDF5 library supporting
4860 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4861 binary files in a language independent format. The HDF5 format can therefore
4862 be used as an alternative to R's save/load mechanism. Since h5 is able to
4863 access only subsets of stored data it can also handle data sets which do not
4865 (license license:bsd-2)))
4867 (define-public r-cgdsr
4874 (uri (cran-uri "cgdsr" version))
4877 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4878 (build-system r-build-system)
4880 `(("r-httr" ,r-httr)
4881 ("r-r-methodss3" ,r-r-methodss3)
4882 ("r-r-oo" ,r-r-oo)))
4883 (home-page "https://github.com/cBioPortal/cgdsr")
4884 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4886 "This package provides a basic set of R functions for querying the Cancer
4887 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4888 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4889 (license license:lgpl3)))
4891 (define-public r-import
4898 (uri (cran-uri "import" version))
4901 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4902 (build-system r-build-system)
4903 (home-page "https://github.com/smbache/import")
4904 (synopsis "Import mechanism for R")
4906 "This is an alternative mechanism for importing objects from packages.
4907 The syntax allows for importing multiple objects from a package with a single
4908 command in an expressive way. The import package bridges some of the gap
4909 between using @code{library} (or @code{require}) and direct (single-object)
4910 imports. Furthermore the imported objects are not placed in the current
4911 environment. It is also possible to import objects from stand-alone @code{.R}
4913 (license license:expat)))
4915 (define-public r-shinyace
4922 (uri (cran-uri "shinyAce" version))
4925 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4926 (properties `((upstream-name . "shinyAce")))
4927 (build-system r-build-system)
4929 `(("r-shiny" ,r-shiny)
4930 ("r-jsonlite" ,r-jsonlite)))
4931 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4932 (synopsis "Ace editor bindings for Shiny")
4934 "This package provides Ace editor bindings to enable a rich text editing
4935 environment within Shiny.")
4936 (license license:expat)))
4938 (define-public r-base64url
4940 (name "r-base64url")
4945 (uri (cran-uri "base64url" version))
4948 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4949 (build-system r-build-system)
4951 `(("r-backports" ,r-backports)))
4952 (home-page "https://github.com/mllg/base64url")
4953 (synopsis "Fast and URL-safe base64 encoder and decoder")
4955 "This package provides a URL-safe base64 encoder and decoder. In
4956 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4957 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4958 encoder does not fill the string with trailing @code{=}. The resulting
4959 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4960 and thus are safe to use in URLs or for file names. The package also comes
4961 with a simple base32 encoder/decoder suited for case insensitive file
4963 (license license:gpl3)))
4965 (define-public r-radiant-data
4967 (name "r-radiant-data")
4972 (uri (cran-uri "radiant.data" version))
4975 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4976 (modules '((guix build utils)))
4979 ;; Delete files that are under CC-NC-SA.
4980 (delete-file-recursively "inst/app/tools/help")
4982 (properties `((upstream-name . "radiant.data")))
4983 (build-system r-build-system)
4985 `(("r-base64enc" ,r-base64enc)
4986 ("r-broom" ,r-broom)
4989 ("r-dplyr" ,r-dplyr)
4992 ("r-ggplot2" ,r-ggplot2)
4993 ("r-gridextra" ,r-gridextra)
4994 ("r-import" ,r-import)
4995 ("r-jsonlite" ,r-jsonlite)
4996 ("r-knitr" ,r-knitr)
4997 ("r-lubridate" ,r-lubridate)
4998 ("r-magrittr" ,r-magrittr)
4999 ("r-markdown" ,r-markdown)
5000 ("r-plotly" ,r-plotly)
5001 ("r-psych" ,r-psych)
5002 ("r-readr" ,r-readr)
5003 ("r-readxl" ,r-readxl)
5004 ("r-rlang" ,r-rlang)
5005 ("r-rmarkdown" ,r-rmarkdown)
5006 ("r-rstudioapi" ,r-rstudioapi)
5007 ("r-scales" ,r-scales)
5008 ("r-shiny" ,r-shiny)
5009 ("r-shinyfiles" ,r-shinyfiles)
5010 ("r-shinyace" ,r-shinyace)
5011 ("r-stringi" ,r-stringi)
5012 ("r-tibble" ,r-tibble)
5013 ("r-tidyr" ,r-tidyr)
5014 ("r-writexl" ,r-writexl)))
5015 (home-page "https://github.com/radiant-rstats/radiant.data")
5016 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5018 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5019 visualizing, summarizing, transforming, and combining data. It also contains
5020 functionality to generate reproducible reports of the analyses conducted in
5022 (license license:agpl3)))
5024 (define-public r-algdesign
5026 (name "r-algdesign")
5031 (uri (cran-uri "AlgDesign" version))
5033 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5034 (properties `((upstream-name . "AlgDesign")))
5035 (build-system r-build-system)
5036 (home-page "https://github.com/jvbraun/AlgDesign")
5037 (synopsis "Algorithmic experimental design")
5039 "This package provides tools to calculate exact and approximate theory
5040 experimental designs for D, A, and I criteria. Very large designs may be
5041 created. Experimental designs may be blocked or blocked designs created from
5042 a candidate list, using several criteria. The blocking can be done when whole
5043 and within plot factors interact.")
5044 (license license:gpl2+)))
5046 (define-public r-signal
5053 (uri (cran-uri "signal" version))
5056 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5057 (build-system r-build-system)
5058 (propagated-inputs `(("r-mass" ,r-mass)))
5059 (native-inputs `(("gfortran" ,gfortran)))
5060 (home-page "https://cran.r-project.org/web/packages/signal/")
5061 (synopsis "Signal processing")
5063 "This package provides a set of signal processing functions originally
5064 written for Matlab and GNU Octave. It includes filter generation utilities,
5065 filtering functions, resampling routines, and visualization of filter models.
5066 It also includes interpolation functions.")
5067 (license license:gpl2)))
5069 (define-public r-gsubfn
5076 (uri (cran-uri "gsubfn" version))
5079 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5080 (build-system r-build-system)
5081 (propagated-inputs `(("r-proto" ,r-proto)))
5082 (home-page "http://gsubfn.googlecode.com")
5083 (synopsis "Utilities for strings and function arguments.")
5085 "This package provides @code{gsubfn} which is like @code{gsub} but can
5086 take a replacement function or certain other objects instead of the
5087 replacement string. Matches and back references are input to the replacement
5088 function and replaced by the function output. @code{gsubfn} can be used to
5089 split strings based on content rather than delimiters and for quasi-perl-style
5090 string interpolation. The package also has facilities for translating
5091 formulas to functions and allowing such formulas in function calls instead of
5093 (license license:gpl2+)))
5095 (define-public r-sqldf
5102 (uri (cran-uri "sqldf" version))
5105 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5106 (build-system r-build-system)
5108 `(("r-chron" ,r-chron)
5110 ("r-gsubfn" ,r-gsubfn)
5111 ("r-proto" ,r-proto)
5112 ("r-rsqlite" ,r-rsqlite)))
5113 (home-page "https://github.com/ggrothendieck/sqldf")
5114 (synopsis "Manipulate R data frames using SQL")
5116 "The @code{sqldf} function is typically passed a single argument which is
5117 an SQL select statement where the table names are ordinary R data frame names.
5118 @code{sqldf} transparently sets up a database, imports the data frames into
5119 that database, performs the SQL statement and returns the result using a
5120 heuristic to determine which class to assign to each column of the returned
5121 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5122 used to read filtered files into R even if the original files are larger than
5123 R itself can handle.")
5124 (license license:gpl2)))
5126 (define-public r-abind
5133 (uri (cran-uri "abind" version))
5136 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5137 (build-system r-build-system)
5138 (home-page "https://cran.r-project.org/web/packages/abind/")
5139 (synopsis "Combine multidimensional arrays")
5141 "This package provides tools to combine multidimensional arrays into a
5142 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5143 works with vectors, matrices, and higher-dimensional arrays. It also provides
5144 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5145 extracting and replacing data in arrays.")
5146 (license license:lgpl2.0+)))
5148 (define-public r-prroc
5155 (uri (cran-uri "PRROC" version))
5158 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5159 (properties `((upstream-name . "PRROC")))
5160 (build-system r-build-system)
5161 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5162 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5164 "This package computes the areas under the @dfn{precision-recall} (PR)
5165 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5166 contrast to other implementations, the interpolation between points of the PR
5167 curve is done by a non-linear piecewise function. In addition to the areas
5168 under the curves, the curves themselves can also be computed and plotted by a
5169 specific S3-method.")
5170 (license license:gpl3)))
5172 (define-public r-vim
5179 (uri (cran-uri "VIM" version))
5182 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5183 (properties `((upstream-name . "VIM")))
5184 (build-system r-build-system)
5187 ("r-colorspace" ,r-colorspace)
5188 ("r-data-table" ,r-data-table)
5189 ("r-e1071" ,r-e1071)
5190 ("r-laeken" ,r-laeken)
5193 ("r-ranger" ,r-ranger)
5195 ("r-robustbase" ,r-robustbase)
5198 (home-page "https://github.com/alexkowa/VIM")
5199 (synopsis "Visualization and imputation of missing values")
5201 "This package provides tools for the visualization of missing and/or
5202 imputed values are introduced, which can be used for exploring the data and
5203 the structure of the missing and/or imputed values. Depending on this
5204 structure of the missing values, the corresponding methods may help to
5205 identify the mechanism generating the missing values and allows to explore the
5206 data including missing values. In addition, the quality of imputation can be
5207 visually explored using various univariate, bivariate, multiple and
5208 multivariate plot methods.")
5209 (license license:gpl2+)))
5211 (define-public r-fnn
5218 (uri (cran-uri "FNN" version))
5221 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5222 (properties `((upstream-name . "FNN")))
5223 (build-system r-build-system)
5224 (home-page "https://cran.r-project.org/web/packages/FNN")
5225 (synopsis "Fast nearest neighbor search algorithms and applications")
5227 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5228 search algorithms. Related applications including KNN classification,
5229 regression and information measures are implemented.")
5230 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5231 ;; later can be used.
5232 (license license:gpl2+)))
5234 (define-public r-smoother
5241 (uri (cran-uri "smoother" version))
5244 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5245 (build-system r-build-system)
5247 `(("r-ttr" ,r-ttr)))
5248 (home-page "http://cran.r-project.org/web/packages/smoother")
5249 (synopsis "Functions relating to the smoothing of numerical data")
5251 "This package provides a collection of methods for smoothing numerical
5252 data, commencing with a port of the Matlab gaussian window smoothing function.
5253 In addition, several functions typically used in smoothing of financial data
5255 (license license:gpl2)))
5257 (define-public r-riverplot
5259 (name "r-riverplot")
5264 (uri (cran-uri "riverplot" version))
5267 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5268 (build-system r-build-system)
5269 (home-page "https://logfc.wordpress.com")
5270 (synopsis "Sankey or ribbon plots")
5272 "Sankey plots are a type of diagram that is convenient to illustrate how
5273 flow of information, resources etc. separates and joins, much like observing
5274 how rivers split and merge. For example, they can be used to compare
5275 different clusterings. This package provides an implementation of Sankey
5277 (license license:gpl2+)))
5279 (define-public r-dyn
5286 (uri (cran-uri "dyn" version))
5289 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5290 (build-system r-build-system)
5292 `(("r-zoo" ,r-zoo)))
5293 (home-page "https://cran.r-project.org/web/packages/dyn")
5294 (synopsis "Time series regression")
5296 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5297 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5298 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5299 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5300 @code{randomForest::randomForest()} and other regression functions, allowing
5301 those functions to be used with time series including specifications that may
5302 contain lags, diffs and missing values.")
5304 (license license:gpl2+)))
5306 (define-public r-catdap
5313 (uri (cran-uri "catdap" version))
5316 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5317 (build-system r-build-system)
5319 `(("gfortran" ,gfortran)))
5320 (home-page "https://cran.r-project.org/web/packages/catdap/")
5321 (synopsis "Tools for categorical data analysis")
5323 "This package provides functions for analyzing multivariate data.
5324 Dependencies of the distribution of the specified variable (response
5325 variable) to other variables (explanatory variables) are derived and
5326 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5327 (license license:gpl2+)))
5329 (define-public r-arules
5336 (uri (cran-uri "arules" version))
5339 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5340 (build-system r-build-system)
5342 `(("r-matrix" ,r-matrix)))
5343 (home-page "https://github.com/mhahsler/arules")
5344 (synopsis "Mining association rules and frequent itemsets")
5346 "This package provides an infrastructure for representing, manipulating
5347 and analyzing transaction data and patterns (frequent itemsets and association rules).
5348 It also provides C implementations of the association mining algorithms Apriori
5350 (license license:gpl3)))
5352 (define-public r-parsedate
5354 (name "r-parsedate")
5359 (uri (cran-uri "parsedate" version))
5362 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5363 (build-system r-build-system)
5365 `(("r-rematch2" ,r-rematch2)))
5366 (home-page "https://github.com/gaborcsardi/parsedate")
5368 "Recognize and parse dates in various formats")
5370 "This package provides three functions for dealing with dates:
5371 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5372 time formats, @code{parse_date} parses dates in unspecified formats,
5373 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5374 (license license:gpl2)))
5376 (define-public r-abc-data
5383 (uri (cran-uri "abc.data" version))
5386 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5387 (properties `((upstream-name . "abc.data")))
5388 (build-system r-build-system)
5389 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5390 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5392 "This package contains data which are used by functions of the abc
5393 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5394 algorithms for performing parameter estimation, model selection, and
5396 (license license:gpl3+)))
5398 (define-public r-abc
5405 (uri (cran-uri "abc" version))
5408 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5409 (build-system r-build-system)
5411 `(("r-abc-data" ,r-abc-data)
5412 ("r-locfit" ,r-locfit)
5415 ("r-quantreg" ,r-quantreg)))
5416 (home-page "https://cran.r-project.org/web/packages/abc/")
5417 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5419 "This package implements several @dfn{Approximate Bayesian
5420 Computation} (ABC) algorithms for performing parameter estimation, model
5421 selection, and goodness-of-fit. Cross-validation tools are also available for
5422 measuring the accuracy of ABC estimates, and to calculate the
5423 misclassification probabilities of different models.")
5424 (license license:gpl3+)))
5426 (define-public r-zip
5433 (uri (cran-uri "zip" version))
5436 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5437 (build-system r-build-system)
5438 (home-page "https://github.com/gaborcsardi/zip")
5439 (synopsis "Cross-platform Zip compression")
5441 "This package provides a cross-platform Zip compression library for R.
5442 It is a replacement for the @code{zip} function, that does not require any
5443 additional external tools on any platform.")
5444 (license license:cc0)))
5446 (define-public r-openxlsx
5453 (uri (cran-uri "openxlsx" version))
5456 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5457 (build-system r-build-system)
5459 `(("r-rcpp" ,r-rcpp)
5460 ("r-stringi" ,r-stringi)
5462 (home-page "https://github.com/awalker89/openxlsx")
5463 (synopsis "Read, write and edit XLSX files")
5465 "This package simplifies the creation of Excel @code{.xlsx} files by
5466 providing a high level interface to writing, styling and editing worksheets.
5467 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5468 and @code{XLConnect} packages with the added benefit of removing the
5469 dependency on Java.")
5470 (license license:gpl3)))
5472 (define-public r-rio
5479 (uri (cran-uri "rio" version))
5482 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5483 (build-system r-build-system)
5485 `(("r-curl" ,r-curl)
5486 ("r-data-table" ,r-data-table)
5487 ("r-foreign" ,r-foreign)
5488 ("r-haven" ,r-haven)
5489 ("r-openxlsx" ,r-openxlsx)
5490 ("r-readxl" ,r-readxl)
5491 ("r-tibble" ,r-tibble)))
5492 (home-page "https://github.com/leeper/rio")
5493 (synopsis "Swiss-army knife for data I/O")
5495 "This package provides streamlined data import and export infrastructure
5496 by making assumptions that the user is probably willing to make: @code{import}
5497 and @code{export} determine the data structure from the file extension,
5498 reasonable defaults are used for data import and export (e.g.,
5499 @code{stringsAsFactors=FALSE}), web-based import is natively
5500 supported (including from SSL/HTTPS), compressed files can be read directly
5501 without explicit decompression, and fast import packages are used where
5502 appropriate. An additional convenience function, @code{convert}, provides a
5503 simple method for converting between file types.")
5504 (license license:gpl2)))
5506 (define-public r-maptools
5513 (uri (cran-uri "maptools" version))
5516 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5517 (build-system r-build-system)
5519 `(("r-foreign" ,r-foreign)
5520 ("r-lattice" ,r-lattice)
5522 (home-page "http://r-forge.r-project.org/projects/maptools/")
5523 (synopsis "Tools for reading and handling spatial objects")
5525 "This package provides a set of tools for manipulating and reading
5526 geographic data, in particular ESRI Shapefiles. It includes binary access to
5527 GSHHG shoreline files. The package also provides interface wrappers for
5528 exchanging spatial objects with other R packages.")
5529 ;; The C source files from shapelib are released under the Expat license.
5530 ;; The R code is released under GPL version 2 or later.
5531 (license (list license:gpl2+
5534 (define-public r-later
5541 (uri (cran-uri "later" version))
5544 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5545 (build-system r-build-system)
5549 ("r-rlang" ,r-rlang)))
5550 (home-page "https://github.com/r-lib/later")
5551 (synopsis "Utilities for delaying function execution")
5553 "This package provides tools to execute arbitrary R or C functions some
5554 time after the current time, after the R execution stack has emptied.")
5555 (license license:gpl2+)))
5557 (define-public r-promises
5564 (uri (cran-uri "promises" version))
5567 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5568 (build-system r-build-system)
5570 `(("r-later" ,r-later)
5571 ("r-magrittr" ,r-magrittr)
5574 ("r-rlang" ,r-rlang)))
5575 (home-page "https://rstudio.github.io/promises")
5576 (synopsis "Abstractions for promise-based asynchronous programming")
5578 "This package provides fundamental abstractions for doing asynchronous
5579 programming in R using promises. Asynchronous programming is useful for
5580 allowing a single R process to orchestrate multiple tasks in the background
5581 while also attending to something else. Semantics are similar to JavaScript
5582 promises, but with a syntax that is idiomatic R.")
5583 (license license:expat)))
5585 (define-public r-dosnow
5592 (uri (cran-uri "doSNOW" version))
5595 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5596 (properties `((upstream-name . "doSNOW")))
5597 (build-system r-build-system)
5599 `(("r-foreach" ,r-foreach)
5600 ("r-iterators" ,r-iterators)
5601 ("r-snow" ,r-snow)))
5602 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5603 (synopsis "Foreach parallel adaptor for the snow package")
5605 "This package provides a parallel backend for the @code{%dopar%} function
5606 using the @code{snow} package.")
5607 (license license:gpl2)))
5609 (define-public r-snowfall
5612 (version "1.84-6.1")
5615 (uri (cran-uri "snowfall" version))
5617 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5618 (build-system r-build-system)
5620 `(("r-snow" ,r-snow)))
5621 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5622 (synopsis "Easier cluster computing")
5623 (description "This package is a usability wrapper around snow for easier
5624 development of parallel R programs. This package offers e.g. extended error
5625 checks, and additional functions. All functions work in sequential mode, too,
5626 if no cluster is present or wished. The package is also designed as connector
5627 to the cluster management tool @code{sfCluster}, but can also used without
5629 (license license:gpl2+)))
5631 (define-public r-rappdirs
5638 (uri (cran-uri "rappdirs" version))
5641 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5642 (build-system r-build-system)
5643 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5644 (synopsis "Determine where to save data, caches, and logs")
5646 "This package provides an easy way to determine which directories on the
5647 user's computer should be used to save data, caches and logs. It is a port of
5648 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5649 (license license:expat)))
5651 (define-public r-renv
5658 (uri (cran-uri "renv" version))
5661 "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr"))))
5662 (properties `((upstream-name . "renv")))
5663 (build-system r-build-system)
5664 (home-page "https://rstudio.github.io/renv")
5665 (synopsis "Project environments")
5667 "This package provides a dependency management toolkit for R. Using
5668 renv, you can create and manage project-local R libraries, save the state of
5669 these libraries to a lockfile, and later restore your library as required.
5670 Together, these tools can help make your projects more isolated, portable, and
5672 (license license:expat)))
5674 (define-public r-learnr
5681 (uri (cran-uri "learnr" version))
5684 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5685 (build-system r-build-system)
5687 `(("r-checkmate" ,r-checkmate)
5688 ("r-ellipsis" ,r-ellipsis)
5689 ("r-evaluate" ,r-evaluate)
5690 ("r-htmltools" ,r-htmltools)
5691 ("r-htmlwidgets" ,r-htmlwidgets)
5692 ("r-jsonlite" ,r-jsonlite)
5693 ("r-knitr" ,r-knitr)
5694 ("r-markdown" ,r-markdown)
5695 ("r-rappdirs" ,r-rappdirs)
5697 ("r-rmarkdown" ,r-rmarkdown)
5698 ("r-rprojroot" ,r-rprojroot)
5699 ("r-shiny" ,r-shiny)
5700 ("r-withr" ,r-withr)))
5701 (home-page "https://rstudio.github.io/learnr/")
5702 (synopsis "Interactive tutorials for R")
5704 "This package provides tools to create interactive tutorials using R
5705 Markdown. Use a combination of narrative, figures, videos, exercises, and
5706 quizzes to create self-paced tutorials for learning about R and R packages.")
5707 (license license:asl2.0)))
5709 (define-public r-analytics
5711 (name "r-analytics")
5716 (uri (cran-uri "analytics" version))
5719 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5720 (build-system r-build-system)
5723 ("r-cluster" ,r-cluster)
5724 ("r-fractal" ,r-fractal)
5725 ("r-lmtest" ,r-lmtest)
5728 ("r-powerplus" ,r-powerplus)
5729 ("r-robust" ,r-robust)
5730 ("r-trend" ,r-trend)
5734 (home-page "https://cran.r-project.org/web/packages/analytics/")
5735 (synopsis "Collection of data analysis tools")
5737 "This package is a collection of data analysis tools. It includes tools
5738 for regression outlier detection in a fitted linear model, stationary
5739 bootstrap using a truncated geometric distribution, a comprehensive test for
5740 weak stationarity, column means by group, weighted biplots, and a heuristic to
5741 obtain a better initial configuration in non-metric MDS.")
5742 (license license:gpl2)))
5744 (define-public r-reticulate
5746 (name "r-reticulate")
5751 (uri (cran-uri "reticulate" version))
5754 "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn"))))
5755 (build-system r-build-system)
5756 (inputs `(("python" ,python)))
5758 `(("r-rappdirs" ,r-rappdirs)
5759 ("r-jsonlite" ,r-jsonlite)
5760 ("r-matrix" ,r-matrix)
5761 ("r-rcpp" ,r-rcpp)))
5762 (home-page "https://github.com/rstudio/reticulate")
5763 (synopsis "R interface to Python")
5765 "This package provides an interface from R to Python modules, classes,
5766 and functions. When calling into Python, R data types are automatically
5767 converted to their equivalent Python types. When values are returned from
5768 Python to R they are converted back to R types.")
5769 (license license:asl2.0)))
5771 (define-public r-bibtex
5778 (uri (cran-uri "bibtex" version))
5781 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5782 (build-system r-build-system)
5783 (propagated-inputs `(("r-stringr" ,r-stringr)))
5784 (home-page "https://github.com/romainfrancois/bibtex")
5785 (synopsis "Bibtex parser")
5786 (description "This package provides a utility for R to parse a bibtex
5788 (license license:gpl2+)))
5790 (define-public r-ggseqlogo
5792 (name "r-ggseqlogo")
5797 (uri (cran-uri "ggseqlogo" version))
5800 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5801 (build-system r-build-system)
5802 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5803 (home-page "https://github.com/omarwagih/ggseqlogo")
5804 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5806 "The range of functions provided by this package makes it possible to
5807 draw highly versatile genomic sequence logos. Features include, but are not
5808 limited to, modifying colour schemes and fonts used to draw the logo,
5809 generating multiple logo plots, and aiding the visualisation with annotations.
5810 Sequence logos can easily be combined with other ggplot2 plots.")
5811 ;; Unspecified version of the LGPL.
5812 (license license:lgpl3+)))
5814 (define-public r-ggsci
5821 (uri (cran-uri "ggsci" version))
5824 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5825 (build-system r-build-system)
5827 `(("r-ggplot2" ,r-ggplot2)
5828 ("r-scales" ,r-scales)))
5829 (home-page "https://nanx.me/ggsci/")
5830 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5832 "This package provides a collection of ggplot2 color palettes inspired by
5833 plots in scientific journals, data visualization libraries, science fiction
5834 movies, and TV shows.")
5835 (license license:gpl3)))
5837 (define-public r-ggsignif
5844 (uri (cran-uri "ggsignif" version))
5847 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5848 (build-system r-build-system)
5850 `(("r-ggplot2" ,r-ggplot2)))
5851 (home-page "https://github.com/const-ae/ggsignif")
5852 (synopsis "Significance brackets for ggplot2")
5854 "Enrich your ggplots with group-wise comparisons. This package provides
5855 an easy way to indicate if two groups are significantly different. Commonly
5856 this is shown by a bracket on top connecting the groups of interest which
5857 itself is annotated with the level of significance. The package provides a
5858 single layer that takes the groups for comparison and the test as arguments
5859 and adds the annotation to the plot.")
5860 (license license:gpl3)))
5862 (define-public r-ggpubr
5869 (uri (cran-uri "ggpubr" version))
5872 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5873 (build-system r-build-system)
5875 `(("r-cowplot" ,r-cowplot)
5876 ("r-dplyr" ,r-dplyr)
5877 ("r-ggplot2" ,r-ggplot2)
5878 ("r-ggrepel" ,r-ggrepel)
5879 ("r-ggsci" ,r-ggsci)
5880 ("r-ggsignif" ,r-ggsignif)
5882 ("r-gridextra" ,r-gridextra)
5883 ("r-magrittr" ,r-magrittr)
5884 ("r-polynom" ,r-polynom)
5885 ("r-purrr" ,r-purrr)
5886 ("r-rlang" ,r-rlang)
5887 ("r-scales" ,r-scales)
5888 ("r-tidyr" ,r-tidyr)))
5889 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5890 (synopsis "ggplot2-based publication-ready plots")
5892 "The ggplot2 package is an excellent and flexible package for elegant
5893 data visualization in R. However the default generated plots require some
5894 formatting before we can send them for publication. The ggpubr package
5895 provides some easy-to-use functions for creating and customizing ggplot2-based
5896 publication-ready plots.")
5897 (license license:gpl2)))
5899 (define-public r-ellipse
5906 (uri (cran-uri "ellipse" version))
5909 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5910 (build-system r-build-system)
5911 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5912 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5914 "This package contains various routines for drawing ellipses and
5915 ellipse-like confidence regions, implementing the plots described in Murdoch
5916 and Chow (1996), A graphical display of large correlation matrices, The
5917 American Statistician 50, 178-180. There are also routines implementing the
5918 profile plots described in Bates and Watts (1988), Nonlinear Regression
5919 Analysis and its Applications.")
5920 (license license:gpl2+)))
5922 (define-public r-flashclust
5924 (name "r-flashclust")
5929 (uri (cran-uri "flashClust" version))
5932 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5933 (properties `((upstream-name . "flashClust")))
5934 (build-system r-build-system)
5935 (native-inputs `(("gfortran" ,gfortran)))
5936 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5937 (synopsis "Implementation of optimal hierarchical clustering")
5939 "This package provides a fast implementation of hierarchical
5941 (license license:gpl2+)))
5943 (define-public r-factominer
5945 (name "r-factominer")
5950 (uri (cran-uri "FactoMineR" version))
5953 "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
5954 (properties `((upstream-name . "FactoMineR")))
5955 (build-system r-build-system)
5958 ("r-cluster" ,r-cluster)
5959 ("r-ellipse" ,r-ellipse)
5960 ("r-flashclust" ,r-flashclust)
5961 ("r-ggplot2" ,r-ggplot2)
5962 ("r-ggrepel" ,r-ggrepel)
5963 ("r-lattice" ,r-lattice)
5964 ("r-leaps" ,r-leaps)
5966 ("r-scatterplot3d" ,r-scatterplot3d)))
5967 (home-page "http://factominer.free.fr")
5968 (synopsis "Multivariate exploratory data analysis and data mining")
5970 "This package provides exploratory data analysis methods to summarize,
5971 visualize and describe datasets. The main principal component methods are
5972 available, those with the largest potential in terms of applications:
5973 principal component analysis (PCA) when variables are quantitative,
5974 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5975 variables are categorical, Multiple Factor Analysis when variables are
5976 structured in groups, etc. and hierarchical cluster analysis.")
5977 (license license:gpl2+)))
5979 (define-public r-factoextra
5981 (name "r-factoextra")
5986 (uri (cran-uri "factoextra" version))
5989 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5990 (build-system r-build-system)
5992 `(("r-abind" ,r-abind)
5993 ("r-cluster" ,r-cluster)
5994 ("r-dendextend" ,r-dendextend)
5995 ("r-factominer" ,r-factominer)
5996 ("r-ggplot2" ,r-ggplot2)
5997 ("r-ggpubr" ,r-ggpubr)
5998 ("r-ggrepel" ,r-ggrepel)
5999 ("r-reshape2" ,r-reshape2)
6000 ("r-tidyr" ,r-tidyr)))
6001 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6002 (synopsis "Extract and visualize the results of multivariate data analyses")
6004 "This package provides some easy-to-use functions to extract and
6005 visualize the output of multivariate data analyses, including
6006 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6007 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6008 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6009 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6010 packages. It contains also functions for simplifying some clustering analysis
6011 steps and provides ggplot2-based elegant data visualization.")
6012 (license license:gpl2)))
6014 (define-public r-fansi
6021 (uri (cran-uri "fansi" version))
6024 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
6025 (build-system r-build-system)
6027 `(("r-knitr" ,r-knitr))) ; for vignettes
6028 (home-page "https://github.com/brodieG/fansi")
6029 (synopsis "ANSI control sequence aware string functions")
6031 "This package provides counterparts to R string manipulation functions
6032 that account for the effects of ANSI text formatting control sequences.")
6033 (license license:gpl2+)))
6035 (define-public r-nbclust
6042 (uri (cran-uri "NbClust" version))
6045 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6046 (properties `((upstream-name . "NbClust")))
6047 (build-system r-build-system)
6048 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6049 (synopsis "Determine the best number of clusters in a data set")
6051 "NbClust provides 30 indexes for determining the optimal number of
6052 clusters in a data set and offers the best clustering scheme from different
6053 results to the user.")
6054 (license license:gpl2)))
6056 (define-public r-hdf5r
6063 (uri (cran-uri "hdf5r" version))
6066 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
6067 (build-system r-build-system)
6072 `(("r-bit64" ,r-bit64)
6074 (home-page "https://hhoeflin.github.io/hdf5r")
6075 (synopsis "Interface to the HDF5 binary data format")
6077 "HDF5 is a data model, library and file format for storing and managing
6078 large amounts of data. This package provides a nearly feature complete,
6079 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6080 functionality is added so that HDF5 objects behave very similar to their
6081 corresponding R counterparts.")
6082 (license license:asl2.0)))
6084 (define-public r-itertools
6086 (name "r-itertools")
6091 (uri (cran-uri "itertools" version))
6094 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6095 (build-system r-build-system)
6097 `(("r-iterators" ,r-iterators)))
6098 (home-page "https://cran.r-project.org/web/packages/itertools/")
6099 (synopsis "Iterator tools")
6101 "This package provides various tools for creating iterators, many
6102 patterned after functions in the Python @code{itertools} module, and others
6103 patterned after functions in the snow package.")
6104 (license license:gpl2)))
6106 (define-public r-polynom
6113 (uri (cran-uri "polynom" version))
6116 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6117 (build-system r-build-system)
6118 (home-page "https://cran.r-project.org/web/packages/polynom/")
6119 (synopsis "Functions for univariate polynomial manipulations")
6121 "This package provides a collection of functions to implement a class for
6122 univariate polynomial manipulations.")
6123 (license license:gpl2)))
6125 (define-public r-gbrd
6132 (uri (cran-uri "gbRd" version))
6135 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6136 (properties `((upstream-name . "gbRd")))
6137 (build-system r-build-system)
6138 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6139 (synopsis "Utilities for processing Rd objects and files")
6141 "This package provides utilities for processing Rd objects and files.
6142 Extract argument descriptions and other parts of the help pages of
6144 (license license:gpl2+)))
6146 (define-public r-rjags
6153 (uri (cran-uri "rjags" version))
6156 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6157 (build-system r-build-system)
6159 `(("r-coda" ,r-coda)))
6163 `(("pkg-config" ,pkg-config)))
6164 (home-page "http://mcmc-jags.sourceforge.net")
6165 (synopsis "Bayesian graphical models using MCMC")
6167 "This package provides an R interface to the JAGS MCMC library. JAGS is
6168 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6169 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6170 (license license:gpl2)))
6172 (define-public r-rdpack
6179 (uri (cran-uri "Rdpack" version))
6182 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6183 (properties `((upstream-name . "Rdpack")))
6184 (build-system r-build-system)
6186 `(("r-bibtex" ,r-bibtex)
6187 ("r-gbrd" ,r-gbrd)))
6188 (home-page "https://github.com/GeoBosh/Rdpack")
6189 (synopsis "Update and manipulate Rd documentation objects")
6191 "This package provides functions for manipulation of R documentation
6192 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6193 updating Rd documentation for functions, methods and classes; it also includes
6194 Rd macros for citations and import of references from bibtex files for use in
6195 Rd files and roxygen2 comments, as well as many functions for manipulation of
6196 references and Rd files.")
6197 (license license:gpl2+)))
6199 (define-public r-officer
6206 (uri (cran-uri "officer" version))
6209 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6210 (build-system r-build-system)
6212 `(("r-base64enc" ,r-base64enc)
6213 ("r-digest" ,r-digest)
6214 ("r-htmltools" ,r-htmltools)
6215 ("r-magrittr" ,r-magrittr)
6218 ("r-rlang" ,r-rlang)
6222 (home-page "https://davidgohel.github.io/officer")
6223 (synopsis "Manipulation of Word and PowerPoint documents")
6225 "This package provides tools to access and manipulate Word and PowerPoint
6226 documents from R. The package focuses on tabular and graphical reporting from
6227 R; it also provides two functions that let users get document content into
6228 data objects. A set of functions lets add and remove images, tables and
6229 paragraphs of text in new or existing documents. When working with PowerPoint
6230 presentations, slides can be added or removed; shapes inside slides can also
6231 be added or removed. When working with Word documents, a cursor can be used
6232 to help insert or delete content at a specific location in the document.")
6233 (license license:gpl3)))
6235 (define-public r-abn
6242 (uri (cran-uri "abn" version))
6245 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6246 (build-system r-build-system)
6250 `(("r-lme4" ,r-lme4)
6254 ("r-rcpparmadillo" ,r-rcpparmadillo)
6255 ("r-rjags" ,r-rjags)))
6256 (home-page "http://www.r-bayesian-networks.org")
6257 (synopsis "Modelling multivariate data with additive bayesian networks")
6259 "Bayesian network analysis is a form of probabilistic graphical models
6260 which derives from empirical data a directed acyclic graph, DAG, describing
6261 the dependency structure between random variables. An additive Bayesian
6262 network model consists of a form of a DAG where each node comprises a
6263 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6264 equivalent to Bayesian multivariate regression using graphical modelling, they
6265 generalises the usual multivariable regression, GLM, to multiple dependent
6266 variables. This package provides routines to help determine optimal Bayesian
6267 network models for a given data set, where these models are used to identify
6268 statistical dependencies in messy, complex data.")
6269 (license license:gpl2+)))
6271 (define-public r-acd
6278 (uri (cran-uri "ACD" version))
6281 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6282 (properties `((upstream-name . "ACD")))
6283 (build-system r-build-system)
6284 (home-page "https://cran.r-project.org/web/packages/ACD/")
6285 (synopsis "Categorical data analysis with complete or missing responses")
6287 "This package provides tools for categorical data analysis with complete
6288 or missing responses.")
6289 (license license:gpl2+)))
6291 (define-public r-acdm
6298 (uri (cran-uri "ACDm" version))
6301 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6302 (properties `((upstream-name . "ACDm")))
6303 (build-system r-build-system)
6305 `(("r-dplyr" ,r-dplyr)
6306 ("r-ggplot2" ,r-ggplot2)
6308 ("r-rsolnp" ,r-rsolnp)
6310 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6311 (synopsis "Tools for Autoregressive Conditional Duration Models")
6313 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6314 and Russell, 1998) models. It creates trade, price or volume durations from
6315 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6317 (license license:gpl2+)))
6319 (define-public r-overlap
6326 (uri (cran-uri "overlap" version))
6329 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6330 (build-system r-build-system)
6331 (home-page "https://cran.r-project.org/web/packages/overlap/")
6332 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6334 "This package provides functions to fit kernel density functions to data
6335 on temporal activity patterns of animals; estimate coefficients of overlapping
6336 of densities for two species; and calculate bootstrap estimates of confidence
6338 (license license:gpl3+)))
6340 (define-public r-snakecase
6342 (name "r-snakecase")
6347 (uri (cran-uri "snakecase" version))
6350 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6351 (build-system r-build-system)
6353 `(("r-stringi" ,r-stringi)
6354 ("r-stringr" ,r-stringr)))
6355 (home-page "https://github.com/Tazinho/snakecase")
6356 (synopsis "Convert strings into any case")
6358 "This package provides a consistent, flexible and easy to use tool to
6359 parse and convert strings into cases like snake or camel among others.")
6360 (license license:gpl3)))
6362 (define-public r-prediction
6364 (name "r-prediction")
6369 (uri (cran-uri "prediction" version))
6372 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6373 (build-system r-build-system)
6375 `(("r-data-table" ,r-data-table)))
6376 (home-page "https://github.com/leeper/prediction")
6377 (synopsis "Tidy, type-safe prediction methods")
6379 "This package provides the @code{prediction()} function, a type-safe
6380 alternative to @code{predict()} that always returns a data frame. The package
6381 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6382 from the @code{stats} package, as well as numerous other model classes from
6383 other add-on packages.")
6384 (license license:expat)))
6386 (define-public r-insight
6393 (uri (cran-uri "insight" version))
6396 "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad"))))
6397 (build-system r-build-system)
6398 (home-page "https://easystats.github.io/insight/")
6399 (synopsis "Easy access to model information for various model objects")
6401 "This package provides a tool to provide an easy, intuitive and
6402 consistent access to information contained in various R models, like model
6403 formulas, model terms, information about random effects, data that was used to
6404 fit the model or data from response variables. The package mainly revolves
6405 around two types of functions: Functions that find (the names of) information,
6406 starting with @code{find_}, and functions that get the underlying data,
6407 starting with @code{get_}. The package has a consistent syntax and works with
6408 many different model objects, where otherwise functions to access these
6409 information are missing.")
6410 (license license:gpl3)))
6412 (define-public r-sjlabelled
6414 (name "r-sjlabelled")
6419 (uri (cran-uri "sjlabelled" version))
6422 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6423 (build-system r-build-system)
6425 `(("r-haven" ,r-haven)
6426 ("r-insight" ,r-insight)
6427 ("r-magrittr" ,r-magrittr)
6428 ("r-purrr" ,r-purrr)
6429 ("r-rlang" ,r-rlang)
6430 ("r-tidyselect" ,r-tidyselect)))
6431 (home-page "https://github.com/strengejacke/sjlabelled")
6432 (synopsis "Labelled data utility functions")
6434 "This package provides a collection of functions dealing with labelled
6435 data, like reading and writing data between R and other statistical software
6436 packages. This includes easy ways to get, set or change value and variable
6437 label attributes, to convert labelled vectors into factors or numeric (and
6438 vice versa), or to deal with multiple declared missing values.")
6439 (license license:gpl3)))
6441 (define-public r-sjmisc
6448 (uri (cran-uri "sjmisc" version))
6451 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6452 (build-system r-build-system)
6454 `(("r-dplyr" ,r-dplyr)
6455 ("r-insight" ,r-insight)
6456 ("r-magrittr" ,r-magrittr)
6457 ("r-purrr" ,r-purrr)
6458 ("r-rlang" ,r-rlang)
6459 ("r-sjlabelled" ,r-sjlabelled)
6460 ("r-tidyselect" ,r-tidyselect)))
6461 (home-page "https://github.com/strengejacke/sjmisc")
6462 (synopsis "Data and variable transformation functions")
6464 "This package is a collection of miscellaneous utility functions,
6465 supporting data transformation tasks like recoding, dichotomizing or grouping
6466 variables, setting and replacing missing values. The data transformation
6467 functions also support labelled data, and all integrate seamlessly into a
6468 tidyverse workflow.")
6469 (license license:gpl3)))
6471 (define-public r-nortest
6478 (uri (cran-uri "nortest" version))
6481 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6482 (build-system r-build-system)
6483 (home-page "https://cran.r-project.org/web/packages/nortest/")
6484 (synopsis "Tests for normality")
6486 "This package provides five omnibus tests for testing the composite
6487 hypothesis of normality.")
6488 (license license:gpl2+)))
6490 (define-public r-moonbook
6497 (uri (cran-uri "moonBook" version))
6500 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6501 (properties `((upstream-name . "moonBook")))
6502 (build-system r-build-system)
6504 `(("r-magrittr" ,r-magrittr)
6505 ("r-nortest" ,r-nortest)
6506 ("r-purrr" ,r-purrr)
6507 ("r-sjmisc" ,r-sjmisc)
6508 ("r-stringr" ,r-stringr)
6509 ("r-survival" ,r-survival)))
6510 (home-page "https://github.com/cardiomoon/moonBook")
6511 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6513 "This package provides several analysis-related functions for the book
6514 entitled \"R statistics and graph for medical articles\" (written in Korean),
6515 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6517 (license license:gpl2)))
6519 (define-public r-flextable
6521 (name "r-flextable")
6526 (uri (cran-uri "flextable" version))
6529 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6530 (build-system r-build-system)
6532 `(("r-base64enc" ,r-base64enc)
6533 ("r-data-table" ,r-data-table)
6534 ("r-gdtools" ,r-gdtools)
6535 ("r-htmltools" ,r-htmltools)
6536 ("r-knitr" ,r-knitr)
6537 ("r-officer" ,r-officer)
6538 ("r-rlang" ,r-rlang)
6539 ("r-rmarkdown" ,r-rmarkdown)
6540 ("r-xml2" ,r-xml2)))
6541 (home-page "https://davidgohel.github.io/flextable")
6542 (synopsis "Functions for tabular reporting")
6544 "This package provides tools to create pretty tables for HTML documents
6545 and other formats. Functions are provided to let users create tables, modify
6546 and format their content. It extends the @code{officer} package and can be
6547 used within R markdown documents when rendering to HTML and to Word
6549 (license license:gpl3)))
6551 (define-public r-writexl
6558 (uri (cran-uri "writexl" version))
6561 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6562 (build-system r-build-system)
6563 (inputs `(("zlib" ,zlib)))
6564 (home-page "https://github.com/ropensci/writexl")
6565 (synopsis "Export data frames to xlsx format")
6567 "This package provides a data frame to xlsx exporter based on
6569 (license license:bsd-2)))
6571 (define-public r-biasedurn
6573 (name "r-biasedurn")
6578 (uri (cran-uri "BiasedUrn" version))
6581 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6582 (properties `((upstream-name . "BiasedUrn")))
6583 (build-system r-build-system)
6584 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6585 (synopsis "Biased Urn model distributions")
6587 "This package provides statistical models of biased sampling in the form
6588 of univariate and multivariate noncentral hypergeometric distributions,
6589 including Wallenius' noncentral hypergeometric distribution and Fisher's
6590 noncentral hypergeometric distribution (also called extended hypergeometric
6592 (license license:gpl3)))
6594 (define-public r-goplot
6601 (uri (cran-uri "GOplot" version))
6604 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6605 (properties `((upstream-name . "GOplot")))
6606 (build-system r-build-system)
6608 `(("r-ggdendro" ,r-ggdendro)
6609 ("r-ggplot2" ,r-ggplot2)
6610 ("r-gridextra" ,r-gridextra)
6611 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6612 (home-page "https://github.com/wencke/wencke.github.io")
6613 (synopsis "Visualization of functional analysis data")
6615 "This package provides an implementation of multilayered visualizations
6616 for enhanced graphical representation of functional analysis data. It
6617 combines and integrates omics data derived from expression and functional
6618 annotation enrichment analyses. Its plotting functions have been developed
6619 with an hierarchical structure in mind: starting from a general overview to
6620 identify the most enriched categories (modified bar plot, bubble plot) to a
6621 more detailed one displaying different types of relevant information for the
6622 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6623 Venn diagram, heatmap).")
6624 (license license:gpl2)))
6626 (define-public r-getopt
6633 (uri (cran-uri "getopt" version))
6636 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6637 (build-system r-build-system)
6638 (home-page "https://github.com/trevorld/getopt")
6639 (synopsis "Command-line option processor for R")
6641 "This package is designed to be used with Rscript to write shebang
6642 scripts that accept short and long options. Many users will prefer to
6643 use the packages @code{optparse} or @code{argparse} which add extra
6644 features like automatically generated help options and usage texts,
6645 support for default values, positional argument support, etc.")
6646 (license license:gpl2+)))
6648 (define-public r-findpython
6650 (name "r-findpython")
6655 (uri (cran-uri "findpython" version))
6658 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6659 (build-system r-build-system)
6660 (home-page "https://github.com/trevorld/findpython")
6661 (synopsis "Functions to find an acceptable Python binary")
6663 "This package was designed to find an acceptable Python binary that
6664 matches version and feature constraints.")
6665 (license license:expat)))
6667 ;; This in not the same as "r-argparser"
6668 (define-public r-argparse
6675 (uri (cran-uri "argparse" version))
6678 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6679 (build-system r-build-system)
6680 (inputs `(("python" ,python)))
6682 `(("r-findpython" ,r-findpython)
6683 ("r-jsonlite" ,r-jsonlite)
6685 (home-page "https://github.com/trevorld/argparse")
6686 (synopsis "Command line optional and positional argument parser")
6688 "This package provides a command line parser to be used with Rscript to
6689 write shebang scripts that gracefully accept positional and optional arguments
6690 and automatically generate usage notices.")
6691 (license license:gpl2+)))
6693 (define-public r-hash
6700 (uri (cran-uri "hash" version))
6703 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6704 (build-system r-build-system)
6705 (home-page "https://cran.r-project.org/web/packages/hash/")
6706 (synopsis "Implementation of hash/associated arrays/dictionaries")
6708 "This package implements a data structure similar to hashes in Perl and
6709 dictionaries in Python but with a purposefully R flavor. For objects of
6710 appreciable size, access using hashes outperforms native named lists and
6712 (license license:gpl2+)))
6714 (define-public r-orddom
6721 (uri (cran-uri "orddom" version))
6724 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6725 (build-system r-build-system)
6726 (propagated-inputs `(("r-psych" ,r-psych)))
6727 (home-page "https://cran.r-project.org/web/packages/orddom/")
6728 (synopsis "Ordinal dominance statistics")
6730 "This package provides tools to compute ordinal, statistics and effect
6731 sizes as an alternative to mean comparison: Cliff's delta or success rate
6732 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6733 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6734 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6735 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6736 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6737 Group (Non-)Overlap considerations.")
6738 (license license:gpl2)))
6740 (define-public r-deriv
6747 (uri (cran-uri "Deriv" version))
6750 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6751 (properties `((upstream-name . "Deriv")))
6752 (build-system r-build-system)
6753 (home-page "https://cran.r-project.org/web/packages/Deriv")
6754 (synopsis "Symbolic differentiation")
6756 "This package provides an R-based solution for symbolic differentiation.
6757 It admits user-defined functions as well as function substitution in arguments
6758 of functions to be differentiated. Some symbolic simplification is part of
6760 (license license:gpl3+)))
6762 (define-public r-doby
6769 (uri (cran-uri "doBy" version))
6772 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6773 (properties `((upstream-name . "doBy")))
6774 (build-system r-build-system)
6776 `(("r-broom" ,r-broom)
6777 ("r-deriv" ,r-deriv)
6778 ("r-dplyr" ,r-dplyr)
6779 ("r-magrittr" ,r-magrittr)
6781 ("r-matrix" ,r-matrix)
6783 ("r-pbkrtest" ,r-pbkrtest)
6784 ("r-tibble" ,r-tibble)))
6785 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6786 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6788 "This package contains:
6791 @item facilities for working with grouped data: @code{do}
6792 something to data stratified @code{by} some variables.
6793 @item implementations of least-squares means, general linear contrasts, and
6794 @item miscellaneous other utilities.
6796 (license license:gpl2+)))
6798 (define-public r-refgenome
6800 (name "r-refgenome")
6805 (uri (cran-uri "refGenome" version))
6808 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6809 (properties `((upstream-name . "refGenome")))
6810 (build-system r-build-system)
6814 ("r-rsqlite" ,r-rsqlite)))
6815 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6817 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6819 "This package contains functionality for importing and managing of
6820 downloaded genome annotation data from the Ensembl genome browser (European
6821 Bioinformatics Institute) and from the UCSC genome browser (University of
6822 California, Santa Cruz) and annotation routines for genomic positions and
6823 splice site positions.")
6824 (license license:gpl2)))
6826 (define-public r-basix
6833 (uri (cran-uri "BASIX" version))
6836 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6837 (properties `((upstream-name . "BASIX")))
6838 (build-system r-build-system)
6839 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6840 (synopsis "Efficient C/C++ toolset for R")
6842 "BASIX provides some efficient C/C++ implementations of native R
6843 procedures to speed up calculations in R.")
6844 (license license:gpl2)))
6846 (define-public r-blockfest
6848 (name "r-blockfest")
6853 (uri (cran-uri "BlockFeST" version))
6856 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6857 (properties `((upstream-name . "BlockFeST")))
6858 (build-system r-build-system)
6859 (propagated-inputs `(("r-basix" ,r-basix)))
6860 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6861 (synopsis "Bayesian calculation of region-specific fixation index")
6863 "This package provides an R implementation of an extension of the
6864 BayeScan software for codominant markers, adding the option to group
6865 individual SNPs into pre-defined blocks. A typical application of this new
6866 approach is the identification of genomic regions, genes, or gene sets
6867 containing one or more SNPs that evolved under directional selection.")
6868 (license license:gpl2)))
6870 (define-public r-proc
6877 (uri (cran-uri "pROC" version))
6880 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6881 (properties `((upstream-name . "pROC")))
6882 (build-system r-build-system)
6884 `(("r-plyr" ,r-plyr)
6885 ("r-rcpp" ,r-rcpp)))
6886 (home-page "http://expasy.org/tools/pROC/")
6887 (synopsis "Display and analyze ROC curves")
6889 "This package provides tools for visualizing, smoothing and comparing
6890 receiver operating characteristic (ROC curves). The area under the
6891 curve (AUC) can be compared with statistical tests based on U-statistics or
6892 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6893 (license license:gpl3+)))
6895 (define-public r-rootsolve
6897 (name "r-rootsolve")
6902 (uri (cran-uri "rootSolve" version))
6905 "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
6906 (properties `((upstream-name . "rootSolve")))
6907 (build-system r-build-system)
6908 (native-inputs `(("gfortran" ,gfortran)))
6909 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6910 (synopsis "Tools for the analysis of ordinary differential equations")
6912 "This package provides routines to find the root of nonlinear functions,
6913 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6914 differential equations} (ODE). It includes routines that:
6917 @item generate gradient and jacobian matrices (full and banded),
6918 @item find roots of non-linear equations by the Newton-Raphson method,
6919 @item estimate steady-state conditions of a system of (differential) equations
6920 in full, banded or sparse form, using the Newton-Raphson method, or by
6921 dynamically running,
6922 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6923 and 3-D partial differential equations, that have been converted to ordinary
6924 differential equations by numerical differencing (using the method-of-lines
6927 (license license:gpl2+)))
6929 (define-public r-abcanalysis
6931 (name "r-abcanalysis")
6936 (uri (cran-uri "ABCanalysis" version))
6938 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6939 (properties `((upstream-name . "ABCanalysis")))
6940 (build-system r-build-system)
6941 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6942 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6943 (synopsis "Computed ABC Analysis")
6945 "Multivariate data sets often differ in several factors or derived statistical
6946 parameters, which have to be selected for a valid interpretation. Basing this
6947 selection on traditional statistical limits leads occasionally to the perception
6948 of losing information from a data set. This package provides tools to calculate
6949 these limits on the basis of the mathematical properties of the distribution of
6950 the analyzed items.")
6951 (license license:gpl3)))
6953 (define-public r-slam
6960 (uri (cran-uri "slam" version))
6962 (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
6963 (build-system r-build-system)
6964 (home-page "https://cran.r-project.org/web/packages/slam/")
6965 (synopsis "Sparse lightweight arrays and matrices")
6967 "This package contains data structures and algorithms for sparse arrays and matrices,
6968 based on index arrays and simple triplet representations, respectively.")
6969 (license license:gpl2)))
6971 (define-public r-manipulatewidget
6973 (name "r-manipulatewidget")
6978 (uri (cran-uri "manipulateWidget" version))
6980 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6982 `((upstream-name . "manipulateWidget")))
6983 (build-system r-build-system)
6985 `(("r-base64enc" ,r-base64enc)
6986 ("r-codetools" ,r-codetools)
6987 ("r-htmltools" ,r-htmltools)
6988 ("r-htmlwidgets" ,r-htmlwidgets)
6989 ("r-knitr" ,r-knitr)
6990 ("r-miniui" ,r-miniui)
6991 ("r-shiny" ,r-shiny)
6992 ("r-webshot" ,r-webshot)))
6993 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6994 (synopsis "Add even more interactivity to interactive charts")
6996 "This package lets you create in just a few lines of R code a nice user interface to
6997 modify the data or the graphical parameters of one or multiple interactive
6998 charts. It is useful to quickly explore visually some data or for package
6999 developers to generate user interfaces easy to maintain.")
7000 (license license:gpl2+)))
7009 (uri (cran-uri "A3" version))
7011 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7012 (properties `((upstream-name . "A3")))
7013 (build-system r-build-system)
7015 `(("r-pbapply" ,r-pbapply)
7016 ("r-xtable" ,r-xtable)))
7017 (home-page "https://cran.r-project.org/web/packages/A3/")
7018 (synopsis "Error metrics for predictive models")
7020 "This package supplies tools for tabulating and analyzing the results of predictive
7021 models. The methods employed are applicable to virtually any predictive model
7022 and make comparisons between different methodologies straightforward.")
7023 (license license:gpl2+)))
7025 (define-public r-infotheo
7032 (uri (cran-uri "infotheo" version))
7035 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7036 (build-system r-build-system)
7037 (home-page "http://homepage.meyerp.com/software")
7038 (synopsis "Information-theoretic measures")
7040 "This package implements various measures of information theory based on
7041 several entropy estimators.")
7042 (license license:gpl3+)))
7044 (define-public r-abcoptim
7051 (uri (cran-uri "ABCoptim" version))
7053 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7054 (properties `((upstream-name . "ABCoptim")))
7055 (build-system r-build-system)
7056 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7057 (home-page "https://github.com/gvegayon/ABCoptim/")
7058 (synopsis "Optimization of Artificial Bee Colony algorithm")
7060 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7061 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7062 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7063 algorithms, and uses only common control parameters such as colony size and
7064 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7065 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7066 This version is a work-in-progress and is written in R code.")
7067 (license license:expat)))
7069 (define-public r-abcp2
7076 (uri (cran-uri "ABCp2" version))
7078 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7079 (properties `((upstream-name . "ABCp2")))
7080 (build-system r-build-system)
7081 (propagated-inputs `(("r-mass" ,r-mass)))
7082 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7083 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7085 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7086 Poisson, and Gamma distribution and estimates the proportional paternity of the
7087 second male (P2) based on the best fit distribution.")
7088 (license license:gpl2)))
7090 (define-public r-abcrf
7097 (uri (cran-uri "abcrf" version))
7099 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7100 (build-system r-build-system)
7102 `(("r-doparallel" ,r-doparallel)
7103 ("r-foreach" ,r-foreach)
7105 ("r-matrixstats" ,r-matrixstats)
7106 ("r-ranger" ,r-ranger)
7108 ("r-rcpparmadillo" ,r-rcpparmadillo)
7109 ("r-readr" ,r-readr)
7110 ("r-stringr" ,r-stringr)))
7111 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7112 (synopsis "Approximate bayesian computation via random forests")
7114 "This package performs approximate bayesian computation (ABC) model choice and
7115 parameter inference via random forests. This machine learning tool named random
7116 forests (RF) can conduct selection among the highly complex models covered by
7118 (license license:gpl2+)))
7120 (define-public r-abctools
7127 (uri (cran-uri "abctools" version))
7129 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7130 (build-system r-build-system)
7133 ("r-abind" ,r-abind)
7134 ("r-hmisc" ,r-hmisc)
7135 ("r-plyr" ,r-plyr)))
7136 (home-page "https://github.com/dennisprangle/abctools/")
7137 (synopsis "Tools for ABC analyses")
7139 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7140 including summary statistic selection and assessing coverage. This includes
7141 recent dimension reduction algorithms to tune the choice of summary statistics,
7142 and coverage methods to tune the choice of threshold.")
7143 (license license:gpl2+)))
7145 (define-public r-ggstance
7152 (uri (cran-uri "ggstance" version))
7154 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7155 (build-system r-build-system)
7157 `(("r-ggplot2" ,r-ggplot2)
7159 ("r-rlang" ,r-rlang)
7160 ("r-withr" ,r-withr)))
7161 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7162 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7164 "This package is a @code{r-ggplot2} extension that provides flipped components:
7166 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7167 @item vertical versions of @code{r-ggplot2} positions.
7169 (license license:gpl3)))
7171 (define-public r-mosaiccore
7173 (name "r-mosaiccore")
7178 (uri (cran-uri "mosaicCore" version))
7180 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7181 (properties `((upstream-name . "mosaicCore")))
7182 (build-system r-build-system)
7184 `(("r-dplyr" ,r-dplyr)
7185 ("r-lazyeval" ,r-lazyeval)
7187 ("r-rlang" ,r-rlang)
7188 ("r-tidyr" ,r-tidyr)))
7189 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7190 (synopsis "Common utilities for mosaic family packages")
7192 "Common utilities used in other Mosaic family packages are collected here.")
7193 (license license:gpl2+)))
7195 (define-public r-ggformula
7197 (name "r-ggformula")
7202 (uri (cran-uri "ggformula" version))
7204 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7205 (build-system r-build-system)
7207 `(("r-ggplot2" ,r-ggplot2)
7208 ("r-ggstance" ,r-ggstance)
7209 ("r-magrittr" ,r-magrittr)
7210 ("r-mosaiccore" ,r-mosaiccore)
7211 ("r-rlang" ,r-rlang)
7212 ("r-stringr" ,r-stringr)
7213 ("r-tibble" ,r-tibble)
7214 ("r-tidyr" ,r-tidyr)))
7215 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7216 (synopsis "Formula interface for the @code{r-ggplot2}")
7218 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7219 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7220 and extends the excellent simplicity of the lattice-graphics formula interface,
7221 while providing the intuitive capabilities of @code{r-ggplot2}.")
7222 (license license:expat)))
7224 (define-public r-mosaicdata
7226 (name "r-mosaicdata")
7231 (uri (cran-uri "mosaicData" version))
7233 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7234 (properties `((upstream-name . "mosaicData")))
7235 (build-system r-build-system)
7236 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7237 (synopsis "Data sets for project Mosaic")
7239 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7240 used to teach mathematics, statistics, computation and modeling.")
7241 (license license:gpl2+)))
7243 (define-public r-raster
7250 (uri (cran-uri "raster" version))
7253 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7254 (build-system r-build-system)
7256 `(("r-rcpp" ,r-rcpp)
7258 (home-page "https://www.rspatial.org/")
7259 (synopsis "Geographic data analysis and modeling")
7261 "The package implements basic and high-level functions for reading,
7262 writing, manipulating, analyzing and modeling of gridded spatial data.
7263 Processing of very large files is supported.")
7264 (license license:gpl3+)))
7266 (define-public r-mosaic
7273 (uri (cran-uri "mosaic" version))
7275 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7276 (build-system r-build-system)
7278 `(("r-broom" ,r-broom)
7279 ("r-dplyr" ,r-dplyr)
7280 ("r-ggdendro" ,r-ggdendro)
7281 ("r-ggformula" ,r-ggformula)
7282 ("r-ggplot2" ,r-ggplot2)
7283 ("r-ggrepel" ,r-ggrepel)
7285 ("r-gridextra" ,r-gridextra)
7286 ("r-lattice" ,r-lattice)
7287 ("r-latticeextra" ,r-latticeextra)
7288 ("r-lazyeval" ,r-lazyeval)
7290 ("r-matrix" ,r-matrix)
7291 ("r-mosaiccore" ,r-mosaiccore)
7292 ("r-mosaicdata" ,r-mosaicdata)
7293 ("r-readr" ,r-readr)
7294 ("r-tidyr" ,r-tidyr)))
7295 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7296 (synopsis "Mathematics, statistics, and computation teaching utilities")
7298 "This package contain data sets and utilities from
7299 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7300 statistics, computation and modeling. Project MOSAIC is a community of
7301 educators working to tie together aspects of quantitative work that students
7302 in science, technology, engineering and mathematics will need in their
7303 professional lives, but which are usually taught in isolation, if at all.")
7304 (license license:gpl2+)))
7306 (define-public r-abd
7313 (uri (cran-uri "abd" version))
7315 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7316 (build-system r-build-system)
7318 `(("r-lattice" ,r-lattice)
7319 ("r-mosaic" ,r-mosaic)
7320 ("r-nlme" ,r-nlme)))
7321 (home-page "https://cran.r-project.org/web/packages/abd/")
7322 (synopsis "Analysis of biological data")
7324 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7325 biological data by Michael Whitlock and Dolph Schluter.")
7326 (license license:gpl2)))
7328 (define-public r-svgui
7335 (uri (cran-uri "svGUI" version))
7337 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7338 (properties `((upstream-name . "svGUI")))
7339 (build-system r-build-system)
7340 (home-page "https://github.com/SciViews/svGUI/")
7341 (synopsis "Functions for managing GUI clients in R")
7343 "The SciViews @code{svGUI} package eases the management of Graphical User
7344 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7345 centralizes info about GUI elements currently used, and it dispatches GUI
7346 calls to the particular toolkits in use in function of the context.")
7347 (license license:gpl2)))
7349 (define-public r-svdialogs
7351 (name "r-svdialogs")
7356 (uri (cran-uri "svDialogs" version))
7358 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7359 (properties `((upstream-name . "svDialogs")))
7360 (build-system r-build-system)
7363 ("zenity" ,zenity)))
7365 `(("r-rstudioapi" ,r-rstudioapi)
7366 ("r-svgui" ,r-svgui)))
7367 (home-page "https://github.com/SciViews/svDialogs/")
7368 (synopsis "Portable dialog boxes")
7370 "This package helps to construct standard dialog boxes for your GUI, including
7371 message boxes, input boxes, list, file or directory selection, and others. In
7372 case R cannot display GUI dialog boxes, a simpler command line version of these
7373 interactive elements is also provided as a fallback solution.")
7374 (license license:gpl2)))
7376 (define-public r-abe
7383 (uri (cran-uri "abe" version))
7386 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7387 (build-system r-build-system)
7388 (home-page "https://cran.r-project.org/web/packages/abe/")
7389 (synopsis "Augmented backward elimination")
7391 "This package performs augmented backward elimination and checks the
7392 stability of the obtained model. Augmented backward elimination combines
7393 significance or information based criteria with the change in estimate to
7394 either select the optimal model for prediction purposes or to serve as a tool
7395 to obtain a practically sound, highly interpretable model.")
7396 (license license:gpl2+)))
7398 (define-public r-abf2
7405 (uri (cran-uri "abf2" version))
7407 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7408 (build-system r-build-system)
7409 (home-page "https://cran.r-project.org/web/packages/abf2/")
7410 (synopsis "Load gap-free axon @code{r-abf2} files")
7412 "This package loads electrophysiology data from ABF2 files, as created by
7413 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7414 mode are currently supported.")
7415 (license license:artistic2.0)))
7417 (define-public r-abhgenotyper
7419 (name "r-abhgenotyper")
7424 (uri (cran-uri "ABHgenotypeR" version))
7426 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7427 (properties `((upstream-name . "ABHgenotypeR")))
7428 (build-system r-build-system)
7430 `(("r-ggplot2" ,r-ggplot2)
7431 ("r-reshape2" ,r-reshape2)))
7432 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7433 (synopsis "Visualize and manipulate ABH genotypes")
7435 "The @code{r-abhgenotyper} package provides simple imputation,
7436 error-correction and plotting capacities for genotype data. The package is
7437 supposed to serve as an intermediate but independent analysis tool between the
7438 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7439 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7440 genotypes as \"graphical genotypes\".")
7441 (license license:gpl3)))
7443 (define-public r-furrr
7450 (uri (cran-uri "furrr" version))
7453 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7454 (build-system r-build-system)
7456 `(("r-future" ,r-future)
7457 ("r-globals" ,r-globals)
7458 ("r-purrr" ,r-purrr)
7459 ("r-rlang" ,r-rlang)))
7460 (home-page "https://github.com/DavisVaughan/furrr")
7461 (synopsis "Apply mapping functions in parallel using futures")
7463 "This package provides implementations of the family of @code{map()}
7464 functions from the @code{purrr} package that can be resolved using any
7465 @code{future}-supported backend, e.g. parallel on the local machine or
7466 distributed on a compute cluster.")
7467 (license license:lgpl2.1+)))
7469 (define-public r-abjutils
7476 (uri (cran-uri "abjutils" version))
7478 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7479 (build-system r-build-system)
7481 `(("r-devtools" ,r-devtools)
7482 ("r-dplyr" ,r-dplyr)
7483 ("r-furrr" ,r-furrr)
7484 ("r-future" ,r-future)
7487 ("r-magrittr" ,r-magrittr)
7488 ("r-progress" ,r-progress)
7489 ("r-purrr" ,r-purrr)
7490 ("r-readr" ,r-readr)
7491 ("r-rlang" ,r-rlang)
7492 ("r-rstudioapi" ,r-rstudioapi)
7493 ("r-scales" ,r-scales)
7494 ("r-stringi" ,r-stringi)
7495 ("r-stringr" ,r-stringr)
7496 ("r-tibble" ,r-tibble)
7497 ("r-tidyr" ,r-tidyr)))
7498 (home-page "https://github.com/abjur/abjutils/")
7499 (synopsis "Collection of tools for jurimetrical analysis")
7501 "This package implements general purpose tools, such as functions for
7502 sampling and basic manipulation of Brazilian lawsuits identification number.
7503 It also implements functions for text cleaning, such as accentuation
7505 (license license:expat)))
7507 (define-public r-abnormality
7509 (name "r-abnormality")
7514 (uri (cran-uri "abnormality" version))
7516 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7517 (build-system r-build-system)
7519 `(("r-mass" ,r-mass)
7520 ("r-matrix" ,r-matrix)))
7521 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7522 (synopsis "Measure a subject's abnormality with respect to a reference population")
7524 "This package contains functions to implement the methodology and
7525 considerations laid out by Marks et al. in the article \"Measuring abnormality
7526 in high dimensional spaces: applications in biomechanical gait analysis\".
7527 Using high-dimensional datasets to measure a subject's overall level of
7528 abnormality as compared to a reference population is often needed in outcomes
7530 (license license:expat)))
7532 (define-public r-abodoutlier
7534 (name "r-abodoutlier")
7539 (uri (cran-uri "abodOutlier" version))
7541 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7542 (properties `((upstream-name . "abodOutlier")))
7543 (build-system r-build-system)
7545 `(("r-cluster" ,r-cluster)))
7546 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7547 (synopsis "Angle-based outlier detection")
7549 "This package performs angle-based outlier detection on a given data
7550 frame. It offers three methods to process data:
7552 @item full but slow implementation using all the data that has cubic
7554 @item a fully randomized method;
7555 @item a method using k-nearest neighbours.
7557 These algorithms are well suited for high dimensional data outlier
7559 (license license:expat)))
7561 (define-public r-abps
7568 (uri (cran-uri "ABPS" version))
7570 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7571 (properties `((upstream-name . "ABPS")))
7572 (build-system r-build-system)
7573 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7574 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7575 (synopsis "Abnormal blood profile score to detect blood doping")
7577 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7578 The ABPS is a part of the Athlete biological passport program of the World
7579 anti-doping agency, which combines several blood parameters into a single
7580 score in order to detect blood doping. The package also contains functions to
7581 calculate other scores used in anti-doping programs, such as the ratio of
7582 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7583 (license license:gpl2+)))
7585 (define-public r-parmigene
7587 (name "r-parmigene")
7592 (uri (cran-uri "parmigene" version))
7595 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7596 (build-system r-build-system)
7597 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7598 (synopsis "Mutual information estimation for gene network reconstruction")
7600 "This package provides a parallel estimation of the mutual information
7601 based on entropy estimates from k-nearest neighbors distances and algorithms
7602 for the reconstruction of gene regulatory networks.")
7603 (license license:agpl3+)))
7605 (define-public r-pscl
7612 (uri (cran-uri "pscl" version))
7614 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7615 (build-system r-build-system)
7617 `(("r-mass" ,r-mass)))
7618 (home-page "https://github.com/atahk/pscl/")
7619 (synopsis "Political science computational laboratory")
7621 "The @code{pscl} is an R package providing classes and methods for:
7623 @item Bayesian analysis of roll call data (item-response models);
7624 @item elementary Bayesian statistics;
7625 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7627 @item utility functions.
7629 (license license:gpl2)))
7631 (define-public r-accelmissing
7633 (name "r-accelmissing")
7638 (uri (cran-uri "accelmissing" version))
7640 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7641 (build-system r-build-system)
7643 `(("r-mice" ,r-mice)
7644 ("r-pscl" ,r-pscl)))
7645 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7646 (synopsis "Missing value imputation for accelerometer data")
7648 "This package provides a statistical method to impute the missing values in
7649 accelerometer data. The methodology includes both parametric and
7650 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7651 model. It also provides multiple functions to preprocess the accelerometer data
7652 previous to the missing data imputation. These include detecting the wearing
7653 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7654 (license license:gpl2+)))
7656 (define-public r-mhsmm
7663 (uri (cran-uri "mhsmm" version))
7665 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7666 (build-system r-build-system)
7667 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7668 (home-page "https://github.com/jaredo/mhsmm/")
7669 (synopsis "Inference for hidden Markov and semi-Markov models")
7671 "The @code{r-mhsmm} package implements estimation and prediction methods for
7672 hidden Markov and semi-Markov models for multiple observation sequences. Such
7673 techniques are of interest when observed data is thought to be dependent on some
7674 unobserved (or hidden) state. Also, this package is suitable for equidistant
7675 time series data, with multivariate and/or missing data. Allows user defined
7676 emission distributions.")
7677 (license license:gpl2+)))
7679 (define-public r-nleqslv
7686 (uri (cran-uri "nleqslv" version))
7688 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7689 (build-system r-build-system)
7690 (native-inputs `(("gfortran" ,gfortran)))
7691 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7692 (synopsis "Solve systems of nonlinear equations")
7694 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7695 Broyden or a Newton method with a choice of global strategies such as line
7696 search and trust region. There are options for using a numerical or user
7697 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7698 singular or ill-conditioned Jacobian.")
7699 (license license:gpl2+)))
7701 (define-public r-physicalactivity
7703 (name "r-physicalactivity")
7708 (uri (cran-uri "PhysicalActivity" version))
7710 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7712 `((upstream-name . "PhysicalActivity")))
7713 (build-system r-build-system)
7714 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7715 (synopsis "Procesing accelerometer data for physical activity measurement")
7717 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7718 for classification of monitor wear and nonwear time intervals in accelerometer
7719 data collected to assess physical activity. The package also contains functions
7720 for making plots of accelerometer data and obtaining the summary of various
7721 information including daily monitor wear time and the mean monitor wear time
7722 during valid days. The revised package version 0.2-1 improved the functions
7723 regarding speed, robustness and add better support for time zones and daylight
7724 saving. In addition, several functions were added:
7726 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7727 @item the @code{markPAI} can categorize physical activity intensity level based
7728 on user-defined cut-points of accelerometer counts.
7730 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7731 @code{queryActigraph} functions.")
7732 (license license:gpl3+)))
7734 (define-public r-acc
7741 (uri (cran-uri "acc" version))
7743 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7744 (build-system r-build-system)
7746 `(("r-circlize" ,r-circlize)
7748 ("r-ggplot2" ,r-ggplot2)
7749 ("r-iterators" ,r-iterators)
7750 ("r-mhsmm" ,r-mhsmm)
7751 ("r-nleqslv" ,r-nleqslv)
7752 ("r-physicalactivity" ,r-physicalactivity)
7754 ("r-r-utils" ,r-r-utils)
7756 ("r-rcpparmadillo" ,r-rcpparmadillo)
7757 ("r-rsqlite" ,r-rsqlite)
7759 (home-page "https://cran.r-project.org/web/packages/acc/")
7760 (synopsis "Exploring accelerometer data")
7762 "This package processes accelerometer data from uni-axial and tri-axial devices
7763 and generates data summaries. Also, includes functions to plot, analyze, and
7764 simulate accelerometer data.")
7765 (license license:gpl2+)))
7767 (define-public r-rbenchmark
7769 (name "r-rbenchmark")
7774 (uri (cran-uri "rbenchmark" version))
7776 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7777 (build-system r-build-system)
7778 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7779 (synopsis "Benchmarking routine for R")
7781 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7782 and is intended to facilitate benchmarking of arbitrary R code. The library
7783 consists of just one function, benchmark, which is a simple wrapper around
7784 system.time. Given a specification of the benchmarking process (counts of
7785 replications, evaluation environment) and an arbitrary number of expressions,
7786 benchmark evaluates each of the expressions in the specified environment,
7787 replicating the evaluation as many times as specified, and returning the results
7788 conveniently wrapped into a data frame.")
7789 (license license:gpl2+)))
7791 (define-public r-mitools
7798 (uri (cran-uri "mitools" version))
7801 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7802 (build-system r-build-system)
7803 (propagated-inputs `(("r-dbi" ,r-dbi)))
7804 (home-page "https://cran.r-project.org/web/packages/mitools/")
7805 (synopsis "Tools for multiple imputation of missing data")
7807 "This package provides tools to perform analyses and combine results from
7808 multiple-imputation datasets.")
7809 (license license:gpl2)))
7811 (define-public r-magick
7818 (uri (cran-uri "magick" version))
7821 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7822 (build-system r-build-system)
7824 `(("imagemagick" ,imagemagick)
7827 `(("r-curl" ,r-curl)
7828 ("r-magrittr" ,r-magrittr)
7829 ("r-rcpp" ,r-rcpp)))
7831 `(("pkg-config" ,pkg-config)))
7832 (home-page "https://github.com/ropensci/magick")
7833 (synopsis "Advanced graphics and image-processing in R")
7835 "This package provides bindings to ImageMagick, a comprehensive image
7836 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7837 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7838 operations are vectorized via the Magick++ STL meaning they operate either on
7839 a single frame or a series of frames for working with layers, collages, or
7840 animation. In RStudio, images are automatically previewed when printed to the
7841 console, resulting in an interactive editing environment.")
7842 (license license:expat)))
7844 (define-public r-survey
7851 (uri (cran-uri "survey" version))
7854 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7855 (build-system r-build-system)
7857 `(("r-lattice" ,r-lattice)
7858 ("r-matrix" ,r-matrix)
7859 ("r-minqa" ,r-minqa)
7860 ("r-mitools" ,r-mitools)
7861 ("r-numderiv" ,r-numderiv)
7862 ("r-survival" ,r-survival)))
7863 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7864 (synopsis "Analysis of complex survey samples")
7866 "This package provides tools for the analysis of complex survey samples.
7867 The provided features include: summary statistics, two-sample tests, rank
7868 tests, generalised linear models, cumulative link models, Cox models,
7869 loglinear models, and general maximum pseudolikelihood estimation for
7870 multistage stratified, cluster-sampled, unequally weighted survey samples;
7871 variances by Taylor series linearisation or replicate weights;
7872 post-stratification, calibration, and raking; two-phase subsampling designs;
7873 graphics; PPS sampling without replacement; principal components, and factor
7875 ;; Either version of the GPL.
7876 (license (list license:gpl2 license:gpl3))))
7878 (define-public r-gee
7885 (uri (cran-uri "gee" version))
7888 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
7889 (properties `((upstream-name . "gee")))
7890 (build-system r-build-system)
7892 `(("gfortran" ,gfortran)))
7893 (home-page "https://cran.r-project.org/web/packages/gee/")
7894 (synopsis "Generalized estimation equation solver")
7896 "This package provides a solver for generalized estimation equations.")
7897 (license license:gpl2)))
7899 (define-public r-tab
7906 (uri (cran-uri "tab" version))
7909 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
7910 (properties `((upstream-name . "tab")))
7911 (build-system r-build-system)
7913 `(("r-dplyr" ,r-dplyr)
7915 ("r-knitr" ,r-knitr)
7917 ("r-survey" ,r-survey)
7918 ("r-survival" ,r-survival)
7919 ("r-xtable" ,r-xtable)))
7920 (home-page "https://cran.r-project.org/web/packages/tab/")
7921 (synopsis "Create summary tables for statistical reports")
7923 "This package contains functions for creating various types of summary
7924 tables, e.g. comparing characteristics across levels of a categorical variable
7925 and summarizing fitted generalized linear models, generalized estimating
7926 equations, and Cox proportional hazards models. Functions are available to
7927 handle data from simple random samples as well as complex surveys.")
7928 (license license:gpl3+)))
7930 (define-public r-dvmisc
7937 (uri (cran-uri "dvmisc" version))
7939 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
7940 (build-system r-build-system)
7942 `(("r-cubature" ,r-cubature)
7943 ("r-data-table" ,r-data-table)
7944 ("r-dplyr" ,r-dplyr)
7945 ("r-ggplot2" ,r-ggplot2)
7947 ("r-mvtnorm" ,r-mvtnorm)
7948 ("r-pracma" ,r-pracma)
7949 ("r-rbenchmark" ,r-rbenchmark)
7951 ("r-survey" ,r-survey)
7953 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7954 (synopsis "Faster computation of common statistics and miscellaneous functions")
7956 "This package implements faster versions of base R functions (e.g. mean, standard
7957 deviation, covariance, weighted mean), mostly written in C++, along with
7958 miscellaneous functions for various purposes (e.g. create the histogram with
7959 fitted probability density function or probability mass function curve, create
7960 the body mass index groups, assess the linearity assumption in logistic
7962 (license license:gpl2)))
7964 (define-public r-accelerometry
7966 (name "r-accelerometry")
7971 (uri (cran-uri "accelerometry" version))
7973 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7974 (build-system r-build-system)
7976 `(("r-dvmisc" ,r-dvmisc)
7977 ("r-rcpp" ,r-rcpp)))
7978 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7979 (synopsis "Functions for processing accelerometer data")
7981 "This package provides a collection of functions that perform operations on
7982 time-series accelerometer data, such as identify the non-wear time, flag minutes
7983 that are part of an activity bout, and find the maximum 10-minute average count
7984 value. The functions are generally very flexible, allowing for a variety of
7985 algorithms to be implemented.")
7986 (license license:gpl3)))
7988 (define-public r-absim
7995 (uri (cran-uri "AbSim" version))
7997 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7998 (properties `((upstream-name . "AbSim")))
7999 (build-system r-build-system)
8002 ("r-powerlaw" ,r-powerlaw)))
8003 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8004 (synopsis "Time resolved simulations of antibody repertoires")
8006 "This package provides simulation methods for the evolution of antibody repertoires.
8007 The heavy and light chain variable region of both human and C57BL/6 mice can
8008 be simulated in a time-dependent fashion. Both single lineages using one set of
8009 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8010 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8011 Upon completion, the main loop of the algorithm begins, with each iteration
8012 representing one simulated time step. Various mutation events are possible at
8013 each time step, contributing to a diverse final repertoire.")
8014 (license license:gpl2)))
8016 (define-public r-quic
8023 (uri (cran-uri "QUIC" version))
8025 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8026 (properties `((upstream-name . "QUIC")))
8027 (build-system r-build-system)
8028 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8029 (synopsis "Regularized sparse inverse covariance matrix estimation")
8031 "This package implements the regularized Gaussian maximum likelihood
8032 estimation of the inverse of a covariance matrix. It uses Newton's method and
8033 coordinate descent to solve the regularized inverse covariance matrix
8034 estimation problem.")
8035 ;; The project home page states that the release is under GPLv3 or later.
8036 ;; The CRAN page only says GPL-3.
8037 (license license:gpl3+)))
8039 (define-public r-abundant
8046 (uri (cran-uri "abundant" version))
8048 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8049 (build-system r-build-system)
8051 `(("r-quic" ,r-quic)))
8052 (home-page "https://cran.r-project.org/web/packages/abundant/")
8053 (synopsis "Abundant regression and high-dimensional principal fitted components")
8055 "This package provides tools to fit and predict with the high-dimensional
8056 principal fitted components model. This model is described by Cook, Forzani,
8057 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8058 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8059 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8060 (license license:gpl2+)))
8062 (define-public r-ac3net
8069 (uri (cran-uri "Ac3net" version))
8071 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8072 (properties `((upstream-name . "Ac3net")))
8073 (build-system r-build-system)
8075 `(("r-data-table" ,r-data-table)))
8076 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8077 (synopsis "Inferring directional conservative causal core gene networks")
8078 (description "This package infers directional Conservative causal core
8079 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8080 directional network.")
8081 (license license:gpl3+)))
8083 (define-public r-aca
8090 (uri (cran-uri "ACA" version))
8092 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8093 (properties `((upstream-name . "ACA")))
8094 (build-system r-build-system)
8095 (home-page "https://cran.r-project.org/web/packages/ACA/")
8096 (synopsis "Abrupt change-point or aberration detection in point series")
8098 "This package offers an interactive function for the detection of breakpoints in
8100 ;; Any version of the GPL
8101 (license (list license:gpl2+ license:gpl3+))))
8103 (define-public r-acceptancesampling
8105 (name "r-acceptancesampling")
8110 (uri (cran-uri "AcceptanceSampling" version))
8112 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8114 `((upstream-name . "AcceptanceSampling")))
8115 (build-system r-build-system)
8116 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8117 (synopsis "Creation and evaluation of acceptance sampling plans")
8119 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8120 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8121 in quality control and improvement. International standards of acceptance
8122 sampling provide sampling plans for specific circumstances. The aim of this
8123 package is to provide an easy-to-use interface to visualize single, double or
8124 multiple sampling plans. In addition, methods have been provided to enable the
8125 user to assess sampling plans against pre-specified levels of performance, as
8126 measured by the probability of acceptance for a given level of quality in the
8128 (license license:gpl3+)))
8130 (define-public r-acclma
8137 (uri (cran-uri "ACCLMA" version))
8139 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8140 (properties `((upstream-name . "ACCLMA")))
8141 (build-system r-build-system)
8142 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8143 (synopsis "ACC & LMA graph plotting")
8145 "This package contains a function that imports data from a @acronym{CSV,
8146 Comma-Separated Values} file, or uses manually entered data from the format (x,
8147 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8148 Curve} vs @acronym{LOI, Line of Independence} graph and
8149 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8150 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8151 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8152 string) was passed, a manual data entry window is opened. The header parameter
8153 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8154 a header row or not. The dataset should contain only one independent variable
8155 (x) and one dependent variable (y) and can contain a weight for each
8157 (license license:gpl2)))
8159 (define-public r-aspi
8166 (uri (cran-uri "aspi" version))
8168 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8169 (build-system r-build-system)
8171 "https://cran.r-project.org/web/packages/aspi/")
8173 "Analysis of symmetry of parasitic infections")
8175 "This package provides tools for the analysis and visualization of bilateral
8176 asymmetry in parasitic infections.")
8177 (license license:gpl3+)))
8179 (define-public r-sandwich
8186 (uri (cran-uri "sandwich" version))
8189 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8190 (build-system r-build-system)
8192 `(("r-zoo" ,r-zoo)))
8193 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8194 (synopsis "Robust Covariance Matrix Estimators")
8196 "This package provides model-robust standard error estimators for
8197 cross-sectional, time series, clustered, panel, and longitudinal data.")
8198 ;; Either version of the license.
8199 (license (list license:gpl2 license:gpl3))))
8201 (define-public r-th-data
8208 (uri (cran-uri "TH.data" version))
8211 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8212 (properties `((upstream-name . "TH.data")))
8213 (build-system r-build-system)
8215 `(("r-mass" ,r-mass)
8216 ("r-survival" ,r-survival)))
8217 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8218 (synopsis "Shared data sets")
8220 "This package contains supporting data sets that are used in other
8221 packages maintained by Torsten Hothorn.")
8222 (license license:gpl3)))
8224 (define-public r-multcomp
8231 (uri (cran-uri "multcomp" version))
8234 "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb"))))
8235 (build-system r-build-system)
8237 `(("r-codetools" ,r-codetools)
8238 ("r-mvtnorm" ,r-mvtnorm)
8239 ("r-sandwich" ,r-sandwich)
8240 ("r-survival" ,r-survival)
8241 ("r-th-data" ,r-th-data)))
8242 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8243 (synopsis "Simultaneous inference in general parametric models")
8245 "Simultaneous tests and confidence intervals for general linear
8246 hypotheses in parametric models, including linear, generalized linear, linear
8247 mixed effects, and survival models. The package includes demos reproducing
8248 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8249 Hothorn, Westfall, 2010, CRC Press).")
8250 (license license:gpl2)))
8252 (define-public r-emmeans
8255 (version "1.4.3.01")
8259 (uri (cran-uri "emmeans" version))
8262 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8263 (build-system r-build-system)
8265 `(("r-estimability" ,r-estimability)
8266 ("r-mvtnorm" ,r-mvtnorm)
8267 ("r-numderiv" ,r-numderiv)
8269 ("r-xtable" ,r-xtable)))
8270 (home-page "https://github.com/rvlenth/emmeans")
8271 (synopsis "Estimated marginal means, aka least-squares means")
8273 "This package provides tools to obtain @dfn{estimated marginal
8274 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8275 be used to compute contrasts or linear functions of EMMs, trends, and
8276 comparisons of slopes.")
8277 ;; Either version of the license.
8278 (license (list license:gpl2 license:gpl3))))
8280 (define-public r-pwr
8287 (uri (cran-uri "pwr" version))
8290 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8291 (build-system r-build-system)
8293 `(("r-knitr" ,r-knitr)))
8294 (home-page "https://github.com/heliosdrm/pwr")
8295 (synopsis "Basic functions for power analysis")
8297 "This package provides power analysis functions along the lines of
8299 (license license:gpl3+)))
8301 (define-public r-libcoin
8308 (uri (cran-uri "libcoin" version))
8311 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8312 (build-system r-build-system)
8313 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8314 (home-page "https://cran.r-project.org/web/packages/libcoin")
8315 (synopsis "Linear test statistics for permutation inference")
8317 "This package provides basic infrastructure for linear test statistics
8318 and permutation inference in the framework of Strasser and Weber (1999).")
8319 (license license:gpl2)))
8321 (define-public r-coin
8328 (uri (cran-uri "coin" version))
8331 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8332 (build-system r-build-system)
8334 `(("r-libcoin" ,r-libcoin)
8335 ("r-matrixstats" ,r-matrixstats)
8336 ("r-modeltools" ,r-modeltools)
8337 ("r-multcomp" ,r-multcomp)
8338 ("r-mvtnorm" ,r-mvtnorm)
8339 ("r-survival" ,r-survival)))
8340 (home-page "http://coin.r-forge.r-project.org")
8341 (synopsis "Conditional inference procedures in a permutation test framework")
8343 "This package provides conditional inference procedures for the general
8344 independence problem including two-sample, K-sample (non-parametric ANOVA),
8345 correlation, censored, ordered and multivariate problems.")
8346 (license license:gpl2)))
8348 (define-public r-bayesplot
8350 (name "r-bayesplot")
8355 (uri (cran-uri "bayesplot" version))
8358 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8359 (build-system r-build-system)
8361 `(("pandoc" ,ghc-pandoc)
8362 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8364 `(("r-dplyr" ,r-dplyr)
8365 ("r-ggplot2" ,r-ggplot2)
8366 ("r-ggridges" ,r-ggridges)
8368 ("r-reshape2" ,r-reshape2)
8369 ("r-rlang" ,r-rlang)
8370 ("r-tibble" ,r-tibble)
8371 ("r-tidyselect" ,r-tidyselect)))
8372 (home-page "http://mc-stan.org/bayesplot")
8373 (synopsis "Plotting for Bayesian models")
8375 "This package provides plotting functions for posterior analysis, model
8376 checking, and MCMC diagnostics. The package is designed not only to provide
8377 convenient functionality for users, but also a common set of functions that
8378 can be easily used by developers working on a variety of R packages for
8379 Bayesian modeling.")
8380 (license license:gpl3+)))
8382 (define-public r-tmb
8389 (uri (cran-uri "TMB" version))
8392 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8393 (properties `((upstream-name . "TMB")))
8394 (build-system r-build-system)
8396 `(("r-matrix" ,r-matrix)
8397 ("r-rcppeigen" ,r-rcppeigen)))
8398 (home-page "http://tmb-project.org")
8399 (synopsis "Template model builder: a general random effect tool")
8401 "With this tool, a user should be able to quickly implement complex
8402 random effect models through simple C++ templates. The package combines
8403 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8404 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8405 from R) to obtain an efficient implementation of the applied Laplace
8406 approximation with exact derivatives. Key features are: Automatic sparseness
8407 detection, parallelism through BLAS and parallel user templates.")
8408 (license license:gpl2)))
8410 (define-public r-sjstats
8417 (uri (cran-uri "sjstats" version))
8419 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8420 (build-system r-build-system)
8422 `(("r-bayestestr" ,r-bayestestr)
8423 ("r-broom" ,r-broom)
8424 ("r-dplyr" ,r-dplyr)
8425 ("r-emmeans" ,r-emmeans)
8426 ("r-insight" ,r-insight)
8428 ("r-magrittr" ,r-magrittr)
8430 ("r-modelr" ,r-modelr)
8431 ("r-parameters" ,r-parameters)
8432 ("r-performance" ,r-performance)
8433 ("r-purrr" ,r-purrr)
8434 ("r-rlang" ,r-rlang)
8435 ("r-sjlabelled" ,r-sjlabelled)
8436 ("r-sjmisc" ,r-sjmisc)
8437 ("r-tidyr" ,r-tidyr)))
8438 (home-page "https://github.com/strengejacke/sjstats")
8439 (synopsis "Functions for common statistical computations")
8441 "This package provides a collection of convenient functions for common
8442 statistical computations, which are not directly provided by R's @code{base}
8443 or @code{stats} packages. This package aims at providing, first, shortcuts
8444 for statistical measures, which otherwise could only be calculated with
8445 additional effort. Second, these shortcut functions are generic, and can be
8446 applied not only to vectors, but also to other objects as well. The focus of
8447 most functions lies on summary statistics or fit measures for regression
8448 models, including generalized linear models, mixed effects models and Bayesian
8450 (license license:gpl3)))
8452 (define-public r-glmmtmb
8459 (uri (cran-uri "glmmTMB" version))
8462 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8463 (properties `((upstream-name . "glmmTMB")))
8464 (build-system r-build-system)
8466 `(("r-lme4" ,r-lme4)
8467 ("r-matrix" ,r-matrix)
8469 ("r-rcppeigen" ,r-rcppeigen)
8472 `(("r-knitr" ,r-knitr))) ; for vignettes
8473 (home-page "https://github.com/glmmTMB")
8474 (synopsis "Generalized linear mixed models")
8476 "Fit linear and generalized linear mixed models with various extensions,
8477 including zero-inflation. The models are fitted using maximum likelihood
8478 estimation via the Template Model Builder. Random effects are assumed to be
8479 Gaussian on the scale of the linear predictor and are integrated out using the
8480 Laplace approximation. Gradients are calculated using automatic
8482 (license license:agpl3+)))
8484 (define-public r-bayestestr
8486 (name "r-bayestestr")
8491 (uri (cran-uri "bayestestR" version))
8494 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8495 (properties `((upstream-name . "bayestestR")))
8496 (build-system r-build-system)
8498 `(("r-insight" ,r-insight)))
8499 (home-page "https://github.com/easystats/bayestestR")
8500 (synopsis "Describe Bayesian models and posterior distributions")
8502 "This package provides utilities to understand and describe posterior
8503 distributions and Bayesian models. It includes point-estimates such as
8504 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8505 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8506 ROPE percentage and pd).")
8507 (license license:gpl3)))
8509 (define-public r-performance
8511 (name "r-performance")
8516 (uri (cran-uri "performance" version))
8519 "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p"))))
8520 (build-system r-build-system)
8522 `(("r-bayestestr" ,r-bayestestr)
8523 ("r-insight" ,r-insight)))
8524 (home-page "https://easystats.github.io/performance/")
8525 (synopsis "Assessment of regression models performance")
8527 "This package provides utilities for computing measures to assess model
8528 quality, which are not directly provided by R's @code{base} or @code{stats}
8529 packages. These include e.g. measures like r-squared, intraclass correlation
8530 coefficient, root mean squared error or functions to check models for
8531 overdispersion, singularity or zero-inflation and more. Functions apply to a
8532 large variety of regression models, including generalized linear models, mixed
8533 effects models and Bayesian models.")
8534 (license license:gpl3)))
8536 (define-public r-ggeffects
8538 (name "r-ggeffects")
8543 (uri (cran-uri "ggeffects" version))
8546 "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw"))))
8547 (build-system r-build-system)
8549 `(("r-insight" ,r-insight)
8550 ("r-magrittr" ,r-magrittr)
8552 ("r-purrr" ,r-purrr)
8553 ("r-sjlabelled" ,r-sjlabelled)
8554 ("r-sjmisc" ,r-sjmisc)))
8555 (home-page "https://github.com/strengejacke/ggeffects")
8556 (synopsis "Create tidy data frames of marginal effects for ggplot")
8558 "This package provides tools to compute marginal effects from statistical
8559 models and return the result as tidy data frames. These data frames are ready
8560 to use with the @code{ggplot2} package. Marginal effects can be calculated
8561 for many different models. Interaction terms, splines and polynomial terms
8562 are also supported. The two main functions are @code{ggpredict()} and
8563 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8564 results using @code{ggplot2}.")
8565 (license license:gpl3)))
8567 (define-public r-effectsize
8569 (name "r-effectsize")
8574 (uri (cran-uri "effectsize" version))
8577 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8578 (properties `((upstream-name . "effectsize")))
8579 (build-system r-build-system)
8581 `(("r-bayestestr" ,r-bayestestr)
8582 ("r-insight" ,r-insight)
8583 ("r-parameters" ,r-parameters)))
8584 (home-page "https://github.com/easystats/effectsize")
8585 (synopsis "Indices of effect size and standardized parameters")
8587 "This package provides utilities to work with indices of effect size and
8588 standardized parameters for a wide variety of models, allowing computation and
8589 conversion of indices such as Cohen's d, r, odds, etc.")
8590 (license license:gpl3)))
8592 (define-public r-sjplot
8599 (uri (cran-uri "sjPlot" version))
8601 (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
8602 (properties `((upstream-name . "sjPlot")))
8603 (build-system r-build-system)
8605 `(("r-bayestestr" ,r-bayestestr)
8606 ("r-dplyr" ,r-dplyr)
8607 ("r-effectsize" ,r-effectsize)
8608 ("r-forcats" ,r-forcats)
8609 ("r-ggeffects" ,r-ggeffects)
8610 ("r-ggplot2" ,r-ggplot2)
8611 ("r-ggrepel" ,r-ggrepel)
8612 ("r-glmmtmb" ,r-glmmtmb)
8613 ("r-insight" ,r-insight)
8614 ("r-knitr" ,r-knitr)
8616 ("r-magrittr" ,r-magrittr)
8618 ("r-modelr" ,r-modelr)
8619 ("r-parameters" ,r-parameters)
8620 ("r-performance" ,r-performance)
8621 ("r-psych" ,r-psych)
8622 ("r-purrr" ,r-purrr)
8623 ("r-rlang" ,r-rlang)
8624 ("r-scales" ,r-scales)
8625 ("r-sjlabelled" ,r-sjlabelled)
8626 ("r-sjmisc" ,r-sjmisc)
8627 ("r-sjstats" ,r-sjstats)
8628 ("r-tidyr" ,r-tidyr)))
8629 (home-page "https://strengejacke.github.io/sjPlot/")
8630 (synopsis "Data visualization for statistics in social science")
8632 "This package represents a collection of plotting and table output
8633 functions for data visualization. Results of various statistical
8634 analyses (that are commonly used in social sciences) can be visualized using
8635 this package, including simple and cross tabulated frequencies, histograms,
8636 box plots, (generalized) linear models, mixed effects models, principal
8637 component analysis and correlation matrices, cluster analyses, scatter plots,
8638 stacked scales, effects plots of regression models (including interaction
8639 terms) and much more. This package supports labelled data.")
8640 (license license:gpl3)))
8642 (define-public r-ini
8649 (uri (cran-uri "ini" version))
8652 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8653 (build-system r-build-system)
8654 (home-page "https://github.com/dvdscripter/ini")
8655 (synopsis "Read and write configuration files")
8657 "This package provides tools to parse simple @code{.ini} configuration
8658 files to an structured list. Users can manipulate this resulting list with
8659 @code{lapply()} functions. This same structured list can be used to write
8660 back to file after modifications.")
8661 (license license:gpl3)))
8670 (uri (cran-uri "gh" version))
8673 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8674 (build-system r-build-system)
8676 `(("r-httr" ,r-httr)
8678 ("r-jsonlite" ,r-jsonlite)))
8679 (home-page "https://github.com/r-lib/gh#readme")
8680 (synopsis "Access the GitHub API via R")
8682 "This package provides a minimal R client to access the GitHub API.")
8683 (license license:expat)))
8692 (uri (cran-uri "fs" version))
8695 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8696 (build-system r-build-system)
8698 `(("r-rcpp" ,r-rcpp)))
8700 `(("pkg-config" ,pkg-config)))
8701 (home-page "http://fs.r-lib.org")
8702 (synopsis "Cross-platform file system operations based on libuv")
8704 "This package provides a cross-platform interface to file system
8705 operations, built on top of the libuv C library.")
8706 (license license:gpl3)))
8708 (define-public r-clisymbols
8710 (name "r-clisymbols")
8715 (uri (cran-uri "clisymbols" version))
8718 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8719 (build-system r-build-system)
8720 (home-page "https://github.com/gaborcsardi/clisymbols")
8721 (synopsis "Unicode symbols at the R prompt")
8723 "This package provides a small subset of Unicode symbols, that are useful
8724 when building command line applications. They fall back to alternatives on
8725 terminals that do not support Unicode.")
8726 (license license:expat)))
8728 (define-public r-usethis
8735 (uri (cran-uri "usethis" version))
8738 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8739 (build-system r-build-system)
8741 `(("r-clipr" ,r-clipr)
8742 ("r-clisymbols" ,r-clisymbols)
8743 ("r-crayon" ,r-crayon)
8748 ("r-git2r" ,r-git2r)
8750 ("r-purrr" ,r-purrr)
8751 ("r-rlang" ,r-rlang)
8752 ("r-rprojroot" ,r-rprojroot)
8753 ("r-rstudioapi" ,r-rstudioapi)
8754 ("r-whisker" ,r-whisker)
8755 ("r-withr" ,r-withr)
8756 ("r-yaml" ,r-yaml)))
8757 (home-page "https://github.com/r-lib/usethis")
8758 (synopsis "Automate R package and project setup")
8760 "This package helps you to automate R package and project setup tasks
8761 that are otherwise performed manually. This includes setting up unit testing,
8762 test coverage, continuous integration, Git, GitHub integration, licenses,
8763 Rcpp, RStudio projects, and more.")
8764 (license license:gpl3)))
8766 (define-public r-sessioninfo
8768 (name "r-sessioninfo")
8773 (uri (cran-uri "sessioninfo" version))
8776 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8777 (build-system r-build-system)
8780 ("r-withr" ,r-withr)))
8781 (home-page "https://github.com/r-lib/sessioninfo#readme")
8782 (synopsis "R session information")
8784 "This package provides tools to query and print information about the
8785 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8786 more information about packages, and where they were installed from.")
8787 (license license:gpl2)))
8789 (define-public r-remotes
8796 (uri (cran-uri "remotes" version))
8799 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8800 (build-system r-build-system)
8801 (home-page "https://github.com/r-lib/remotes#readme")
8802 (synopsis "R package installation from remote repositories")
8804 "Download and install R packages stored in GitHub, BitBucket, or plain
8805 subversion or git repositories. This package is a lightweight replacement of
8806 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8807 the code was copied over from @code{devtools}.")
8808 (license license:gpl2+)))
8810 (define-public r-xopen
8817 (uri (cran-uri "xopen" version))
8820 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8821 (build-system r-build-system)
8823 `(("r-processx" ,r-processx)))
8824 (home-page "https://github.com/r-lib/xopen#readme")
8825 (synopsis "Open system files, URLs, anything")
8827 "This package provides a cross-platform solution to open files,
8828 directories or URLs with their associated programs.")
8829 (license license:expat)))
8831 (define-public r-rcmdcheck
8833 (name "r-rcmdcheck")
8838 (uri (cran-uri "rcmdcheck" version))
8841 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8842 (build-system r-build-system)
8844 `(("r-callr" ,r-callr)
8846 ("r-crayon" ,r-crayon)
8848 ("r-digest" ,r-digest)
8849 ("r-pkgbuild" ,r-pkgbuild)
8850 ("r-prettyunits" ,r-prettyunits)
8852 ("r-rprojroot" ,r-rprojroot)
8853 ("r-sessioninfo" ,r-sessioninfo)
8854 ("r-withr" ,r-withr)
8855 ("r-xopen" ,r-xopen)))
8856 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8857 (synopsis "Run R CMD check from R and capture results")
8859 "Run @code{R CMD check} from R programmatically, and capture the results
8860 of the individual checks.")
8861 (license license:expat)))
8863 (define-public r-rapportools
8865 (name "r-rapportools")
8870 (uri (cran-uri "rapportools" version))
8873 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8874 (build-system r-build-system)
8876 `(("r-pander" ,r-pander)
8878 ("r-reshape" ,r-reshape)))
8879 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8880 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8882 "This package provides helper functions that act as wrappers to more
8883 advanced statistical methods with the advantage of having sane defaults for
8885 (license license:agpl3+)))
8887 (define-public r-pander
8894 (uri (cran-uri "pander" version))
8897 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8898 (build-system r-build-system)
8900 `(("r-digest" ,r-digest)
8901 ("r-rcpp" ,r-rcpp)))
8902 (home-page "https://rapporter.github.io/pander")
8903 (synopsis "Render R objects into Pandoc's markdown")
8905 "The main aim of the pander R package is to provide a minimal and easy
8906 tool for rendering R objects into Pandoc's markdown. The package is also
8907 capable of exporting/converting complex Pandoc documents (reports) in various
8909 ;; This package is licensed under either the AGPLv3+ or the very rarely
8911 (license license:agpl3+)))
8913 (define-public r-summarytools
8915 (name "r-summarytools")
8920 (uri (cran-uri "summarytools" version))
8923 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8924 (build-system r-build-system)
8926 `(("r-checkmate" ,r-checkmate)
8927 ("r-dplyr" ,r-dplyr)
8928 ("r-htmltools" ,r-htmltools)
8929 ("r-lubridate" ,r-lubridate)
8930 ("r-magick" ,r-magick)
8931 ("r-matrixstats" ,r-matrixstats)
8932 ("r-pander" ,r-pander)
8934 ("r-rapportools" ,r-rapportools)
8935 ("r-rcurl" ,r-rcurl)
8936 ("r-tibble" ,r-tibble)
8937 ("r-tidyr" ,r-tidyr)))
8938 (home-page "https://github.com/dcomtois/summarytools")
8939 (synopsis "Tools to quickly and neatly summarize data")
8941 "This package provides tools for data frame summaries, cross-tabulations,
8942 weight-enabled frequency tables and common univariate statistics in concise
8943 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8944 good point-of-entry for exploring data, both for experienced and new R
8946 (license license:gpl2)))
8948 (define-public r-lsei
8955 (uri (cran-uri "lsei" version))
8958 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8959 (build-system r-build-system)
8961 `(("gfortran" ,gfortran)))
8962 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8963 (synopsis "Solve regression problems under equality/inequality constraints")
8965 "It contains functions that solve least squares linear regression
8966 problems under linear equality/inequality constraints. Functions for solving
8967 quadratic programming problems are also available, which transform such
8968 problems into least squares ones first.")
8969 (license license:gpl2+)))
8971 (define-public r-npsurv
8978 (uri (cran-uri "npsurv" version))
8981 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8982 (build-system r-build-system)
8984 `(("r-lsei" ,r-lsei)))
8985 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8986 (synopsis "Nonparametric survival analysis")
8988 "This package contains functions for non-parametric survival analysis of
8989 exact and interval-censored observations.")
8990 (license license:gpl2+)))
8992 (define-public r-clusteval
8994 (name "r-clusteval")
8999 (uri (cran-uri "clusteval" version))
9002 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9003 (build-system r-build-system)
9005 `(("r-mvtnorm" ,r-mvtnorm)
9006 ("r-rcpp" ,r-rcpp)))
9007 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9008 (synopsis "Evaluation of clustering algorithms")
9010 "This R package provides a suite of tools to evaluate clustering
9011 algorithms, clusterings, and individual clusters.")
9012 (license license:expat)))
9014 (define-public r-tweedie
9021 (uri (cran-uri "tweedie" version))
9024 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9025 (build-system r-build-system)
9026 (native-inputs `(("gfortran" ,gfortran)))
9027 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9028 (synopsis "Evaluation of Tweedie exponential family models")
9030 "Maximum likelihood computations for Tweedie families, including the
9031 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9032 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9033 and related methods.")
9034 (license license:gpl2+)))
9036 (define-public r-rcppgsl
9043 (uri (cran-uri "RcppGSL" version))
9045 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9046 (properties `((upstream-name . "RcppGSL")))
9047 (build-system r-build-system)
9049 `(("r-rcpp" ,r-rcpp)
9052 `(("r-knitr" ,r-knitr))) ; for vignettes
9053 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9054 (synopsis "Rcpp integration for GSL vectors and matrices")
9056 "The GNU Scientific Library (or GSL) is a collection of numerical
9057 routines for scientific computing. It is particularly useful for C and C++
9058 programs as it provides a standard C interface to a wide range of mathematical
9059 routines. There are over 1000 functions in total with an extensive test
9060 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9061 structures and R using concepts from Rcpp which is itself a package that eases
9062 the interfaces between R and C++.")
9063 (license license:gpl2+)))
9065 (define-public r-mvabund
9072 (uri (cran-uri "mvabund" version))
9075 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
9076 (build-system r-build-system)
9078 `(("r-mass" ,r-mass)
9080 ("r-rcppgsl" ,r-rcppgsl)
9081 ("r-statmod" ,r-statmod)
9082 ("r-tweedie" ,r-tweedie)))
9083 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9084 (synopsis "Statistical methods for analysing multivariate abundance data")
9086 "This package provides a set of tools for displaying, modeling and
9087 analysing multivariate abundance data in community ecology.")
9088 (license license:lgpl2.1+)))
9090 (define-public r-afex
9097 (uri (cran-uri "afex" version))
9100 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
9101 (build-system r-build-system)
9105 ("r-lmertest" ,r-lmertest)
9106 ("r-pbkrtest" ,r-pbkrtest)
9107 ("r-reshape2" ,r-reshape2)))
9108 (home-page "https://afex.singmann.science/")
9109 (synopsis "Analysis of factorial experiments")
9111 "This package provides convenience functions for analyzing factorial
9112 experiments using ANOVA or mixed models.")
9113 (license license:gpl2+)))
9115 (define-public r-lmertest
9122 (uri (cran-uri "lmerTest" version))
9125 "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
9126 (properties `((upstream-name . "lmerTest")))
9127 (build-system r-build-system)
9129 `(("r-ggplot2" ,r-ggplot2)
9132 ("r-numderiv" ,r-numderiv)))
9133 (home-page "https://github.com/runehaubo/lmerTestR")
9134 (synopsis "Tests in linear mixed effects models")
9136 "This package provides p-values in type I, II or III anova and summary
9137 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9138 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9139 package. Model selection methods include step, drop1 and anova-like tables
9140 for random effects (ranova). Methods for Least-Square means (LS-means) and
9141 tests of linear contrasts of fixed effects are also available.")
9142 (license license:gpl2+)))
9144 (define-public r-r2glmm
9151 (uri (cran-uri "r2glmm" version))
9154 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9155 (build-system r-build-system)
9157 `(("r-afex" ,r-afex)
9158 ("r-data-table" ,r-data-table)
9159 ("r-dplyr" ,r-dplyr)
9160 ("r-ggplot2" ,r-ggplot2)
9161 ("r-gridextra" ,r-gridextra)
9162 ("r-lmertest" ,r-lmertest)
9164 ("r-matrix" ,r-matrix)
9166 ("r-pbkrtest" ,r-pbkrtest)))
9167 (home-page "https://github.com/bcjaeger/r2glmm")
9168 (synopsis "Compute R squared for mixed (multilevel) models")
9170 "This package computes model and semi partial R squared with confidence
9171 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9172 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9173 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9175 (license license:gpl2)))
9177 (define-public r-weights
9184 (uri (cran-uri "weights" version))
9187 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9188 (build-system r-build-system)
9190 `(("r-gdata" ,r-gdata)
9191 ("r-hmisc" ,r-hmisc)
9192 ("r-mice" ,r-mice)))
9194 "https://cran.r-project.org/web/packages/weights/")
9195 (synopsis "Weighting and weighted statistics")
9196 (description "This package Provides a variety of functions for producing
9197 simple weighted statistics, such as weighted Pearson's correlations, partial
9198 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9199 includes some software for quickly recoding survey data and plotting point
9200 estimates from interaction terms in regressions (and multiply imputed
9201 regressions). NOTE: Weighted partial correlation calculations pulled to
9203 (license license:gpl2+)))
9205 (define-public r-rcppannoy
9207 (name "r-rcppannoy")
9212 (uri (cran-uri "RcppAnnoy" version))
9215 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9216 (properties `((upstream-name . "RcppAnnoy")))
9217 (build-system r-build-system)
9219 `(("r-rcpp" ,r-rcpp)))
9221 `(("r-knitr" ,r-knitr))) ; for vignettes
9222 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9223 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9225 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9226 for efficient memory usage as well an ability to load from and save to disk.
9227 This package provides an R interface.")
9228 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9230 (license (list license:gpl2+ license:asl2.0))))
9232 (define-public r-rcpphnsw
9239 (uri (cran-uri "RcppHNSW" version))
9242 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9243 (properties `((upstream-name . "RcppHNSW")))
9244 (build-system r-build-system)
9245 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9246 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9247 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9249 "Hnswlib is a C++ library for approximate nearest neighbors. This
9250 package provides a minimal R interface by relying on the Rcpp package.")
9251 ;; hnswlib is released under Version 2.0 of the Apache License.
9252 (license (list license:gpl3 license:asl2.0))))
9254 (define-public r-rcppparallel
9256 (name "r-rcppparallel")
9261 (uri (cran-uri "RcppParallel" version))
9264 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9265 (properties `((upstream-name . "RcppParallel")))
9266 (build-system r-build-system)
9267 (home-page "http://rcppcore.github.io/RcppParallel")
9268 (synopsis "Parallel programming tools for Rcpp")
9270 "This package provides high level functions for parallel programming with
9271 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9272 the work of a standard serial @code{for} loop into a parallel one and the
9273 @code{parallelReduce()} function can be used for accumulating aggregates or
9275 (license license:gpl2)))
9277 (define-public r-ncdf4
9284 (uri (cran-uri "ncdf4" version))
9287 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9288 (build-system r-build-system)
9290 `(("netcdf" ,netcdf)
9292 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9293 (synopsis "R interface to Unidata netCDF format data files")
9295 "This package provides a high-level R interface to data files written
9296 using Unidata's netCDF library (version 4 or earlier), which are binary data
9297 files that are portable across platforms and include metadata information in
9298 addition to the data sets. Using this package, netCDF files can be opened and
9299 data sets read in easily. It is also easy to create new netCDF dimensions,
9300 variables, and files, in either version 3 or 4 format, and manipulate existing
9302 (license license:gpl3+)))
9304 (define-public r-biocmanager
9306 (name "r-biocmanager")
9311 (uri (cran-uri "BiocManager" version))
9313 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9314 (properties `((upstream-name . "BiocManager")))
9315 (build-system r-build-system)
9316 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9317 (synopsis "Access the Bioconductor project package repository")
9319 "This package provides a convenient tool to install and update
9320 Bioconductor packages.")
9321 (license license:artistic2.0)))
9323 (define-public r-rgl
9326 (version "0.100.30")
9330 (uri (cran-uri "rgl" version))
9333 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9334 (build-system r-build-system)
9336 `(("pkg-config" ,pkg-config)))
9338 `(("freetype" ,freetype)
9342 ("ghc-pandoc" ,ghc-pandoc)
9345 `(("r-crosstalk" ,r-crosstalk)
9346 ("r-htmltools" ,r-htmltools)
9347 ("r-htmlwidgets" ,r-htmlwidgets)
9348 ("r-jsonlite" ,r-jsonlite)
9349 ("r-knitr" ,r-knitr)
9350 ("r-magrittr" ,r-magrittr)
9351 ("r-manipulatewidget" ,r-manipulatewidget)
9352 ("r-shiny" ,r-shiny)))
9353 (home-page "https://r-forge.r-project.org/projects/rgl/")
9354 (synopsis "3D visualization using OpenGL")
9356 "This package provides medium to high level functions for 3D interactive graphics,
9357 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9358 as functions for constructing representations of geometric
9359 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9360 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9361 image formats, including PNG, Postscript, SVG, PGF.")
9362 ;; Any version of the GPL.
9363 (license (list license:gpl2+ license:gpl3+))))
9365 (define-public r-multicool
9367 (name "r-multicool")
9372 (uri (cran-uri "multicool" version))
9375 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9376 (build-system r-build-system)
9377 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9378 (home-page "https://cran.r-project.org/web/packages/multicool/")
9379 (synopsis "Permutations of multisets in cool-lex order")
9381 "This package provides a set of tools to permute multisets without loops
9382 or hash tables and to generate integer partitions. Cool-lex order is similar
9383 to colexicographical order.")
9384 (license license:gpl2)))
9386 (define-public r-misc3d
9393 (uri (cran-uri "misc3d" version))
9396 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9397 (build-system r-build-system)
9398 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9399 (synopsis "Miscellaneous 3D Plots")
9401 "This package provides a collection of miscellaneous 3d plots, including
9403 ;; Any version of the GPL.
9404 (license (list license:gpl2+ license:gpl3+))))
9413 (uri (cran-uri "ks" version))
9415 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9416 (build-system r-build-system)
9419 ("r-kernlab" ,r-kernlab)
9420 ("r-kernsmooth" ,r-kernsmooth)
9421 ("r-matrix" ,r-matrix)
9422 ("r-mclust" ,r-mclust)
9424 ("r-multicool" ,r-multicool)
9425 ("r-mvtnorm" ,r-mvtnorm)))
9426 (home-page "http://www.mvstat.net/tduong/")
9427 (synopsis "Kernel smoothing")
9429 "This package provides kernel smoothers for univariate and multivariate
9430 data, including density functions, density derivatives, cumulative
9431 distributions, modal clustering, discriminant analysis, and two-sample
9432 hypothesis testing.")
9433 ;; Either version of the GPL.
9434 (license (list license:gpl2 license:gpl3))))
9436 (define-public r-feature
9443 (uri (cran-uri "feature" version))
9446 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9447 (build-system r-build-system)
9450 ("r-misc3d" ,r-misc3d)
9452 (home-page "http://www.mvstat.net/tduong/")
9453 (synopsis "Inferential feature significance for kernel density estimation")
9455 "The feature package contains functions to display and compute kernel
9456 density estimates, significant gradient and significant curvature regions.
9457 Significant gradient and/or curvature regions often correspond to significant
9458 features (e.g. local modes).")
9459 ;; Either version of the GPL.
9460 (license (list license:gpl2 license:gpl3))))
9462 (define-public r-arm
9469 (uri (cran-uri "arm" version))
9472 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9473 (build-system r-build-system)
9475 `(("r-abind" ,r-abind)
9479 ("r-matrix" ,r-matrix)
9480 ("r-nlme" ,r-nlme)))
9481 (home-page "https://cran.r-project.org/web/packages/arm/")
9482 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9484 "This package provides functions to accompany A. Gelman and J. Hill,
9485 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9486 University Press, 2007.")
9487 (license license:gpl3+)))
9489 (define-public r-circular
9496 (uri (cran-uri "circular" version))
9499 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9500 (build-system r-build-system)
9502 `(("r-boot" ,r-boot)
9503 ("r-mvtnorm" ,r-mvtnorm)))
9505 `(("gfortran" ,gfortran)))
9506 (home-page "https://cran.r-project.org/web/packages/circular/")
9507 (synopsis "Circular statistics")
9509 "This package provides tools for circular statistics, from \"Topics in
9510 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9512 (license license:gpl2+)))
9514 (define-public r-activity
9521 (uri (cran-uri "activity" version))
9524 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9525 (build-system r-build-system)
9527 `(("r-circular" ,r-circular)
9528 ("r-insol" ,r-insol)
9529 ("r-pbapply" ,r-pbapply)))
9530 (home-page "https://cran.r-project.org/web/packages/activity/")
9531 (synopsis "Animal activity statistics")
9533 "This package provides functions to fit kernel density functions to
9534 animal activity time data; plot activity distributions; quantify overall
9535 levels of activity; statistically compare activity metrics through
9536 bootstrapping; and evaluate variation in linear variables with time (or other
9537 circular variables).")
9538 (license license:gpl3)))
9540 (define-public r-ouch
9547 (uri (cran-uri "ouch" version))
9550 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9551 (build-system r-build-system)
9552 (propagated-inputs `(("r-subplex" ,r-subplex)))
9553 (home-page "http://kingaa.github.io/ouch/")
9554 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9556 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9557 for evolution along a phylogenetic tree.")
9558 (license license:gpl2+)))
9560 (define-public r-fmsb
9567 (uri (cran-uri "fmsb" version))
9570 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9571 (build-system r-build-system)
9572 (home-page "http://minato.sip21c.org/msb/")
9573 (synopsis "Functions for medical statistics book with demographic data")
9575 "This package provides several utility functions for the book entitled
9576 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9577 Japan, 2007) with Japanese demographic data and some demographic analysis
9578 related functions.")
9579 (license license:gpl2+)))
9581 (define-public r-stabledist
9583 (name "r-stabledist")
9588 (uri (cran-uri "stabledist" version))
9591 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9592 (build-system r-build-system)
9593 (home-page "http://www.rmetrics.org")
9594 (synopsis "Stable distribution functions")
9596 "This package provides density, probability and quantile functions, and
9597 random number generation for (skew) stable distributions, using the
9598 parametrizations of Nolan.")
9599 (license license:gpl2+)))
9601 (define-public r-gsl
9608 (uri (cran-uri "gsl" version))
9611 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9612 (build-system r-build-system)
9615 (home-page "https://cran.r-project.org/web/packages/gsl")
9616 (synopsis "Wrapper for the GNU Scientific Library")
9618 "This package provides an R wrapper for the special functions and quasi
9619 random number generators of the GNU Scientific Library.")
9620 (license license:gpl2+)))
9622 (define-public r-adgoftest
9624 (name "r-adgoftest")
9629 (uri (cran-uri "ADGofTest" version))
9632 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9633 (properties `((upstream-name . "ADGofTest")))
9634 (build-system r-build-system)
9635 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9636 (synopsis "Anderson-Darling GoF test")
9638 "This package provides an implementation of the Anderson-Darling GoF test
9639 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9640 Anderson-Darling Distribution\".")
9641 ;; Any version of the GPL.
9642 (license license:gpl3+)))
9644 (define-public r-softimpute
9646 (name "r-softimpute")
9651 (uri (cran-uri "softImpute" version))
9654 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9655 (properties `((upstream-name . "softImpute")))
9656 (build-system r-build-system)
9658 `(("r-matrix" ,r-matrix)))
9660 `(("gfortran" ,gfortran)))
9661 (home-page "https://cran.r-project.org/web/packages/softImpute")
9662 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9664 "This package provides iterative methods for matrix completion that use
9665 nuclear-norm regularization. The package includes procedures for centering
9666 and scaling rows, columns or both, and for computing low-rank @dfn{single
9667 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9669 (license license:gpl2)))
9671 (define-public r-fftwtools
9673 (name "r-fftwtools")
9678 (uri (cran-uri "fftwtools" version))
9681 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9682 (build-system r-build-system)
9683 (inputs `(("fftw" ,fftw)))
9684 (home-page "https://github.com/krahim/fftwtools")
9685 (synopsis "Wrapper for FFTW3")
9687 "This package provides a wrapper for several FFTW functions. It provides
9688 access to the two-dimensional FFT, the multivariate FFT, and the
9689 one-dimensional real to complex FFT using the FFTW3 library. The package
9690 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9691 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9692 The FFT functions have a parameter that allows them to not return the
9693 redundant complex conjugate when the input is real data.")
9694 (license license:gpl2+)))
9696 (define-public r-tiff
9703 (uri (cran-uri "tiff" version))
9706 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9707 (build-system r-build-system)
9709 `(("libtiff" ,libtiff)
9710 ("libjpeg" ,libjpeg)
9712 (home-page "http://www.rforge.net/tiff/")
9713 (synopsis "Read and write TIFF images")
9715 "This package provides an easy and simple way to read, write and display
9716 bitmap images stored in the TIFF format. It can read and write both files and
9717 in-memory raw vectors.")
9718 ;; Either of these two license versions.
9719 (license (list license:gpl2 license:gpl3))))
9721 (define-public r-nlp
9728 (uri (cran-uri "NLP" version))
9731 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9732 (properties `((upstream-name . "NLP")))
9733 (build-system r-build-system)
9734 (home-page "https://cran.r-project.org/web/packages/NLP/")
9735 (synopsis "Natural language processing infrastructure")
9737 "This package provides basic classes and methods for Natural Language
9739 (license license:gpl3)))
9748 (uri (cran-uri "tm" version))
9751 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9752 (properties `((upstream-name . "tm")))
9753 (build-system r-build-system)
9759 ("r-xml2" ,r-xml2)))
9760 (home-page "http://tm.r-forge.r-project.org/")
9761 (synopsis "Text mining package")
9763 "This package provides a framework for text mining applications within R.")
9764 (license license:gpl3)))
9766 (define-public r-waveslim
9773 (uri (cran-uri "waveslim" version))
9776 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9777 (build-system r-build-system)
9779 `(("gfortran" ,gfortran)))
9780 (home-page "http://waveslim.blogspot.com")
9781 (synopsis "Basic wavelet routines for signal processing")
9783 "This package provides basic wavelet routines for time series (1D),
9784 image (2D) and array (3D) analysis. The code provided here is based on
9785 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9786 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9787 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9788 pairs (Selesnick 2001, 2002).")
9789 (license license:bsd-3)))
9791 (define-public r-wordcloud
9793 (name "r-wordcloud")
9798 (uri (cran-uri "wordcloud" version))
9801 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9802 (build-system r-build-system)
9804 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9806 ;; The "tm" package is only "suggested" according to CRAN, but the
9807 ;; wordcloud package cannot be loaded without it.
9809 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9810 (synopsis "Word clouds")
9812 "This package provides functionality to create pretty word clouds,
9813 visualize differences and similarity between documents, and avoid
9814 over-plotting in scatter plots with text.")
9815 (license license:lgpl2.1)))
9817 (define-public r-colorramps
9819 (name "r-colorramps")
9824 (uri (cran-uri "colorRamps" version))
9827 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9828 (properties `((upstream-name . "colorRamps")))
9829 (build-system r-build-system)
9830 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9831 (synopsis "Build color tables")
9832 (description "This package provides features to build gradient color
9834 ;; Any version of the GPL
9835 (license license:gpl3+)))
9837 (define-public r-tidytree
9844 (uri (cran-uri "tidytree" version))
9846 (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7"))))
9847 (build-system r-build-system)
9850 ("r-dplyr" ,r-dplyr)
9851 ("r-lazyeval" ,r-lazyeval)
9852 ("r-magrittr" ,r-magrittr)
9853 ("r-rlang" ,r-rlang)
9854 ("r-tibble" ,r-tibble)))
9855 (home-page "https://github.com/GuangchuangYu/tidytree")
9856 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9858 "Phylogenetic trees generally contain multiple components including nodes,
9859 edges, branches and associated data. This package provides an approach to
9860 convert tree objects to tidy data frames. It also provides tidy interfaces to
9861 manipulate tree data.")
9862 (license license:artistic2.0)))
9864 (define-public r-rvcheck
9871 (uri (cran-uri "rvcheck" version))
9873 (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
9874 (build-system r-build-system)
9876 `(("r-biocmanager" ,r-biocmanager)
9877 ("r-rlang" ,r-rlang)))
9878 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9879 (synopsis "R package version check")
9881 "This package provides tools to check the latest release version of R and
9882 R packages (on CRAN, Bioconductor or Github).")
9883 (license license:artistic2.0)))
9885 (define-public r-docopt
9892 (uri (cran-uri "docopt" version))
9895 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9896 (build-system r-build-system)
9897 (home-page "https://github.com/docopt/docopt.R")
9898 (synopsis "Command-line interface specification language")
9900 "This package enables you to define a command-line interface by just
9901 giving it a description in the specific format.")
9902 (license license:expat)))
9904 (define-public r-sparsesvd
9906 (name "r-sparsesvd")
9911 (uri (cran-uri "sparsesvd" version))
9914 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9915 (build-system r-build-system)
9916 (propagated-inputs `(("r-matrix" ,r-matrix)))
9917 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9918 (synopsis "Sparse truncated singular value decomposition")
9920 "This package provides a Wrapper around the SVDLIBC library
9921 for (truncated) singular value decomposition of a sparse matrix. Currently,
9922 only sparse real matrices in Matrix package format are supported.")
9923 ;; SVDLIBC is released under BSD-2. The R interface is released under
9925 (license (list license:bsd-3 license:bsd-2))))
9927 (define-public r-speedglm
9934 (uri (cran-uri "speedglm" version))
9937 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9938 (build-system r-build-system)
9940 `(("r-mass" ,r-mass)
9941 ("r-matrix" ,r-matrix)))
9942 (home-page "https://cran.r-project.org/web/packages/speedglm")
9943 (synopsis "Fit linear and generalized linear models to large data sets")
9945 "This package provides tools for fitting linear models and generalized
9946 linear models to large data sets by updating algorithms.")
9947 ;; Any version of the GPL
9948 (license license:gpl2+)))
9950 (define-public r-densityclust
9952 (name "r-densityclust")
9957 (uri (cran-uri "densityClust" version))
9960 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9961 (properties `((upstream-name . "densityClust")))
9962 (build-system r-build-system)
9965 ("r-ggplot2" ,r-ggplot2)
9966 ("r-ggrepel" ,r-ggrepel)
9967 ("r-gridextra" ,r-gridextra)
9968 ("r-rcolorbrewer" ,r-rcolorbrewer)
9970 ("r-rtsne" ,r-rtsne)))
9971 (home-page "https://cran.r-project.org/web/packages/densityClust")
9972 (synopsis "Clustering by fast search and find of density peaks")
9974 "This package provides an improved implementation (based on k-nearest
9975 neighbors) of the density peak clustering algorithm, originally described by
9976 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9977 large datasets (> 100,000 samples) very efficiently.")
9978 (license license:gpl2+)))
9980 (define-public r-combinat
9987 (uri (cran-uri "combinat" version))
9990 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9991 (build-system r-build-system)
9992 (home-page "https://cran.r-project.org/web/packages/combinat")
9993 (synopsis "Combinatorics utilities")
9994 (description "This package provides assorted routines for combinatorics.")
9995 (license license:gpl2)))
9997 (define-public r-qlcmatrix
9999 (name "r-qlcmatrix")
10004 (uri (cran-uri "qlcMatrix" version))
10007 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10008 (properties `((upstream-name . "qlcMatrix")))
10009 (build-system r-build-system)
10011 `(("r-docopt" ,r-docopt)
10012 ("r-matrix" ,r-matrix)
10014 ("r-sparsesvd" ,r-sparsesvd)))
10015 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10016 (synopsis "Sparse matrix functions for quantitative language comparison")
10018 "This package provides an extension of the functionality of the Matrix
10019 package for using sparse matrices. Some of the functions are very general,
10020 while other are highly specific for the special data format used for
10021 @dfn{quantitative language comparison} (QLC).")
10022 (license license:gpl3)))
10024 (define-public r-ddrtree
10031 (uri (cran-uri "DDRTree" version))
10034 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10035 (properties `((upstream-name . "DDRTree")))
10036 (build-system r-build-system)
10039 ("r-irlba" ,r-irlba)
10041 ("r-rcppeigen" ,r-rcppeigen)))
10042 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10043 (synopsis "Learning principal graphs with DDRTree")
10045 "This package provides an implementation of the framework of
10046 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10047 dimensional space while constructs a principal tree which passes through the
10048 middle of the data simultaneously. DDRTree shows superiority to
10049 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10050 intrinsic structure of single cell genomics data. In general, it could be
10051 used to reconstruct the temporal progression as well as the bifurcation
10052 structure of any data type.")
10053 (license license:asl2.0)))
10055 (define-public r-corpcor
10062 (uri (cran-uri "corpcor" version))
10065 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10066 (build-system r-build-system)
10067 (home-page "http://strimmerlab.org/software/corpcor/")
10068 (synopsis "Efficient estimation of covariance and (partial) correlation")
10070 "This package implements a James-Stein-type shrinkage estimator for the
10071 covariance matrix, with separate shrinkage for variances and correlations.
10072 Furthermore, functions are available for fast singular value decomposition,
10073 for computing the pseudoinverse, and for checking the rank and positive
10074 definiteness of a matrix.")
10075 (license license:gpl3+)))
10077 (define-public r-rspectra
10079 (name "r-rspectra")
10084 (uri (cran-uri "RSpectra" version))
10087 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10088 (properties `((upstream-name . "RSpectra")))
10089 (build-system r-build-system)
10091 `(("r-matrix" ,r-matrix)
10093 ("r-rcppeigen" ,r-rcppeigen)))
10094 (home-page "https://github.com/yixuan/RSpectra")
10095 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10097 "This package provides an R interface to the Spectra library for
10098 large-scale eigenvalue and SVD problems. It is typically used to compute a
10099 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10100 which is usually more efficient than @code{eigen()} if k << n.")
10102 (license license:mpl2.0)))
10104 (define-public r-vbsr
10111 (uri (cran-uri "vbsr" version))
10114 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10115 (build-system r-build-system)
10116 (home-page "https://cran.r-project.org/web/packages/vbsr")
10117 (synopsis "Variational Bayes spike regression regularized linear models")
10119 "This package provides an efficient algorithm for solving ultra-sparse
10120 regularized regression models using a variational Bayes algorithm with a spike
10121 prior. The algorithm is solved on a path, with coordinate updates, and is
10122 capable of generating very sparse models. Very general model
10123 diagnostics for controlling type-1 errors are also provided.")
10124 (license license:gpl2)))
10126 (define-public r-flare
10129 (version "1.6.0.2")
10133 (uri (cran-uri "flare" version))
10136 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10137 (build-system r-build-system)
10139 `(("r-igraph" ,r-igraph)
10140 ("r-lattice" ,r-lattice)
10142 ("r-matrix" ,r-matrix)))
10143 (home-page "https://cran.r-project.org/web/packages/flare")
10144 (synopsis "Family of Lasso regression implementations")
10146 "This package provides implementations of a family of Lasso variants
10147 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10148 high dimensional sparse linear models.")
10149 (license license:gpl2)))
10151 (define-public r-lassopv
10158 (uri (cran-uri "lassopv" version))
10161 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10162 (build-system r-build-system)
10163 (propagated-inputs `(("r-lars" ,r-lars)))
10164 (home-page "https://github.com/lingfeiwang/lassopv")
10165 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10167 "This package enables you to estimate the p-values for predictors x
10168 against target variable y in Lasso regression, using the regularization
10169 strength when each predictor enters the active set of regularization path for
10170 the first time as the statistic.")
10171 (license license:gpl3)))
10173 (define-public r-splitstackshape
10175 (name "r-splitstackshape")
10180 (uri (cran-uri "splitstackshape" version))
10183 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10184 (build-system r-build-system)
10186 `(("r-data-table" ,r-data-table)))
10187 (home-page "https://github.com/mrdwab/splitstackshape")
10188 (synopsis "Stack and reshape datasets after splitting concatenated values")
10190 "Online data collection tools like Google Forms often export
10191 multiple-response questions with data concatenated in cells. The
10192 @code{concat.split} (cSplit) family of functions provided by this package
10193 splits such data into separate cells. This package also includes functions to
10194 stack groups of columns and to reshape wide data, even when the data are
10195 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10196 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10198 (license license:gpl3)))
10200 (define-public r-tfmpvalue
10202 (name "r-tfmpvalue")
10207 (uri (cran-uri "TFMPvalue" version))
10210 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10211 (properties `((upstream-name . "TFMPvalue")))
10212 (build-system r-build-system)
10213 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10214 (home-page "https://github.com/ge11232002/TFMPvalue")
10215 (synopsis "P-value computation for position weight matrices")
10217 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10218 identification from sequence/alignments, we are interested in the significance
10219 of certain match scores. TFMPvalue provides the accurate calculation of a
10220 p-value with a score threshold for position weight matrices, or the score with
10221 a given p-value. It is an interface to code originally made available by
10222 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10223 Touzet and Varre (2007).")
10224 (license license:gpl2)))
10226 (define-public r-rnifti
10233 (uri (cran-uri "RNifti" version))
10236 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10237 (properties `((upstream-name . "RNifti")))
10238 (build-system r-build-system)
10239 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10240 (home-page "https://github.com/jonclayden/RNifti")
10241 (synopsis "Fast R and C++ access to NIfTI images")
10243 "This package provides very fast read and write access to images stored
10244 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10245 compiled C and interpreted R code. It also provides a C/C++ API that can be
10246 used by other packages.")
10247 (license license:gpl2)))
10249 (define-public r-shades
10256 (uri (cran-uri "shades" version))
10259 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10260 (build-system r-build-system)
10261 (home-page "https://github.com/jonclayden/shades")
10262 (synopsis "Simple color manipulation")
10264 "This package provides functions for easily manipulating colors,
10265 creating color scales and calculating color distances.")
10266 (license license:bsd-3)))
10268 (define-public r-ore
10275 (uri (cran-uri "ore" version))
10277 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10278 (build-system r-build-system)
10279 (home-page "https://github.com/jonclayden/ore")
10280 (synopsis "R interface to the Onigmo regular expression library")
10282 "This package provides an alternative to R's built-in functionality for
10283 handling regular expressions, based on the Onigmo library. It offers
10284 first-class compiled regex objects, partial matching and function-based
10285 substitutions, amongst other features.")
10286 (license license:bsd-3)))
10288 (define-public r-reportr
10295 (uri (cran-uri "reportr" version))
10298 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10299 (build-system r-build-system)
10300 (propagated-inputs `(("r-ore" ,r-ore)))
10301 (home-page "https://github.com/jonclayden/reportr")
10302 (synopsis "General message and error reporting system")
10304 "This package provides a system for reporting messages, which offers
10305 certain useful features over the standard R system, such as the incorporation
10306 of output consolidation, message filtering, assertions, expression
10307 substitution, automatic generation of stack traces for debugging, and
10308 conditional reporting based on the current \"output level\".")
10309 (license license:gpl2)))
10311 (define-public r-tractor-base
10313 (name "r-tractor-base")
10318 (uri (cran-uri "tractor.base" version))
10321 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10322 (properties `((upstream-name . "tractor.base")))
10323 (build-system r-build-system)
10326 ("r-reportr" ,r-reportr)
10327 ("r-rnifti" ,r-rnifti)
10328 ("r-shades" ,r-shades)))
10329 (home-page "http://www.tractor-mri.org.uk")
10330 (synopsis "Read, manipulate and visualize magnetic resonance images")
10332 "This package provides functions for working with magnetic resonance
10333 images. It supports reading and writing of popular file formats (DICOM,
10334 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10335 visualization; flexible image manipulation; metadata and sparse image
10337 (license license:gpl2)))
10339 (define-public r-grimport
10341 (name "r-grimport")
10346 (uri (cran-uri "grImport" version))
10349 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10350 (properties `((upstream-name . "grImport")))
10351 (build-system r-build-system)
10353 `(("ghostscript" ,ghostscript)))
10355 `(("r-xml" ,r-xml)))
10356 (home-page "https://cran.r-project.org/web/packages/grImport")
10357 (synopsis "Convert, import, and draw PostScript pictures")
10359 "This package provides functions for converting, importing, and drawing
10360 PostScript pictures in R plots.")
10361 (license license:gpl2+)))
10363 (define-public r-grimport2
10365 (name "r-grimport2")
10370 (uri (cran-uri "grImport2" version))
10373 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10374 (properties `((upstream-name . "grImport2")))
10375 (build-system r-build-system)
10377 `(("r-base64enc" ,r-base64enc)
10381 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10382 (synopsis "Import SVG graphics")
10384 "This package provides functions for importing external vector images and
10385 drawing them as part of R plots. This package is different from the
10386 @code{grImport} package because, where that package imports PostScript format
10387 images, this package imports SVG format images. Furthermore, this package
10388 imports a specific subset of SVG, so external images must be preprocessed
10389 using a package like @code{rsvg} to produce SVG that this package can import.
10390 SVG features that are not supported by R graphics, such as gradient fills, can
10391 be imported and then exported via the @code{gridSVG} package.")
10392 (license license:gpl2+)))
10394 (define-public r-kohonen
10401 (uri (cran-uri "kohonen" version))
10404 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10405 (build-system r-build-system)
10407 `(("r-rcpp" ,r-rcpp)))
10408 (home-page "https://cran.r-project.org/web/packages/kohonen")
10409 (synopsis "Supervised and unsupervised self-organising maps")
10411 "This package provides functions to train @dfn{self-organising
10412 maps} (SOMs). Also interrogation of the maps and prediction using trained
10413 maps are supported. The name of the package refers to Teuvo Kohonen, the
10414 inventor of the SOM.")
10415 (license license:gpl2+)))
10417 (define-public r-nnls
10424 (uri (cran-uri "nnls" version))
10427 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10428 (build-system r-build-system)
10429 (native-inputs `(("gfortran" ,gfortran)))
10430 (home-page "https://cran.r-project.org/web/packages/nnls")
10431 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10433 "This package provides an R interface to the Lawson-Hanson implementation
10434 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10435 the combination of non-negative and non-positive constraints.")
10436 (license license:gpl2+)))
10438 (define-public r-iso
10445 (uri (cran-uri "Iso" version))
10448 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10449 (properties `((upstream-name . "Iso")))
10450 (build-system r-build-system)
10451 (native-inputs `(("gfortran" ,gfortran)))
10452 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10453 (synopsis "Functions to perform isotonic regression")
10455 "This package provides support for linear order and unimodal
10456 order (univariate) isotonic regression and bivariate isotonic regression with
10457 linear order on both variables.")
10458 (license license:gpl2+)))
10460 (define-public r-chemometricswithr
10462 (name "r-chemometricswithr")
10467 (uri (cran-uri "ChemometricsWithR" version))
10470 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10472 `((upstream-name . "ChemometricsWithR")))
10473 (build-system r-build-system)
10475 `(("r-devtools" ,r-devtools)
10476 ("r-kohonen" ,r-kohonen)
10479 (home-page "https://github.com/rwehrens/CWR")
10480 (synopsis "Chemometrics with R")
10482 "This package provides functions and scripts used in the book
10483 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10484 Life Sciences\" by Ron Wehrens, Springer (2011).")
10485 (license license:gpl2+)))
10487 (define-public r-als
10494 (uri (cran-uri "ALS" version))
10497 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10498 (properties `((upstream-name . "ALS")))
10499 (build-system r-build-system)
10502 ("r-nnls" ,r-nnls)))
10503 (home-page "https://cran.r-project.org/web/packages/ALS")
10504 (synopsis "Multivariate curve resolution alternating least squares")
10506 "Alternating least squares is often used to resolve components
10507 contributing to data with a bilinear structure; the basic technique may be
10508 extended to alternating constrained least squares. This package provides an
10509 implementation of @dfn{multivariate curve resolution alternating least
10510 squares} (MCR-ALS).
10512 Commonly applied constraints include unimodality, non-negativity, and
10513 normalization of components. Several data matrices may be decomposed
10514 simultaneously by assuming that one of the two matrices in the bilinear
10515 decomposition is shared between datasets.")
10516 (license license:gpl2+)))
10518 (define-public r-strucchange
10520 (name "r-strucchange")
10525 (uri (cran-uri "strucchange" version))
10528 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10529 (build-system r-build-system)
10531 `(("r-sandwich" ,r-sandwich)
10533 (home-page "https://cran.r-project.org/web/packages/strucchange")
10534 (synopsis "Testing, monitoring, and dating structural changes")
10536 "This package provides tools for testing, monitoring and dating
10537 structural changes in (linear) regression models. It features tests/methods
10538 from the generalized fluctuation test framework as well as from the F
10539 test (Chow test) framework. This includes methods to fit, plot and test
10540 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10541 statistics, respectively. It is possible to monitor incoming data online
10542 using fluctuation processes. Finally, the breakpoints in regression models
10543 with structural changes can be estimated together with confidence intervals.
10544 Emphasis is always given to methods for visualizing the data.")
10545 ;; Either of these two GPL versions
10546 (license (list license:gpl2 license:gpl3))))
10548 (define-public r-pixmap
10555 (uri (cran-uri "pixmap" version))
10558 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10559 (build-system r-build-system)
10560 (home-page "https://cran.r-project.org/web/packages/pixmap")
10561 (synopsis "Tools for bitmap images")
10563 "This package provides functions for importing, exporting, plotting and
10564 other manipulations of bitmapped images.")
10565 (license license:gpl2)))
10567 (define-public r-rapidjsonr
10569 (name "r-rapidjsonr")
10574 (uri (cran-uri "rapidjsonr" version))
10577 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10578 (build-system r-build-system)
10579 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10580 (synopsis "JSON parser")
10582 "This package provides JSON parsing capability through the Rapidjson
10584 (license license:expat)))
10586 (define-public r-ontologyindex
10588 (name "r-ontologyindex")
10593 (uri (cran-uri "ontologyIndex" version))
10596 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10597 (properties `((upstream-name . "ontologyIndex")))
10598 (build-system r-build-system)
10599 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10600 (synopsis "Functions for processing ontologies in R")
10602 "This package provides functions for reading ontologies into R as lists
10603 and manipulating sets of ontological terms.")
10604 (license license:gpl2+)))
10606 (define-public r-gargle
10613 (uri (cran-uri "gargle" version))
10616 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10617 (build-system r-build-system)
10622 ("r-jsonlite" ,r-jsonlite)
10623 ("r-rlang" ,r-rlang)
10624 ("r-withr" ,r-withr)))
10625 (home-page "https://gargle.r-lib.org")
10626 (synopsis "Utilities for working with Google APIs")
10628 "This package provides utilities for working with Google APIs. This
10629 includes functions and classes for handling common credential types and for
10630 preparing, executing, and processing HTTP requests.")
10631 (license license:expat)))
10633 (define-public r-bigrquery
10635 (name "r-bigrquery")
10640 (uri (cran-uri "bigrquery" version))
10643 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10644 (build-system r-build-system)
10646 `(("r-assertthat" ,r-assertthat)
10647 ("r-bit64" ,r-bit64)
10650 ("r-gargle" ,r-gargle)
10653 ("r-jsonlite" ,r-jsonlite)
10654 ("r-prettyunits" ,r-prettyunits)
10655 ("r-progress" ,r-progress)
10656 ("r-rapidjsonr" ,r-rapidjsonr)
10658 ("r-rlang" ,r-rlang)
10659 ("r-tibble" ,r-tibble)))
10660 (home-page "https://github.com/rstats-db/bigrquery")
10661 (synopsis "R interface to Google's BigQuery API")
10663 "This package provides an R interface to Google's BigQuery database.")
10664 (license license:gpl3)))
10666 (define-public r-gmp
10669 (version "0.5-13.5")
10673 (uri (cran-uri "gmp" version))
10676 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10677 (build-system r-build-system)
10680 (modify-phases %standard-phases
10681 (add-after 'unpack 'set-CC
10682 (lambda _ (setenv "CC" "gcc") #t)))))
10683 (inputs `(("gmp" ,gmp)))
10684 (home-page "https://cran.r-project.org/web/packages/gmp")
10685 (synopsis "Multiple precision arithmetic")
10687 "This package supports multiple precision arithmetic (big integers and
10688 rationals, prime number tests, matrix computation), \"arithmetic without
10689 limitations\" using the GNU Multiple Precision library.")
10690 ;; Any version of the GPL.
10691 (license license:gpl3+)))
10693 (define-public r-rmpfr
10700 (uri (cran-uri "Rmpfr" version))
10703 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10704 (properties `((upstream-name . "Rmpfr")))
10705 (build-system r-build-system)
10709 `(("r-gmp" ,r-gmp)))
10710 (home-page "http://rmpfr.r-forge.r-project.org/")
10711 (synopsis "R bindings to the MPFR library")
10713 "This package supports arithmetic (via S4 classes and methods) for
10714 arbitrary precision floating point numbers, including transcendental
10715 functions. To this end, the package interfaces with the @dfn{Multiple
10716 Precision Floating-Point Reliable} (MPFR) library.")
10717 (license license:gpl2+)))
10719 (define-public r-assertive-base
10721 (name "r-assertive-base")
10726 (uri (cran-uri "assertive.base" version))
10729 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10731 `((upstream-name . "assertive.base")))
10732 (build-system r-build-system)
10733 (home-page "https://bitbucket.org/richierocks/assertive.base")
10734 (synopsis "Core of the assertive package")
10736 "This package provides a minimal set of predicates and assertions used by
10737 the assertive package. This is mainly for use by other package developers who
10738 want to include run-time testing features in their own packages.")
10739 (license license:gpl3+)))
10741 (define-public r-assertive-properties
10743 (name "r-assertive-properties")
10748 (uri (cran-uri "assertive.properties" version))
10751 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10753 `((upstream-name . "assertive.properties")))
10754 (build-system r-build-system)
10756 `(("r-assertive-base" ,r-assertive-base)))
10757 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10758 (synopsis "Assertions to check properties of variables")
10760 "This package provides a set of predicates and assertions for checking
10761 the properties of variables, such as length, names and attributes. This is
10762 mainly for use by other package developers who want to include run-time
10763 testing features in their own packages.")
10764 (license license:gpl3+)))
10766 (define-public r-assertive-numbers
10768 (name "r-assertive-numbers")
10773 (uri (cran-uri "assertive.numbers" version))
10776 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10778 `((upstream-name . "assertive.numbers")))
10779 (build-system r-build-system)
10781 `(("r-assertive-base" ,r-assertive-base)))
10782 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10783 (synopsis "Assertions to check properties of numbers")
10785 "This package provides a set of predicates and assertions for checking
10786 the properties of numbers. This is mainly for use by other package developers
10787 who want to include run-time testing features in their own packages.")
10788 (license license:gpl3+)))
10790 (define-public r-assertive-sets
10792 (name "r-assertive-sets")
10797 (uri (cran-uri "assertive.sets" version))
10800 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10802 `((upstream-name . "assertive.sets")))
10803 (build-system r-build-system)
10805 `(("r-assertive-base" ,r-assertive-base)))
10806 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10807 (synopsis "Assertions to check properties of sets")
10809 "This package provides a set of predicates and assertions for checking
10810 the properties of sets. This is mainly for use by other package developers
10811 who want to include run-time testing features in their own packages.")
10812 (license license:gpl3+)))
10814 (define-public r-assertive-matrices
10816 (name "r-assertive-matrices")
10821 (uri (cran-uri "assertive.matrices" version))
10824 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10826 `((upstream-name . "assertive.matrices")))
10827 (build-system r-build-system)
10829 `(("r-assertive-base" ,r-assertive-base)))
10830 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10831 (synopsis "Assertions to check properties of matrices")
10833 "This package provides a set of predicates and assertions for checking
10834 the properties of matrices. This is mainly for use by other package
10835 developers who want to include run-time testing features in their own
10837 (license license:gpl3+)))
10839 (define-public r-assertive-models
10841 (name "r-assertive-models")
10846 (uri (cran-uri "assertive.models" version))
10849 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10851 `((upstream-name . "assertive.models")))
10852 (build-system r-build-system)
10854 `(("r-assertive-base" ,r-assertive-base)))
10855 (home-page "https://bitbucket.org/richierocks/assertive.models")
10856 (synopsis "Assertions to check properties of models")
10858 "This package provides a set of predicates and assertions for checking
10859 the properties of models. This is mainly for use by other package developers
10860 who want to include run-time testing features in their own packages.")
10861 (license license:gpl3+)))
10863 (define-public r-assertive-reflection
10865 (name "r-assertive-reflection")
10870 (uri (cran-uri "assertive.reflection" version))
10873 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10875 `((upstream-name . "assertive.reflection")))
10876 (build-system r-build-system)
10878 `(("r-assertive-base" ,r-assertive-base)))
10879 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10880 (synopsis "Assertions for checking the state of R")
10882 "This package provides a set of predicates and assertions for checking
10883 the state and capabilities of R, the operating system it is running on, and
10884 the IDE being used. This is mainly for use by other package developers who
10885 want to include run-time testing features in their own packages.")
10886 (license license:gpl3+)))
10888 (define-public r-assertive-types
10890 (name "r-assertive-types")
10895 (uri (cran-uri "assertive.types" version))
10898 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10900 `((upstream-name . "assertive.types")))
10901 (build-system r-build-system)
10903 `(("r-assertive-base" ,r-assertive-base)
10904 ("r-assertive-properties" ,r-assertive-properties)
10905 ("r-codetools" ,r-codetools)))
10906 (home-page "https://bitbucket.org/richierocks/assertive.types")
10907 (synopsis "Assertions to check types of variables")
10909 "This package provides a set of predicates and assertions for checking
10910 the types of variables. This is mainly for use by other package developers
10911 who want to include run-time testing features in their own packages.")
10912 (license license:gpl3+)))
10914 (define-public r-assertive-files
10916 (name "r-assertive-files")
10921 (uri (cran-uri "assertive.files" version))
10924 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10926 `((upstream-name . "assertive.files")))
10927 (build-system r-build-system)
10929 `(("r-assertive-base" ,r-assertive-base)
10930 ("r-assertive-numbers" ,r-assertive-numbers)))
10931 (home-page "https://bitbucket.org/richierocks/assertive.files")
10932 (synopsis "Assertions to check properties of files")
10934 "This package provides a set of predicates and assertions for checking
10935 the properties of files and connections. This is mainly for use by other
10936 package developers who want to include run-time testing features in their own
10938 (license license:gpl3+)))
10940 (define-public r-assertive-code
10942 (name "r-assertive-code")
10947 (uri (cran-uri "assertive.code" version))
10950 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10952 `((upstream-name . "assertive.code")))
10953 (build-system r-build-system)
10955 `(("r-assertive-base" ,r-assertive-base)
10956 ("r-assertive-properties" ,r-assertive-properties)
10957 ("r-assertive-types" ,r-assertive-types)))
10958 (home-page "https://bitbucket.org/richierocks/assertive.code")
10959 (synopsis "Assertions to check properties of code")
10961 "This package provides a set of predicates and assertions for checking
10962 the properties of code. This is mainly for use by other package developers
10963 who want to include run-time testing features in their own packages.")
10964 (license license:gpl3+)))
10966 (define-public r-assertive-datetimes
10968 (name "r-assertive-datetimes")
10973 (uri (cran-uri "assertive.datetimes" version))
10976 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10978 `((upstream-name . "assertive.datetimes")))
10979 (build-system r-build-system)
10981 `(("r-assertive-base" ,r-assertive-base)
10982 ("r-assertive-types" ,r-assertive-types)))
10983 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10984 (synopsis "Assertions to check properties of dates and times")
10986 "This package provides a set of predicates and assertions for checking
10987 the properties of dates and times. This is mainly for use by other package
10988 developers who want to include run-time testing features in their own
10990 (license license:gpl3+)))
10992 (define-public r-assertive-strings
10994 (name "r-assertive-strings")
10999 (uri (cran-uri "assertive.strings" version))
11002 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11004 `((upstream-name . "assertive.strings")))
11005 (build-system r-build-system)
11007 `(("r-assertive-base" ,r-assertive-base)
11008 ("r-assertive-types" ,r-assertive-types)
11009 ("r-stringi" ,r-stringi)))
11010 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11011 (synopsis "Assertions to check properties of strings")
11013 "This package provides a set of predicates and assertions for checking
11014 the properties of strings. This is mainly for use by other package developers
11015 who want to include run-time testing features in their own packages.")
11016 (license license:gpl3+)))
11018 (define-public r-assertive-data-us
11020 (name "r-assertive-data-us")
11025 (uri (cran-uri "assertive.data.us" version))
11028 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11030 `((upstream-name . "assertive.data.us")))
11031 (build-system r-build-system)
11033 `(("r-assertive-base" ,r-assertive-base)
11034 ("r-assertive-strings" ,r-assertive-strings)))
11035 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11036 (synopsis "Assertions to check properties of strings")
11038 "This package provides a set of predicates and assertions for checking
11039 the properties of US-specific complex data types. This is mainly for use by
11040 other package developers who want to include run-time testing features in
11041 their own packages.")
11042 (license license:gpl3+)))
11044 (define-public r-assertive-data-uk
11046 (name "r-assertive-data-uk")
11051 (uri (cran-uri "assertive.data.uk" version))
11054 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11056 `((upstream-name . "assertive.data.uk")))
11057 (build-system r-build-system)
11059 `(("r-assertive-base" ,r-assertive-base)
11060 ("r-assertive-strings" ,r-assertive-strings)))
11061 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11062 (synopsis "Assertions to check properties of strings")
11064 "This package provides a set of predicates and assertions for checking
11065 the properties of UK-specific complex data types. This is mainly for use by
11066 other package developers who want to include run-time testing features in
11067 their own packages.")
11068 (license license:gpl3+)))
11070 (define-public r-assertive-data
11072 (name "r-assertive-data")
11077 (uri (cran-uri "assertive.data" version))
11080 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11082 `((upstream-name . "assertive.data")))
11083 (build-system r-build-system)
11085 `(("r-assertive-base" ,r-assertive-base)
11086 ("r-assertive-strings" ,r-assertive-strings)))
11087 (home-page "https://bitbucket.org/richierocks/assertive.data")
11088 (synopsis "Assertions to check properties of data")
11090 "This package provides a set of predicates and assertions for checking
11091 the properties of (country independent) complex data types. This is mainly
11092 for use by other package developers who want to include run-time testing
11093 features in their own packages.")
11094 (license license:gpl3+)))
11096 (define-public r-assertive
11098 (name "r-assertive")
11103 (uri (cran-uri "assertive" version))
11106 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11107 (build-system r-build-system)
11109 `(("r-assertive-base" ,r-assertive-base)
11110 ("r-assertive-code" ,r-assertive-code)
11111 ("r-assertive-data" ,r-assertive-data)
11112 ("r-assertive-data-uk" ,r-assertive-data-uk)
11113 ("r-assertive-data-us" ,r-assertive-data-us)
11114 ("r-assertive-datetimes" ,r-assertive-datetimes)
11115 ("r-assertive-files" ,r-assertive-files)
11116 ("r-assertive-matrices" ,r-assertive-matrices)
11117 ("r-assertive-models" ,r-assertive-models)
11118 ("r-assertive-numbers" ,r-assertive-numbers)
11119 ("r-assertive-properties" ,r-assertive-properties)
11120 ("r-assertive-reflection" ,r-assertive-reflection)
11121 ("r-assertive-sets" ,r-assertive-sets)
11122 ("r-assertive-strings" ,r-assertive-strings)
11123 ("r-assertive-types" ,r-assertive-types)
11124 ("r-knitr" ,r-knitr)))
11125 (home-page "https://bitbucket.org/richierocks/assertive")
11126 (synopsis "Readable check functions to ensure code integrity")
11128 "This package provides lots of predicates (@code{is_*} functions) to
11129 check the state of your variables, and assertions (@code{assert_*} functions)
11130 to throw errors if they aren't in the right form.")
11131 (license license:gpl3+)))
11133 (define-public r-dotcall64
11135 (name "r-dotcall64")
11140 (uri (cran-uri "dotCall64" version))
11143 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11144 (properties `((upstream-name . "dotCall64")))
11145 (build-system r-build-system)
11146 (native-inputs `(("gfortran" ,gfortran)))
11147 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11148 (synopsis "Enhanced foreign function interface supporting long vectors")
11150 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11151 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11152 supports long vectors, arguments of type 64-bit integer, and provides a
11153 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11154 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11155 (license license:gpl2+)))
11157 (define-public r-spam
11164 (uri (cran-uri "spam" version))
11166 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11167 (build-system r-build-system)
11169 `(("r-dotcall64" ,r-dotcall64)))
11170 (native-inputs `(("gfortran" ,gfortran)))
11171 (home-page "https://www.math.uzh.ch/pages/spam/")
11172 (synopsis "Sparse matrix algebra")
11174 "This package provides a set of functions for sparse matrix algebra.
11175 Differences with other sparse matrix packages are:
11178 @item it only supports (essentially) one sparse matrix format;
11179 @item it is based on transparent and simple structure(s);
11180 @item it is tailored for MCMC calculations within G(M)RF;
11181 @item and it is fast and scalable (with the extension package @code{spam64}).
11183 ;; Either of these licenses
11184 (license (list license:bsd-3 license:lgpl2.0))))
11186 (define-public r-fields
11193 (uri (cran-uri "fields" version))
11195 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11196 (build-system r-build-system)
11198 `(("r-maps" ,r-maps)
11199 ("r-spam" ,r-spam)))
11201 `(("gfortran" ,gfortran)))
11202 (home-page "https://www.image.ucar.edu/fields")
11203 (synopsis "Tools for spatial data")
11205 "This is a package for curve, surface and function fitting with an
11206 emphasis on splines, spatial data and spatial statistics. The major methods
11207 include cubic, and thin plate splines, Kriging, and compactly supported
11208 covariance functions for large data sets.")
11209 (license license:gpl2+)))
11211 (define-public r-spatialextremes
11213 (name "r-spatialextremes")
11214 (version "2.0-7.2")
11218 (uri (cran-uri "SpatialExtremes" version))
11221 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11223 `((upstream-name . "SpatialExtremes")))
11224 (build-system r-build-system)
11226 `(("r-fields" ,r-fields)
11227 ("r-maps" ,r-maps)))
11228 (home-page "http://spatialextremes.r-forge.r-project.org/")
11229 (synopsis "Modelling spatial extremes")
11231 "This package provides tools for the statistical modelling of spatial
11232 extremes using max-stable processes, copula or Bayesian hierarchical models.
11233 More precisely, this package allows (conditional) simulations from various
11234 parametric max-stable models, analysis of the extremal spatial dependence, the
11235 fitting of such processes using composite likelihoods or least square (simple
11236 max-stable processes only), model checking and selection and prediction.")
11237 (license license:gpl2+)))
11239 (define-public r-drc
11246 (uri (cran-uri "drc" version))
11249 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11250 (build-system r-build-system)
11253 ("r-gtools" ,r-gtools)
11255 ("r-multcomp" ,r-multcomp)
11256 ("r-plotrix" ,r-plotrix)
11257 ("r-scales" ,r-scales)))
11258 (home-page "https://cran.r-project.org/web/packages/drc")
11259 (synopsis "Analysis of dose-response curves")
11261 "This package provides a suite of flexible and versatile model fitting
11262 and after-fitting functions for the analysis of dose-response data.")
11263 (license license:gpl2+)))
11265 (define-public r-rmeta
11272 (uri (cran-uri "rmeta" version))
11275 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11276 (build-system r-build-system)
11277 (home-page "https://cran.r-project.org/web/packages/rmeta")
11278 (synopsis "Tools for meta-analysis")
11280 "This package provides functions for simple fixed and random effects
11281 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11282 draws standard summary plots, funnel plots, and computes summaries and tests
11283 for association and heterogeneity.")
11284 (license license:gpl2)))
11286 (define-public r-bootstrap
11288 (name "r-bootstrap")
11293 (uri (cran-uri "bootstrap" version))
11296 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11297 (build-system r-build-system)
11298 (native-inputs `(("gfortran" ,gfortran)))
11299 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11300 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11302 "This package provides software and data for the book \"An Introduction
11303 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11304 This package is primarily provided for projects already based on it, and for
11305 support of the book. New projects should preferentially use the recommended
11306 package \"boot\".")
11307 (license license:bsd-3)))
11309 (define-public r-survivalroc
11311 (name "r-survivalroc")
11316 (uri (cran-uri "survivalROC" version))
11319 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11320 (properties `((upstream-name . "survivalROC")))
11321 (build-system r-build-system)
11322 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11323 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11325 "Compute time-dependent ROC curve from censored survival data using
11326 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11327 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11328 (license license:gpl2+)))
11330 (define-public r-longitudinal
11332 (name "r-longitudinal")
11337 (uri (cran-uri "longitudinal" version))
11340 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11341 (build-system r-build-system)
11342 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11343 (home-page "http://strimmerlab.org/software/longitudinal/")
11344 (synopsis "Analysis of multiple time course data")
11346 "This package contains general data structures and functions for
11347 longitudinal data with multiple variables, repeated measurements, and
11348 irregularly spaced time points. It also implements a shrinkage estimator of
11349 dynamical correlation and dynamical covariance.")
11350 (license license:gpl3+)))
11352 (define-public r-genenet
11359 (uri (cran-uri "GeneNet" version))
11362 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11363 (properties `((upstream-name . "GeneNet")))
11364 (build-system r-build-system)
11366 `(("r-corpcor" ,r-corpcor)
11367 ("r-fdrtool" ,r-fdrtool)
11368 ("r-longitudinal" ,r-longitudinal)))
11369 (home-page "http://strimmerlab.org/software/genenet/")
11370 (synopsis "Modeling and inferring gene networks")
11372 "This package analyzes gene expression (time series) data with focus on
11373 the inference of gene networks. In particular, GeneNet implements the methods
11374 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11375 for learning large-scale gene association networks (including assignment of
11376 putative directions).")
11377 (license license:gpl3+)))
11379 (define-public r-rbamtools
11381 (name "r-rbamtools")
11382 (version "2.16.17")
11386 (uri (cran-uri "rbamtools" version))
11389 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11390 (build-system r-build-system)
11391 (inputs `(("zlib" ,zlib)))
11393 `(("r-refgenome" ,r-refgenome)))
11394 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11395 (synopsis "Read and write BAM (binary alignment) files")
11397 "This package provides an R interface to functions of the SAMtools
11399 (license license:artistic2.0)))
11401 (define-public r-protviz
11408 (uri (cran-uri "protViz" version))
11411 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11412 (properties `((upstream-name . "protViz")))
11413 (build-system r-build-system)
11414 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11415 (home-page "https://github.com/protViz/protViz/")
11416 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11418 "This package helps with quality checks, visualizations and analysis of
11419 mass spectrometry data, coming from proteomics experiments. The package is
11420 developed, tested and used at the Functional Genomics Center Zurich, where it
11421 is used mainly for prototyping, teaching, and having fun with proteomics data.
11422 But it can also be used to do data analysis for small scale data sets.")
11423 (license license:gpl3)))
11425 (define-public r-cmprsk
11432 (uri (cran-uri "cmprsk" version))
11434 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11435 (build-system r-build-system)
11437 `(("r-survival" ,r-survival)))
11439 `(("gfortran" ,gfortran)))
11440 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11441 (synopsis "Subdistribution analysis of competing risks")
11443 "This package provides tool for estimation, testing and regression
11444 modeling of subdistribution functions in competing risks, as described in
11445 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11446 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11447 A proportional hazards model for the subdistribution of a competing risk,
11448 JASA, 94:496-509.")
11449 (license license:gpl2+)))
11451 (define-public r-etm
11458 (uri (cran-uri "etm" version))
11461 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11462 (build-system r-build-system)
11464 `(("r-data-table" ,r-data-table)
11465 ("r-lattice" ,r-lattice)
11467 ("r-rcpparmadillo" ,r-rcpparmadillo)
11468 ("r-survival" ,r-survival)))
11469 (home-page "https://cran.r-project.org/web/packages/etm")
11470 (synopsis "Empirical transition matrix")
11472 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11473 the matrix of transition probabilities for any time-inhomogeneous multistate
11474 model with finite state space using the Aalen-Johansen estimator.")
11475 (license license:expat)))
11477 (define-public r-epi
11484 (uri (cran-uri "Epi" version))
11487 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11488 (properties `((upstream-name . "Epi")))
11489 (build-system r-build-system)
11491 `(("r-cmprsk" ,r-cmprsk)
11492 ("r-data-table" ,r-data-table)
11495 ("r-matrix" ,r-matrix)
11497 ("r-numderiv" ,r-numderiv)
11499 ("r-survival" ,r-survival)
11501 (home-page "http://BendixCarstensen.com/Epi/")
11502 (synopsis "Statistical analysis in epidemiology")
11504 "This package provides functions for demographic and epidemiological
11505 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11506 particular representation, manipulation and simulation of multistate data -
11507 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11508 @code{etm} and @code{cmprsk} packages. It also contains functions for
11509 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11510 data and some useful functions for tabulation and plotting, as well as a
11511 number of epidemiological data sets.")
11512 (license license:gpl2)))
11514 (define-public r-ppls
11517 (version "1.6-1.1")
11521 (uri (cran-uri "ppls" version))
11524 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11525 (build-system r-build-system)
11526 (propagated-inputs `(("r-mass" ,r-mass)))
11527 (home-page "https://cran.r-project.org/web/packages/ppls")
11528 (synopsis "Penalized partial least squares")
11530 "This package contains linear and nonlinear regression methods based on
11531 partial least squares and penalization techniques. Model parameters are
11532 selected via cross-validation, and confidence intervals ans tests for the
11533 regression coefficients can be conducted via jackknifing.")
11534 (license license:gpl2+)))
11536 (define-public r-huge
11543 (uri (cran-uri "huge" version))
11545 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11546 (build-system r-build-system)
11548 `(("r-igraph" ,r-igraph)
11550 ("r-matrix" ,r-matrix)
11552 ("r-rcppeigen" ,r-rcppeigen)))
11553 (home-page "https://cran.r-project.org/web/packages/huge")
11554 (synopsis "High-dimensional undirected graph estimation")
11556 "This package provides a general framework for high-dimensional
11557 undirected graph estimation. It integrates data preprocessing, neighborhood
11558 screening, graph estimation, and model selection techniques into a pipeline.")
11559 (license license:gpl2)))
11561 (define-public r-parcor
11568 (uri (cran-uri "parcor" version))
11571 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11572 (build-system r-build-system)
11575 ("r-genenet" ,r-genenet)
11576 ("r-glmnet" ,r-glmnet)
11578 ("r-ppls" ,r-ppls)))
11579 (home-page "https://cran.r-project.org/web/packages/parcor")
11580 (synopsis "Regularized estimation of partial correlation matrices")
11582 "This package estimates the matrix of partial correlations based on
11583 different regularized regression methods: lasso, adaptive lasso, PLS, and
11584 Ridge Regression. In addition, the package provides model selection for
11585 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11586 (license license:gpl2+)))
11588 (define-public r-mcmc
11595 (uri (cran-uri "mcmc" version))
11598 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11599 (build-system r-build-system)
11600 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11601 (synopsis "Markov chain Monte Carlo")
11603 "This package simulates continuous distributions of random vectors using
11604 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11605 function that evaluates the log unnormalized density. Algorithms are random
11606 walk Metropolis algorithm (function @code{metrop}), simulated
11607 tempering (function @code{temper}), and morphometric random walk
11608 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11609 by change of variable.")
11610 (license license:expat)))
11612 (define-public r-listenv
11619 (uri (cran-uri "listenv" version))
11622 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11623 (build-system r-build-system)
11625 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11626 (home-page "https://github.com/HenrikBengtsson/listenv")
11627 (synopsis "Environments behaving (almost) as lists")
11629 "This package implements list environments. List environments are
11630 environments that have list-like properties. For instance, the elements of a
11631 list environment are ordered and can be accessed and iterated over using index
11633 (license license:lgpl2.1+)))
11635 (define-public r-globals
11642 (uri (cran-uri "globals" version))
11645 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11646 (build-system r-build-system)
11648 `(("r-codetools" ,r-codetools)))
11649 (home-page "https://github.com/HenrikBengtsson/globals")
11650 (synopsis "Identify global objects in R expressions")
11652 "This package provides tools to identify global (\"unknown\" or \"free\")
11653 objects in R expressions by code inspection using various strategies, e.g.
11654 conservative or liberal. The objective of this package is to make it as
11655 simple as possible to identify global objects for the purpose of exporting
11656 them in distributed compute environments.")
11657 (license license:lgpl2.1+)))
11659 (define-public r-future
11666 (uri (cran-uri "future" version))
11669 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11670 (build-system r-build-system)
11672 `(("r-digest" ,r-digest)
11673 ("r-globals" ,r-globals)
11674 ("r-listenv" ,r-listenv)))
11676 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11677 (home-page "https://github.com/HenrikBengtsson/future")
11678 (synopsis "Unified parallel and distributed processing in R")
11680 "The purpose of this package is to provide a lightweight and unified
11681 Future API for sequential and parallel processing of R expression via futures.
11682 This package implements sequential, multicore, multisession, and cluster
11683 futures. With these, R expressions can be evaluated on the local machine, in
11684 parallel a set of local machines, or distributed on a mix of local and remote
11685 machines. Extensions to this package implement additional backends for
11686 processing futures via compute cluster schedulers etc. Because of its unified
11687 API, there is no need to modify any code in order to switch from sequential on
11688 the local machine to, say, distributed processing on a remote compute cluster.")
11689 (license license:lgpl2.1+)))
11691 (define-public r-future-apply
11693 (name "r-future-apply")
11698 (uri (cran-uri "future.apply" version))
11701 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11702 (properties `((upstream-name . "future.apply")))
11703 (build-system r-build-system)
11705 `(("r-future" ,r-future)
11706 ("r-globals" ,r-globals)))
11708 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11709 (home-page "https://github.com/HenrikBengtsson/future.apply")
11710 (synopsis "Apply function to elements in parallel using futures")
11712 "This package provides implementations of @code{apply()},
11713 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11714 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11715 can be resolved using any future-supported backend, e.g. parallel on the local
11716 machine or distributed on a compute cluster.")
11717 (license license:gpl2+)))
11719 (define-public r-rsvd
11726 (uri (cran-uri "rsvd" version))
11729 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11730 (build-system r-build-system)
11732 `(("r-matrix" ,r-matrix)))
11733 (home-page "https://github.com/erichson/rSVD")
11734 (synopsis "Randomized singular value decomposition")
11736 "Low-rank matrix decompositions are fundamental tools and widely used for
11737 data analysis, dimension reduction, and data compression. Classically, highly
11738 accurate deterministic matrix algorithms are used for this task. However, the
11739 emergence of large-scale data has severely challenged our computational
11740 ability to analyze big data. The concept of randomness has been demonstrated
11741 as an effective strategy to quickly produce approximate answers to familiar
11742 problems such as the @dfn{singular value decomposition} (SVD). This package
11743 provides several randomized matrix algorithms such as the randomized singular
11744 value decomposition (@code{rsvd}), randomized principal component
11745 analysis (@code{rpca}), randomized robust principal component
11746 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11747 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11748 functions are provided.")
11749 (license license:gpl3+)))
11751 (define-public r-sloop
11758 (uri (cran-uri "sloop" version))
11761 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11762 (build-system r-build-system)
11764 `(("r-codetools" ,r-codetools)
11765 ("r-crayon" ,r-crayon)
11766 ("r-purrr" ,r-purrr)
11767 ("r-rlang" ,r-rlang)
11768 ("r-tibble" ,r-tibble)))
11769 (home-page "https://github.com/r-lib/sloop")
11770 (synopsis "Helpers for object-oriented programming in R")
11772 "This package provides a collection of helper functions designed to
11773 help you to better understand object oriented programming in R, particularly
11775 (license license:gpl3)))
11777 (define-public r-capushe
11784 (uri (cran-uri "capushe" version))
11787 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11788 (build-system r-build-system)
11789 (propagated-inputs `(("r-mass" ,r-mass)))
11790 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11791 (synopsis "Calibrating penalties using slope heuristics")
11793 "This package provides tools for the calibration of penalized criteria
11794 for model selection. The calibration methods available are based on the slope
11796 (license license:gpl2+)))
11798 (define-public r-dorng
11805 (uri (cran-uri "doRNG" version))
11808 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11809 (properties `((upstream-name . "doRNG")))
11810 (build-system r-build-system)
11812 `(("r-foreach" ,r-foreach)
11813 ("r-iterators" ,r-iterators)
11814 ("r-pkgmaker" ,r-pkgmaker)
11815 ("r-rngtools" ,r-rngtools)))
11816 (home-page "https://renozao.github.io/doRNG/")
11817 (synopsis "Generic reproducible parallel backend for foreach loops")
11819 "This package provides functions to perform reproducible parallel
11820 @code{foreach} loops, using independent random streams as generated by
11821 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11822 convert standard @code{%dopar%} loops into fully reproducible loops,
11823 independently of the number of workers, the task scheduling strategy, or the
11824 chosen parallel environment and associated foreach backend.")
11825 (license license:gpl2+)))
11827 (define-public r-blockmodeling
11829 (name "r-blockmodeling")
11834 (uri (cran-uri "blockmodeling" version))
11837 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11838 (build-system r-build-system)
11840 `(("r-doparallel" ,r-doparallel)
11841 ("r-dorng" ,r-dorng)
11842 ("r-foreach" ,r-foreach)
11843 ("r-matrix" ,r-matrix)))
11844 (native-inputs `(("gfortran" ,gfortran)))
11845 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11846 (synopsis "Generalized and classical blockmodeling of valued networks")
11848 "This package is primarily meant as an implementation of generalized
11849 blockmodeling for valued networks. In addition, measures of similarity or
11850 dissimilarity based on structural equivalence and regular equivalence (REGE
11851 algorithms) can be computed and partitioned matrices can be plotted.")
11852 (license license:gpl2+)))
11854 (define-public r-upsetr
11861 (uri (cran-uri "UpSetR" version))
11864 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11865 (properties `((upstream-name . "UpSetR")))
11866 (build-system r-build-system)
11868 `(("r-ggplot2" ,r-ggplot2)
11869 ("r-gridextra" ,r-gridextra)
11871 ("r-scales" ,r-scales)))
11872 (home-page "https://github.com/hms-dbmi/UpSetR")
11873 (synopsis "Visualize intersecting sets")
11875 "This package provides a more scalable alternative to Venn and Euler
11876 diagrams for visualizing intersecting sets. Create visualizations of
11877 intersecting sets using a novel matrix design, along with visualizations of
11878 several common set, element and attribute related tasks.")
11879 (license license:expat)))
11881 ;; This package includes a JavaScript file, which is not minified. When
11882 ;; upgrading please check that there are no new minified JavaScript files.
11883 (define-public r-shinybs
11890 (uri (cran-uri "shinyBS" version))
11893 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11894 (properties `((upstream-name . "shinyBS")))
11895 (build-system r-build-system)
11896 ;; The tests spawn Shiny browser apps. They cannot be run
11897 ;; non-interactively.
11898 (arguments '(#:tests? #f))
11900 `(("r-htmltools" ,r-htmltools)
11901 ("r-shiny" ,r-shiny)))
11902 (home-page "https://ebailey78.github.io/shinyBS/")
11903 (synopsis "Twitter Bootstrap components for Shiny")
11905 "This package adds additional Twitter Bootstrap components to Shiny.")
11906 (license license:gpl3)))
11908 (define-public r-outliers
11910 (name "r-outliers")
11915 (uri (cran-uri "outliers" version))
11918 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11919 (build-system r-build-system)
11920 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11921 (synopsis "Tests for outliers")
11923 "This package provides a collection of some tests commonly used for
11924 identifying outliers.")
11925 (license license:gpl2+)))
11927 (define-public r-bayesm
11934 (uri (cran-uri "bayesm" version))
11936 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11937 (build-system r-build-system)
11939 `(("r-rcpp" ,r-rcpp)
11940 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11941 (home-page "http://www.perossi.org/home/bsm-1")
11942 (synopsis "Bayesian inference for marketing/micro-econometrics")
11944 "This package covers many important models used in marketing and
11945 micro-econometrics applications, including Bayes Regression (univariate or
11946 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11947 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11948 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11949 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11950 Estimation with normal base, Hierarchical Linear Models with normal prior and
11951 covariates, Hierarchical Linear Models with a mixture of normals prior and
11952 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11953 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11954 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11955 analysis of choice-based conjoint data, Bayesian treatment of linear
11956 instrumental variables models, Analysis of Multivariate Ordinal survey data
11957 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11958 Coefficient Logit Models.")
11959 (license license:gpl2+)))
11961 (define-public r-tensora
11968 (uri (cran-uri "tensorA" version))
11971 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11972 (properties `((upstream-name . "tensorA")))
11973 (build-system r-build-system)
11974 (home-page "http://www.stat.boogaart.de/tensorA")
11975 (synopsis "Advanced tensor arithmetic with named indices")
11977 "This package provides convenience functions for advanced linear algebra
11978 with tensors and computation with datasets of tensors on a higher level
11979 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11980 co- and contravariate indices, and parallel computations on sequences of
11982 (license license:gpl2+)))
11984 (define-public r-rarpack
11991 (uri (cran-uri "rARPACK" version))
11994 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11995 (properties `((upstream-name . "rARPACK")))
11996 (build-system r-build-system)
11997 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11998 (home-page "https://github.com/yixuan/rARPACK")
11999 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12001 "This package was previously an R wrapper of the ARPACK library, and now
12002 a shell of the R package RSpectra, an R interface to the Spectra library for
12003 solving large scale eigenvalue/vector problems. The current version of
12004 rARPACK simply imports and exports the functions provided by RSpectra. New
12005 users of rARPACK are advised to switch to the RSpectra package.")
12006 (license license:bsd-3)))
12008 (define-public r-compositions
12010 (name "r-compositions")
12015 (uri (cran-uri "compositions" version))
12018 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
12019 (build-system r-build-system)
12021 `(("r-bayesm" ,r-bayesm)
12022 ("r-robustbase" ,r-robustbase)
12023 ("r-tensora" ,r-tensora)))
12024 (home-page "http://www.stat.boogaart.de/compositions")
12025 (synopsis "Compositional data analysis")
12027 "This package provides functions for the consistent analysis of
12028 compositional data (e.g. portions of substances) and positive
12029 numbers (e.g. concentrations).")
12030 (license license:gpl2+)))
12032 (define-public r-cobs
12039 (uri (cran-uri "cobs" version))
12042 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
12043 (build-system r-build-system)
12045 `(("r-quantreg" ,r-quantreg)
12046 ("r-sparsem" ,r-sparsem)))
12047 (home-page "https://cran.r-project.org/web/packages/cobs")
12048 (synopsis "Constrained B-Splines (sparse matrix based)")
12050 "This package provides qualitatively constrained (regression) smoothing
12051 splines via linear programming and sparse matrices.")
12052 (license license:gpl2+)))
12054 (define-public r-drimpute
12056 (name "r-drimpute")
12061 (uri (cran-uri "DrImpute" version))
12064 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12065 (properties `((upstream-name . "DrImpute")))
12066 (build-system r-build-system)
12068 `(("r-rcpp" ,r-rcpp)
12069 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12070 (home-page "https://github.com/ikwak2/DrImpute")
12071 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12073 "This is an R package for imputing dropout events. Many statistical
12074 methods in cell type identification, visualization and lineage reconstruction
12075 do not account for dropout events. DrImpute can improve the performance of
12076 such software by imputing dropout events.")
12077 (license license:gpl3)))
12079 (define-public r-gamlss-dist
12081 (name "r-gamlss-dist")
12086 (uri (cran-uri "gamlss.dist" version))
12088 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
12089 (properties `((upstream-name . "gamlss.dist")))
12090 (build-system r-build-system)
12091 (propagated-inputs `(("r-mass" ,r-mass)))
12092 (home-page "http://www.gamlss.org/")
12093 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12095 "This package provides a set of distributions which can be used for
12096 modelling the response variables in Generalized Additive Models for Location
12097 Scale and Shape. The distributions can be continuous, discrete or mixed
12098 distributions. Extra distributions can be created, by transforming, any
12099 continuous distribution defined on the real line, to a distribution defined on
12100 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12101 transformation, respectively.")
12102 ;; Either version of the GPL.
12103 (license (list license:gpl2 license:gpl3))))
12105 ;; This package includes JavaScript files, which are not minified. When
12106 ;; upgrading please check that there are no new minified JavaScript files.
12107 (define-public r-shinyjs
12114 (uri (cran-uri "shinyjs" version))
12117 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
12118 (build-system r-build-system)
12120 `(("r-digest" ,r-digest)
12121 ("r-htmltools" ,r-htmltools)
12122 ("r-jsonlite" ,r-jsonlite)
12123 ("r-shiny" ,r-shiny)))
12124 (home-page "https://deanattali.com/shinyjs")
12125 (synopsis "Improve the user experience of your Shiny apps")
12127 "Perform common useful JavaScript operations in Shiny apps that will
12128 greatly improve your apps without having to know any JavaScript. Examples
12129 include: hiding an element, disabling an input, resetting an input back to its
12130 original value, delaying code execution by a few seconds, and many more useful
12131 functions for both the end user and the developer. Shinyjs can also be used
12132 to easily call your own custom JavaScript functions from R.")
12133 (license license:agpl3+)))
12135 ;; This package includes minified JavaScript files. When upgrading please
12136 ;; check that there are no new minified JavaScript files.
12137 (define-public r-colourpicker
12139 (name "r-colourpicker")
12144 (uri (cran-uri "colourpicker" version))
12147 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12148 (build-system r-build-system)
12150 `(#:modules ((guix build utils)
12151 (guix build r-build-system)
12155 (modify-phases %standard-phases
12156 (add-after 'unpack 'process-javascript
12157 (lambda* (#:key inputs #:allow-other-keys)
12158 (with-directory-excursion "inst"
12162 `((,(assoc-ref inputs "js-salvattore")
12163 "examples/colourInput/www/salvattore.min.js")
12164 (,(assoc-ref inputs "js-jquery")
12165 "htmlwidgets/lib/jquery/jquery.min.js")
12166 ("www/shared/colourpicker/js/colourpicker.js"
12167 "www/shared/colourpicker/js/colourpicker.min.js"))))
12168 (lambda (sources targets)
12169 (for-each (lambda (source target)
12170 (format #t "Processing ~a --> ~a~%"
12172 (delete-file target)
12173 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12174 (call-with-output-file target
12176 (dump-port minified port)))))
12177 sources targets))))
12180 `(("r-ggplot2" ,r-ggplot2)
12181 ("r-htmltools" ,r-htmltools)
12182 ("r-htmlwidgets" ,r-htmlwidgets)
12183 ("r-jsonlite" ,r-jsonlite)
12184 ("r-miniui" ,r-miniui)
12185 ("r-shiny" ,r-shiny)
12186 ("r-shinyjs" ,r-shinyjs)))
12188 `(("uglify-js" ,uglify-js)
12192 (uri "https://code.jquery.com/jquery-3.3.1.js")
12195 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12199 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12202 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12203 (home-page "https://github.com/daattali/colourpicker")
12204 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12206 "This package provides a color picker that can be used as an input in
12207 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12208 custom color palettes, and many more options. A plot color helper tool is
12209 available as an RStudio Addin, which helps you pick colors to use in your
12210 plots. A more generic color picker RStudio Addin is also provided to let you
12211 select colors to use in your R code.")
12212 (license license:expat)))
12214 (define-public r-ggextra
12221 (uri (cran-uri "ggExtra" version))
12224 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12225 (properties `((upstream-name . "ggExtra")))
12226 (build-system r-build-system)
12228 `(("r-colourpicker" ,r-colourpicker)
12229 ("r-ggplot2" ,r-ggplot2)
12230 ("r-gtable" ,r-gtable)
12231 ("r-miniui" ,r-miniui)
12233 ("r-scales" ,r-scales)
12234 ("r-shiny" ,r-shiny)
12235 ("r-shinyjs" ,r-shinyjs)))
12236 (home-page "https://github.com/daattali/ggExtra")
12237 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12239 "This package is a collection of functions and layers to enhance ggplot2.
12240 The flagship function is @code{ggMarginal()}, which can be used to add
12241 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12242 (license license:expat)))
12244 (define-public r-minpack-lm
12246 (name "r-minpack-lm")
12251 (uri (cran-uri "minpack.lm" version))
12254 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12255 (properties `((upstream-name . "minpack.lm")))
12256 (build-system r-build-system)
12257 (native-inputs `(("gfortran" ,gfortran)))
12258 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12259 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12261 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12262 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12263 problems by a modification of the Levenberg-Marquardt algorithm, with support
12264 for lower and upper parameter bounds. The implementation can be used via
12265 @code{nls}-like calls using the @code{nlsLM} function.")
12266 (license license:gpl3)))
12268 (define-public r-moments
12275 (uri (cran-uri "moments" version))
12278 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12279 (build-system r-build-system)
12280 (home-page "https://cran.r-project.org/web/packages/moments")
12281 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12283 "This package provides functions to calculate: moments, Pearson's
12284 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12285 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12286 (license license:gpl2+)))
12288 (define-public r-msir
12295 (uri (cran-uri "msir" version))
12298 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12299 (build-system r-build-system)
12301 `(("r-mclust" ,r-mclust)))
12302 (home-page "https://cran.r-project.org/web/packages/msir")
12303 (synopsis "Model-based sliced inverse regression")
12305 "This is an R package for dimension reduction based on finite Gaussian
12306 mixture modeling of inverse regression.")
12307 (license license:gpl2+)))
12309 (define-public r-pbivnorm
12311 (name "r-pbivnorm")
12316 (uri (cran-uri "pbivnorm" version))
12319 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12320 (build-system r-build-system)
12321 (native-inputs `(("gfortran" ,gfortran)))
12322 (home-page "https://github.com/brentonk/pbivnorm")
12323 (synopsis "Vectorized bivariate normal CDF")
12325 "This package provides a vectorized R function for calculating
12326 probabilities from a standard bivariate normal CDF.")
12327 (license license:gpl2+)))
12329 (define-public r-lavaan
12336 (uri (cran-uri "lavaan" version))
12339 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12340 (build-system r-build-system)
12342 `(("r-mass" ,r-mass)
12343 ("r-mnormt" ,r-mnormt)
12344 ("r-numderiv" ,r-numderiv)
12345 ("r-pbivnorm" ,r-pbivnorm)))
12346 (home-page "http://lavaan.ugent.be")
12347 (synopsis "Latent variable analysis")
12349 "This package provides tools to fit a variety of latent variable models,
12350 including confirmatory factor analysis, structural equation modeling and
12351 latent growth curve models.")
12352 (license license:gpl2+)))
12354 (define-public r-nonnest2
12356 (name "r-nonnest2")
12361 (uri (cran-uri "nonnest2" version))
12364 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12365 (build-system r-build-system)
12367 `(("r-compquadform" ,r-compquadform)
12368 ("r-lavaan" ,r-lavaan)
12369 ("r-mvtnorm" ,r-mvtnorm)
12370 ("r-sandwich" ,r-sandwich)))
12371 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12372 (synopsis "Tests of non-nested models")
12374 "This package allows for testing of non-nested models. It includes tests
12375 of model distinguishability and of model fit that can be applied to both
12376 nested and non-nested models. The package also includes functionality to
12377 obtain confidence intervals associated with AIC and BIC.")
12378 ;; Either version of the GPL.
12379 (license (list license:gpl2 license:gpl3))))
12381 (define-public r-penalized
12383 (name "r-penalized")
12388 (uri (cran-uri "penalized" version))
12391 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12392 (build-system r-build-system)
12394 `(("r-rcpp" ,r-rcpp)
12395 ("r-rcpparmadillo" ,r-rcpparmadillo)
12396 ("r-survival" ,r-survival)))
12397 (home-page "https://cran.r-project.org/web/packages/penalized/")
12398 (synopsis "Penalized estimation in GLMs and in the Cox model")
12400 "This package provides tools for fitting possibly high dimensional
12401 penalized regression models. The penalty structure can be any combination of
12402 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12403 constraint on the regression coefficients. The supported regression models
12404 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12405 model. Cross-validation routines allow optimization of the tuning
12407 (license license:gpl2+)))
12409 (define-public r-zim
12416 (uri (cran-uri "ZIM" version))
12419 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12420 (properties `((upstream-name . "ZIM")))
12421 (build-system r-build-system)
12422 (propagated-inputs `(("r-mass" ,r-mass)))
12423 (home-page "https://github.com/biostatstudio/ZIM")
12424 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12426 "Analyze count time series with excess zeros. Two types of statistical
12427 models are supported: Markov regression and state-space models. They are also
12428 known as observation-driven and parameter-driven models respectively in the
12429 time series literature. The functions used for Markov regression or
12430 observation-driven models can also be used to fit ordinary regression models
12431 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12432 negative binomial (ZINB) assumption. The package also contains miscellaneous
12433 functions to compute density, distribution, quantile, and generate random
12434 numbers from ZIP and ZINB distributions.")
12435 (license license:gpl3)))
12437 (define-public r-nor1mix
12444 (uri (cran-uri "nor1mix" version))
12447 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12448 (build-system r-build-system)
12449 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12450 (synopsis "Normal (1-d) mixture models")
12452 "This package provides S3 classes and methods for one-dimensional normal
12453 mixture models, for, e.g., density estimation or clustering algorithms
12454 research and teaching; it provides the widely used Marron-Wand densities. It
12455 also provides tools for efficient random number generation and graphics.")
12456 (license license:gpl2+)))
12458 (define-public r-beanplot
12460 (name "r-beanplot")
12465 (uri (cran-uri "beanplot" version))
12468 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12469 (build-system r-build-system)
12470 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12471 (synopsis "Visualization via beanplots")
12473 "This package provides beanplots, an alternative to
12474 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12476 (license license:gpl2)))
12478 (define-public r-pbdzmq
12485 (uri (cran-uri "pbdZMQ" version))
12488 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12489 (properties `((upstream-name . "pbdZMQ")))
12490 (build-system r-build-system)
12492 `(("zeromq" ,zeromq)
12495 `(("pkg-config" ,pkg-config)))
12496 (home-page "https://pbdr.org/")
12497 (synopsis "R interface to ZeroMQ")
12499 "ZeroMQ is a well-known library for high-performance asynchronous
12500 messaging in scalable, distributed applications. This package provides high
12501 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12502 interactive client/server programming frameworks. A few wrapper functions
12503 compatible with @code{rzmq} are also provided.")
12504 (license license:gpl3)))
12506 (define-public r-repr
12513 (uri (cran-uri "repr" version))
12516 "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw"))))
12517 (build-system r-build-system)
12519 `(("r-base64enc" ,r-base64enc)
12520 ("r-htmltools" ,r-htmltools)
12521 ("r-jsonlite" ,r-jsonlite)
12522 ("r-pillar" ,r-pillar)))
12523 (home-page "https://cran.r-project.org/web/packages/repr/")
12524 (synopsis "Serializable representations")
12526 "This package provides string and binary representations of objects for
12527 several formats and MIME types.")
12528 (license license:gpl3)))
12530 (define-public r-irdisplay
12532 (name "r-irdisplay")
12537 (uri (cran-uri "IRdisplay" version))
12540 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12541 (properties `((upstream-name . "IRdisplay")))
12542 (build-system r-build-system)
12544 `(("r-repr" ,r-repr)))
12545 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12546 (synopsis "Jupyter display machinery")
12548 "This package provides an interface to the rich display capabilities of
12549 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12550 running IRkernel session.")
12551 (license license:expat)))
12553 (define-public r-irkernel
12555 (name "r-irkernel")
12560 (uri (cran-uri "IRkernel" version))
12563 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12564 (properties `((upstream-name . "IRkernel")))
12565 (build-system r-build-system)
12568 (modify-phases %standard-phases
12569 (add-after 'install 'install-kernelspec
12570 (lambda* (#:key outputs #:allow-other-keys)
12571 (let ((out (assoc-ref outputs "out")))
12572 (setenv "HOME" "/tmp")
12573 (invoke "jupyter" "kernelspec" "install"
12576 (string-append out "/site-library/IRkernel/kernelspec"))
12579 `(("jupyter" ,jupyter)))
12581 `(("r-crayon" ,r-crayon)
12582 ("r-digest" ,r-digest)
12583 ("r-evaluate" ,r-evaluate)
12584 ("r-irdisplay" ,r-irdisplay)
12585 ("r-jsonlite" ,r-jsonlite)
12586 ("r-pbdzmq" ,r-pbdzmq)
12588 ("r-uuid" ,r-uuid)))
12589 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12590 (synopsis "Native R kernel for Jupyter")
12592 "The R kernel for the Jupyter environment executes R code which the
12593 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12595 (license license:expat)))
12597 (define-public r-gmodels
12604 (uri (cran-uri "gmodels" version))
12607 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12608 (build-system r-build-system)
12610 `(("r-gdata" ,r-gdata)
12611 ("r-mass" ,r-mass)))
12612 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12613 (synopsis "Various R programming tools for model fitting")
12615 "This package provides various R programming tools for model fitting.")
12616 (license license:gpl2)))
12618 (define-public r-apcluster
12620 (name "r-apcluster")
12625 (uri (cran-uri "apcluster" version))
12628 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12629 (build-system r-build-system)
12631 `(("r-matrix" ,r-matrix)
12632 ("r-rcpp" ,r-rcpp)))
12633 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12634 (synopsis "Affinity propagation clustering")
12636 "This package implements affinity propagation clustering introduced by
12637 Frey and Dueck (2007). The package further provides leveraged affinity
12638 propagation and an algorithm for exemplar-based agglomerative clustering that
12639 can also be used to join clusters obtained from affinity propagation. Various
12640 plotting functions are available for analyzing clustering results.")
12641 (license license:gpl2+)))
12643 (define-public r-valr
12650 (uri (cran-uri "valr" version))
12653 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12654 (build-system r-build-system)
12656 `(("r-broom" ,r-broom)
12657 ("r-dplyr" ,r-dplyr)
12658 ("r-ggplot2" ,r-ggplot2)
12660 ("r-readr" ,r-readr)
12661 ("r-rlang" ,r-rlang)
12662 ("r-stringr" ,r-stringr)
12663 ("r-tibble" ,r-tibble)))
12664 (home-page "http://github.com/rnabioco/valr")
12665 (synopsis "Genome interval arithmetic in R")
12667 "This package enables you to read and manipulate genome intervals and
12668 signals. It provides functionality similar to command-line tool suites within
12669 R, enabling interactive analysis and visualization of genome-scale data.")
12670 (license license:expat)))
12672 (define-public r-rematch2
12674 (name "r-rematch2")
12679 (uri (cran-uri "rematch2" version))
12682 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12683 (build-system r-build-system)
12685 `(("r-tibble" ,r-tibble)))
12686 (home-page "https://github.com/r-lib/rematch2")
12687 (synopsis "Tidy output from regular expression matching")
12689 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12690 return the match results in tidy data frames.")
12691 (license license:expat)))
12693 (define-public r-picante
12700 (uri (cran-uri "picante" version))
12703 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12704 (build-system r-build-system)
12708 ("r-vegan" ,r-vegan)))
12709 (home-page "https://cran.r-project.org/web/packages/picante/")
12710 (synopsis "Integrating phylogenies and ecology")
12712 "This package provides functions for phylocom integration, community
12713 analyses, null-models, traits and evolution. It implements numerous
12714 ecophylogenetic approaches including measures of community phylogenetic and
12715 trait diversity, phylogenetic signal, estimation of trait values for
12716 unobserved taxa, null models for community and phylogeny randomizations, and
12717 utility functions for data input/output and phylogeny plotting. A full
12718 description of package functionality and methods are provided by Kembel et
12720 (license license:gpl2)))
12722 (define-public r-reinforcelearn
12724 (name "r-reinforcelearn")
12729 (uri (cran-uri "reinforcelearn" version))
12732 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12733 (build-system r-build-system)
12735 `(("r-checkmate" ,r-checkmate)
12737 ("r-purrr" ,r-purrr)
12739 (home-page "https://markusdumke.github.io/reinforcelearn")
12740 (synopsis "Reinforcement learning")
12742 "This package implements reinforcement learning environments and
12743 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12744 can be used with function approximation, eligibility traces (Singh & Sutton,
12745 1996) and experience replay (Mnih et al., 2013).")
12746 (license license:expat)))
12748 (define-public r-lemon
12755 (uri (cran-uri "lemon" version))
12758 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12759 (build-system r-build-system)
12761 `(("r-ggplot2" ,r-ggplot2)
12762 ("r-gridextra" ,r-gridextra)
12763 ("r-gtable" ,r-gtable)
12764 ("r-knitr" ,r-knitr)
12765 ("r-lattice" ,r-lattice)
12767 ("r-scales" ,r-scales)))
12768 (home-page "https://github.com/stefanedwards/lemon")
12769 (synopsis "Freshen up your ggplot2 plots")
12771 "This package provides functions for working with legends and axis lines
12772 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12774 (license license:gpl3)))
12776 (define-public r-wgaim
12783 (uri (cran-uri "wgaim" version))
12785 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12786 (build-system r-build-system)
12788 `(("r-ggplot2" ,r-ggplot2)
12790 (home-page "https://cran.r-project.org/web/packages/wgaim")
12791 (synopsis "Whole genome average interval mapping for QTL detection")
12793 "This package integrates sophisticated mixed modelling methods with a
12794 whole genome approach to detecting significant QTL in linkage maps.")
12795 (license license:gpl2+)))
12797 (define-public r-bedr
12804 (uri (cran-uri "bedr" version))
12807 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12808 (build-system r-build-system)
12810 `(("r-data-table" ,r-data-table)
12811 ("r-r-utils" ,r-r-utils)
12812 ("r-testthat" ,r-testthat)
12813 ("r-venndiagram" ,r-venndiagram)
12816 ("bedtools" ,bedtools)
12817 ("htslib" ,htslib))) ; for tabix
12819 `(("r-knitr" ,r-knitr))) ; for vignettes
12820 (home-page "https://cran.r-project.org/web/packages/bedr")
12821 (synopsis "Genomic region processing")
12823 "This package is for genomic regions processing using command line tools
12824 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12825 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12826 The bedr package's API enhances access to these tools as well as offers
12827 additional utilities for genomic regions processing.")
12828 (license license:gpl2)))
12830 (define-public r-sets
12837 (uri (cran-uri "sets" version))
12840 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12841 (properties `((upstream-name . "sets")))
12842 (build-system r-build-system)
12843 (home-page "https://cran.r-project.org/web/packages/sets")
12844 (synopsis "Sets, generalized sets, customizable sets and intervals")
12846 "This package provides data structures and basic operations for ordinary
12847 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12848 customizable sets, and intervals.")
12849 (license license:gpl2)))
12851 (define-public r-partitions
12853 (name "r-partitions")
12858 (uri (cran-uri "partitions" version))
12861 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12862 (build-system r-build-system)
12865 ("r-polynom" ,r-polynom)
12866 ("r-sets" ,r-sets)))
12867 (home-page "https://cran.r-project.org/web/packages/partitions")
12868 (synopsis "Additive partitions of integers")
12870 "This package provides tools to enumerates the partitions, unequal
12871 partitions, and restricted partitions of an integer; the three corresponding
12872 partition functions are also given.")
12873 ;; Any version of the GPL
12874 (license license:gpl2+)))
12876 (define-public r-brobdingnag
12878 (name "r-brobdingnag")
12883 (uri (cran-uri "Brobdingnag" version))
12886 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12887 (properties `((upstream-name . "Brobdingnag")))
12888 (build-system r-build-system)
12889 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12890 (synopsis "Very large numbers in R")
12892 "This package handles very large numbers in R. Real numbers are held
12893 using their natural logarithms, plus a logical flag indicating sign. The
12894 package includes a vignette that gives a step-by-step introduction to using S4
12896 ;; Any version of the GPL
12897 (license license:gpl2+)))
12899 (define-public r-untb
12906 (uri (cran-uri "untb" version))
12909 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12910 (build-system r-build-system)
12912 `(("r-brobdingnag" ,r-brobdingnag)
12913 ("r-partitions" ,r-partitions)
12914 ("r-polynom" ,r-polynom)))
12915 (home-page "https://github.com/RobinHankin/untb.git")
12916 (synopsis "Ecological drift under the UNTB")
12918 "This package provides numerical simulations, and visualizations, of
12919 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12920 (license license:gpl2+)))
12922 (define-public r-stepwise
12924 (name "r-stepwise")
12929 (uri (cran-uri "stepwise" version))
12932 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12933 (build-system r-build-system)
12934 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12935 (synopsis "Stepwise detection of recombination breakpoints")
12937 "This package provides a stepwise approach to identifying recombination
12938 breakpoints in a genomic sequence alignment.")
12939 (license license:gpl2+)))
12941 (define-public r-snpmaxsel
12943 (name "r-snpmaxsel")
12948 (uri (cran-uri "SNPmaxsel" version))
12951 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12952 (properties `((upstream-name . "SNPmaxsel")))
12953 (build-system r-build-system)
12955 `(("r-combinat" ,r-combinat)
12956 ("r-mvtnorm" ,r-mvtnorm)))
12957 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12958 (synopsis "Maximally selected statistics for SNP data")
12960 "This package implements asymptotic methods related to maximally selected
12961 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12963 (license license:gpl2+)))
12965 (define-public r-acsnminer
12967 (name "r-acsnminer")
12968 (version "0.16.8.25")
12971 (uri (cran-uri "ACSNMineR" version))
12974 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12975 (properties `((upstream-name . "ACSNMineR")))
12976 (build-system r-build-system)
12978 `(("r-ggplot2" ,r-ggplot2)
12979 ("r-gridextra" ,r-gridextra)))
12980 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12981 (synopsis "Gene enrichment analysis")
12983 "This package provides tools to compute and represent gene set enrichment
12984 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12985 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12986 enrichment can be run with hypergeometric test or Fisher exact test, and can
12987 use multiple corrections. Visualization of data can be done either by
12988 barplots or heatmaps.")
12989 (license license:gpl2+)))
12991 (define-public r-seqinr
12998 (uri (cran-uri "seqinr" version))
13001 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13002 (build-system r-build-system)
13004 `(("r-ade4" ,r-ade4)
13005 ("r-segmented" ,r-segmented)))
13008 (home-page "http://seqinr.r-forge.r-project.org/")
13009 (synopsis "Biological sequences retrieval and analysis")
13011 "This package provides tools for exploratory data analysis and data
13012 visualization of biological sequence (DNA and protein) data. It also includes
13013 utilities for sequence data management under the ACNUC system.")
13014 (license license:gpl2+)))
13016 (define-public r-units
13023 (uri (cran-uri "units" version))
13026 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
13027 (build-system r-build-system)
13029 `(("udunits" ,udunits)))
13031 `(("r-rcpp" ,r-rcpp)))
13032 (home-page "https://github.com/r-quantities/units/")
13033 (synopsis "Measurement Units for R Vectors")
13035 "This package provides support for measurement units in R vectors,
13036 matrices and arrays: automatic propagation, conversion, derivation and
13037 simplification of units; raising errors in case of unit incompatibility. It
13038 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13040 (license license:gpl2)))
13042 (define-public r-classint
13044 (name "r-classint")
13049 (uri (cran-uri "classInt" version))
13052 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
13053 (properties `((upstream-name . "classInt")))
13054 (build-system r-build-system)
13056 `(("r-class" ,r-class)
13057 ("r-e1071" ,r-e1071)
13058 ("r-kernsmooth" ,r-kernsmooth)))
13059 (native-inputs `(("gfortran" ,gfortran)))
13060 (home-page "https://github.com/r-spatial/classInt/")
13061 (synopsis "Choose univariate class intervals")
13063 "This package provides selected commonly used methods for choosing
13064 univariate class intervals for mapping or other graphics purposes.")
13065 (license license:gpl2+)))
13067 (define-public r-spdata
13074 (uri (cran-uri "spData" version))
13077 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
13078 (properties `((upstream-name . "spData")))
13079 (build-system r-build-system)
13080 (home-page "https://github.com/Nowosad/spData")
13081 (synopsis "Datasets for spatial analysis")
13083 "This a package containing diverse spatial datasets for demonstrating,
13084 benchmarking and teaching spatial data analysis. It includes R data of class
13085 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13086 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13087 of the datasets are designed to illustrate specific analysis techniques.
13088 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13089 illustrate point pattern analysis techniques.")
13090 (license license:cc0)))
13092 (define-public r-learnbayes
13094 (name "r-learnbayes")
13099 (uri (cran-uri "LearnBayes" version))
13102 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13103 (properties `((upstream-name . "LearnBayes")))
13104 (build-system r-build-system)
13105 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13106 (synopsis "Functions for learning Bayesian inference")
13108 "This package provides a collection of functions helpful in learning the
13109 basic tenets of Bayesian statistical inference. It contains functions for
13110 summarizing basic one and two parameter posterior distributions and predictive
13111 distributions. It contains MCMC algorithms for summarizing posterior
13112 distributions defined by the user. It also contains functions for regression
13113 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13115 (license license:gpl2+)))
13117 (define-public r-deldir
13124 (uri (cran-uri "deldir" version))
13127 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
13128 (build-system r-build-system)
13129 (native-inputs `(("gfortran" ,gfortran)))
13130 (home-page "https://cran.r-project.org/web/packages/deldir")
13131 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13133 "This package provides tools for calculating the Delaunay triangulation
13134 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13135 of a planar point set. It plots triangulations and tessellations in various
13136 ways, clips tessellations to sub-windows, calculates perimeters of
13137 tessellations, and summarizes information about the tiles of the
13139 (license license:gpl2+)))
13141 (define-public r-sf
13148 (uri (cran-uri "sf" version))
13151 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
13152 (build-system r-build-system)
13159 `(("r-classint" ,r-classint)
13161 ("r-magrittr" ,r-magrittr)
13163 ("r-units" ,r-units)))
13164 (native-inputs `(("pkg-config" ,pkg-config)))
13165 (home-page "https://github.com/r-spatial/sf/")
13166 (synopsis "Simple features for R")
13168 "This package provides support for simple features, a standardized way to
13169 encode spatial vector data. It binds to GDAL for reading and writing data, to
13170 GEOS for geometrical operations, and to PROJ for projection conversions and
13171 datum transformations.")
13172 ;; Either of these licenses
13173 (license (list license:gpl2 license:expat))))
13175 (define-public r-spdep
13182 (uri (cran-uri "spdep" version))
13185 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13186 (build-system r-build-system)
13188 `(("r-boot" ,r-boot)
13190 ("r-deldir" ,r-deldir)
13192 ("r-gmodels" ,r-gmodels)
13193 ("r-learnbayes" ,r-learnbayes)
13195 ("r-matrix" ,r-matrix)
13199 ("r-spdata" ,r-spdata)))
13200 (home-page "https://github.com/r-spatial/spdep/")
13201 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13203 "This package provides a collection of functions to create spatial
13204 weights matrix objects from polygon contiguities, from point patterns by
13205 distance and tessellations, for summarizing these objects, and for permitting
13206 their use in spatial data analysis, including regional aggregation by minimum
13208 (license license:gpl2+)))
13210 (define-public r-adegenet
13212 (name "r-adegenet")
13217 (uri (cran-uri "adegenet" version))
13220 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13221 (build-system r-build-system)
13223 `(("r-ade4" ,r-ade4)
13226 ("r-dplyr" ,r-dplyr)
13227 ("r-ggplot2" ,r-ggplot2)
13228 ("r-igraph" ,r-igraph)
13230 ("r-reshape2" ,r-reshape2)
13231 ("r-seqinr" ,r-seqinr)
13232 ("r-shiny" ,r-shiny)
13233 ("r-spdep" ,r-spdep)
13234 ("r-vegan" ,r-vegan)))
13235 (home-page "https://github.com/thibautjombart/adegenet")
13236 (synopsis "Exploratory analysis of genetic and genomic data")
13238 "This package provides a toolset for the exploration of genetic and
13239 genomic data. Adegenet provides formal (S4) classes for storing and handling
13240 various genetic data, including genetic markers with varying ploidy and
13241 hierarchical population structure (@code{genind} class), alleles counts by
13242 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13243 also implements original multivariate methods (DAPC, sPCA), graphics,
13244 statistical tests, simulation tools, distance and similarity measures, and
13245 several spatial methods. A range of both empirical and simulated datasets is
13246 also provided to illustrate various methods.")
13247 (license license:gpl2+)))
13249 (define-public r-pegas
13256 (uri (cran-uri "pegas" version))
13258 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13259 (build-system r-build-system)
13261 `(("r-adegenet" ,r-adegenet)
13263 (home-page "http://ape-package.ird.fr/pegas.html")
13264 (synopsis "Population and evolutionary genetics analysis system")
13266 "This package provides functions for reading, writing, plotting,
13267 analysing, and manipulating allelic and haplotypic data, including from VCF
13268 files, and for the analysis of population nucleotide sequences and
13269 micro-satellites including coalescent analyses, linkage disequilibrium,
13270 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13271 minimum spanning tree and network, and median-joining networks.")
13272 (license license:gpl2+)))
13274 (define-public r-rmetasim
13276 (name "r-rmetasim")
13281 (uri (cran-uri "rmetasim" version))
13284 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13285 (build-system r-build-system)
13287 `(("r-ade4" ,r-ade4)
13288 ("r-adegenet" ,r-adegenet)
13289 ("r-gtools" ,r-gtools)
13290 ("r-pegas" ,r-pegas)))
13291 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13292 (synopsis "Individual-based population genetic simulation environment")
13294 "This package provides an interface between R and the metasim simulation
13295 engine. The simulation environment is documented in: Strand, A.(2002),
13296 Metasim 1.0: an individual-based environment for simulating population
13297 genetics of complex population dynamics.")
13299 (license license:gpl2+)))
13301 (define-public r-genetics
13303 (name "r-genetics")
13304 (version "1.3.8.1.2")
13308 (uri (cran-uri "genetics" version))
13311 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13312 (build-system r-build-system)
13314 `(("r-combinat" ,r-combinat)
13315 ("r-gdata" ,r-gdata)
13316 ("r-gtools" ,r-gtools)
13318 ("r-mvtnorm" ,r-mvtnorm)))
13319 (home-page "https://cran.r-project.org/web/packages/genetics/")
13320 (synopsis "Population genetics")
13322 "This package provides classes and methods for handling genetic data.
13323 It includes classes to represent genotypes and haplotypes at single markers up
13324 to multiple markers on multiple chromosomes. Function include allele
13325 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13326 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13327 and testing for linkage disequilibrium, ...")
13328 ;; Any GPL version.
13329 (license license:gpl2+)))
13331 (define-public r-snp-plotter
13333 (name "r-snp-plotter")
13338 (uri (cran-uri "snp.plotter" version))
13341 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13342 (properties `((upstream-name . "snp.plotter")))
13343 (build-system r-build-system)
13344 (propagated-inputs `(("r-genetics" ,r-genetics)))
13345 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13346 (synopsis "Plot p-values using single SNP and/or haplotype data")
13348 "This package helps you create plots of p-values using single SNP and/or
13349 haplotype data. Main features of the package include options to display a
13350 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13351 datasets simultaneously. Plots can be created using global and/or individual
13352 haplotype p-values along with single SNP p-values. Images are created as
13353 either PDF/EPS files.")
13354 (license license:gpl2+)))
13356 (define-public r-polspline
13358 (name "r-polspline")
13363 (uri (cran-uri "polspline" version))
13365 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13366 (build-system r-build-system)
13367 (native-inputs `(("gfortran" ,gfortran)))
13368 (home-page "https://cran.r-project.org/web/packages/polspline/")
13369 (synopsis "Polynomial spline routines")
13371 "This package provides routines for the polynomial spline fitting
13372 routines hazard regression, hazard estimation with flexible tails, logspline,
13373 lspec, polyclass, and polymars.")
13374 (license license:gpl2+)))
13376 (define-public r-rms
13383 (uri (cran-uri "rms" version))
13385 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13386 (build-system r-build-system)
13388 `(("r-ggplot2" ,r-ggplot2)
13389 ("r-hmisc" ,r-hmisc)
13390 ("r-htmltable" ,r-htmltable)
13391 ("r-htmltools" ,r-htmltools)
13392 ("r-lattice" ,r-lattice)
13393 ("r-multcomp" ,r-multcomp)
13395 ("r-polspline" ,r-polspline)
13396 ("r-quantreg" ,r-quantreg)
13397 ("r-rpart" ,r-rpart)
13398 ("r-sparsem" ,r-sparsem)
13399 ("r-survival" ,r-survival)))
13400 (native-inputs `(("gfortran" ,gfortran)))
13401 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13402 (synopsis "Regression modeling strategies")
13404 "This is a package for regression modeling, testing, estimation,
13405 validation, graphics, prediction, and typesetting by storing enhanced model
13406 design attributes in the fit. The rms package is a collection of functions
13407 that assist with and streamline modeling. It also contains functions for
13408 binary and ordinal logistic regression models, ordinal models for continuous Y
13409 with a variety of distribution families, and the Buckley-James multiple
13410 regression model for right-censored responses, and implements penalized
13411 maximum likelihood estimation for logistic and ordinary linear models. The
13412 package works with almost any regression model, but it was especially written
13413 to work with binary or ordinal regression models, Cox regression, accelerated
13414 failure time models, ordinary linear models, the Buckley-James model,
13415 generalized least squares for serially or spatially correlated observations,
13416 generalized linear models, and quantile regression.")
13417 (license license:gpl2+)))
13419 (define-public r-haplo-stats
13421 (name "r-haplo-stats")
13426 (uri (cran-uri "haplo.stats" version))
13429 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13430 (properties `((upstream-name . "haplo.stats")))
13431 (build-system r-build-system)
13433 `(("r-rms" ,r-rms)))
13435 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13436 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13437 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13439 "This package provides routines for the analysis of indirectly measured
13440 haplotypes. The statistical methods assume that all subjects are unrelated
13441 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13442 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13443 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13444 examples in the vignette.")
13445 (license license:gpl2+)))
13447 (define-public r-bqtl
13454 (uri (cran-uri "bqtl" version))
13457 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13458 (build-system r-build-system)
13459 (native-inputs `(("gfortran" ,gfortran)))
13460 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13461 (synopsis "Bayesian QTL mapping toolkit")
13463 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13464 lines. It includes maximum likelihood and Bayesian tools.")
13465 (license license:gpl2+)))
13467 (define-public r-ibdreg
13474 (uri (cran-uri "ibdreg" version))
13477 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13478 (build-system r-build-system)
13479 (home-page "https://www.mayo.edu/research/labs/\
13480 statistical-genetics-genetic-epidemiology/software")
13481 (synopsis "Regression methods for IBD linkage with covariates")
13483 "This package provides a method to test genetic linkage with covariates
13484 by regression methods with response IBD sharing for relative pairs. Account
13485 for correlations of IBD statistics and covariates for relative pairs within
13486 the same pedigree.")
13487 (license license:gpl2+)))
13489 (define-public r-dlmap
13496 (uri (cran-uri "dlmap" version))
13499 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13500 (build-system r-build-system)
13502 `(("r-ibdreg" ,r-ibdreg)
13506 ("r-wgaim" ,r-wgaim)))
13507 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13508 (synopsis "Detection localization mapping for QTL")
13510 "This is package for QTL mapping in a mixed model framework with separate
13511 detection and localization stages. The first stage detects the number of QTL
13512 on each chromosome based on the genetic variation due to grouped markers on
13513 the chromosome; the second stage uses this information to determine the most
13514 likely QTL positions. The mixed model can accommodate general fixed and
13515 random effects, including spatial effects in field trials and pedigree
13516 effects. It is applicable to backcrosses, doubled haploids, recombinant
13517 inbred lines, F2 intercrosses, and association mapping populations.")
13518 (license license:gpl2)))
13520 (define-public r-ldheatmap
13522 (name "r-ldheatmap")
13527 (uri (cran-uri "LDheatmap" version))
13530 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13531 (properties `((upstream-name . "LDheatmap")))
13532 (build-system r-build-system)
13534 `(("r-genetics" ,r-genetics)
13536 ("r-snpstats" ,r-snpstats)))
13537 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13538 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13540 "This package provides tools to produce a graphical display, as a heat
13541 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13542 optionally include the physical locations or genetic map distances of each SNP
13544 (license license:gpl3)))
13546 (define-public r-hwde
13553 (uri (cran-uri "hwde" version))
13556 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13557 (build-system r-build-system)
13558 (home-page "https://cran.r-project.org/web/packages/hwde/")
13559 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13561 "This package fits models for genotypic disequilibria, as described in
13562 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13563 terms are available that account for first order interactions between loci.
13564 It also implements, for a single locus in a single population, a conditional
13565 exact test for Hardy-Weinberg equilibrium.")
13566 (license license:gpl2+)))
13568 (define-public r-tdthap
13575 (uri (cran-uri "tdthap" version))
13578 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13579 (build-system r-build-system)
13580 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13581 (synopsis "TDT tests for extended haplotypes")
13583 "Functions and examples are provided for transmission/disequilibrium
13584 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13585 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13586 (license license:artistic2.0)))
13588 (define-public r-sparql
13594 (uri (cran-uri "SPARQL" version))
13597 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13598 (properties `((upstream-name . "SPARQL")))
13599 (build-system r-build-system)
13601 `(("r-rcurl" ,r-rcurl)
13603 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13604 (synopsis "SPARQL client for R")
13605 (description "This package provides an interface to use SPARQL to pose
13606 SELECT or UPDATE queries to an end-point.")
13607 ;; The only license indication is found in the DESCRIPTION file,
13608 ;; which states GPL-3. So we cannot assume GPLv3+.
13609 (license license:gpl3)))
13611 (define-public r-bookdown
13613 (name "r-bookdown")
13617 (uri (cran-uri "bookdown" version))
13620 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13621 (build-system r-build-system)
13623 `(("r-htmltools" ,r-htmltools)
13624 ("r-knitr" ,r-knitr)
13625 ("r-rmarkdown" ,r-rmarkdown)
13626 ("r-tinytex" ,r-tinytex)
13628 ("pandoc" ,ghc-pandoc)))
13629 (home-page "https://github.com/rstudio/bookdown")
13630 (synopsis "Authoring books and technical documents with R markdown")
13631 (description "This package provides output formats and utilities for
13632 authoring books and technical documents with R Markdown.")
13633 (license license:gpl3)))
13635 (define-public r-optparse
13637 (name "r-optparse")
13642 (uri (cran-uri "optparse" version))
13645 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13646 (build-system r-build-system)
13648 `(("r-getopt" ,r-getopt)))
13649 (home-page "https://github.com/trevorld/optparse")
13650 (synopsis "Command line option parser")
13652 "This package provides a command line parser inspired by Python's
13653 @code{optparse} library to be used with Rscript to write shebang scripts
13654 that accept short and long options.")
13655 (license license:gpl2+)))
13657 (define-public r-wgcna
13664 (uri (cran-uri "WGCNA" version))
13667 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13668 (properties `((upstream-name . "WGCNA")))
13669 (build-system r-build-system)
13671 `(("r-annotationdbi" ,r-annotationdbi)
13672 ("r-doparallel" ,r-doparallel)
13673 ("r-dynamictreecut" ,r-dynamictreecut)
13674 ("r-fastcluster" ,r-fastcluster)
13675 ("r-foreach" ,r-foreach)
13676 ("r-go-db" ,r-go-db)
13677 ("r-hmisc" ,r-hmisc)
13678 ("r-impute" ,r-impute)
13680 ("r-robust" ,r-robust)
13681 ("r-survival" ,r-survival)
13682 ("r-matrixstats" ,r-matrixstats)
13683 ("r-preprocesscore" ,r-preprocesscore)))
13685 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13686 (synopsis "Weighted correlation network analysis")
13688 "This package provides functions necessary to perform Weighted
13689 Correlation Network Analysis on high-dimensional data. It includes functions
13690 for rudimentary data cleaning, construction and summarization of correlation
13691 networks, module identification and functions for relating both variables and
13692 modules to sample traits. It also includes a number of utility functions for
13693 data manipulation and visualization.")
13694 (license license:gpl2+)))
13696 (define-public r-kernlab
13703 (uri (cran-uri "kernlab" version))
13705 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13706 (build-system r-build-system)
13707 (home-page "https://cran.r-project.org/web/packages/kernlab")
13708 (synopsis "Kernel-based machine learning tools")
13710 "This package provides kernel-based machine learning methods for
13711 classification, regression, clustering, novelty detection, quantile regression
13712 and dimensionality reduction. Among other methods @code{kernlab} includes
13713 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13715 (license license:gpl2)))
13717 (define-public r-hierfstat
13719 (name "r-hierfstat")
13720 (version "0.04-22")
13724 (uri (cran-uri "hierfstat" version))
13727 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13728 (build-system r-build-system)
13730 `(("r-ade4" ,r-ade4)
13731 ("r-adegenet" ,r-adegenet)
13732 ("r-gtools" ,r-gtools)))
13733 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13734 (synopsis "Estimation and tests of hierarchical F-statistics")
13736 "This package allows the estimation of hierarchical F-statistics from
13737 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13738 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13739 are also given to test via randomisations the significance of each F and
13740 variance components, using the likelihood-ratio statistics G.")
13741 (license license:gpl2+)))
13743 (define-public r-hapassoc
13745 (name "r-hapassoc")
13750 (uri (cran-uri "hapassoc" version))
13753 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13754 (build-system r-build-system)
13755 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13756 (synopsis "Inference of trait associations with SNP haplotypes")
13758 "Hapassoc performs likelihood inference of trait associations with
13759 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13760 functions are developed primarily for data collected in cohort or
13761 cross-sectional studies. They can accommodate uncertain haplotype phase and
13762 handle missing genotypes at some SNPs.")
13763 (license license:gpl2)))
13765 (define-public r-sampling
13767 (name "r-sampling")
13772 (uri (cran-uri "sampling" version))
13775 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13776 (build-system r-build-system)
13778 `(("r-lpsolve" ,r-lpsolve)
13779 ("r-mass" ,r-mass)))
13780 (home-page "https://cran.r-project.org/web/packages/sampling/")
13781 (synopsis "Survey sampling")
13783 "This package provides functions for drawing and calibrating samples.")
13784 (license license:gpl2+)))
13786 (define-public r-r2html
13793 (uri (cran-uri "R2HTML" version))
13796 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13797 (properties `((upstream-name . "R2HTML")))
13798 (build-system r-build-system)
13799 (home-page "https://github.com/nalimilan/R2HTML")
13800 (synopsis "HTML export for R objects")
13802 "This package includes HTML functions and methods to write in an HTML
13803 file. Thus, making HTML reports is easy. It includes a function that allows
13804 redirection on the fly, which appears to be very useful for teaching purposes,
13805 as the student can keep a copy of the produced output to keep all that they
13806 did during the course. The package comes with a vignette describing how to
13807 write HTML reports for statistical analysis. Finally, a driver for Sweave
13808 allows to parse HTML flat files containing R code and to automatically write
13809 the corresponding outputs (tables and graphs).")
13810 (license license:gpl2+)))
13812 (define-public r-rjava
13819 (uri (cran-uri "rJava" version))
13822 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13823 (properties `((upstream-name . "rJava")))
13824 (build-system r-build-system)
13826 `(#:modules ((guix build utils)
13827 (guix build r-build-system)
13830 (modify-phases %standard-phases
13831 (add-after 'unpack 'set-JAVA_HOME
13832 (lambda* (#:key inputs #:allow-other-keys)
13833 (let ((jdk (assoc-ref inputs "jdk")))
13834 (setenv "JAVA_HOME" jdk)
13835 (setenv "JAVA" (which "java"))
13836 (setenv "JAR" (which "jar"))
13837 (setenv "JAVAC" (which "javac"))
13838 (setenv "JAVAH" (which "javah"))
13839 (setenv "JAVA_CPPFLAGS"
13840 (string-append "-I" jdk "/include "
13841 "-I" jdk "/include/linux"))
13842 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13843 ((lib) (setenv "JAVA_LIBS" lib))
13844 (_ (error "Could not find libjvm.so"))))
13848 ("jdk" ,icedtea-8 "jdk")
13851 (home-page "http://www.rforge.net/rJava/")
13852 (synopsis "Low-Level R to Java interface")
13854 "This package provides a low-level interface to the Java VM very much
13855 like .C/.Call and friends. It allows the creation of objects, calling methods
13856 and accessing fields.")
13857 (license license:gpl2)))
13859 (define-public r-svmisc
13866 (uri (cran-uri "svMisc" version))
13869 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13870 (properties `((upstream-name . "svMisc")))
13871 (build-system r-build-system)
13872 (home-page "https://github.com/SciViews/svMisc")
13873 (synopsis "Miscellaneous functions for SciViews")
13875 "This package provides miscellaneous functions for SciViews or general
13876 use, including tools to manage a temporary environment attached to the search
13877 path for temporary variables you do not want to @code{save()} or
13878 @code{load()}; test the current platform; showing progress bars, etc.")
13879 (license license:gpl2)))
13881 (define-public r-xyz
13888 (uri (cran-uri "xyz" version))
13891 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13892 (build-system r-build-system)
13894 `(("r-rcpp" ,r-rcpp)))
13895 (home-page "https://cran.r-project.org/web/packages/xyz/")
13896 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13898 "High dimensional interaction search by brute force requires a quadratic
13899 computational cost in the number of variables. The xyz algorithm provably
13900 finds strong interactions in almost linear time. For details of the algorithm
13901 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13902 interaction search in high-dimensional data.")
13903 ;; Any version of the GPL.
13904 (license license:gpl2+)))
13906 (define-public r-rttf2pt1
13908 (name "r-rttf2pt1")
13913 (uri (cran-uri "Rttf2pt1" version))
13916 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13917 (properties `((upstream-name . "Rttf2pt1")))
13918 (build-system r-build-system)
13919 (home-page "https://github.com/wch/Rttf2pt1")
13920 (synopsis "Font conversion utility")
13922 "This package contains the program @code{ttf2pt1}, for use with the
13923 @code{extrafont} package.")
13924 ;; Most of the files are covered under the Expat license. Some files are
13925 ;; covered under BSD-3. Deviations for individual files are recorded in
13926 ;; the LICENSE file.
13927 (license (list license:bsd-3 license:expat
13928 (license:non-copyleft "file://LICENSE")))))
13930 (define-public r-extrafontdb
13932 (name "r-extrafontdb")
13937 (uri (cran-uri "extrafontdb" version))
13940 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13941 (build-system r-build-system)
13942 (home-page "https://github.com/wch/extrafontdb")
13943 (synopsis "Database for the extrafont package")
13945 "This package holds the database for the @code{extrafont} package.")
13946 (license license:gpl2)))
13948 (define-public r-extrafont
13950 (name "r-extrafont")
13955 (uri (cran-uri "extrafont" version))
13958 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13959 (build-system r-build-system)
13961 `(("r-extrafontdb" ,r-extrafontdb)
13962 ("r-rttf2pt1" ,r-rttf2pt1)))
13963 (home-page "https://github.com/wch/extrafont")
13964 (synopsis "Tools for using fonts in R")
13966 "The extrafont package makes it easier to use fonts other than the basic
13967 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13968 used with PDF or PostScript output files. There are two hurdles for using
13969 fonts in PDF (or Postscript) output files:
13972 @item Making R aware of the font and the dimensions of the characters.
13973 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13974 properly on a device that doesn't have the font. This is usually needed if
13975 you want to print the PDF file or share it with others.
13978 The extrafont package makes both of these things easier.")
13979 (license license:gpl2)))
13981 (define-public r-xkcd
13988 (uri (cran-uri "xkcd" version))
13991 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13992 (build-system r-build-system)
13994 `(("r-extrafont" ,r-extrafont)
13995 ("r-ggplot2" ,r-ggplot2)
13996 ("r-hmisc" ,r-hmisc)))
13997 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13998 (synopsis "Plot ggplot2 graphics in the XKCD style")
14000 "This package provides the means to plot ggplot2 graphs in the style of
14001 the XKCD web comic.")
14002 (license license:gpl3)))
14004 (define-public r-msigdbr
14011 (uri (cran-uri "msigdbr" version))
14014 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14015 (build-system r-build-system)
14017 `(("r-dplyr" ,r-dplyr)
14018 ("r-magrittr" ,r-magrittr)
14019 ("r-rlang" ,r-rlang)
14020 ("r-tibble" ,r-tibble)))
14021 (home-page "https://github.com/igordot/msigdbr")
14022 (synopsis "MSigDB gene sets for multiple organisms")
14024 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14025 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14026 software in a standard R data frame with key-value pairs. Included are the
14027 original human gene symbols and Entrez IDs as well as the equivalents for
14028 various frequently studied model organisms such as mouse, rat, pig, fly, and
14030 ;; The package is covered under the Expat license, but the upstream MSigDB
14031 ;; files are made available under the Creative Commons Attribution 4.0
14032 ;; International license.
14033 (license (list license:expat license:cc-by4.0))))
14035 (define-public r-gridgraphics
14037 (name "r-gridgraphics")
14042 (uri (cran-uri "gridGraphics" version))
14045 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
14046 (properties `((upstream-name . "gridGraphics")))
14047 (build-system r-build-system)
14048 (home-page "https://github.com/pmur002/gridgraphics")
14049 (synopsis "Redraw base graphics using @code{grid} graphics")
14051 "This package provides functions to convert a page of plots drawn with
14052 the @code{graphics} package into identical output drawn with the @code{grid}
14053 package. The result looks like the original @code{graphics}-based plot, but
14054 consists of @code{grid} grobs and viewports that can then be manipulated with
14055 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14056 (license license:gpl2+)))
14058 (define-public r-farver
14065 (uri (cran-uri "farver" version))
14068 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
14069 (build-system r-build-system)
14070 (home-page "https://github.com/thomasp85/farver")
14071 (synopsis "Vectorized color conversion and comparison")
14073 "The encoding of color can be handled in many different ways, using
14074 different color spaces. As different color spaces have different uses,
14075 efficient conversion between these representations are important. This
14076 package provides a set of functions that gives access to very fast color space
14077 conversion and comparisons implemented in C++, and offers 100-fold speed
14078 improvements over the @code{convertColor} function in the @code{grDevices}
14080 (license license:expat)))
14082 (define-public r-ggplotify
14084 (name "r-ggplotify")
14089 (uri (cran-uri "ggplotify" version))
14092 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
14093 (build-system r-build-system)
14095 `(("r-ggplot2" ,r-ggplot2)
14096 ("r-gridgraphics" ,r-gridgraphics)
14097 ("r-rvcheck" ,r-rvcheck)))
14098 (home-page "https://github.com/GuangchuangYu/ggplotify")
14099 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14101 "This package provides tools to convert plot function calls (using
14102 expression or formula) to @code{grob} or @code{ggplot} objects that are
14103 compatible with the @code{grid} and @code{ggplot2} environment. With this
14104 package, we are able to e.g. use @code{cowplot} to align plots produced by
14105 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14106 converting them to @code{ggplot} objects.")
14107 (license license:artistic2.0)))
14109 (define-public r-triebeard
14111 (name "r-triebeard")
14116 (uri (cran-uri "triebeard" version))
14119 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14120 (build-system r-build-system)
14121 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14122 (home-page "https://github.com/Ironholds/triebeard/")
14123 (synopsis "Radix trees in Rcpp")
14125 "Radix trees, or tries, are key-value data structures optimized for
14126 efficient lookups, similar in purpose to hash tables. This package provides
14127 an implementation of radix trees for use in R programming and in developing
14128 packages with Rcpp.")
14129 (license license:expat)))
14131 (define-public r-tweenr
14138 (uri (cran-uri "tweenr" version))
14141 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14142 (build-system r-build-system)
14144 `(("r-farver" ,r-farver)
14145 ("r-magrittr" ,r-magrittr)
14147 ("r-rlang" ,r-rlang)))
14148 (home-page "https://github.com/thomasp85/tweenr")
14149 (synopsis "Interpolate data for smooth animations")
14151 "In order to create smooth animation between states of data, tweening is
14152 necessary. This package provides a range of functions for creating tweened
14153 data that can be used as basis for animation. Furthermore it adds a number of
14154 vectorized interpolaters for common R data types such as numeric, date and
14156 (license license:expat)))
14158 (define-public r-polyclip
14160 (name "r-polyclip")
14165 (uri (cran-uri "polyclip" version))
14168 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14169 (build-system r-build-system)
14170 (native-inputs `(("pkg-config" ,pkg-config)))
14171 (home-page "http://www.angusj.com/delphi/clipper.php")
14172 (synopsis "Polygon clipping")
14174 "This package provides an R port of the library Clipper. It performs
14175 polygon clipping operations (intersection, union, set minus, set difference)
14176 for polygonal regions of arbitrary complexity, including holes. It computes
14177 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14178 dilations) for polygonal regions and polygonal lines. It computes the
14179 Minkowski Sum of general polygons. There is a function for removing
14180 self-intersections from polygon data.")
14181 (license license:boost1.0)))
14183 (define-public r-urltools
14185 (name "r-urltools")
14190 (uri (cran-uri "urltools" version))
14193 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14194 (build-system r-build-system)
14196 `(("r-rcpp" ,r-rcpp)
14197 ("r-triebeard" ,r-triebeard)))
14198 (home-page "https://github.com/Ironholds/urltools/")
14199 (synopsis "Vectorized tools for URL handling and parsing")
14201 "This package provides a toolkit for all URL-handling needs, including
14202 encoding and decoding, parsing, parameter extraction and modification. All
14203 functions are designed to be both fast and entirely vectorized. It is
14204 intended to be useful for people dealing with web-related datasets, such as
14205 server-side logs, although may be useful for other situations involving large
14207 (license license:expat)))
14209 (define-public r-ggforce
14216 (uri (cran-uri "ggforce" version))
14219 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14220 (build-system r-build-system)
14222 `(("r-ggplot2" ,r-ggplot2)
14223 ("r-gtable" ,r-gtable)
14225 ("r-polyclip" ,r-polyclip)
14227 ("r-rcppeigen" ,r-rcppeigen)
14228 ("r-rlang" ,r-rlang)
14229 ("r-scales" ,r-scales)
14230 ("r-tidyselect" ,r-tidyselect)
14231 ("r-tweenr" ,r-tweenr)
14232 ("r-withr" ,r-withr)))
14233 (home-page "https://ggforce.data-imaginist.com")
14234 (synopsis "Accelerating ggplot2")
14236 "The aim of the ggplot2 package is to aid in visual data investigations.
14237 This focus has led to a lack of facilities for composing specialized plots.
14238 Thi package aims to be a collection of mainly new statistics and geometries
14239 that fills this gap.")
14240 (license license:expat)))
14242 (define-public r-europepmc
14244 (name "r-europepmc")
14249 (uri (cran-uri "europepmc" version))
14252 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14253 (build-system r-build-system)
14255 `(("r-dplyr" ,r-dplyr)
14257 ("r-jsonlite" ,r-jsonlite)
14259 ("r-progress" ,r-progress)
14260 ("r-purrr" ,r-purrr)
14261 ("r-urltools" ,r-urltools)
14262 ("r-xml2" ,r-xml2)))
14263 (home-page "https://github.com/ropensci/europepmc/")
14264 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14266 "This package provides an R Client for the
14267 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14268 Service}. It gives access to both metadata on life science literature and
14269 open access full texts. Europe PMC indexes all PubMed content and other
14270 literature sources including Agricola, a bibliographic database of citations
14271 to the agricultural literature, or Biological Patents. In addition to
14272 bibliographic metadata, the client allows users to fetch citations and
14273 reference lists. Links between life-science literature and other EBI
14274 databases, including ENA, PDB or ChEMBL are also accessible.")
14275 (license license:gpl3)))
14277 (define-public r-ggraph
14284 (uri (cran-uri "ggraph" version))
14287 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14288 (build-system r-build-system)
14290 `(("r-digest" ,r-digest)
14291 ("r-dplyr" ,r-dplyr)
14292 ("r-ggforce" ,r-ggforce)
14293 ("r-ggplot2" ,r-ggplot2)
14294 ("r-ggrepel" ,r-ggrepel)
14295 ("r-graphlayouts" ,r-graphlayouts)
14296 ("r-gtable" ,r-gtable)
14297 ("r-igraph" ,r-igraph)
14300 ("r-rlang" ,r-rlang)
14301 ("r-scales" ,r-scales)
14302 ("r-tidygraph" ,r-tidygraph)
14303 ("r-viridis" ,r-viridis)))
14304 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14305 (synopsis "Implementation of grammar of graphics for graphs and networks")
14307 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14308 graph and network visualizations due to its reliance on tabular data input.
14309 The ggraph package is an extension of the ggplot2 API tailored to graph
14310 visualizations and provides the same flexible approach to building up plots
14312 (license license:gpl3)))
14314 (define-public r-varselrf
14316 (name "r-varselrf")
14321 (uri (cran-uri "varSelRF" version))
14324 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14325 (properties `((upstream-name . "varSelRF")))
14326 (build-system r-build-system)
14328 `(("r-randomforest" ,r-randomforest)))
14329 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14330 (synopsis "Variable selection using random forests")
14332 "This package provides tools for the variable selection from random
14333 forests using both backwards variable elimination (for the selection of small
14334 sets of non-redundant variables) and selection based on the importance
14335 spectrum (somewhat similar to scree plots; for the selection of large,
14336 potentially highly-correlated variables). The main applications are in
14337 high-dimensional data (e.g., microarray data, and other genomics and
14338 proteomics applications).")
14339 (license license:gpl2+)))
14341 (define-public r-pamr
14348 (uri (cran-uri "pamr" version))
14351 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14352 (build-system r-build-system)
14354 `(("r-cluster" ,r-cluster)
14355 ("r-survival" ,r-survival)))
14356 (native-inputs `(("gfortran" ,gfortran)))
14357 (home-page "https://cran.r-project.org/web/packages/pamr/")
14358 (synopsis "Prediction Analysis for Microarrays")
14360 "This package provides some functions for sample classification in
14362 (license license:gpl2)))
14364 (define-public r-rda
14367 (version "1.0.2-2.1")
14371 (uri (cran-uri "rda" version))
14374 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14375 (build-system r-build-system)
14376 (home-page "https://cran.r-project.org/web/packages/rda/")
14377 (synopsis "Shrunken centroids regularized discriminant analysis")
14379 "This package provides tools for shrunken centroids regularized
14380 discriminant analysis for the purpose of classifying high dimensional data.")
14381 (license license:gpl2+)))
14383 (define-public r-ggvis
14390 (uri (cran-uri "ggvis" version))
14393 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14394 (build-system r-build-system)
14396 `(("r-assertthat" ,r-assertthat)
14397 ("r-dplyr" ,r-dplyr)
14398 ("r-htmltools" ,r-htmltools)
14399 ("r-jsonlite" ,r-jsonlite)
14400 ("r-lazyeval" ,r-lazyeval)
14401 ("r-magrittr" ,r-magrittr)
14402 ("r-shiny" ,r-shiny)))
14403 (home-page "https://ggvis.rstudio.com/")
14404 (synopsis "Interactive grammar of graphics")
14406 "This package is a data visualization package for R providing an
14407 implementation of an interactive grammar of graphics, taking the best parts of
14408 ggplot2, combining them with the reactive framework of Shiny and drawing web
14409 graphics using Vega.")
14410 (license license:gpl2)))
14412 (define-public r-gbm
14419 (uri (cran-uri "gbm" version))
14422 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14423 (build-system r-build-system)
14425 `(("r-gridextra" ,r-gridextra)
14426 ("r-lattice" ,r-lattice)
14427 ("r-survival" ,r-survival)))
14428 (home-page "https://github.com/gbm-developers/gbm")
14429 (synopsis "Generalized boosted regression models")
14431 "This package is an implementation of extensions to Freund and Schapire's
14432 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14433 regression methods for least squares, absolute loss, t-distribution loss,
14434 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14435 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14436 and Learning to Rank measures (LambdaMart).")
14437 (license license:gpl2+)))
14439 (define-public r-threejs
14446 (uri (cran-uri "threejs" version))
14449 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14450 (build-system r-build-system)
14452 `(#:modules ((guix build utils)
14453 (guix build r-build-system)
14457 (modify-phases %standard-phases
14458 (add-after 'unpack 'process-javascript
14459 (lambda* (#:key inputs #:allow-other-keys)
14460 (with-directory-excursion "inst"
14464 `((,(assoc-ref inputs "js-jquery")
14465 "htmlwidgets/lib/jquery/jquery.min.js")
14466 (,(assoc-ref inputs "js-threejs-85")
14467 "htmlwidgets/lib/threejs-85/three.min.js"))))
14468 (lambda (sources targets)
14469 (for-each (lambda (source target)
14470 (format #t "Processing ~a --> ~a~%"
14472 (delete-file target)
14473 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14474 (call-with-output-file target
14476 (dump-port minified port)))))
14477 sources targets))))
14480 `(("r-base64enc" ,r-base64enc)
14481 ("r-crosstalk" ,r-crosstalk)
14482 ("r-htmlwidgets" ,r-htmlwidgets)
14483 ("r-igraph" ,r-igraph)))
14485 `(("uglify-js" ,uglify-js)
14489 (uri "https://code.jquery.com/jquery-3.3.1.js")
14492 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14496 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14499 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14500 (home-page "https://bwlewis.github.io/rthreejs")
14501 (synopsis "Interactive 3D scatter plots, networks and globes")
14503 "Create interactive 3D scatter plots, network plots, and globes in R
14504 using the three.js visualization library.")
14505 (license license:expat)))
14507 (define-public r-mlbench
14514 (uri (cran-uri "mlbench" version))
14517 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14518 (build-system r-build-system)
14519 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14520 (synopsis "Machine learning benchmark problems")
14522 "This package provides a collection of artificial and real-world machine
14523 learning benchmark problems, including, e.g., several data sets from the UCI
14525 (license license:gpl2)))
14527 (define-public r-mpm
14534 (uri (cran-uri "mpm" version))
14537 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14538 (build-system r-build-system)
14540 `(("r-kernsmooth" ,r-kernsmooth)
14541 ("r-mass" ,r-mass)))
14542 (home-page "http://mpm.r-forge.r-project.org")
14543 (synopsis "Multivariate projection methods")
14545 "This is a package for exploratory graphical analysis of multivariate
14546 data, specifically gene expression data with different projection methods:
14547 principal component analysis, correspondence analysis, spectral map
14549 (license license:gpl2+)))
14551 (define-public r-png
14557 (uri (cran-uri "png" version))
14560 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14561 (build-system r-build-system)
14563 `(("libpng" ,libpng)
14565 (home-page "http://www.rforge.net/png/")
14566 (synopsis "Read and write PNG images")
14568 "This package provides an easy and simple way to read, write and display
14569 bitmap images stored in the PNG format. It can read and write both files and
14570 in-memory raw vectors.")
14571 ;; Any of these GPL versions.
14572 (license (list license:gpl2 license:gpl3))))
14574 (define-public r-ggcorrplot
14576 (name "r-ggcorrplot")
14581 (uri (cran-uri "ggcorrplot" version))
14584 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14585 (build-system r-build-system)
14587 `(("r-ggplot2" ,r-ggplot2)
14588 ("r-reshape2" ,r-reshape2)))
14589 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14590 (synopsis "Visualization of a correlation matrix using ggplot2")
14592 "The ggcorrplot package can be used to visualize easily a correlation
14593 matrix using ggplot2. It provides a solution for reordering the correlation
14594 matrix and displays the significance level on the plot. It also includes a
14595 function for computing a matrix of correlation p-values.")
14596 (license license:gpl2)))
14598 (define-public r-flexdashboard
14600 (name "r-flexdashboard")
14601 (version "0.5.1.1")
14605 (uri (cran-uri "flexdashboard" version))
14608 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14609 (build-system r-build-system)
14611 `(#:modules ((guix build utils)
14612 (guix build r-build-system)
14616 (ice-9 textual-ports))
14618 (modify-phases %standard-phases
14619 (add-after 'unpack 'process-javascript
14620 (lambda* (#:key inputs #:allow-other-keys)
14621 (with-directory-excursion "inst"
14622 ;; Concatenate all components of prism.js
14623 (let ((contents (string-join
14624 (map (lambda (name)
14625 (call-with-input-file
14626 (assoc-ref inputs name)
14630 "js-prism-line-numbers"))
14632 (call-with-output-file "prism-src.js"
14633 (cut display contents <>)))
14637 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14638 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14640 "www/sly/sly.min.js")
14642 "www/prism/prism.js")
14643 (,(assoc-ref inputs "js-raphael")
14644 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14645 (,(assoc-ref inputs "js-featherlight")
14646 "www/featherlight/featherlight.min.js"))))
14647 (lambda (sources targets)
14648 (for-each (lambda (source target)
14649 (format #t "Processing ~a --> ~a~%"
14651 (delete-file target)
14652 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14653 (call-with-output-file target
14655 (dump-port minified port)))))
14656 sources targets))))
14659 `(("r-htmltools" ,r-htmltools)
14660 ("r-htmlwidgets" ,r-htmlwidgets)
14661 ("r-jsonlite" ,r-jsonlite)
14662 ("r-knitr" ,r-knitr)
14663 ("r-rmarkdown" ,r-rmarkdown)
14664 ("r-shiny" ,r-shiny)))
14666 `(("uglify-js" ,uglify-js)
14670 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14673 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14677 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14680 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14684 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14687 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14688 ("js-prism-line-numbers"
14691 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14694 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14698 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14701 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14702 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14703 (synopsis "R Markdown format for flexible dashboards")
14705 "This package provides an R Markdown format for converting an R Markdown
14706 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14707 of its components to the containing web page.")
14708 (license license:expat)))
14710 (define-public r-preseqr
14717 (uri (cran-uri "preseqR" version))
14720 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14721 (properties `((upstream-name . "preseqR")))
14722 (build-system r-build-system)
14724 `(("r-polynom" ,r-polynom)))
14725 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14726 (synopsis "Predicting species accumulation curves")
14728 "This package can be used to predict the r-species accumulation
14729 curve (r-SAC), which is the number of species represented at least r times as
14730 a function of the sampling effort. When r = 1, the curve is known as the
14731 species accumulation curve, or the library complexity curve in high-throughput
14732 genomic sequencing. The package includes both parametric and nonparametric
14733 methods, as described by Deng C, et al. (2018).")
14734 (license license:gpl3)))
14736 (define-public r-mapplots
14738 (name "r-mapplots")
14743 (uri (cran-uri "mapplots" version))
14746 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14747 (build-system r-build-system)
14748 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14749 (synopsis "Data visualization on maps")
14751 "This package helps you create simple maps; add sub-plots like pie plots
14752 to a map or any other plot; format, plot and export gridded data. The package
14753 was developed for displaying fisheries data but most functions can be used for
14754 more generic data visualisation.")
14755 (license license:gpl2+)))
14757 (define-public r-pmcmr
14764 (uri (cran-uri "PMCMR" version))
14767 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14768 (properties `((upstream-name . "PMCMR")))
14769 (build-system r-build-system)
14770 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14771 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14773 "This is a deprecated package for calculating pairwise multiple
14774 comparisons of mean rank sums. This package is superseded by the novel
14775 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14776 compatibility of dependent packages for some time.")
14777 (license license:gpl3+)))
14779 (define-public r-downloader
14781 (name "r-downloader")
14786 (uri (cran-uri "downloader" version))
14789 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14790 (build-system r-build-system)
14792 `(("r-digest" ,r-digest)))
14793 (home-page "https://github.com/wch/downloader")
14794 (synopsis "Download files over HTTP and HTTPS")
14796 "This package provides a wrapper for the @code{download.file} function,
14797 making it possible to download files over HTTPS across platforms. The
14798 @code{RCurl} package provides this functionality (and much more) but has
14799 external dependencies. This package has is implemented purely in R.")
14800 (license license:gpl2)))
14802 (define-public r-rex
14809 (uri (cran-uri "rex" version))
14812 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14813 (build-system r-build-system)
14815 `(("r-lazyeval" ,r-lazyeval)
14816 ("r-magrittr" ,r-magrittr)))
14817 (home-page "https://github.com/kevinushey/rex")
14818 (synopsis "Friendly regular expressions")
14820 "This package provides a friendly interface for the construction of
14821 regular expressions. Regular expressions are a very powerful feature, however
14822 they are often difficult to interpret. Rex allows you to build complex
14823 regular expressions from human readable expressions")
14824 (license license:expat)))
14826 (define-public r-xmlparsedata
14828 (name "r-xmlparsedata")
14833 (uri (cran-uri "xmlparsedata" version))
14836 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14837 (properties `((upstream-name . "xmlparsedata")))
14838 (build-system r-build-system)
14839 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14840 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14842 "This package provides tools to convert the output of
14843 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14844 @code{XPath}, and is easier to manipulate in general.")
14845 (license license:expat)))
14847 (define-public r-cyclocomp
14849 (name "r-cyclocomp")
14854 (uri (cran-uri "cyclocomp" version))
14857 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14858 (properties `((upstream-name . "cyclocomp")))
14859 (build-system r-build-system)
14861 `(("r-callr" ,r-callr)
14862 ("r-crayon" ,r-crayon)
14864 ("r-remotes" ,r-remotes)
14865 ("r-withr" ,r-withr)))
14866 (home-page "https://github.com/MangoTheCat/cyclocomp")
14867 (synopsis "Cyclomatic complexity of R code")
14869 "Cyclomatic complexity is a software metric, used to indicate the
14870 complexity of a program. It is a quantitative measure of the number of
14871 linearly independent paths through a program's source code. This package
14872 provides tools to compute this metric.")
14873 (license license:expat)))
14875 (define-public r-lintr
14882 (uri (cran-uri "lintr" version))
14885 "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb"))))
14886 (properties `((upstream-name . "lintr")))
14887 (build-system r-build-system)
14889 `(("r-codetools" ,r-codetools)
14890 ("r-crayon" ,r-crayon)
14891 ("r-cyclocomp" ,r-cyclocomp)
14892 ("r-digest" ,r-digest)
14894 ("r-jsonlite" ,r-jsonlite)
14895 ("r-knitr" ,r-knitr)
14897 ("r-rstudioapi" ,r-rstudioapi)
14898 ("r-stringdist" ,r-stringdist)
14899 ("r-testthat" ,r-testthat)
14901 ("r-xmlparsedata" ,r-xmlparsedata)))
14902 (home-page "https://github.com/jimhester/lintr")
14903 (synopsis "Linter for R code")
14904 (description "This package checks adherence to a given style, syntax
14905 errors and possible semantic issues. It supports on the fly checking of R
14906 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14907 (license license:expat)))
14909 (define-public r-sctransform
14911 (name "r-sctransform")
14916 (uri (cran-uri "sctransform" version))
14919 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
14920 (build-system r-build-system)
14922 `(("r-future-apply" ,r-future-apply)
14923 ("r-ggplot2" ,r-ggplot2)
14924 ("r-gridextra" ,r-gridextra)
14926 ("r-matrix" ,r-matrix)
14928 ("r-rcppeigen" ,r-rcppeigen)
14929 ("r-reshape2" ,r-reshape2)))
14930 (home-page "https://github.com/ChristophH/sctransform")
14931 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14933 "This package provides a normalization method for single-cell UMI count
14934 data using a variance stabilizing transformation. The transformation is based
14935 on a negative binomial regression model with regularized parameters. As part
14936 of the same regression framework, this package also provides functions for
14937 batch correction, and data correction.")
14938 (license license:gpl3)))
14940 (define-public r-styler
14947 (uri (cran-uri "styler" version))
14950 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14951 (build-system r-build-system)
14953 `(("r-backports" ,r-backports)
14955 ("r-magrittr" ,r-magrittr)
14956 ("r-purrr" ,r-purrr)
14957 ("r-rematch2" ,r-rematch2)
14958 ("r-rlang" ,r-rlang)
14959 ("r-rprojroot" ,r-rprojroot)
14960 ("r-tibble" ,r-tibble)
14961 ("r-withr" ,r-withr)
14962 ("r-xfun" ,r-xfun)))
14963 (home-page "https://github.com/r-lib/styler")
14964 (synopsis "Non-invasive pretty printing of R code")
14966 "This is a package for pretty-printing R code without changing the user's
14967 formatting intent.")
14968 (license license:gpl3)))
14970 (define-public r-scrime
14977 (uri (cran-uri "scrime" version))
14980 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14981 (build-system r-build-system)
14982 (home-page "https://cran.r-project.org/web/packages/scrime/")
14983 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14985 "This package provides tools for the analysis of high-dimensional data
14986 developed/implemented at the group \"Statistical Complexity Reduction In
14987 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14988 the functions can also be applied to other types of categorical data.")
14989 (license license:gpl2)))
14991 (define-public r-pbmcapply
14993 (name "r-pbmcapply")
14998 (uri (cran-uri "pbmcapply" version))
15001 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15002 (build-system r-build-system)
15003 (home-page "https://github.com/kvnkuang/pbmcapply")
15004 (synopsis "Track the progress of apply procedures with a progress bar")
15006 "This light-weight package helps you track and visualize the progress of
15007 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15008 (license license:expat)))
15010 (define-public r-blme
15017 (uri (cran-uri "blme" version))
15020 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15021 (build-system r-build-system)
15022 (propagated-inputs `(("r-lme4" ,r-lme4)))
15023 (home-page "https://github.com/vdorie/blme")
15024 (synopsis "Bayesian linear mixed-effects models")
15026 "This package provides tools for maximum a posteriori estimation for
15027 linear and generalized linear mixed-effects models in a Bayesian setting. It
15028 extends the lme4 package.")
15029 (license license:gpl2+)))
15031 (define-public r-batchtools
15033 (name "r-batchtools")
15038 (uri (cran-uri "batchtools" version))
15041 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
15042 (build-system r-build-system)
15044 `(("r-backports" ,r-backports)
15045 ("r-base64url" ,r-base64url)
15047 ("r-checkmate" ,r-checkmate)
15048 ("r-data-table" ,r-data-table)
15049 ("r-digest" ,r-digest)
15051 ("r-progress" ,r-progress)
15053 ("r-rappdirs" ,r-rappdirs)
15054 ("r-stringi" ,r-stringi)
15055 ("r-withr" ,r-withr)))
15056 (home-page "https://github.com/mllg/batchtools")
15057 (synopsis "Tools for computation on batch systems")
15059 "As a successor of the packages BatchJobs and BatchExperiments, this
15060 package provides a parallel implementation of the Map function for high
15061 performance computing systems managed by various schedulers. A multicore and
15062 socket mode allow the parallelization on a local machines, and multiple
15063 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15064 the package provides an abstraction mechanism to define large-scale computer
15065 experiments in a well-organized and reproducible way.")
15066 (license license:lgpl3)))
15068 (define-public r-clue
15075 (uri (cran-uri "clue" version))
15078 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15079 (build-system r-build-system)
15080 (propagated-inputs `(("r-cluster" ,r-cluster)))
15081 (home-page "https://cran.r-project.org/web/packages/clue/")
15082 (synopsis "Tools for analyzing cluster ensembles")
15083 (description "Cluster ensembles are collections of individual solutions to
15084 a given clustering problem which are useful or necessary to consider in a wide
15085 range of applications. This R package provides an extensible computational
15086 environment for creating and analyzing cluster ensembles, with basic data
15087 structures for representing partitions and hierarchies, and facilities for
15088 computing on them, including methods for measuring proximity and obtaining
15089 consensus and secondary clusterings.")
15090 (license license:gpl2)))
15092 (define-public r-sitmo
15099 (uri (cran-uri "sitmo" version))
15102 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15103 (build-system r-build-system)
15104 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15105 (home-page "https://github.com/coatless/sitmo/")
15106 (synopsis "Parallel pseudo random number generator header files")
15108 "This package provides two high quality and fast PPRNGs that may be used
15109 in an OpenMP parallel environment. In addition, there is a generator for one
15110 dimensional low-discrepancy sequence.")
15111 (license license:expat)))
15113 (define-public r-dqrng
15120 (uri (cran-uri "dqrng" version))
15123 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15124 (build-system r-build-system)
15128 ("r-sitmo" ,r-sitmo)))
15129 (home-page "https://www.daqana.org/dqrng")
15130 (synopsis "Fast pseudo random number generators")
15132 "Several fast random number generators are provided as C++ header-only
15133 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15134 Additionally, fast functions for generating random numbers according to a
15135 uniform, normal and exponential distribution are included. The latter two use
15136 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15137 functions are exported to R and as a C++ interface and are enabled for use
15138 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15139 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15140 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15141 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15142 ;; whole is distributed under the terms of the AGPL 3.
15143 (license license:agpl3)))
15145 (define-public r-dalex
15152 (uri (cran-uri "DALEX" version))
15155 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
15156 (properties `((upstream-name . "DALEX")))
15157 (build-system r-build-system)
15158 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15159 (home-page "https://pbiecek.github.io/DALEX/")
15160 (synopsis "Descriptive machine learning explanations")
15162 "Machine Learning models are widely used and have various applications in
15163 classification or regression. Models created with boosting, bagging, stacking
15164 or similar techniques are often used due to their high performance, but such
15165 black-box models usually lack interpretability. The DALEX package contains
15166 various explainers that help to understand the link between input variables
15167 and model output.")
15168 ;; Any version of the GPL
15169 (license license:gpl3+)))
15171 (define-public r-enrichr
15178 (uri (cran-uri "enrichR" version))
15181 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15182 (properties `((upstream-name . "enrichR")))
15183 (build-system r-build-system)
15185 `(("r-httr" ,r-httr)
15186 ("r-rjson" ,r-rjson)))
15187 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15188 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15190 "This package provides an R interface to all Enrichr databases, a
15191 web-based tool for analyzing gene sets and returns any enrichment of common
15192 annotated biological functions.")
15193 (license license:gpl2+)))
15195 (define-public r-plot3d
15202 (uri (cran-uri "plot3D" version))
15205 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15206 (properties `((upstream-name . "plot3D")))
15207 (build-system r-build-system)
15208 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15209 (home-page "https://cran.r-project.org/web/packages/plot3D")
15210 (synopsis "Plot multi-dimensional data")
15212 "This package provides functions for viewing 2D and 3D data, including
15213 perspective plots, slice plots, surface plots, scatter plots, etc. It
15214 includes data sets from oceanography.")
15215 (license license:gpl3+)))
15217 (define-public r-ggfortify
15219 (name "r-ggfortify")
15224 (uri (cran-uri "ggfortify" version))
15227 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15228 (build-system r-build-system)
15230 `(("r-dplyr" ,r-dplyr)
15231 ("r-ggplot2" ,r-ggplot2)
15232 ("r-gridextra" ,r-gridextra)
15233 ("r-scales" ,r-scales)
15234 ("r-stringr" ,r-stringr)
15235 ("r-tibble" ,r-tibble)
15236 ("r-tidyr" ,r-tidyr)))
15237 (home-page "https://github.com/sinhrks/ggfortify")
15238 (synopsis "Data visualization tools for statistical analysis results")
15240 "This package provides unified plotting tools for statistics commonly
15241 used, such as GLM, time series, PCA families, clustering and survival
15242 analysis. The package offers a single plotting interface for these analysis
15243 results and plots in a unified style using the @code{ggplot2} package.")
15244 (license license:gpl2)))
15246 (define-public r-refmanager
15248 (name "r-refmanager")
15253 (uri (cran-uri "RefManageR" version))
15256 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15257 (properties `((upstream-name . "RefManageR")))
15258 (build-system r-build-system)
15260 `(("r-bibtex" ,r-bibtex)
15262 ("r-jsonlite" ,r-jsonlite)
15263 ("r-lubridate" ,r-lubridate)
15265 ("r-stringr" ,r-stringr)
15266 ("r-xml2" ,r-xml2)))
15267 (home-page "https://github.com/ropensci/RefManageR/")
15268 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15270 "This package provides tools for importing and working with bibliographic
15271 references. It greatly enhances the @code{bibentry} class by providing a
15272 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15273 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15274 by various formats for name lists (author by last names, translator by full
15275 names, etc.). Entries can be updated, combined, sorted, printed in a number
15276 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15277 into R and converted to @code{BibEntry} objects.")
15278 ;; Any of these licenses may be picked.
15279 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15281 (define-public r-citr
15288 (uri (cran-uri "citr" version))
15291 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15292 (build-system r-build-system)
15294 `(("r-assertthat" ,r-assertthat)
15297 ("r-miniui" ,r-miniui)
15298 ("r-refmanager" ,r-refmanager)
15299 ("r-rstudioapi" ,r-rstudioapi)
15300 ("r-shiny" ,r-shiny)
15301 ("r-shinyjs" ,r-shinyjs)
15302 ("r-yaml" ,r-yaml)))
15303 (home-page "https://github.com/crsh/citr")
15304 (synopsis "RStudio add-in to insert Markdown citations")
15306 "This package provides functions and an RStudio add-in that search a
15307 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15308 the current document.")
15309 (license license:expat)))
15311 (define-public r-xgboost
15314 (version "0.90.0.2")
15318 (uri (cran-uri "xgboost" version))
15321 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15322 (build-system r-build-system)
15324 `(("r-data-table" ,r-data-table)
15325 ("r-magrittr" ,r-magrittr)
15326 ("r-matrix" ,r-matrix)
15327 ("r-stringi" ,r-stringi)))
15328 (home-page "https://github.com/dmlc/xgboost")
15329 (synopsis "Extreme gradient boosting")
15331 "This package provides an R interface to Extreme Gradient Boosting, which
15332 is an efficient implementation of the gradient boosting framework from Chen
15333 and Guestrin (2016). The package includes efficient linear model solver and
15334 tree learning algorithms. The package can automatically do parallel
15335 computation on a single machine. It supports various objective functions,
15336 including regression, classification and ranking. The package is made to be
15337 extensible, so that users are also allowed to define their own objectives
15339 (license license:asl2.0)))
15341 (define-public r-umap
15344 (version "0.2.4.0")
15348 (uri (cran-uri "umap" version))
15351 "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch"))))
15352 (build-system r-build-system)
15354 `(("r-openssl" ,r-openssl)
15356 ("r-reticulate" ,r-reticulate)
15357 ("r-rspectra" ,r-rspectra)))
15358 (home-page "https://github.com/tkonopka/umap")
15359 (synopsis "Uniform manifold approximation and projection")
15361 "Uniform manifold approximation and projection is a technique for
15362 dimension reduction. This package provides an interface to the UMAP algorithm
15363 in R, including a translation of the original algorithm into R.")
15364 (license license:expat)))
15366 (define-public r-uwot
15373 (uri (cran-uri "uwot" version))
15376 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15377 (build-system r-build-system)
15379 `(("r-dqrng" ,r-dqrng)
15381 ("r-irlba" ,r-irlba)
15382 ("r-matrix" ,r-matrix)
15384 ("r-rcppannoy" ,r-rcppannoy)
15385 ("r-rcppparallel" ,r-rcppparallel)
15386 ("r-rcppprogress" ,r-rcppprogress)
15387 ("r-rspectra" ,r-rspectra)))
15388 (home-page "https://github.com/jlmelville/uwot")
15389 (synopsis "Uniform manifold approximation and projection")
15391 "This package provides an implementation of the Uniform Manifold
15392 Approximation and Projection dimensionality reduction by McInnes et
15393 al. (2018). It also provides means to transform new data and to carry out
15394 supervised dimensionality reduction. An implementation of the related
15395 LargeVis method of Tang et al. (2016) is also provided.")
15396 (license license:gpl3)))
15398 (define-public r-kableextra
15400 (name "r-kableextra")
15405 (uri (cran-uri "kableExtra" version))
15408 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15409 (properties `((upstream-name . "kableExtra")))
15410 (build-system r-build-system)
15412 `(("r-digest" ,r-digest)
15414 ("r-htmltools" ,r-htmltools)
15415 ("r-knitr" ,r-knitr)
15416 ("r-magrittr" ,r-magrittr)
15417 ("r-readr" ,r-readr)
15418 ("r-rmarkdown" ,r-rmarkdown)
15419 ("r-rstudioapi" ,r-rstudioapi)
15420 ("r-rvest" ,r-rvest)
15421 ("r-scales" ,r-scales)
15422 ("r-stringr" ,r-stringr)
15423 ("r-viridislite" ,r-viridislite)
15424 ("r-webshot" ,r-webshot)
15425 ("r-xml2" ,r-xml2)))
15426 (home-page "https://haozhu233.github.io/kableExtra/")
15427 (synopsis "Construct complex tables with pipe syntax")
15429 "Build complex HTML or LaTeX tables using @code{kable()} from
15430 @code{knitr} and the piping syntax from @code{magrittr}. The function
15431 @code{kable()} is a light weight table generator coming from @code{knitr}.
15432 This package simplifies the way to manipulate the HTML or LaTeX codes
15433 generated by @code{kable()} and allows users to construct complex tables and
15434 customize styles using a readable syntax.")
15435 (license license:expat)))
15437 (define-public r-glasso
15444 (uri (cran-uri "glasso" version))
15446 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15447 (build-system r-build-system)
15448 (native-inputs `(("gfortran" ,gfortran)))
15449 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15450 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15452 "This is a package for estimation of a sparse inverse covariance matrix
15453 using a lasso (L1) penalty. Facilities are provided for estimates along a
15454 path of values for the regularization parameter.")
15455 (license license:gpl2)))
15457 (define-public r-rhpcblasctl
15459 (name "r-rhpcblasctl")
15460 (version "0.18-205")
15464 (uri (cran-uri "RhpcBLASctl" version))
15467 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15468 (properties `((upstream-name . "RhpcBLASctl")))
15469 (build-system r-build-system)
15470 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15471 (synopsis "Control the number of threads on BLAS")
15473 "This package allows you to control the number of threads the BLAS
15474 library uses. It is also possible to control the number of threads in
15476 (license license:agpl3+)))
15478 (define-public r-lda
15485 (uri (cran-uri "lda" version))
15488 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15489 (build-system r-build-system)
15490 (home-page "https://cran.r-project.org/web/packages/lda/")
15491 (synopsis "Collapsed Gibbs sampling methods for topic models")
15493 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15494 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15495 mixed-membership stochastic blockmodel. Inference for all of these models is
15496 implemented via a fast collapsed Gibbs sampler written in C. Utility
15497 functions for reading/writing data typically used in topic models, as well as
15498 tools for examining posterior distributions are also included.")
15499 ;; Any version of the LGPL
15500 (license license:lgpl3+)))
15502 (define-public r-rann-l1
15509 (uri (cran-uri "RANN.L1" version))
15512 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15513 (properties `((upstream-name . "RANN.L1")))
15514 (build-system r-build-system)
15515 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15516 (synopsis "Fast nearest neighbour search using L1 metric")
15518 "This package provides tools to find the k nearest neighbours for every
15519 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15520 library. There is support for approximate as well as exact searches, fixed
15521 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15522 computed using the L1 (Manhattan, taxicab) metric.")
15523 (license license:gpl3+)))
15525 (define-public r-leiden
15532 (uri (cran-uri "leiden" version))
15535 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15536 (properties `((upstream-name . "leiden")))
15537 (build-system r-build-system)
15539 `(("r-igraph" ,r-igraph)
15540 ("r-matrix" ,r-matrix)
15541 ("r-reticulate" ,r-reticulate)))
15542 (home-page "https://github.com/TomKellyGenetics/leiden")
15543 (synopsis "R implementation of Leiden clustering algorithm")
15545 "This package implements the Python @code{leidenalg} module to be called
15546 in R. It enables clustering using the Leiden algorithm for partitioning a
15547 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15548 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15549 (license license:gpl3)))
15551 (define-public r-patchwork
15552 ;; There has been no public release yet.
15553 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15556 (name "r-patchwork")
15557 (version (git-version "0.0.1" revision commit))
15561 (uri (git-reference
15562 (url "https://github.com/thomasp85/patchwork.git")
15564 (file-name (git-file-name name version))
15567 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15568 (build-system r-build-system)
15570 `(("r-ggplot2" ,r-ggplot2)
15571 ("r-gtable" ,r-gtable)))
15572 (home-page "https://github.com/thomasp85/patchwork")
15573 (synopsis "Compose ggplot2 plots")
15575 "The @code{ggplot2} package provides a strong API for sequentially
15576 building up a plot, but does not concern itself with composition of multiple
15577 plots. Patchwork is a package that expands the API to allow for arbitrarily
15578 complex composition of plots by providing mathmatical operators for combining
15580 (license license:expat))))
15582 (define-public r-liger
15589 (uri (git-reference
15590 (url "https://github.com/MacoskoLab/liger.git")
15591 (commit (string-append "v" version))))
15592 (file-name (git-file-name name version))
15595 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15596 (modules '((guix build utils)))
15599 (delete-file "inst/java/ModularityOptimizer.jar")
15601 (build-system r-build-system)
15604 (modify-phases %standard-phases
15605 (add-after 'unpack 'build-java-part
15606 (lambda* (#:key inputs #:allow-other-keys)
15607 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15608 (for-each (lambda (file) (invoke "javac" file))
15609 (find-files "." "\\.java$"))
15610 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15611 (find-files "." "\\.class$"))
15614 `(("r-cowplot" ,r-cowplot)
15615 ("r-dosnow" ,r-dosnow)
15616 ("r-dplyr" ,r-dplyr)
15618 ("r-foreach" ,r-foreach)
15619 ("r-ggplot2" ,r-ggplot2)
15620 ("r-ggrepel" ,r-ggrepel)
15621 ("r-hmisc" ,r-hmisc)
15623 ("r-irlba" ,r-irlba)
15624 ("r-matrix" ,r-matrix)
15625 ("r-mclust" ,r-mclust)
15626 ("r-patchwork" ,r-patchwork)
15628 ("r-rann-l1" ,r-rann-l1)
15630 ("r-rcpparmadillo" ,r-rcpparmadillo)
15631 ("r-riverplot" ,r-riverplot)
15632 ("r-rtsne" ,r-rtsne)
15633 ("r-snow" ,r-snow)))
15635 `(("jdk" ,icedtea "jdk")
15636 ;; See https://github.com/MacoskoLab/liger/issues/96
15637 ;; The optimizer is released under the Expat license.
15641 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15644 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15646 ("r-knitr" ,r-knitr))) ; for vignettes
15647 (home-page "https://github.com/MacoskoLab/liger")
15648 (synopsis "Integrate and analyze multiple single-cell datasets")
15650 "LIGER is a package for integrating and analyzing multiple single-cell
15651 datasets, developed and maintained by the Macosko lab. It relies on
15652 integrative non-negative matrix factorization to identify shared and
15653 dataset-specific factors.")
15654 (license license:gpl3)))
15656 (define-public r-harmony
15657 ;; There are no tagged commits
15658 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15662 (version (git-version "1.0" revision commit))
15666 (uri (git-reference
15667 (url "https://github.com/immunogenomics/harmony")
15669 (file-name (git-file-name name version))
15672 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15673 (build-system r-build-system)
15675 `(("r-cowplot" ,r-cowplot)
15676 ("r-dplyr" ,r-dplyr)
15677 ("r-ggplot2" ,r-ggplot2)
15678 ("r-irlba" ,r-irlba)
15679 ("r-matrix" ,r-matrix)
15681 ("r-rcpparmadillo" ,r-rcpparmadillo)
15682 ("r-rcppprogress" ,r-rcppprogress)
15683 ("r-rlang" ,r-rlang)
15684 ("r-tibble" ,r-tibble)
15685 ("r-tidyr" ,r-tidyr)))
15686 (home-page "https://github.com/immunogenomics/harmony")
15687 (synopsis "Integration of single cell sequencing data")
15689 "This package provides an implementation of the Harmony algorithm for
15690 single cell integration, described in Korsunsky et al
15691 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15692 function and interfaces to external frameworks.")
15693 (license license:gpl3))))
15695 (define-public r-covr
15702 (uri (cran-uri "covr" version))
15704 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15705 (properties `((upstream-name . "covr")))
15706 (build-system r-build-system)
15708 `(("r-crayon" ,r-crayon)
15709 ("r-digest" ,r-digest)
15711 ("r-jsonlite" ,r-jsonlite)
15713 ("r-withr" ,r-withr)
15714 ("r-yaml" ,r-yaml)))
15715 (home-page "https://github.com/r-lib/covr")
15716 (synopsis "Test coverage for R packages")
15718 "Thisp package enables you to track and report code coverage for your
15719 package and (optionally) upload the results to a coverage service. Code
15720 coverage is a measure of the amount of code being exercised by a set of tests.
15721 It is an indirect measure of test quality and completeness. This package is
15722 compatible with any testing methodology or framework and tracks coverage of
15723 both R code and compiled C/C++/FORTRAN code.")
15724 (license license:gpl3)))
15726 (define-public r-systemfonts
15728 (name "r-systemfonts")
15733 (uri (cran-uri "systemfonts" version))
15736 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15737 (properties `((upstream-name . "systemfonts")))
15738 (build-system r-build-system)
15740 `(("fontconfig" ,fontconfig)
15741 ("freetype" ,freetype)
15744 `(("pkg-config" ,pkg-config)))
15745 (home-page "https://github.com/r-lib/systemfonts")
15746 (synopsis "System native font finding")
15748 "This package provides system native access to the font catalogue. As
15749 font handling varies between systems it is difficult to correctly locate
15750 installed fonts across different operating systems. The 'systemfonts' package
15751 provides bindings to the native libraries for finding font files that can then
15752 be used further by e.g. graphic devices.")
15753 (license license:expat)))
15755 (define-public r-graphlayouts
15757 (name "r-graphlayouts")
15762 (uri (cran-uri "graphlayouts" version))
15765 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15766 (properties `((upstream-name . "graphlayouts")))
15767 (build-system r-build-system)
15769 `(("r-igraph" ,r-igraph)
15771 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15772 (home-page "https://github.com/schochastics/graphlayouts")
15773 (synopsis "Additional layout algorithms for network visualizations")
15775 "This package provides several layout algorithms to visualize networks
15776 which are not part of the igraph library. Most are based on the concept of
15777 stress majorization by Gansner et al. (2004)
15778 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15779 emphasize hidden group structures in networks or focus on specific nodes.")
15780 (license license:expat)))
15782 (define-public r-tidygraph
15784 (name "r-tidygraph")
15789 (uri (cran-uri "tidygraph" version))
15792 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15793 (properties `((upstream-name . "tidygraph")))
15794 (build-system r-build-system)
15796 `(("r-dplyr" ,r-dplyr)
15797 ("r-igraph" ,r-igraph)
15798 ("r-magrittr" ,r-magrittr)
15799 ("r-pillar" ,r-pillar)
15802 ("r-rlang" ,r-rlang)
15803 ("r-tibble" ,r-tibble)
15804 ("r-tidyr" ,r-tidyr)))
15805 (home-page "https://github.com/thomasp85/tidygraph")
15806 (synopsis "Tidy API for graph manipulation")
15808 "This package provides a graph implementation that can be thought of as
15809 two tidy data frames describing node and edge data respectively. It provides
15810 an approach to manipulate these two virtual data frames using the API defined
15811 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15812 common graph algorithms.")
15813 (license license:expat)))
15815 (define-public r-soupx
15816 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15820 (version (git-version "0.3.1" revision commit))
15824 (uri (git-reference
15825 (url "https://github.com/constantAmateur/SoupX")
15827 (file-name (git-file-name name version))
15830 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15831 (properties `((upstream-name . "SoupX")))
15832 (build-system r-build-system)
15834 `(("r-ggplot2" ,r-ggplot2)
15835 ("r-matrix" ,r-matrix)
15836 ("r-seurat" ,r-seurat)))
15837 (home-page "https://github.com/constantAmateur/SoupX")
15838 (synopsis "Single cell mRNA Soup eXterminator")
15840 "This package provides a package for quantifying, profiling and
15841 removing cell free mRNA contamination (the \"soup\") from droplet based single
15842 cell RNA-seq experiments.")
15843 (license license:gpl2))))
15845 (define-public r-assertr
15852 (uri (cran-uri "assertr" version))
15855 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15856 (build-system r-build-system)
15858 `(("r-dplyr" ,r-dplyr)
15860 ("r-rlang" ,r-rlang)))
15862 `(("r-knitr" ,r-knitr))) ; needed for vignette
15863 (home-page "https://github.com/ropensci/assertr")
15864 (synopsis "Assertive programming for R analysis pipelines")
15866 "This package provides functionality to assert conditions that have to be
15867 met so that errors in data used in analysis pipelines can fail quickly. It is
15868 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15870 (license license:expat)))
15872 (define-public r-parameters
15874 (name "r-parameters")
15879 (uri (cran-uri "parameters" version))
15882 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15883 (properties `((upstream-name . "parameters")))
15884 (build-system r-build-system)
15886 `(("r-bayestestr" ,r-bayestestr)
15887 ("r-insight" ,r-insight)))
15888 (home-page "https://cran.r-project.org/web/packages/parameters")
15889 (synopsis "Processing of model parameters")
15891 "This package provides utilities for processing the parameters of various
15892 statistical models. Beyond computing p values, CIs, and other indices for a
15893 wide variety of models, this package implements features like standardization
15894 or bootstrapping of parameters and models, feature reduction (feature
15895 extraction and variable selection) as well as conversion between indices of
15897 (license license:gpl3)))
15899 (define-public r-rgdal
15906 (uri (cran-uri "rgdal" version))
15908 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15909 (properties `((upstream-name . "rgdal")))
15910 (build-system r-build-system)
15918 `(("pkg-config" ,pkg-config)))
15919 (home-page "http://rgdal.r-forge.r-project.org")
15920 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15922 "This package provides bindings to the Geospatial Data Abstraction
15923 Library (GDAL) and access to projection/transformation operations from the
15925 (license license:gpl2+)))
15927 (define-public r-insol
15934 (uri (cran-uri "insol" version))
15937 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
15938 (properties `((upstream-name . "insol")))
15939 (build-system r-build-system)
15941 `(("r-raster" ,r-raster)))
15943 `(("gfortran" ,gfortran)))
15944 (home-page "https://meteoexploration.com/R/insol/index.html")
15945 (synopsis "Tools for calculating solar radiation")
15947 "This package provides functions to compute insolation on tilted
15948 surfaces, computes atmospheric transmittance and related parameters such as:
15949 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15950 time, vector in the direction of the sun, vector normal to surface, and some
15951 atmospheric physics.")
15952 (license license:gpl2+)))
15954 (define-public r-lifecycle
15956 (name "r-lifecycle")
15961 (uri (cran-uri "lifecycle" version))
15964 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15965 (properties `((upstream-name . "lifecycle")))
15966 (build-system r-build-system)
15968 `(("r-glue" ,r-glue)
15969 ("r-rlang" ,r-rlang)))
15970 (home-page "https://github.com/r-lib/lifecycle")
15971 (synopsis "Manage the life cycle of your package functions")
15973 "Manage the life cycle of your exported functions with shared
15974 conventions, documentation badges, and non-invasive deprecation warnings. The
15975 lifecycle package defines four development stages (experimental, maturing,
15976 stable, and questioning) and three deprecation stages (soft-deprecated,
15977 deprecated, and defunct). It makes it easy to insert badges corresponding to
15978 these stages in your documentation. Usage of deprecated functions are
15979 signalled with increasing levels of non-invasive verbosity.")
15980 (license license:gpl3)))
15982 (define-public r-assertable
15984 (name "r-assertable")
15989 (uri (cran-uri "assertable" version))
15992 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15993 (build-system r-build-system)
15995 `(("r-data-table" ,r-data-table)))
15996 (home-page "https://cran.r-project.org/web/packages/assertable/")
15997 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15998 (description "This package provides simple, flexible assertions on
15999 data.frame or data.table objects with verbose output for vetting. While other
16000 assertion packages apply towards more general use-cases, @code{assertable} is
16001 tailored towards tabular data. It includes functions to check variable names
16002 and values, whether the dataset contains all combinations of a given set of
16003 unique identifiers, and whether it is a certain length. In addition,
16004 @code{assertable} includes utility functions to check the existence of target
16005 files and to efficiently import multiple tabular data files into one
16007 (license license:gpl3)))
16009 (define-public r-quadprog
16011 (name "r-quadprog")
16016 (uri (cran-uri "quadprog" version))
16018 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16019 (build-system r-build-system)
16021 `(("gfortran" ,gfortran)))
16022 (home-page "https://cran.r-project.org/web/packages/quadprog")
16023 (synopsis "Functions to solve quadratic programming problems")
16025 "This package contains routines and documentation for solving quadratic
16026 programming problems.")
16027 (license license:gpl3+)))
16029 (define-public r-desolve
16036 (uri (cran-uri "deSolve" version))
16038 (base32 "1qhjq4vxlxd9qmhf6i26x1k7bzhldlxzbby1zgcplicdvlqk951d"))))
16039 (properties `((upstream-name . "deSolve")))
16040 (build-system r-build-system)
16042 `(("gfortran" ,gfortran)))
16043 (home-page "https://desolve.r-forge.r-project.org/")
16044 (synopsis "Solvers for initial value problems of differential equations")
16045 (description "This package provides functions that solve initial value
16046 problems of a system of first-order @dfn{ordinary differential
16047 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16048 @dfn{differential algebraic equations} (DAE), and of delay differential
16049 equations. The functions provide an interface to the FORTRAN functions
16050 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16051 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16052 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16053 time steps. The package contains routines designed for solving ODEs resulting
16054 from 1-D, 2-D and 3-D partial differential equations that have been converted
16055 to ODEs by numerical differencing.")
16056 (license license:gpl2+)))
16058 (define-public r-pracma
16064 (uri (cran-uri "pracma" version))
16066 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16067 (build-system r-build-system)
16068 (home-page "https://cran.r-project.org/web/packages/pracma/")
16069 (synopsis "Practical numerical math functions")
16070 (description "This package provides functions for numerical analysis and
16071 linear algebra, numerical optimization, differential equations, plus some
16072 special functions. It uses Matlab function names where appropriate to simplify
16074 (license license:gpl3+)))
16076 (define-public r-subplex
16083 (uri (cran-uri "subplex" version))
16086 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
16087 (build-system r-build-system)
16089 `(("gfortran" ,gfortran)))
16090 (home-page "https://cran.r-project.org/web/packages/subplex")
16091 (synopsis "Unconstrained optimization using the subplex algorithm")
16093 "This package implements the Subplex optimization algorithm.
16094 It solves unconstrained optimization problems using a simplex method on
16095 subspaces. The method is well suited for optimizing objective functions that
16096 are noisy or are discontinuous at the solution.")
16097 (license license:gpl3+)))
16099 (define-public r-txtplot
16106 (uri (cran-uri "txtplot" version))
16109 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16110 (build-system r-build-system)
16111 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16112 (synopsis "Text-based plotting")
16113 (description "This package provides functions to produce rudimentary ASCII
16114 graphics directly in the terminal window. This package provides a basic
16115 plotting function (and equivalents of curve, density, acf and barplot) as well
16116 as a boxplot function.")
16117 (license license:lgpl3+)))
16119 (define-public r-bio3d
16126 (uri (cran-uri "bio3d" version))
16129 "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
16130 (properties `((upstream-name . "bio3d")))
16131 (build-system r-build-system)
16132 (inputs `(("zlib" ,zlib)))
16133 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16134 (home-page "http://thegrantlab.org/bio3d/")
16135 (synopsis "Biological structure analysis")
16137 "This package provides utilities to process, organize and explore protein
16138 structure, sequence and dynamics data. Features include the ability to read
16139 and write structure, sequence and dynamic trajectory data, perform sequence
16140 and structure database searches, data summaries, atom selection, alignment,
16141 superposition, rigid core identification, clustering, torsion analysis,
16142 distance matrix analysis, structure and sequence conservation analysis, normal
16143 mode analysis, principal component analysis of heterogeneous structure data,
16144 and correlation network analysis from normal mode and molecular dynamics data.
16145 In addition, various utility functions are provided to enable the statistical
16146 and graphical power of the R environment to work with biological sequence and
16148 (license license:gpl2+)))
16150 (define-public r-bios2cor
16152 (name "r-bios2cor")
16157 (uri (cran-uri "Bios2cor" version))
16160 "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
16161 (properties `((upstream-name . "Bios2cor")))
16162 (build-system r-build-system)
16164 `(("r-bigmemory" ,r-bigmemory)
16165 ("r-bio3d" ,r-bio3d)
16166 ("r-circular" ,r-circular)
16167 ("r-igraph" ,r-igraph)))
16168 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16169 (synopsis "From biological sequences and simulations to correlation analysis")
16171 "This package provides utilities for computation and analysis of
16172 correlation/covariation in multiple sequence alignments and in side chain
16173 motions during molecular dynamics simulations. Features include the
16174 computation of correlation/covariation scores using a variety of scoring
16175 functions between either sequence positions in alignments or side chain
16176 dihedral angles in molecular dynamics simulations and utilities to analyze the
16177 correlation/covariation matrix through a variety of tools including network
16178 representation and principal components analysis. In addition, several
16179 utility functions are based on the R graphical environment to provide friendly
16180 tools for help in data interpretation.")
16181 (license license:gpl2+)))
16183 ;; This package includes minified JavaScript files. When upgrading please
16184 ;; check that there are no new minified JavaScript files.
16185 (define-public r-networkd3
16187 (name "r-networkd3")
16192 (uri (cran-uri "networkD3" version))
16195 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16198 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16200 (properties `((upstream-name . "networkD3")))
16201 (build-system r-build-system)
16203 `(#:modules ((guix build utils)
16204 (guix build r-build-system)
16208 (modify-phases %standard-phases
16209 (add-after 'unpack 'process-javascript
16210 (lambda* (#:key inputs #:allow-other-keys)
16211 (with-directory-excursion "inst/htmlwidgets/lib/"
16215 `((,(assoc-ref inputs "d3.v4.js")
16216 "d3-4.5.0/d3.min.js"))))
16217 (lambda (sources targets)
16218 (for-each (lambda (source target)
16219 (format #t "Processing ~a --> ~a~%"
16221 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16222 (call-with-output-file target
16224 (dump-port minified port)))))
16225 sources targets))))
16228 `(("uglify-js" ,uglify-js)
16229 ;; NOTE: Make sure that this version of d3 is still valid when
16230 ;; upgrading the package.
16234 (uri "https://d3js.org/d3.v4.js")
16237 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16239 `(("r-htmlwidgets" ,r-htmlwidgets)
16240 ("r-igraph" ,r-igraph)
16241 ("r-magrittr" ,r-magrittr)))
16242 (home-page "https://cran.r-project.org/package=networkD3")
16243 (synopsis "D3 JavaScript network graphs from R")
16245 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16247 (license license:gpl3+)))
16249 (define-public r-aasea
16256 (uri (cran-uri "aaSEA" version))
16259 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16260 (properties `((upstream-name . "aaSEA")))
16261 (build-system r-build-system)
16263 `(("r-bios2cor" ,r-bios2cor)
16265 ("r-hmisc" ,r-hmisc)
16266 ("r-magrittr" ,r-magrittr)
16267 ("r-networkd3" ,r-networkd3)
16268 ("r-plotly" ,r-plotly)
16269 ("r-seqinr" ,r-seqinr)
16270 ("r-shiny" ,r-shiny)
16271 ("r-shinydashboard" ,r-shinydashboard)))
16272 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16273 (synopsis "Amino acid substitution effect analyzer")
16275 "Given a protein multiple sequence alignment, it is a daunting task to
16276 assess the effects of substitutions along sequence length. The aaSEA package
16277 is intended to help researchers to rapidly analyze property changes caused by
16278 single, multiple and correlated amino acid substitutions in proteins.")
16279 (license license:gpl3)))
16281 (define-public r-abacus
16288 (uri (cran-uri "ABACUS" version))
16291 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16292 (properties `((upstream-name . "ABACUS")))
16293 (build-system r-build-system)
16295 `(("r-ggplot2" ,r-ggplot2)
16296 ("r-shiny" ,r-shiny)))
16297 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16298 (synopsis "Apps-based activities for communicating and understanding statistics")
16300 "This package provides a set of Shiny apps for effective communication
16301 and understanding in statistics. The current version includes properties of
16302 normal distribution, properties of sampling distribution, one-sample z and t
16303 tests, two samples independent (unpaired) t test and analysis of variance.")
16304 (license license:gpl3)))
16306 (define-public r-abc-rap
16313 (uri (cran-uri "ABC.RAP" version))
16316 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16317 (properties `((upstream-name . "ABC.RAP")))
16318 (build-system r-build-system)
16319 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16320 (synopsis "Array-based CpG region analysis pipeline")
16322 "This package aims to identify candidate genes that are differentially
16323 methylated between cases and controls. It applies Student's t-test and delta
16324 beta analysis to identify candidate genes containing multiple CpG sites.")
16325 (license license:gpl3)))
16327 (define-public r-abcadm
16334 (uri (cran-uri "abcADM" version))
16337 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16338 (properties `((upstream-name . "abcADM")))
16339 (build-system r-build-system)
16342 ("r-rcpp" ,r-rcpp)))
16343 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16344 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16346 "This package provides tools to estimate parameters of accumulated
16347 damage (load duration) models based on failure time data under a Bayesian
16348 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16349 long-term reliability under stochastic load profiles.")
16350 (license license:gpl3)))
16352 (define-public r-rglpk
16359 (uri (cran-uri "Rglpk" version))
16362 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16363 (properties `((upstream-name . "Rglpk")))
16364 (build-system r-build-system)
16366 `(("r-slam" ,r-slam)))
16369 (home-page "http://R-Forge.R-project.org/projects/rglp/")
16370 (synopsis "R interface to the GNU Linear Programming Kit")
16372 "This package provides an R interface to the GNU Linear Programming Kit,
16373 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16374 integer linear programming} (MILP) and other related problems.")
16376 (license (list license:gpl2 license:gpl3))))
16378 (define-public r-abcdefba
16380 (name "r-abcdefba")
16385 (uri (cran-uri "abcdeFBA" version))
16388 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16389 (properties `((upstream-name . "abcdeFBA")))
16390 (build-system r-build-system)
16392 `(("r-corrplot" ,r-corrplot)
16393 ("r-lattice" ,r-lattice)
16395 ("r-rglpk" ,r-rglpk)))
16396 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16397 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16399 "This package provides functions for Constraint Based Simulation using
16400 Flux Balance Analysis and informative analysis of the data generated during
16402 (license license:gpl2)))
16404 (define-public r-abcrlda
16411 (uri (cran-uri "abcrlda" version))
16414 "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
16415 (properties `((upstream-name . "abcrlda")))
16416 (build-system r-build-system)
16417 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16418 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16420 "This package offers methods to perform @dfn{asymptotically
16421 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16422 cost-sensitive binary classification. The bias-correction is an estimate of
16423 the bias term added to regularized discriminant analysis that minimizes the
16425 (license license:gpl3)))
16427 (define-public r-abemus
16434 (uri (cran-uri "abemus" version))
16437 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16438 (properties `((upstream-name . "abemus")))
16439 (build-system r-build-system)
16441 `(("r-data-table" ,r-data-table)))
16442 (home-page "https://cran.r-project.org/web/packages/abemus/")
16443 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16445 "This package provides an implementation of @dfn{Adaptive Base Error
16446 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16447 platform-specific genetic knowledge and empirical signal to readily detect and
16448 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16449 cell free DNA} (cfDNA).")
16450 (license license:gpl3)))
16452 ;; This package includes minified JavaScript files. When upgrading please
16453 ;; check that there are no new minified JavaScript files.
16454 (define-public r-rintrojs
16456 (name "r-rintrojs")
16461 (uri (cran-uri "rintrojs" version))
16464 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16465 (properties `((upstream-name . "rintrojs")))
16466 (build-system r-build-system)
16468 `(#:modules ((guix build utils)
16469 (guix build r-build-system)
16473 (modify-phases %standard-phases
16474 (add-after 'unpack 'process-javascript
16475 (lambda* (#:key inputs #:allow-other-keys)
16476 (with-directory-excursion "inst/javascript/introjs/"
16480 `((,(assoc-ref inputs "intro.js")
16482 (lambda (sources targets)
16483 (for-each (lambda (source target)
16484 (format #t "Processing ~a --> ~a~%"
16486 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16487 (call-with-output-file target
16489 (dump-port minified port)))))
16490 sources targets))))
16493 `(("uglify-js" ,uglify-js)
16497 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16500 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16502 `(("r-jsonlite" ,r-jsonlite)
16503 ("r-shiny" ,r-shiny)))
16504 (home-page "https://github.com/carlganz/rintrojs")
16505 (synopsis "Wrapper for the Intro.js library")
16507 "This package provides a wrapper for the @url{http://www.introjs.com,
16508 Intro.js} library. This package makes it easy to include step-by-step
16509 introductions, and clickable hints in a Shiny application. It supports both
16510 static introductions in the UI, and programmatic introductions from the
16512 (license license:agpl3+)))
16514 (define-public r-sysfonts
16516 (name "r-sysfonts")
16521 (uri (cran-uri "sysfonts" version))
16524 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16525 (properties `((upstream-name . "sysfonts")))
16526 (build-system r-build-system)
16528 `(("freetype" ,freetype)
16532 `(("pkg-config" ,pkg-config)))
16533 (home-page "https://github.com/yixuan/sysfonts")
16534 (synopsis "Loading fonts into R")
16536 "This is a package to simplify loading of system fonts and Google Fonts
16537 into R, in order to support other packages.")
16538 (license license:gpl2)))
16540 (define-public r-showtextdb
16542 (name "r-showtextdb")
16547 (uri (cran-uri "showtextdb" version))
16550 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16551 (properties `((upstream-name . "showtextdb")))
16552 (build-system r-build-system)
16554 `(("r-sysfonts" ,r-sysfonts)))
16555 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16556 (synopsis "Font files for the 'showtext' package")
16558 "This package provides font files that can be used by the @code{showtext}
16560 (license license:asl2.0)))
16562 (define-public r-showtext
16564 (name "r-showtext")
16569 (uri (cran-uri "showtext" version))
16572 "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
16573 (properties `((upstream-name . "showtext")))
16574 (build-system r-build-system)
16576 `(("freetype" ,freetype)
16580 `(("r-showtextdb" ,r-showtextdb)
16581 ("r-sysfonts" ,r-sysfonts)))
16582 (native-inputs `(("pkg-config" ,pkg-config)))
16583 (home-page "https://github.com/yixuan/showtext")
16584 (synopsis "Using fonts more easily in R graphs")
16586 "This package aims to make it easy to use various types of
16587 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16588 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16589 will be converted into polygons or raster images, hence after the plot has
16590 been created, it no longer relies on the font files. No external software
16591 such as Ghostscript is needed to use this package.")
16592 (license license:asl2.0)))
16594 (define-public r-emojifont
16596 (name "r-emojifont")
16601 (uri (cran-uri "emojifont" version))
16604 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16605 (properties `((upstream-name . "emojifont")))
16606 (build-system r-build-system)
16608 `(("r-ggplot2" ,r-ggplot2)
16609 ("r-proto" ,r-proto)
16610 ("r-showtext" ,r-showtext)
16611 ("r-sysfonts" ,r-sysfonts)))
16612 (home-page "https://guangchuangyu.github.io/emojifont")
16613 (synopsis "Emoji and Font Awesome in R graphics")
16615 "This package enables the use of emoji and the Font Awesome glyphs in
16616 both base and ggplot2 graphics.")
16617 (license license:artistic2.0)))
16619 (define-public r-abstractr
16621 (name "r-abstractr")
16626 (uri (cran-uri "abstractr" version))
16629 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16630 (properties `((upstream-name . "abstractr")))
16631 (build-system r-build-system)
16633 `(("r-colourpicker" ,r-colourpicker)
16634 ("r-emojifont" ,r-emojifont)
16635 ("r-ggplot2" ,r-ggplot2)
16636 ("r-gridextra" ,r-gridextra)
16637 ("r-rintrojs" ,r-rintrojs)
16638 ("r-shiny" ,r-shiny)
16639 ("r-shinythemes" ,r-shinythemes)))
16640 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16641 (synopsis "R-Shiny application for creating visual abstracts")
16643 "This package provides an R Shiny application to create visual abstracts
16644 for original research. A variety of user defined options and formatting are
16646 (license license:gpl3)))
16648 (define-public r-abtest
16655 (uri (cran-uri "abtest" version))
16658 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16659 (properties `((upstream-name . "abtest")))
16660 (build-system r-build-system)
16662 `(("r-matrix" ,r-matrix)
16663 ("r-mvtnorm" ,r-mvtnorm)
16664 ("r-plotrix" ,r-plotrix)
16665 ("r-rcolorbrewer" ,r-rcolorbrewer)
16668 ("r-truncnorm" ,r-truncnorm)
16669 ("r-vgam" ,r-vgam)))
16670 (home-page "https://cran.r-project.org/web/packages/abtest/")
16671 (synopsis "Bayesian A/B testing")
16673 "This package provides functions for Bayesian A/B testing including prior
16674 elicitation options based on Kass and Vaidyanathan (1992)
16675 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16676 (license license:gpl2+)))
16678 (define-public r-accept
16685 (uri (cran-uri "accept" version))
16688 "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
16689 (properties `((upstream-name . "accept")))
16690 (build-system r-build-system)
16692 `(("r-dplyr" ,r-dplyr)
16693 ("r-extrafont" ,r-extrafont)
16695 ("r-plotly" ,r-plotly)
16696 ("r-stringr" ,r-stringr)
16697 ("r-viridis" ,r-viridis)))
16698 (home-page "https://cran.r-project.org/web/packages/accept/")
16699 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16701 "This package allows clinicians to predict the rate and severity of
16702 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16703 Disease} (COPD) patients, based on the clinical prediction model published in
16704 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16705 (license license:gpl3)))
16707 (define-public r-smpracticals
16709 (name "r-smpracticals")
16714 (uri (cran-uri "SMPracticals" version))
16717 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16718 (properties `((upstream-name . "SMPracticals")))
16719 (build-system r-build-system)
16721 `(("r-ellipse" ,r-ellipse)
16724 ("r-survival" ,r-survival)))
16725 (home-page "http://statwww.epfl.ch/davison/SM/")
16726 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16728 "This package contains the datasets and a few functions for use with the
16729 practicals outlined in Appendix A of the book Statistical Models (Davison,
16730 2003, Cambridge University Press). The practicals themselves can be found at
16731 @url{http://statwww.epfl.ch/davison/SM/}.")
16732 (license license:gpl2+)))
16734 (define-public r-fgui
16741 (uri (cran-uri "fgui" version))
16744 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16745 (properties `((upstream-name . "fgui")))
16746 (build-system r-build-system)
16748 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16749 (synopsis "Create GUI for R functions")
16751 "Rapidly create a GUI for a function you created by automatically
16752 creating widgets for arguments of the function. This package automatically
16753 parses help routines for context-sensitive help to these arguments. The
16754 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16755 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16756 incorporated into the interface for greater customization for the more
16758 ;; Any version of the GPL.
16759 (license (list license:gpl2+ license:gpl3+))))
16761 (define-public r-tcltk2
16768 (uri (cran-uri "tcltk2" version))
16771 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16772 (properties `((upstream-name . "tcltk2")))
16773 (build-system r-build-system)
16777 (home-page "http://www.sciviews.org/SciViews-R")
16778 (synopsis "Tcl/Tk additions")
16780 "This package provides a series of additional Tcl commands and Tk widgets
16781 with style and various functions to supplement the tcltk package")
16782 (license license:lgpl3)))
16784 (define-public r-accrual
16791 (uri (cran-uri "accrual" version))
16794 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16795 (properties `((upstream-name . "accrual")))
16796 (build-system r-build-system)
16798 `(("r-fgui" ,r-fgui)
16799 ("r-smpracticals" ,r-smpracticals)
16800 ("r-tcltk2" ,r-tcltk2)))
16801 (home-page "https://cran.r-project.org/web/packages/accrual/")
16802 (synopsis "Bayesian accrual prediction")
16804 "Subject recruitment for medical research is challenging. Slow patient
16805 accrual leads to delay in research. Accrual monitoring during the process of
16806 recruitment is critical. Researchers need reliable tools to manage the
16807 accrual rate. This package provides an implementation of a Bayesian method
16808 that integrates researcher's experience on previous trials and data from the
16809 current study, providing reliable prediction on accrual rate for clinical
16810 studies. It provides functions for Bayesian accrual prediction which can be
16811 easily used by statisticians and clinical researchers.")
16812 (license license:gpl2)))
16814 (define-public r-accrued
16821 (uri (cran-uri "accrued" version))
16824 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16825 (properties `((upstream-name . "accrued")))
16826 (build-system r-build-system)
16827 (home-page "https://cran.r-project.org/web/packages/accrued/")
16828 (synopsis "Data quality visualization tools for partially accruing data")
16830 "This is a package for visualizing data quality of partially accruing
16832 (license license:gpl3)))
16834 (define-public r-mda
16841 (uri (cran-uri "mda" version))
16844 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16845 (properties `((upstream-name . "mda")))
16846 (build-system r-build-system)
16847 (propagated-inputs `(("r-class" ,r-class)))
16848 (native-inputs `(("gfortran" ,gfortran)))
16849 (home-page "https://cran.r-project.org/web/packages/mda/")
16850 (synopsis "Mixture and flexible discriminant analysis")
16852 "This is a package for mixture and flexible discriminant analysis,
16853 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16854 (license license:gpl2)))
16856 (define-public r-elasticnet
16858 (name "r-elasticnet")
16863 (uri (cran-uri "elasticnet" version))
16866 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16867 (properties `((upstream-name . "elasticnet")))
16868 (build-system r-build-system)
16870 `(("r-lars" ,r-lars)))
16871 (home-page "http://www.stat.umn.edu/~hzou")
16872 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16874 "This package provides functions for fitting the entire solution path of
16875 the Elastic-Net and also provides functions for estimating sparse Principal
16876 Components. The Lasso solution paths can be computed by the same function.")
16877 (license license:gpl2+)))
16879 (define-public r-sparselda
16881 (name "r-sparselda")
16886 (uri (cran-uri "sparseLDA" version))
16889 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16890 (properties `((upstream-name . "sparseLDA")))
16891 (build-system r-build-system)
16893 `(("r-elasticnet" ,r-elasticnet)
16896 (home-page "http://www.imm.dtu.dk/~lhc")
16897 (synopsis "Sparse discriminant analysis")
16899 "This package performs sparse linear discriminant analysis for Gaussians
16900 and mixture of Gaussian models.")
16901 (license license:gpl2+)))
16903 (define-public r-accsda
16910 (uri (cran-uri "accSDA" version))
16913 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
16914 (properties `((upstream-name . "accSDA")))
16915 (build-system r-build-system)
16917 `(("r-ggplot2" ,r-ggplot2)
16918 ("r-ggthemes" ,r-ggthemes)
16919 ("r-gridextra" ,r-gridextra)
16921 ("r-rarpack" ,r-rarpack)
16922 ("r-sparselda" ,r-sparselda)))
16923 (home-page "https://github.com/gumeo/accSDA/wiki")
16924 (synopsis "Accelerated sparse discriminant analysis")
16926 "This package provides an implementation of sparse linear discriminant
16927 analysis, which is a supervised classification method for multiple classes.
16928 Various novel optimization approaches to this problem are implemented
16929 including @dfn{alternating direction method of multipliers} (ADMM),
16930 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
16931 Functions for performing cross validation are also supplied along with basic
16932 prediction and plotting functions. @dfn{Sparse zero variance
16933 discriminant} (SZVD) analysis is also included in the package.")
16934 (license license:gpl2+)))
16936 (define-public r-ace2fastq
16938 (name "r-ace2fastq")
16943 (uri (cran-uri "ace2fastq" version))
16946 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
16947 (properties `((upstream-name . "ace2fastq")))
16948 (build-system r-build-system)
16950 `(("r-stringr" ,r-stringr)))
16951 (home-page "https://github.com/c5sire/ace2fastq")
16952 (synopsis "ACE file to FASTQ converter")
16954 "The ACE file format is used in genomics to store contigs from sequencing
16955 machines. This tools converts it into FASTQ format. Both formats contain the
16956 sequence characters and their corresponding quality information. Unlike the
16957 FASTQ file, the ACE file stores the quality values numerically. The
16958 conversion algorithm uses the standard Sanger formula. The package
16959 facilitates insertion into pipelines, and content inspection.")
16960 (license license:gpl3)))
16962 (define-public r-rngwell
16969 (uri (cran-uri "rngWELL" version))
16972 "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
16973 (properties `((upstream-name . "rngWELL")))
16974 (build-system r-build-system)
16975 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
16976 (synopsis "Toolbox for WELL random number generators")
16978 "This is a dedicated package to WELL pseudo random generators, which were
16979 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
16980 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
16981 (license license:bsd-3)))
16983 (define-public r-randtoolbox
16985 (name "r-randtoolbox")
16990 (uri (cran-uri "randtoolbox" version))
16993 "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd"))))
16994 (properties `((upstream-name . "randtoolbox")))
16995 (build-system r-build-system)
16997 `(("r-rngwell" ,r-rngwell)))
16999 `(("gfortran" ,gfortran)))
17000 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17001 (synopsis "Toolbox for pseudo and quasi random number generation")
17003 "This package provides
17006 @item pseudo random generators, such as general linear
17007 congruential generators, multiple recursive generators and generalized
17008 feedback shift register (SF-Mersenne Twister algorithm and WELL
17011 @item quasi random generators, such as the Torus algorithm, the Sobol
17012 sequence, the Halton sequence (including the Van der Corput sequence), and
17014 @item some generator tests: the gap test, the serial test, the poker test.
17017 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17018 (license license:bsd-3)))
17020 (define-public r-lhs
17027 (uri (cran-uri "lhs" version))
17030 "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
17031 (properties `((upstream-name . "lhs")))
17032 (build-system r-build-system)
17033 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17034 (home-page "https://github.com/bertcarnell/lhs")
17035 (synopsis "Latin Hypercube Samples")
17037 "This package provides a number of methods for creating and augmenting
17038 Latin Hypercube Samples.")
17039 (license license:gpl3)))
17041 (define-public r-acebayes
17043 (name "r-acebayes")
17048 (uri (cran-uri "acebayes" version))
17051 "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln"))))
17052 (properties `((upstream-name . "acebayes")))
17053 (build-system r-build-system)
17055 `(("r-compare" ,r-compare)
17057 ("r-randtoolbox" ,r-randtoolbox)
17059 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17060 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17061 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17063 "Finding an optimal Bayesian experimental design involves maximizing an
17064 objective function given by the expectation of some appropriately chosen
17065 utility function with respect to the joint distribution of unknown
17066 quantities (including responses). This objective function is usually not
17067 available in closed form and the design space can be continuous and of high
17068 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17069 to maximise an approximation to the expectation of the utility function.")
17070 (license license:gpl2)))
17072 (define-public r-acet
17079 (uri (cran-uri "ACEt" version))
17082 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17083 (properties `((upstream-name . "ACEt")))
17084 (build-system r-build-system)
17089 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17090 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17091 (synopsis "Estimating dynamic heritability and twin model comparison")
17093 "This package supports twin models that are able to estimate the dynamic
17094 behaviour of the variance components in the classical twin models with respect
17095 to age using B-splines and P-splines.")
17096 (license license:gpl2+)))
17098 (define-public r-acfmperiod
17100 (name "r-acfmperiod")
17105 (uri (cran-uri "acfMPeriod" version))
17108 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17109 (properties `((upstream-name . "acfMPeriod")))
17110 (build-system r-build-system)
17112 `(("r-mass" ,r-mass)))
17113 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17114 (synopsis "Estimation of the ACF from the M-periodogram")
17116 "This package support non-robust and robust computations of the sample
17117 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17118 univariate and multivariate processes. The methodology consists in reversing
17119 the diagonalization procedure involving the periodogram or the
17120 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17121 ACOVF or the ACF as discussed in Fuller (1995)
17122 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17123 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17124 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17125 (license license:gpl2+)))
17127 (define-public r-gamlss-data
17129 (name "r-gamlss-data")
17134 (uri (cran-uri "gamlss.data" version))
17137 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17138 (properties `((upstream-name . "gamlss.data")))
17139 (build-system r-build-system)
17140 (home-page "http://www.gamlss.org/")
17141 (synopsis "GAMLSS data")
17143 "This package provides data used as examples to demonstrate GAMLSS
17145 ;; Either version of the license
17146 (license (list license:gpl2 license:gpl3))))
17148 (define-public r-gamlss
17155 (uri (cran-uri "gamlss" version))
17158 "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc"))))
17159 (properties `((upstream-name . "gamlss")))
17160 (build-system r-build-system)
17162 `(("r-gamlss-data" ,r-gamlss-data)
17163 ("r-gamlss-dist" ,r-gamlss-dist)
17166 ("r-survival" ,r-survival)))
17167 (home-page "http://www.gamlss.org/")
17168 (synopsis "Generalized additive models for location scale and shape")
17170 "This package provides functions for fitting the generalized additive
17171 models for location scale and shape introduced by Rigby and
17172 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17173 use a distributional regression approach where all the parameters of the
17174 conditional distribution of the response variable are modelled using
17175 explanatory variables.")
17176 ;; Either version of the license
17177 (license (list license:gpl2 license:gpl3))))
17179 (define-public r-acid
17186 (uri (cran-uri "acid" version))
17189 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17190 (properties `((upstream-name . "acid")))
17191 (build-system r-build-system)
17193 `(("r-gamlss" ,r-gamlss)
17194 ("r-gamlss-dist" ,r-gamlss-dist)
17195 ("r-hmisc" ,r-hmisc)))
17196 (home-page "https://cran.r-project.org/web/packages/acid/")
17197 (synopsis "Analysing conditional income distributions")
17199 "This package provides functions for the analysis of income distributions
17200 for subgroups of the population as defined by a set of variables like age,
17201 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17202 distribution as well as functions for moments, inequality measures, entropy
17203 measures and polarisation measures of income distributions. This package thus
17204 aides the analysis of income inequality by offering tools for the exploratory
17205 analysis of income distributions at the disaggregated level.")
17206 (license license:gpl3)))
17208 (define-public r-acm4r
17215 (uri (cran-uri "acm4r" version))
17218 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17219 (properties `((upstream-name . "acm4r")))
17220 (build-system r-build-system)
17221 (propagated-inputs `(("r-mass" ,r-mass)))
17222 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17223 (synopsis "Align-and-count method comparisons of RFLP data")
17225 "This is a package to compare sequence fragment lengths or molecular
17226 weights from pairs of lanes. The number of matching bands in the
17227 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17228 the align-and-count method.")
17229 ;; Any version of the GPL
17230 (license (list license:gpl2+ license:gpl3+))))
17232 (define-public r-filematrix
17234 (name "r-filematrix")
17239 (uri (cran-uri "filematrix" version))
17242 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17243 (properties `((upstream-name . "filematrix")))
17244 (build-system r-build-system)
17245 ;; These inputs are needed for vignettes
17247 `(("r-knitr" ,r-knitr)
17248 ("r-rmarkdown" ,r-rmarkdown)
17249 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17250 (home-page "https://github.com/andreyshabalin/filematrix")
17251 (synopsis "File-backed matrix class with convenient read and write access")
17253 "This package provides an interface for working with large matrices
17254 stored in files, not in computer memory. It supports multiple non-character
17255 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17256 byte real values). Access to parts of the matrix is done by indexing, exactly
17257 as with usual R matrices. It supports very large matrices; the package has
17258 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17259 columns, ad allows for quick addition of extra columns to a filematrix.")
17260 (license license:lgpl3)))
17262 (define-public r-acmeeqtl
17264 (name "r-acmeeqtl")
17269 (uri (cran-uri "ACMEeqtl" version))
17272 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17273 (properties `((upstream-name . "ACMEeqtl")))
17274 (build-system r-build-system)
17276 `(("r-filematrix" ,r-filematrix)))
17277 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17278 (synopsis "Estimation of interpretable eQTL effect sizes")
17280 "This package provides a non-linear model, termed ACME, that reflects a
17281 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17282 With non-linear least-squares algorithm the maximum likelihood parameters can
17283 be estimated. The ACME model provides interpretable effect size estimates and
17284 p-values with well controlled Type-I error.")
17285 (license license:lgpl3)))
17287 (define-public r-acmer
17294 (uri (cran-uri "acmeR" version))
17297 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17298 (properties `((upstream-name . "acmeR")))
17299 (build-system r-build-system)
17300 (propagated-inputs `(("r-foreign" ,r-foreign)))
17301 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17302 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17304 "This package provides an implementation of the ACME estimator, described
17305 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17306 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17307 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17308 as carcasses age; variable bleed-through at successive searches; and interval
17309 mortality estimates. The package provides, based on search data, functions
17310 for estimating the mortality inflation factor in Frequentist and Bayesian
17312 (license license:expat)))
17314 (define-public r-r-huge
17321 (uri (cran-uri "R.huge" version))
17324 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17325 (properties `((upstream-name . "R.huge")))
17326 (build-system r-build-system)
17328 `(("r-r-methodss3" ,r-r-methodss3)
17330 ("r-r-utils" ,r-r-utils)))
17331 (home-page "https://github.com/HenrikBengtsson/R.huge")
17332 (synopsis "Methods for accessing huge amounts of data")
17334 "This is a deprecated package for accessing huge amounts of data.
17335 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17336 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17337 the @code{aroma.affymetrix} package.")
17338 (license license:lgpl2.1+)))
17340 (define-public r-r-filesets
17342 (name "r-r-filesets")
17347 (uri (cran-uri "R.filesets" version))
17350 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17351 (properties `((upstream-name . "R.filesets")))
17352 (build-system r-build-system)
17354 `(("r-digest" ,r-digest)
17355 ("r-r-cache" ,r-r-cache)
17356 ("r-r-methodss3" ,r-r-methodss3)
17358 ("r-r-utils" ,r-r-utils)))
17359 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17360 (synopsis "Easy handling of and access to files")
17362 "This package provides classes and methods to locate, setup, subset,
17363 navigate and iterate file sets, i.e. sets of files located in one or more
17364 directories on the file system. The API is designed such that these classes
17365 can be extended via inheritance to provide a richer API for special file
17366 formats. Moreover, a specific name format is defined such that filenames and
17367 directories can be considered to have full names which consists of a name
17368 followed by comma-separated tags. This adds additional flexibility to
17369 identify file sets and individual files.")
17370 (license license:lgpl2.1+)))
17372 (define-public r-r-devices
17374 (name "r-r-devices")
17379 (uri (cran-uri "R.devices" version))
17382 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17383 (properties `((upstream-name . "R.devices")))
17384 (build-system r-build-system)
17386 `(("r-base64enc" ,r-base64enc)
17387 ("r-r-methodss3" ,r-r-methodss3)
17389 ("r-r-utils" ,r-r-utils)))
17390 (home-page "https://github.com/HenrikBengtsson/R.devices")
17391 (synopsis "Unified handling of graphics devices")
17393 "This package provides functions for creating plots and image files in a
17394 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17395 Default device options as well as scales and aspect ratios are controlled in a
17396 uniform way across all device types. Switching output format requires minimal
17397 changes in code. This package is ideal for large-scale batch processing,
17398 because it will never leave open graphics devices or incomplete image files
17399 behind, even on errors or user interrupts.")
17400 (license license:lgpl2.1+)))
17402 (define-public r-acnr
17409 (uri (cran-uri "acnr" version))
17412 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17413 (properties `((upstream-name . "acnr")))
17414 (build-system r-build-system)
17415 (home-page "https://github.com/mpierrejean/acnr")
17416 (synopsis "Annotated copy-number regions")
17418 "This package provides SNP array data from different types of copy-number
17419 regions. These regions were identified manually by the authors of the package
17420 and may be used to generate realistic data sets with known truth.")
17421 (license license:lgpl2.1+)))
17423 (define-public r-acopula
17430 (uri (cran-uri "acopula" version))
17433 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17434 (properties `((upstream-name . "acopula")))
17435 (build-system r-build-system)
17436 (home-page "https://cran.r-project.org/web/packages/acopula/")
17437 (synopsis "Modelling dependence with multivariate Archimax copulas")
17439 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17440 package provides definitions of several parametric families of generator and
17441 dependence function, computes CDF and PDF, estimates parameters, tests for
17442 goodness of fit, generates random sample and checks copula properties for
17443 custom constructs. In the 2-dimensional case explicit formulas for density
17444 are used, contrary to higher dimensions when all derivatives are linearly
17445 approximated. Several non-archimax families (normal, FGM, Plackett) are
17446 provided as well.")
17447 (license license:gpl2)))
17449 (define-public r-tuner
17456 (uri (cran-uri "tuneR" version))
17459 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17460 (properties `((upstream-name . "tuneR")))
17461 (build-system r-build-system)
17462 (propagated-inputs `(("r-signal" ,r-signal)))
17463 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17464 (synopsis "Analysis of music and speech")
17466 "This is a package for the analysis of music and speech. Analyze music
17467 and speech, extract features like MFCCs, handle wave files and their
17468 representation in various ways, read MP3, read MIDI, perform steps of a
17469 transcription, ...")
17470 ;; Either of these versions.
17471 (license (list license:gpl2 license:gpl3))))
17473 (define-public r-seewave
17480 (uri (cran-uri "seewave" version))
17483 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17484 (properties `((upstream-name . "seewave")))
17485 (build-system r-build-system)
17487 `(("r-tuner" ,r-tuner)))
17488 (home-page "http://rug.mnhn.fr/seewave")
17489 (synopsis "Sound analysis and synthesis")
17491 "This package provides functions for analysing, manipulating, displaying,
17492 editing and synthesizing time waves (particularly sound). This package
17493 processes time analysis (oscillograms and envelopes), spectral content,
17494 resonance quality factor, entropy, cross correlation and autocorrelation,
17495 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17496 and 3D spectrograms and many other analyses.")
17497 (license license:gpl2+)))
17499 (define-public r-acousticndlcoder
17501 (name "r-acousticndlcoder")
17506 (uri (cran-uri "AcousticNDLCodeR" version))
17509 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17511 `((upstream-name . "AcousticNDLCodeR")))
17512 (build-system r-build-system)
17514 `(("r-seewave" ,r-seewave)
17515 ("r-tuner" ,r-tuner)
17517 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17518 (synopsis "Coding sound files for use with NDL")
17520 "Make acoustic cues to use with the R package @code{ndl}.
17521 The package implements functions used in the PLoS ONE paper \"Words from
17522 spontaneous conversational speech can be recognized with human-like accuracy
17523 by an error-driven learning algorithm that discriminates between meanings
17524 straight from smart acoustic features, bypassing the phoneme as recognition
17525 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17526 (license license:gpl2+)))
17528 (define-public r-acp
17535 (uri (cran-uri "acp" version))
17538 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17539 (properties `((upstream-name . "acp")))
17540 (build-system r-build-system)
17542 `(("r-quantmod" ,r-quantmod)
17543 ("r-tseries" ,r-tseries)))
17544 (home-page "https://cran.r-project.org/web/packages/acp/")
17545 (synopsis "Autoregressive conditional Poisson")
17547 "This package supports the analysis of count data exhibiting
17548 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17549 model (ACP(p,q)) proposed by Heinen (2003).")
17550 (license license:gpl2)))
17552 (define-public r-ada
17559 (uri (cran-uri "ada" version))
17562 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17563 (properties `((upstream-name . "ada")))
17564 (build-system r-build-system)
17565 (propagated-inputs `(("r-rpart" ,r-rpart)))
17566 (home-page "https://cran.r-project.org/web/packages/ada/")
17567 (synopsis "Stochastic boosting")
17569 "This package provides a straightforward, well-documented, and broad
17570 boosting routine for classification, ideally suited for small to
17571 moderate-sized data sets. It performs discrete, real, and gentle boost under
17572 both exponential and logistic loss on a given data set.")
17573 ;; Any version of the GPL.
17574 (license (list license:gpl2+ license:gpl3+))))
17576 (define-public r-genalg
17583 (uri (cran-uri "genalg" version))
17586 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17587 (properties `((upstream-name . "genalg")))
17588 (build-system r-build-system)
17589 (home-page "https://github.com/egonw/genalg")
17590 (synopsis "R based genetic algorithm")
17592 "This package provides an R based genetic algorithm for binary and
17593 floating point chromosomes.")
17594 (license license:gpl2)))
17596 (define-public r-kernelfactory
17598 (name "r-kernelfactory")
17603 (uri (cran-uri "kernelFactory" version))
17606 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17607 (properties `((upstream-name . "kernelFactory")))
17608 (build-system r-build-system)
17611 ("r-genalg" ,r-genalg)
17612 ("r-kernlab" ,r-kernlab)
17613 ("r-randomforest" ,r-randomforest)))
17614 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17615 (synopsis "Ensemble of kernel machines")
17617 "Kernel factory is an ensemble method where each base classifier (random
17618 forest) is fit on the kernel matrix of a subset of the training data.")
17619 (license license:gpl2+)))
17621 (define-public r-dummies
17628 (uri (cran-uri "dummies" version))
17631 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17632 (properties `((upstream-name . "dummies")))
17633 (build-system r-build-system)
17634 (home-page "http://www.decisionpatterns.com")
17635 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17637 "This package lets you expand factors, characters and other eligible
17638 classes into dummy/indicator variables.")
17639 (license license:gpl2+)))
17641 (define-public r-acrm
17648 (uri (cran-uri "aCRM" version))
17651 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17652 (properties `((upstream-name . "aCRM")))
17653 (build-system r-build-system)
17656 ("r-dummies" ,r-dummies)
17657 ("r-kernelfactory" ,r-kernelfactory)
17658 ("r-randomforest" ,r-randomforest)))
17659 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17660 (synopsis "Convenience functions for analytical customer relationship management")
17662 "This package provides convenience functions for data preparation and
17663 modeling often used in @dfn{analytical customer relationship
17664 management} (aCRM).")
17665 (license license:gpl2+)))
17667 (define-public r-treeclust
17669 (name "r-treeclust")
17674 (uri (cran-uri "treeClust" version))
17677 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
17678 (properties `((upstream-name . "treeClust")))
17679 (build-system r-build-system)
17681 `(("r-cluster" ,r-cluster)
17682 ("r-rpart" ,r-rpart)))
17683 (home-page "https://cran.r-project.org/web/packages/treeClust/")
17684 (synopsis "Cluster distances through trees")
17686 "This package provides tools to create a measure of inter-point
17687 dissimilarity useful for clustering mixed data, and, optionally, perform the
17689 (license license:gpl2+)))
17691 (define-public r-acrosstic
17693 (name "r-acrosstic")
17698 (uri (cran-uri "AcrossTic" version))
17701 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
17702 (properties `((upstream-name . "AcrossTic")))
17703 (build-system r-build-system)
17705 `(("r-lpsolve" ,r-lpsolve)
17706 ("r-treeclust" ,r-treeclust)))
17707 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
17708 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
17710 "This is a package for constructing minimum-cost regular spanning
17711 subgraph as part of a non-parametric two-sample test for equality of
17713 (license license:gpl2+)))
17715 (define-public r-acrt
17722 (uri (cran-uri "acrt" version))
17725 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
17726 (properties `((upstream-name . "acrt")))
17727 (build-system r-build-system)
17729 `(("r-rcpp" ,r-rcpp)
17730 ("r-rcppeigen" ,r-rcppeigen)
17731 ("r-sandwich" ,r-sandwich)))
17732 (home-page "https://cran.r-project.org/web/packages/acrt/")
17733 (synopsis "Autocorrelation robust testing")
17735 "This package provides functions for testing affine hypotheses on the
17736 regression coefficient vector in regression models with autocorrelated
17738 (license license:gpl2)))
17740 (define-public r-acs
17747 (uri (cran-uri "acs" version))
17750 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
17751 (properties `((upstream-name . "acs")))
17752 (build-system r-build-system)
17754 `(("r-httr" ,r-httr)
17757 ("r-stringr" ,r-stringr)
17759 (home-page "http://dusp.mit.edu/faculty/ezra-glenn")
17760 (synopsis "Work with data from the US Census")
17762 "This package provides a general toolkit for downloading, managing,
17763 analyzing, and presenting data from the
17764 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
17765 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
17766 American Community Survey (ACS). Confidence intervals provided with ACS data
17767 are converted to standard errors to be bundled with estimates in complex
17768 @code{acs} objects. The package provides new methods to conduct standard
17769 operations on @code{acs} objects and present/plot data in statistically
17770 appropriate ways.")
17771 (license license:gpl3)))
17773 (define-public r-acss-data
17775 (name "r-acss-data")
17780 (uri (cran-uri "acss.data" version))
17783 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
17784 (properties `((upstream-name . "acss.data")))
17785 (build-system r-build-system)
17786 (home-page "http://complexitycalculator.com/methodology.html")
17787 (synopsis "Data for algorithmic complexity of short strings")
17789 "This is a data only package providing the algorithmic complexity of
17790 short strings, computed using the coding theorem method. For a given set of
17791 symbols in a string, all possible or a large number of random samples of
17792 Turing machines with a given number of states (e.g., 5) and number of symbols
17793 corresponding to the number of symbols in the strings were simulated until
17794 they reached a halting state or failed to end. This package contains data on
17795 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
17796 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
17797 distribution of the halting states.")
17798 (license license:gpl2+)))
17800 (define-public r-acss
17807 (uri (cran-uri "acss" version))
17810 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
17811 (properties `((upstream-name . "acss")))
17812 (build-system r-build-system)
17814 `(("r-acss-data" ,r-acss-data)
17816 (home-page "http://complexitycalculator.com/methodology.html")
17817 (synopsis "Algorithmic complexity for short strings")
17819 "The main purpose of this package is to provide the algorithmic
17820 complexity for short strings, an approximation of the Kolmogorov Complexity of
17821 a short string using the coding theorem method. While the database containing
17822 the complexity is provided in the data only package @code{acss.data}, this
17823 package provides functions accessing the data such as @code{prob_random}
17824 returning the posterior probability that a given string was produced by a
17825 random process. In addition, two traditional (but problematic) measures of
17826 complexity are also provided: entropy and change complexity.")
17827 (license license:gpl2+)))
17829 (define-public r-acswr
17836 (uri (cran-uri "ACSWR" version))
17839 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
17840 (properties `((upstream-name . "ACSWR")))
17841 (build-system r-build-system)
17843 `(("r-mass" ,r-mass)))
17844 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
17845 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
17847 "This is a companion package for the book \"A Course in Statistics with
17848 R\" (ISBN 978-1-119-15272-9.)")
17849 (license license:gpl2)))
17851 (define-public r-alabama
17854 (version "2015.3-1")
17858 (uri (cran-uri "alabama" version))
17861 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
17862 (properties `((upstream-name . "alabama")))
17863 (build-system r-build-system)
17864 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
17865 (home-page "https://cran.r-project.org/web/packages/alabama/")
17866 (synopsis "Constrained nonlinear optimization")
17868 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
17869 Algorithm; it is used for optimizing smooth nonlinear objective functions with
17870 constraints. Linear or nonlinear equality and inequality constraints are
17872 (license license:gpl2+)))
17874 (define-public r-gdina
17881 (uri (cran-uri "GDINA" version))
17884 "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx"))))
17885 (properties `((upstream-name . "GDINA")))
17886 (build-system r-build-system)
17888 `(("r-alabama" ,r-alabama)
17889 ("r-ggplot2" ,r-ggplot2)
17891 ("r-nloptr" ,r-nloptr)
17892 ("r-numderiv" ,r-numderiv)
17894 ("r-rcpparmadillo" ,r-rcpparmadillo)
17895 ("r-rsolnp" ,r-rsolnp)
17896 ("r-shiny" ,r-shiny)
17897 ("r-shinydashboard" ,r-shinydashboard)))
17898 (home-page "https://github.com/Wenchao-Ma/GDINA")
17899 (synopsis "Generalized DINA model framework")
17901 "This package provides a set of psychometric tools for cognitive
17902 diagnosis modeling based on the generalized deterministic inputs, noisy and
17903 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
17904 and its extensions, including the sequential G-DINA model by Ma and de la
17905 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
17906 polytomous G-DINA model by Chen and de la Torre
17907 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
17908 distribution can be independent, saturated, higher-order, loglinear smoothed
17909 or structured. Q-matrix validation, item and model fit statistics, model
17910 comparison at test and item level and differential item functioning can also
17911 be conducted. A graphical user interface is also provided.")
17912 (license license:gpl3)))
17914 (define-public r-actcd
17921 (uri (cran-uri "ACTCD" version))
17924 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
17925 (properties `((upstream-name . "ACTCD")))
17926 (build-system r-build-system)
17928 `(("r-gdina" ,r-gdina)
17929 ("r-r-methodss3" ,r-r-methodss3)))
17931 `(("gfortran" ,gfortran)))
17932 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
17933 (synopsis "Asymptotic classification theory for cognitive diagnosis")
17935 "This is a package supporting cluster analysis for cognitive diagnosis
17936 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
17937 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
17938 sum-scores, cluster analysis techniques can be used to classify examinees into
17939 latent classes based on their attribute patterns. In addition to the
17940 algorithms used to classify data, three labeling approaches are proposed to
17941 label clusters so that examinees' attribute profiles can be obtained.")
17942 (license license:gpl2+)))
17944 (define-public r-ineq
17951 (uri (cran-uri "ineq" version))
17954 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
17955 (properties `((upstream-name . "ineq")))
17956 (build-system r-build-system)
17957 (home-page "https://cran.r-project.org/web/packages/ineq/")
17958 (synopsis "Measuring inequality, concentration, and poverty")
17960 "This package provides tools for measuring inequality, concentration, and
17961 poverty measures. It provides both empirical and theoretical Lorenz curves.")
17962 ;; Either of these two versions.
17963 (license (list license:gpl2 license:gpl3))))
17965 (define-public r-actfrag
17972 (uri (cran-uri "ActFrag" version))
17975 "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d"))))
17976 (properties `((upstream-name . "ActFrag")))
17977 (build-system r-build-system)
17979 `(("r-accelerometry" ,r-accelerometry)
17980 ("r-dplyr" ,r-dplyr)
17982 ("r-survival" ,r-survival)
17983 ("r-tidyr" ,r-tidyr)))
17984 (home-page "https://github.com/junruidi/ActFrag")
17985 (synopsis "Activity fragmentation metrics extraction")
17987 "This package provides functions to extract commonly used fragmentation
17988 metrics to quantify time accumulation strategies based on minute level
17989 actigraphy-measured activity counts data.")
17990 (license license:gpl3)))
17992 (define-public r-fda
17999 (uri (cran-uri "fda" version))
18002 "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2"))))
18003 (properties `((upstream-name . "fda")))
18004 (build-system r-build-system)
18006 `(("r-matrix" ,r-matrix)))
18007 (home-page "http://www.functionaldata.org")
18008 (synopsis "Functional data analysis")
18010 "These functions were developed to support functional data analysis as
18011 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18012 Analysis. The package includes data sets and script files working many
18014 (license license:gpl2+)))
18016 (define-public r-actigraphy
18018 (name "r-actigraphy")
18023 (uri (cran-uri "Actigraphy" version))
18026 "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574"))))
18027 (properties `((upstream-name . "Actigraphy")))
18028 (build-system r-build-system)
18031 ("r-sdmtools" ,r-sdmtools)))
18032 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18033 (synopsis "Actigraphy data analysis")
18035 "This package provides tools for functional linear modeling and analysis
18036 of actigraphy data.")
18037 (license license:asl2.0)))
18039 (define-public r-activedriver
18041 (name "r-activedriver")
18046 (uri (cran-uri "ActiveDriver" version))
18049 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18050 (properties `((upstream-name . "ActiveDriver")))
18051 (build-system r-build-system)
18053 `(("r-mass" ,r-mass)))
18054 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18055 (synopsis "Tools for finding cancer driver proteins")
18057 "This package provides a mutation analysis tool that discovers cancer
18058 driver genes with frequent mutations in protein signalling sites such as
18059 post-translational modifications (phosphorylation, ubiquitination, etc). The
18060 Poisson generalized linear regression model identifies genes where cancer
18061 mutations in signalling sites are more frequent than expected from the
18062 sequence of the entire gene. Integration of mutations with signalling
18063 information helps find new driver genes and propose candidate mechanisms to
18065 (license license:gpl2+)))
18067 (define-public r-activitycounts
18069 (name "r-activitycounts")
18074 (uri (cran-uri "activityCounts" version))
18077 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18079 `((upstream-name . "activityCounts")))
18080 (build-system r-build-system)
18082 `(("r-lubridate" ,r-lubridate)
18083 ("r-magrittr" ,r-magrittr)
18084 ("r-seewave" ,r-seewave)
18085 ("r-signal" ,r-signal)
18086 ("r-tibble" ,r-tibble)))
18087 (home-page "https://github.com/walkabillylab/activityCounts")
18088 (synopsis "Generate ActiLife counts")
18090 "ActiLife generates activity counts from data collected by Actigraph
18091 accelerometers. Actigraph is one of the most common research-grade
18092 accelerometers. There is considerable research validating and developing
18093 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18094 counts are proprietary and difficult to implement if researchers use different
18095 accelerometer brands. The code creates ActiLife counts from raw acceleration
18096 data for different accelerometer brands.")
18097 (license license:gpl3)))
18099 (define-public r-activityindex
18101 (name "r-activityindex")
18106 (uri (cran-uri "ActivityIndex" version))
18109 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18110 (properties `((upstream-name . "ActivityIndex")))
18111 (build-system r-build-system)
18113 `(("r-data-table" ,r-data-table)
18114 ("r-matrixstats" ,r-matrixstats)
18115 ("r-r-utils" ,r-r-utils)))
18116 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18117 (synopsis "Activity Index calculation using raw accelerometry data")
18119 "This is a package to read raw accelerometry from GT3X+ accelerometry
18120 data and plain table data to calculate the Activity Index from Bai et
18121 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18122 (license license:gpl3)))
18124 (define-public r-activpal
18126 (name "r-activpal")
18131 (uri (cran-uri "activPAL" version))
18134 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18135 (properties `((upstream-name . "activPAL")))
18136 (build-system r-build-system)
18138 `(("r-devtools" ,r-devtools)
18139 ("r-dplyr" ,r-dplyr)
18140 ("r-ggplot2" ,r-ggplot2)
18141 ("r-lubridate" ,r-lubridate)
18142 ("r-magrittr" ,r-magrittr)
18143 ("r-tidyr" ,r-tidyr)))
18144 (home-page "https://cran.r-project.org/web/packages/activPAL")
18145 (synopsis "Processing and chart generation from activPAL events files")
18147 "This package contains functions to generate pre-defined summary
18148 statistics from activPAL events files. The package also contains functions to
18149 produce informative graphics that visualize physical activity behaviour and
18150 trends. This includes generating graphs that align physical activity
18151 behaviour with additional time based observations described by other data
18152 sets, such as sleep diaries and continuous glucose monitoring data.")
18153 (license license:gpl3)))
18155 (define-public r-activpalprocessing
18157 (name "r-activpalprocessing")
18162 (uri (cran-uri "activpalProcessing" version))
18165 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18167 `((upstream-name . "activpalProcessing")))
18168 (build-system r-build-system)
18170 `(("r-chron" ,r-chron)))
18171 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18172 (synopsis "Process activPAL events files")
18174 "This package performs estimation of physical activity and sedentary
18175 behavior variables from activPAL events files.")
18176 ;; Either version of the GPL.
18177 (license (list license:gpl2 license:gpl3))))
18179 (define-public r-actogrammr
18181 (name "r-actogrammr")
18186 (uri (cran-uri "actogrammr" version))
18189 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18190 (properties `((upstream-name . "actogrammr")))
18191 (build-system r-build-system)
18193 `(("r-dplyr" ,r-dplyr)
18194 ("r-ggplot2" ,r-ggplot2)
18195 ("r-lubridate" ,r-lubridate)
18196 ("r-readr" ,r-readr)
18197 ("r-tidyr" ,r-tidyr)))
18198 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18199 (synopsis "Read in activity data and plot actograms")
18201 "Read in activity measurements from standard file formats used by
18202 circadian rhythm researchers, currently only ClockLab format, and process and
18203 plot the data. The central type of plot is the actogram, as first described
18204 in \"Activity and distribution of certain wild mice in relation to biotic
18205 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18206 (license license:gpl3)))
18208 (define-public r-expint
18215 (uri (cran-uri "expint" version))
18218 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18219 (properties `((upstream-name . "expint")))
18220 (build-system r-build-system)
18221 (home-page "https://gitlab.com/vigou3/expint")
18222 (synopsis "Exponential integral and incomplete Gamma function")
18224 "This package provides the exponential integrals @code{E_1(x)},
18225 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18226 function @code{G(a, x)} defined for negative values of its first argument.
18227 The package also gives easy access to the underlying C routines through an
18228 API; see the package vignette for details.")
18229 (license license:gpl2+)))
18231 (define-public r-actuar
18238 (uri (cran-uri "actuar" version))
18241 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18242 (properties `((upstream-name . "actuar")))
18243 (build-system r-build-system)
18244 (propagated-inputs `(("r-expint" ,r-expint)))
18245 (home-page "https://gitlab.com/vigou3/actuar")
18246 (synopsis "Actuarial functions and heavy tailed distributions")
18248 "This package provides functions and data sets for actuarial science:
18249 modeling of loss distributions; risk theory and ruin theory; simulation of
18250 compound models, discrete mixtures and compound hierarchical models;
18251 credibility theory. It boasts support for many additional probability
18252 distributions to model insurance loss amounts and loss frequency: 19
18253 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18254 distribution; zero-truncated and zero-modified extensions of the standard
18255 discrete distributions. It also supports phase-type distributions commonly
18256 used to compute ruin probabilities.")
18257 (license license:gpl2+)))
18259 (define-public r-bmp
18266 (uri (cran-uri "bmp" version))
18269 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18270 (properties `((upstream-name . "bmp")))
18271 (build-system r-build-system)
18272 (home-page "https://cran.r-project.org/web/packages/bmp/")
18273 (synopsis "Read Bitmap (BMP) images")
18275 "This package provides pure R tools to read BMP format images. It is
18276 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18277 (license license:gpl2+)))
18279 (define-public r-readbitmap
18281 (name "r-readbitmap")
18286 (uri (cran-uri "readbitmap" version))
18289 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18290 (properties `((upstream-name . "readbitmap")))
18291 (build-system r-build-system)
18293 `(("libjpeg" ,libjpeg)
18294 ("libpng" ,libpng)))
18299 ("r-tiff" ,r-tiff)))
18300 (home-page "https://github.com/jefferis/readbitmap")
18301 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18303 "This package provides tools to identify and read BMP, JPEG, PNG, and
18304 TIFF format bitmap images. Identification defaults to the use of the magic
18305 number embedded in the file rather than the file extension.")
18306 (license license:gpl2+)))
18308 (define-public r-imager
18315 (uri (cran-uri "imager" version))
18318 "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v"))))
18319 (properties `((upstream-name . "imager")))
18320 (build-system r-build-system)
18323 ("libtiff" ,libtiff)
18327 `(("r-cairo" ,r-cairo)
18328 ("r-downloader" ,r-downloader)
18329 ("r-igraph" ,r-igraph)
18331 ("r-magrittr" ,r-magrittr)
18334 ("r-purrr" ,r-purrr)
18336 ("r-readbitmap" ,r-readbitmap)
18337 ("r-stringr" ,r-stringr)))
18338 (native-inputs `(("pkg-config" ,pkg-config)))
18339 (home-page "http://dahtah.github.io/imager")
18340 (synopsis "Image processing library")
18342 "This is a package for fast image processing for images in up to 4
18343 dimensions (two spatial dimensions, one time/depth dimension, one color
18344 dimension). It provides most traditional image processing tools (filtering,
18345 morphology, transformations, etc.) as well as various functions for easily
18346 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18347 simple, modern C++ library for image processing.")
18348 (license license:lgpl3)))
18350 (define-public r-acuityview
18352 (name "r-acuityview")
18357 (uri (cran-uri "AcuityView" version))
18360 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18361 (properties `((upstream-name . "AcuityView")))
18362 (build-system r-build-system)
18364 `(("r-fftwtools" ,r-fftwtools)
18365 ("r-imager" ,r-imager)
18366 ("r-plotrix" ,r-plotrix)))
18367 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18368 (synopsis "Display scenes as seen by an animal with less acute vision")
18370 "This package provides a simple method for representing a visual scene as
18371 it may be seen by an animal with less acute vision.")
18372 (license license:gpl2+)))
18374 (define-public r-adabag
18381 (uri (cran-uri "adabag" version))
18384 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18385 (properties `((upstream-name . "adabag")))
18386 (build-system r-build-system)
18388 `(("r-caret" ,r-caret)
18389 ("r-doparallel" ,r-doparallel)
18390 ("r-foreach" ,r-foreach)
18391 ("r-rpart" ,r-rpart)))
18392 (home-page "https://cran.r-project.org/web/packages/adabag/")
18393 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18395 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18396 Breiman's Bagging algorithm using classification trees as individual
18397 classifiers. Once these classifiers have been trained, they can be used to
18398 predict on new data. Also, cross validation estimation of the error can be
18400 (license license:gpl2+)))
18402 (define-public r-adagio
18409 (uri (cran-uri "adagio" version))
18412 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18413 (properties `((upstream-name . "adagio")))
18414 (build-system r-build-system)
18415 (native-inputs `(("gfortran" ,gfortran)))
18416 (home-page "https://cran.r-project.org/web/packages/adagio/")
18417 (synopsis "Discrete and global optimization routines")
18419 "This package provides methods and algorithms for discrete optimization,
18420 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18421 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18423 (license license:gpl3+)))
18425 (define-public r-univoutl
18427 (name "r-univoutl")
18432 (uri (cran-uri "univOutl" version))
18435 "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
18436 (properties `((upstream-name . "univOutl")))
18437 (build-system r-build-system)
18439 `(("r-hmisc" ,r-hmisc)
18440 ("r-robustbase" ,r-robustbase)))
18441 (home-page "https://github.com/marcellodo/univOutl")
18442 (synopsis "Detection of univariate outliers")
18444 "This package provides well-known outlier detection techniques in the
18445 univariate case. Methods to deal with skewed distribution are included too.
18446 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18447 historical data is implemented as well. When available, survey weights can be
18448 used in outliers detection.")
18449 (license license:gpl2+)))
18451 (define-public r-tolerance
18453 (name "r-tolerance")
18458 (uri (cran-uri "tolerance" version))
18461 "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86"))))
18462 (properties `((upstream-name . "tolerance")))
18463 (build-system r-build-system)
18465 `(("r-rgl" ,r-rgl)))
18466 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18467 (synopsis "Statistical tolerance intervals and regions")
18469 "This package provides functions for estimating tolerance
18470 limits (intervals) for various univariate distributions (binomial, Cauchy,
18471 discrete Pareto, exponential, two-parameter exponential, extreme value,
18472 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18473 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18474 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18475 nonparametric tolerance intervals, tolerance bands for regression
18476 settings (linear regression, nonlinear regression, nonparametric regression,
18477 and multivariate regression), and analysis of variance tolerance intervals.
18478 Visualizations are also available for most of these settings.")
18479 (license license:gpl2+)))
18481 (define-public r-additivitytests
18483 (name "r-additivitytests")
18488 (uri (cran-uri "additivityTests" version))
18491 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18493 `((upstream-name . "additivityTests")))
18494 (build-system r-build-system)
18495 (home-page "https://github.com/simecek/additivityTests")
18496 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18498 "This package provides an implementation of the Tukey, Mandel,
18499 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18500 (license license:gpl3)))
18502 (define-public r-flexclust
18504 (name "r-flexclust")
18509 (uri (cran-uri "flexclust" version))
18512 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18513 (properties `((upstream-name . "flexclust")))
18514 (build-system r-build-system)
18516 `(("r-class" ,r-class)
18517 ("r-lattice" ,r-lattice)
18518 ("r-modeltools" ,r-modeltools)))
18519 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18520 (synopsis "Flexible cluster algorithms")
18522 "The main function @code{kcca} implements a general framework for
18523 k-centroids cluster analysis supporting arbitrary distance measures and
18524 centroid computation. Further cluster methods include hard competitive
18525 learning, neural gas, and QT clustering. There are numerous visualization
18526 methods for cluster results (neighborhood graphs, convex cluster hulls,
18527 barcharts of centroids, ...), and bootstrap methods for the analysis of
18528 cluster stability.")
18529 (license license:gpl2)))
18531 (define-public r-biclust
18538 (uri (cran-uri "biclust" version))
18541 "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0"))))
18542 (properties `((upstream-name . "biclust")))
18543 (build-system r-build-system)
18545 `(("r-additivitytests" ,r-additivitytests)
18546 ("r-colorspace" ,r-colorspace)
18547 ("r-flexclust" ,r-flexclust)
18548 ("r-ggplot2" ,r-ggplot2)
18549 ("r-lattice" ,r-lattice)
18551 ("r-tidyr" ,r-tidyr)))
18552 (home-page "https://cran.r-project.org/web/packages/biclust/")
18553 (synopsis "BiCluster algorithms")
18555 "The main function @code{biclust()} provides several algorithms to find
18556 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18557 In addition, the package provides methods for data
18558 preprocessing (normalization and discretization), visualization, and
18559 validation of bicluster solutions.")
18560 (license license:gpl3)))
18562 (define-public r-icge
18569 (uri (cran-uri "ICGE" version))
18572 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18573 (properties `((upstream-name . "ICGE")))
18574 (build-system r-build-system)
18576 `(("r-cluster" ,r-cluster)
18577 ("r-mass" ,r-mass)))
18578 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18579 (synopsis "Cluster estimation and identification of atypical units")
18581 "ICGE is a package that helps to estimate the number of real clusters in
18582 data as well as to identify atypical units. The underlying methods are based
18583 on distances rather than on unit x variables.")
18584 (license license:gpl2+)))
18586 (define-public r-depth
18589 (version "2.1-1.1")
18593 (uri (cran-uri "depth" version))
18596 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18597 (properties `((upstream-name . "depth")))
18598 (build-system r-build-system)
18600 `(("r-abind" ,r-abind)
18601 ("r-circular" ,r-circular)
18604 `(("gfortran" ,gfortran)))
18605 (home-page "https://cran.r-project.org/web/packages/depth/")
18606 (synopsis "Nonparametric depth functions for multivariate analysis")
18608 "This package provides tools for depth functions methodology applied to
18609 multivariate analysis. Besides allowing calculation of depth values and
18610 depth-based location estimators, the package includes functions or drawing
18611 contour plots and perspective plots of depth functions. Euclidian and
18612 spherical depths are supported.")
18613 (license license:gpl2)))
18615 (define-public r-archetypes
18617 (name "r-archetypes")
18618 (version "2.2-0.1")
18622 (uri (cran-uri "archetypes" version))
18625 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18626 (properties `((upstream-name . "archetypes")))
18627 (build-system r-build-system)
18629 `(("r-modeltools" ,r-modeltools)
18630 ("r-nnls" ,r-nnls)))
18631 (home-page "https://cran.r-project.org/web/packages/archetypes")
18632 (synopsis "Archetypal analysis")
18634 "The main function @code{archetypes} implements a framework for
18635 archetypal analysis supporting arbitrary problem solving mechanisms for the
18636 different conceptual parts of the algorithm.")
18637 (license license:gpl2+)))
18639 (define-public r-shapes
18646 (uri (cran-uri "shapes" version))
18649 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
18650 (properties `((upstream-name . "shapes")))
18651 (build-system r-build-system)
18653 `(("r-mass" ,r-mass)
18654 ("r-minpack-lm" ,r-minpack-lm)
18656 ("r-scatterplot3d" ,r-scatterplot3d)))
18657 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
18658 (synopsis "Statistical shape analysis")
18660 "This package provides routines for the statistical analysis of landmark
18661 shapes, including Procrustes analysis, graphical displays, principal
18662 components analysis, permutation and bootstrap tests, thin-plate spline
18663 transformation grids and comparing covariance matrices. See Dryden, I.L. and
18664 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
18665 Edition), John Wiley and Sons.")
18666 (license license:gpl2)))
18668 (define-public r-anthropometry
18670 (name "r-anthropometry")
18675 (uri (cran-uri "Anthropometry" version))
18678 "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
18679 (properties `((upstream-name . "Anthropometry")))
18680 (build-system r-build-system)
18682 `(("r-archetypes" ,r-archetypes)
18683 ("r-biclust" ,r-biclust)
18684 ("r-cluster" ,r-cluster)
18685 ("r-depth" ,r-depth)
18690 ("r-shapes" ,r-shapes)))
18691 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
18692 (synopsis "Statistical methods for anthropometric data")
18694 "This package provides statistical methods especially developed to
18695 analyze anthropometric data. These methods are aimed at providing effective
18696 solutions to some commons problems related to Ergonomics and Anthropometry.
18697 They are based on clustering, the statistical concept of data depth,
18698 statistical shape analysis and archetypal analysis.")
18699 (license license:gpl2+)))
18701 (define-public r-adamethods
18703 (name "r-adamethods")
18708 (uri (cran-uri "adamethods" version))
18711 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
18712 (properties `((upstream-name . "adamethods")))
18713 (build-system r-build-system)
18715 `(("r-anthropometry" ,r-anthropometry)
18716 ("r-archetypes" ,r-archetypes)
18718 ("r-foreach" ,r-foreach)
18720 ("r-tolerance" ,r-tolerance)
18721 ("r-univoutl" ,r-univoutl)))
18722 (home-page "https://cran.r-project.org/web/packages/adamethods/")
18723 (synopsis "Archetypoid algorithms and anomaly detection")
18725 "This package is a collection of several algorithms to obtain
18726 archetypoids with small and large databases and with both classical
18727 multivariate data and functional data (univariate and multivariate). Some of
18728 these algorithms also allow to detect anomalies (outliers).")
18729 (license license:gpl2+)))
18731 (define-public r-idpmisc
18738 (uri (cran-uri "IDPmisc" version))
18741 "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
18742 (properties `((upstream-name . "IDPmisc")))
18743 (build-system r-build-system)
18745 `(("r-lattice" ,r-lattice)))
18746 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
18747 (synopsis "Functions for data analyses and visualization")
18749 "This package provides different high-level graphics functions for
18750 displaying large datasets, displaying circular data in a very flexible way,
18751 finding local maxima, brewing color ramps, drawing nice arrows, zooming
18752 2D-plots, creating figures with differently colored margin and plot region.
18753 In addition, the package contains auxiliary functions for data manipulation
18754 like omitting observations with irregular values or selecting data by logical
18755 vectors, which include NAs. Other functions are especially useful in
18756 spectroscopy and analyses of environmental data: robust baseline fitting,
18757 finding peaks in spectra, converting humidity measures.")
18758 (license license:gpl3+)))
18760 (define-public r-qqman
18767 (uri (cran-uri "qqman" version))
18770 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
18771 (properties `((upstream-name . "qqman")))
18772 (build-system r-build-system)
18774 `(("r-calibrate" ,r-calibrate)))
18775 (home-page "https://cran.r-project.org/web/packages/qqman/")
18776 (synopsis "Q-Q and Manhattan plots for GWAS data")
18778 "This package allows you to create Q-Q and Manhattan plots for GWAS data
18779 from PLINK results.")
18780 (license license:gpl3)))
18782 (define-public r-ggplot-multistats
18784 (name "r-ggplot-multistats")
18789 (uri (cran-uri "ggplot.multistats" version))
18792 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
18794 `((upstream-name . "ggplot.multistats")))
18795 (build-system r-build-system)
18797 `(("r-ggplot2" ,r-ggplot2)
18798 ("r-hexbin" ,r-hexbin)
18799 ("r-rlang" ,r-rlang)
18800 ("r-scales" ,r-scales)))
18801 (home-page "https://github.com/flying-sheep/ggplot.multistats")
18802 (synopsis "Multiple summary statistics for binned stats/geometries")
18804 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
18805 which functions similar to its singular form, but allows the use of multiple
18806 statistics per bin. Those statistics can be mapped to multiple bin
18808 (license license:gpl3)))
18810 (define-public r-knn-covertree
18812 (name "r-knn-covertree")
18817 (uri (cran-uri "knn.covertree" version))
18820 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
18821 (properties `((upstream-name . "knn.covertree")))
18822 (build-system r-build-system)
18824 `(("r-matrix" ,r-matrix)
18826 ("r-rcppeigen" ,r-rcppeigen)))
18827 (home-page "https://github.com/flying-sheep/knn.covertree")
18828 (synopsis "Accurate kNN Implementation with multiple distance measures")
18830 "Similarly to the FNN package, this package allows calculation of the k
18831 nearest neighbors (kNN) of a data matrix. The implementation is based on
18832 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
18833 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
18834 (license license:agpl3+)))
18836 (define-public r-poibin
18843 (uri (cran-uri "poibin" version))
18846 "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2"))))
18847 (properties `((upstream-name . "poibin")))
18848 (build-system r-build-system)
18849 (home-page "https://cran.r-project.org/web/packages/poibin/")
18850 (synopsis "Poisson binomial distribution")
18852 "This package provides an implementation of both the exact and
18853 approximation methods for computing the @dfn{cumulative distribution
18854 function} (CDF) of the Poisson binomial distribution. It also provides the
18855 @dfn{probability mass function} (PMF), quantile function, and random number
18856 generation for the Poisson binomial distribution.")
18857 (license license:gpl2)))
18859 (define-public r-diagram
18866 (uri (cran-uri "diagram" version))
18869 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
18870 (properties `((upstream-name . "diagram")))
18871 (build-system r-build-system)
18873 `(("r-shape" ,r-shape)))
18874 (home-page "https://cran.r-project.org/web/packages/diagram/")
18875 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
18877 "This package provides tools to visualize simple graphs (networks) based
18878 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
18879 electrical networks, etc. It also includes supporting material for the book
18880 \"A practical guide to ecological modelling - using R as a simulation
18881 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
18882 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
18883 Francesca Mazzia (2012).")
18884 (license license:gpl2+)))
18886 (define-public r-lim
18893 (uri (cran-uri "LIM" version))
18896 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
18897 (properties `((upstream-name . "LIM")))
18898 (build-system r-build-system)
18900 `(("r-diagram" ,r-diagram)
18901 ("r-limsolve" ,r-limsolve)))
18902 (home-page "https://cran.r-project.org/web/packages/LIM/")
18903 (synopsis "Linear inverse model examples and solution methods")
18905 "This package provides functions that read and solve linear inverse
18906 problems (food web problems, linear programming problems).")
18907 (license license:gpl2+)))
18909 (define-public r-shinycssloaders
18911 (name "r-shinycssloaders")
18916 (uri (cran-uri "shinycssloaders" version))
18919 "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4"))))
18921 `((upstream-name . "shinycssloaders")))
18922 (build-system r-build-system)
18924 `(("r-digest" ,r-digest)
18926 ("r-shiny" ,r-shiny)))
18927 (home-page "https://github.com/andrewsali/shinycssloaders")
18928 (synopsis "Add CSS loading animations to Shiny outputs")
18930 "This package provides tools to create a lightweight Shiny wrapper for
18931 the css-loaders created by Luke Hass
18932 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
18933 automatically show a loader when the output is (re)calculating.")
18934 (license license:gpl3)))
18936 (define-public r-rsvg
18943 (uri (cran-uri "rsvg" version))
18946 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
18947 (properties `((upstream-name . "rsvg")))
18948 (build-system r-build-system)
18950 `(("librsvg" ,librsvg)
18953 `(("pkg-config" ,pkg-config)))
18954 (home-page "https://github.com/jeroen/rsvg#readme")
18955 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
18957 "This package allows you to render vector-based SVG images into
18958 high-quality custom-size bitmap arrays using the librsvg2 library. The
18959 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
18960 addition, the package can convert images directly to various formats such as
18961 PDF or PostScript.")
18962 (license license:expat)))
18964 (define-public r-influencer
18966 (name "r-influencer")
18971 (uri (cran-uri "influenceR" version))
18974 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
18975 (properties `((upstream-name . "influenceR")))
18976 (build-system r-build-system)
18978 `(("r-igraph" ,r-igraph)
18979 ("r-matrix" ,r-matrix)))
18980 (home-page "https://github.com/rcc-uchicago/influenceR")
18981 (synopsis "Tools to quantify structural importance of nodes in a network")
18983 "This package provides functionality to compute various node centrality
18984 measures on networks. Included are functions to compute betweenness
18985 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
18986 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
18987 algorithm to identify key players, and Valente's bridging metric. The
18988 betweenness, Key Players, and bridging implementations are parallelized with
18990 (license license:gpl2)))