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@posteo.net>
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 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
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 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
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-bbmle
2371 (uri (cran-uri "bbmle" version))
2374 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2375 (build-system r-build-system)
2377 `(("r-lattice" ,r-lattice)
2379 ("r-numderiv" ,r-numderiv)))
2380 (home-page "https://cran.r-project.org/web/packages/bbmle")
2381 (synopsis "Tools for General Maximum Likelihood Estimation")
2383 "This package provides methods and functions for fitting maximum
2384 likelihood models in R. This package modifies and extends the @code{mle}
2385 classes in the @code{stats4} package.")
2386 ;; Any version of the GPL
2387 (license license:gpl2+)))
2389 (define-public r-emdbook
2396 (uri (cran-uri "emdbook" version))
2399 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2400 (build-system r-build-system)
2402 `(("r-bbmle" ,r-bbmle)
2404 ("r-lattice" ,r-lattice)
2407 ("r-rcpp" ,r-rcpp)))
2408 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2409 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2411 "This package provides auxiliary functions and data sets for \"Ecological
2412 Models and Data\", a book presenting maximum likelihood estimation and related
2413 topics for ecologists (ISBN 978-0-691-12522-0).")
2415 (license (list license:gpl2 license:gpl3))))
2417 (define-public r-lpsolve
2420 (version "5.6.13.3")
2424 (uri (cran-uri "lpSolve" version))
2427 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2428 (properties `((upstream-name . "lpSolve")))
2429 (build-system r-build-system)
2430 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2431 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2433 "Lp_solve is software for solving linear, integer and mixed integer
2434 programs. This implementation supplies a \"wrapper\" function in C and some R
2435 functions that solve general linear/integer problems, assignment problems, and
2436 transportation problems.")
2437 (license license:lgpl2.0)))
2439 (define-public r-limsolve
2446 (uri (cran-uri "limSolve" version))
2449 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2450 (properties `((upstream-name . "limSolve")))
2451 (build-system r-build-system)
2453 `(("r-lpsolve" ,r-lpsolve)
2455 ("r-quadprog" ,r-quadprog)))
2456 (native-inputs `(("gfortran" ,gfortran)))
2457 (home-page "https://cran.r-project.org/web/packages/limSolve")
2458 (synopsis "Solving linear inverse models")
2460 "This package provides functions that:
2463 @item find the minimum/maximum of a linear or quadratic function,
2464 @item sample an underdetermined or overdetermined system,
2465 @item solve a linear system Ax=B for the unknown x.
2468 It includes banded and tridiagonal linear systems. The package calls Fortran
2469 functions from LINPACK.")
2471 (license (list license:gpl2+ license:gpl3+))))
2473 (define-public r-fitdistrplus
2475 (name "r-fitdistrplus")
2480 (uri (cran-uri "fitdistrplus" version))
2483 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2484 (build-system r-build-system)
2486 `(("r-mass" ,r-mass)
2487 ("r-npsurv" ,r-npsurv)
2488 ("r-survival" ,r-survival)))
2489 (home-page "http://riskassessment.r-forge.r-project.org")
2490 (synopsis "Fitting a parametric distribution from data")
2492 "This package extends the @code{fitdistr} function of the MASS package
2493 with several functions to help the fit of a parametric distribution to
2494 non-censored or censored data. Censored data may contain left-censored,
2495 right-censored and interval-censored values, with several lower and upper
2496 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2497 provides moment matching (MME), quantile matching (QME) and maximum
2498 goodness-of-fit estimation (MGE) methods (available only for non-censored
2499 data). Weighted versions of MLE, MME and QME are available.")
2500 (license license:gpl2+)))
2502 (define-public r-energy
2509 (uri (cran-uri "energy" version))
2512 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2513 (build-system r-build-system)
2515 `(("r-boot" ,r-boot)
2516 ("r-rcpp" ,r-rcpp)))
2517 (home-page "https://cran.r-project.org/web/packages/energy")
2518 (synopsis "Multivariate inference via the energy of data")
2520 "This package provides e-statistics (energy) tests and statistics for
2521 multivariate and univariate inference, including distance correlation,
2522 one-sample, two-sample, and multi-sample tests for comparing multivariate
2523 distributions, are implemented. Measuring and testing multivariate
2524 independence based on distance correlation, partial distance correlation,
2525 multivariate goodness-of-fit tests, clustering based on energy distance,
2526 testing for multivariate normality, distance components (disco) for
2527 non-parametric analysis of structured data, and other energy
2528 statistics/methods are implemented.")
2529 (license license:gpl2+)))
2531 (define-public r-suppdists
2533 (name "r-suppdists")
2538 (uri (cran-uri "SuppDists" version))
2541 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2542 (properties `((upstream-name . "SuppDists")))
2543 (build-system r-build-system)
2544 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2545 (synopsis "Supplementary distributions")
2547 "This package provides ten distributions supplementing those built into
2548 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2549 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2550 coefficient, Johnson distributions, normal scores and generalized
2551 hypergeometric distributions. In addition two random number generators of
2552 George Marsaglia are included.")
2553 (license license:gpl2+)))
2555 (define-public r-ksamples
2562 (uri (cran-uri "kSamples" version))
2565 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2566 (properties `((upstream-name . "kSamples")))
2567 (build-system r-build-system)
2569 `(("r-suppdists" ,r-suppdists)))
2570 (home-page "https://cran.r-project.org/web/packages/kSamples")
2571 (synopsis "K-Sample rank tests and their combinations")
2573 "This package provides tools to compares k samples using the
2574 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2575 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2576 test. It computes asymptotic, simulated or (limited) exact P-values, all
2577 valid under randomization, with or without ties, or conditionally under random
2578 sampling from populations, given the observed tie pattern. Except for Steel's
2579 test and the JT test it also combines these tests across several blocks of
2581 (license license:gpl2+)))
2583 (define-public r-cvst
2590 (uri (cran-uri "CVST" version))
2593 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2594 (properties `((upstream-name . "CVST")))
2595 (build-system r-build-system)
2597 `(("r-kernlab" ,r-kernlab)
2598 ("r-matrix" ,r-matrix)))
2599 (home-page "https://cran.r-project.org/web/packages/CVST")
2600 (synopsis "Fast cross-validation via sequential testing")
2602 "This package implements the fast cross-validation via sequential
2603 testing (CVST) procedure. CVST is an improved cross-validation procedure
2604 which uses non-parametric testing coupled with sequential analysis to
2605 determine the best parameter set on linearly increasing subsets of the data.
2606 Additionally to the CVST the package contains an implementation of the
2607 ordinary k-fold cross-validation with a flexible and powerful set of helper
2608 objects and methods to handle the overall model selection process. The
2609 implementations of the Cochran's Q test with permutations and the sequential
2610 testing framework of Wald are generic and can therefore also be used in other
2612 (license license:gpl2+)))
2614 (define-public r-squarem
2617 (version "2017.10-1")
2621 (uri (cran-uri "SQUAREM" version))
2624 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2625 (properties `((upstream-name . "SQUAREM")))
2626 (build-system r-build-system)
2627 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2628 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2630 "This package provides algorithms for accelerating the convergence of
2631 slow, monotone sequences from smooth, contraction mapping such as the EM
2632 algorithm. It can be used to accelerate any smooth, linearly convergent
2633 acceleration scheme. A tutorial style introduction to this package is
2634 available in a vignette.")
2635 (license license:gpl2+)))
2637 (define-public r-lava
2644 (uri (cran-uri "lava" version))
2647 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2648 (build-system r-build-system)
2650 `(("r-numderiv" ,r-numderiv)
2651 ("r-squarem" ,r-squarem)
2652 ("r-survival" ,r-survival)))
2653 (home-page "https://github.com/kkholst/lava")
2654 (synopsis "Latent variable models")
2656 "This package provides tools for the estimation and simulation of latent
2658 (license license:gpl3)))
2660 (define-public r-drr
2667 (uri (cran-uri "DRR" version))
2670 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2671 (properties `((upstream-name . "DRR")))
2672 (build-system r-build-system)
2674 `(("r-cvst" ,r-cvst)
2675 ("r-kernlab" ,r-kernlab)
2676 ("r-matrix" ,r-matrix)))
2677 (home-page "https://cran.r-project.org/web/packages/DRR")
2678 (synopsis "Dimensionality reduction via regression")
2680 "This package provides an implementation of dimensionality reduction via
2681 regression using Kernel Ridge Regression.")
2682 (license license:gpl3)))
2684 (define-public r-prodlim
2687 (version "2019.11.13")
2691 (uri (cran-uri "prodlim" version))
2694 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2695 (build-system r-build-system)
2697 `(("r-kernsmooth" ,r-kernsmooth)
2700 ("r-survival" ,r-survival)))
2701 (home-page "https://cran.r-project.org/web/packages/prodlim")
2702 (synopsis "Product-limit estimation for censored event history analysis")
2704 "This package provides a fast and user-friendly implementation of
2705 nonparametric estimators for censored event history (survival) analysis with
2706 the Kaplan-Meier and Aalen-Johansen methods.")
2707 (license license:gpl2+)))
2709 (define-public r-dimred
2716 (uri (cran-uri "dimRed" version))
2719 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2720 (properties `((upstream-name . "dimRed")))
2721 (build-system r-build-system)
2724 ("r-magrittr" ,r-magrittr)))
2725 (home-page "https://github.com/gdkrmr/dimRed")
2726 (synopsis "Framework for dimensionality reduction")
2728 "This package provides a collection of dimensionality reduction
2729 techniques from R packages and provides a common interface for calling the
2731 (license license:gpl3)))
2733 (define-public r-timedate
2736 (version "3043.102")
2740 (uri (cran-uri "timeDate" version))
2743 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2744 (properties `((upstream-name . "timeDate")))
2745 (build-system r-build-system)
2746 (home-page "https://www.rmetrics.org")
2747 (synopsis "Chronological and calendar objects")
2749 "This package provides an environment for teaching \"Financial
2750 Engineering and Computational Finance\" and for managing chronological and
2752 (license license:gpl2+)))
2754 (define-public r-magic
2761 (uri (cran-uri "magic" version))
2764 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2765 (build-system r-build-system)
2767 `(("r-abind" ,r-abind)))
2768 (home-page "https://github.com/RobinHankin/magic.git")
2769 (synopsis "Create and investigate magic squares")
2771 "This package provides a collection of efficient, vectorized algorithms
2772 for the creation and investigation of magic squares and hypercubes, including
2773 a variety of functions for the manipulation and analysis of arbitrarily
2774 dimensioned arrays.")
2775 (license license:gpl2)))
2777 (define-public r-rmysql
2784 (uri (cran-uri "RMySQL" version))
2787 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2788 (properties `((upstream-name . "RMySQL")))
2789 (build-system r-build-system)
2791 `(("mariadb" ,mariadb "lib")
2792 ("mariadb-dev" ,mariadb "dev")
2795 `(("r-dbi" ,r-dbi)))
2796 (home-page "https://github.com/r-dbi/RMySQL")
2797 (synopsis "Database interface and MySQL driver for R")
2799 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2800 package contains an old implementation based on legacy code from S-PLUS which
2801 is being phased out. A modern MySQL client based on Rcpp is available from
2802 the RMariaDB package.")
2803 (license license:gpl2)))
2805 (define-public r-rpostgresql
2807 (name "r-rpostgresql")
2812 (uri (cran-uri "RPostgreSQL" version))
2815 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2816 (properties `((upstream-name . "RPostgreSQL")))
2817 (build-system r-build-system)
2819 `(("postgresql" ,postgresql)))
2821 `(("r-dbi" ,r-dbi)))
2822 (home-page "https://github.com/tomoakin/RPostgreSQL")
2823 (synopsis "R interface to the PostgreSQL database system")
2825 "This package provides a Database Interface (DBI) compliant driver for R
2826 to access PostgreSQL database systems.")
2827 ;; The whole package is released under GPL version 2. It includes code
2828 ;; under the PostgreSQL license.
2829 (license license:gpl2)))
2831 (define-public r-linprog
2838 (uri (cran-uri "linprog" version))
2841 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2842 (build-system r-build-system)
2843 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2844 (home-page "http://linprog.r-forge.r-project.org/")
2845 (synopsis "Linear programming and optimization")
2847 "This package can be used to solve Linear Programming / Linear
2848 Optimization problems by using the simplex algorithm.")
2849 (license license:gpl2+)))
2851 (define-public r-geometry
2858 (uri (cran-uri "geometry" version))
2861 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2862 (build-system r-build-system)
2864 `(("r-magic" ,r-magic)
2865 ("r-linprog" ,r-linprog)
2866 ("r-lpsolve" ,r-lpsolve)
2868 ("r-rcppprogress" ,r-rcppprogress)))
2869 (home-page "http://geometry.r-forge.r-project.org/")
2870 (synopsis "Mesh generation and surface tesselation")
2872 "This package makes the qhull library available in R, in a similar manner
2873 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2874 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2875 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2876 and higher dimensions. It implements the Quickhull algorithm for computing
2877 the convex hull. Qhull does not support constrained Delaunay triangulations,
2878 or mesh generation of non-convex objects, but the package does include some R
2879 functions that allow for this. Currently the package only gives access to
2880 Delaunay triangulation and convex hull computation.")
2881 ;; The Qhull sources are included and are distributed under a custom
2882 ;; non-copyleft license. The R sources are released under GPL version 2.
2883 (license (list license:gpl2
2884 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2886 (define-public r-ddalpha
2893 (uri (cran-uri "ddalpha" version))
2896 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2897 (build-system r-build-system)
2900 ("r-class" ,r-class)
2901 ("r-geometry" ,r-geometry)
2904 ("r-robustbase" ,r-robustbase)
2905 ("r-sfsmisc" ,r-sfsmisc)))
2907 `(("gfortran" ,gfortran)))
2908 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2909 (synopsis "Depth-Based classification and calculation of data depth")
2911 "This package contains procedures for depth-based supervised learning,
2912 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2913 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2914 statistical depth function to a compact low-dimensional space, where the final
2915 classification is done. It also offers an extension to functional data and
2916 routines for calculating certain notions of statistical depth functions. 50
2917 multivariate and 5 functional classification problems are included.")
2918 (license license:gpl2)))
2920 (define-public r-gower
2927 (uri (cran-uri "gower" version))
2930 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2931 (build-system r-build-system)
2932 (home-page "https://github.com/markvanderloo/gower")
2933 (synopsis "Gower's distance")
2935 "This package provides tools to compute Gower's distance (or similarity)
2936 coefficient between records, and to compute the top-n matches between records.
2937 Core algorithms are executed in parallel on systems supporting OpenMP.")
2938 (license license:gpl3)))
2940 (define-public r-rcpproll
2947 (uri (cran-uri "RcppRoll" version))
2950 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2951 (properties `((upstream-name . "RcppRoll")))
2952 (build-system r-build-system)
2954 `(("r-rcpp" ,r-rcpp)))
2955 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2956 (synopsis "Efficient rolling and windowed operations")
2958 "This package provides fast and efficient routines for common rolling /
2959 windowed operations. Routines for the efficient computation of windowed mean,
2960 median, sum, product, minimum, maximum, standard deviation and variance are
2962 (license license:gpl2+)))
2964 (define-public r-ipred
2971 (uri (cran-uri "ipred" version))
2974 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2975 (build-system r-build-system)
2977 `(("r-class" ,r-class)
2980 ("r-prodlim" ,r-prodlim)
2981 ("r-rpart" ,r-rpart)
2982 ("r-survival" ,r-survival)))
2983 (home-page "https://cran.r-project.org/web/packages/ipred")
2984 (synopsis "Improved predictors")
2986 "This package provides improved predictive models by indirect
2987 classification and bagging for classification, regression and survival
2988 problems as well as resampling based estimators of prediction error.")
2989 (license license:gpl2+)))
2991 (define-public r-psych
2998 (uri (cran-uri "psych" version))
3001 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
3002 (build-system r-build-system)
3004 `(("r-foreign" ,r-foreign)
3005 ("r-lattice" ,r-lattice)
3006 ("r-mnormt" ,r-mnormt)
3007 ("r-nlme" ,r-nlme)))
3008 (home-page "https://cran.r-project.org/web/packages/psych/")
3009 (synopsis "Procedures for psychological, psychometric, and personality research")
3011 "This package provides a general purpose toolbox for personality,
3012 psychometric theory and experimental psychology. Functions are primarily for
3013 multivariate analysis and scale construction using factor analysis, principal
3014 component analysis, cluster analysis and reliability analysis, although others
3015 provide basic descriptive statistics. Item Response Theory is done using
3016 factor analysis of tetrachoric and polychoric correlations. Functions for
3017 analyzing data at multiple levels include within and between group statistics,
3018 including correlations and factor analysis. Functions for simulating and
3019 testing particular item and test structures are included. Several functions
3020 serve as a useful front end for structural equation modeling. Graphical
3021 displays of path diagrams, factor analysis and structural equation models are
3022 created using basic graphics.")
3023 (license license:gpl2+)))
3025 (define-public r-generics
3032 (uri (cran-uri "generics" version))
3035 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3036 (build-system r-build-system)
3037 (home-page "https://github.com/r-lib/generics")
3038 (synopsis "Common S3 generics not provided by base R methods")
3040 "In order to reduce potential package dependencies and conflicts,
3041 generics provides a number of commonly used S3 generics that are not provided
3042 by base R methods related to model fitting.")
3043 (license license:gpl2)))
3045 (define-public r-broom
3052 (uri (cran-uri "broom" version))
3055 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
3056 (build-system r-build-system)
3058 `(("r-backports" ,r-backports)
3059 ("r-dplyr" ,r-dplyr)
3060 ("r-generics" ,r-generics)
3062 ("r-purrr" ,r-purrr)
3063 ("r-reshape2" ,r-reshape2)
3064 ("r-stringr" ,r-stringr)
3065 ("r-tibble" ,r-tibble)
3066 ("r-tidyr" ,r-tidyr)))
3067 (home-page "https://github.com/tidyverse/broom")
3068 (synopsis "Convert statistical analysis objects into tidy data frames")
3070 "This package provides tools to convert statistical analysis objects from
3071 R into tidy data frames, so that they can more easily be combined, reshaped
3072 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3073 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3074 summarizes a model's statistical findings such as coefficients of a
3075 regression; @code{augment}, which adds columns to the original data such as
3076 predictions, residuals and cluster assignments; and @code{glance}, which
3077 provides a one-row summary of model-level statistics.")
3078 (license license:expat)))
3080 (define-public r-recipes
3087 (uri (cran-uri "recipes" version))
3090 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
3091 (build-system r-build-system)
3093 `(("r-dplyr" ,r-dplyr)
3094 ("r-generics" ,r-generics)
3096 ("r-gower" ,r-gower)
3097 ("r-ipred" ,r-ipred)
3098 ("r-lubridate" ,r-lubridate)
3099 ("r-magrittr" ,r-magrittr)
3100 ("r-matrix" ,r-matrix)
3101 ("r-purrr" ,r-purrr)
3102 ("r-rlang" ,r-rlang)
3103 ("r-tibble" ,r-tibble)
3104 ("r-tidyr" ,r-tidyr)
3105 ("r-tidyselect" ,r-tidyselect)
3106 ("r-timedate" ,r-timedate)
3107 ("r-withr" ,r-withr)))
3108 (home-page "https://github.com/topepo/recipes")
3109 (synopsis "Preprocessing tools to create design matrices")
3111 "Recipes is an extensible framework to create and preprocess design
3112 matrices. Recipes consist of one or more data manipulation and analysis
3113 \"steps\". Statistical parameters for the steps can be estimated from an
3114 initial data set and then applied to other data sets. The resulting design
3115 matrices can then be used as inputs into statistical or machine learning
3117 (license license:gpl2)))
3119 (define-public r-pdist
3126 (uri (cran-uri "pdist" version))
3129 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3130 (build-system r-build-system)
3131 (home-page "https://github.com/jeffwong/pdist")
3132 (synopsis "Partitioned distance function")
3134 "Pdist computes the euclidean distance between rows of a matrix X and
3135 rows of another matrix Y. Previously, this could be done by binding the two
3136 matrices together and calling @code{dist}, but this creates unnecessary
3137 computation by computing the distances between a row of X and another row of
3138 X, and likewise for Y. Pdist strictly computes distances across the two
3139 matrices, not within the same matrix, making computations significantly faster
3140 for certain use cases.")
3141 (license license:gpl3+)))
3143 (define-public r-ggrepel
3150 (uri (cran-uri "ggrepel" version))
3153 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3154 (build-system r-build-system)
3156 `(("r-ggplot2" ,r-ggplot2)
3158 ("r-scales" ,r-scales)))
3159 (home-page "http://github.com/slowkow/ggrepel")
3160 (synopsis "Repulsive text and label geometries for ggplot2")
3162 "This package provides text and label geometries for ggplot2 that help to
3163 avoid overlapping text labels. Labels repel away from each other and away
3164 from the data points.")
3165 (license license:gpl3)))
3167 (define-public r-corrplot
3174 (uri (cran-uri "corrplot" version))
3177 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3178 (build-system r-build-system)
3179 (home-page "https://github.com/taiyun/corrplot")
3180 (synopsis "Visualization of a correlation matrix")
3182 "This package provides a graphical display of a correlation matrix or
3183 general matrix. It also contains some algorithms to do matrix reordering. In
3184 addition, corrplot is good at details, including choosing color, text labels,
3185 color labels, layout, etc.")
3186 ;; Any version of the GPL
3187 (license license:gpl2+)))
3189 (define-public r-stringdist
3191 (name "r-stringdist")
3196 (uri (cran-uri "stringdist" version))
3198 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3199 (build-system r-build-system)
3200 (home-page "https://github.com/markvanderloo/stringdist")
3201 (synopsis "Approximate string matching and string distance functions")
3203 "This package implements an approximate string matching version of R's
3204 native @code{match} function. It can calculate various string distances based
3205 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3206 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3207 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3208 can be computed between character vectors while taking proper care of encoding
3209 or between integer vectors representing generic sequences.")
3210 (license license:gpl3+)))
3212 (define-public r-ucminf
3219 (uri (cran-uri "ucminf" version))
3222 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3223 (build-system r-build-system)
3224 (native-inputs `(("gfortran" ,gfortran)))
3225 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3226 (synopsis "General-purpose unconstrained non-linear optimization")
3228 "This package provides an implementation of an algorithm for
3229 general-purpose unconstrained non-linear optimization. The algorithm is of
3230 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3231 search with a trust region type monitoring of the input to the line search
3232 algorithm. The interface of @code{ucminf} is designed for easy interchange
3233 with the package @code{optim}.")
3234 (license license:gpl2+)))
3236 (define-public r-ordinal
3239 (version "2019.4-25")
3243 (uri (cran-uri "ordinal" version))
3246 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3247 (build-system r-build-system)
3249 `(("r-mass" ,r-mass)
3250 ("r-matrix" ,r-matrix)
3251 ("r-numderiv" ,r-numderiv)
3252 ("r-ucminf" ,r-ucminf)))
3253 (home-page "https://github.com/runehaubo/ordinal")
3254 (synopsis "Regression models for ordinal data")
3256 "This package provides an implementation of cumulative link (mixed)
3257 models also known as ordered regression models, proportional odds models,
3258 proportional hazards models for grouped survival times and ordered models.
3259 Estimation is via maximum likelihood and mixed models are fitted with the
3260 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3261 (license license:gpl2+)))
3263 (define-public r-jomo
3270 (uri (cran-uri "jomo" version))
3273 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3274 (build-system r-build-system)
3276 `(("r-lme4" ,r-lme4)
3278 ("r-ordinal" ,r-ordinal)
3279 ("r-survival" ,r-survival)))
3280 (home-page "https://cran.r-project.org/web/packages/jomo/")
3281 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3283 "Similarly to Schafer's package pan, jomo is a package for multilevel
3284 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3285 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3286 possibility of handling binary and categorical data through latent normal
3287 variables, the option to use cluster-specific covariance matrices and to
3288 impute compatibly with the substantive model.")
3289 (license license:gpl2)))
3291 (define-public r-pan
3298 (uri (cran-uri "pan" version))
3301 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3302 (build-system r-build-system)
3303 (native-inputs `(("gfortran" ,gfortran)))
3304 (home-page "https://cran.r-project.org/web/packages/pan/")
3305 (synopsis "Multiple imputation for multivariate panel or clustered data")
3307 "This package implements multiple imputation for multivariate panel or
3309 (license license:gpl3)))
3311 (define-public r-mitml
3318 (uri (cran-uri "mitml" version))
3321 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3322 (build-system r-build-system)
3324 `(("r-haven" ,r-haven)
3327 (home-page "https://cran.r-project.org/web/packages/mitml/")
3328 (synopsis "Tools for multiple imputation in multilevel modeling")
3330 "This package provides tools for multiple imputation of missing data in
3331 multilevel modeling. It includes a user-friendly interface to the packages
3332 pan and jomo, and several functions for visualization, data management and the
3333 analysis of multiply imputed data sets.")
3334 (license license:gpl2+)))
3336 (define-public r-mice
3343 (uri (cran-uri "mice" version))
3346 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3347 (build-system r-build-system)
3349 `(("r-broom" ,r-broom)
3350 ("r-dplyr" ,r-dplyr)
3351 ("r-lattice" ,r-lattice)
3353 ("r-mitml" ,r-mitml)
3356 ("r-rlang" ,r-rlang)
3357 ("r-rpart" ,r-rpart)
3358 ("r-survival" ,r-survival)))
3359 (home-page "https://cran.r-project.org/web/packages/mice/")
3360 (synopsis "Multivariate imputation by chained equations")
3362 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3363 implemented by the MICE algorithm as described in @url{Van Buuren and
3364 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3365 variable has its own imputation model. Built-in imputation models are
3366 provided for continuous data (predictive mean matching, normal), binary
3367 data (logistic regression), unordered categorical data (polytomous logistic
3368 regression) and ordered categorical data (proportional odds). MICE can also
3369 impute continuous two-level data (normal model, pan, second-level variables).
3370 Passive imputation can be used to maintain consistency between variables.
3371 Various diagnostic plots are available to inspect the quality of the
3373 ;; Any of these two versions.
3374 (license (list license:gpl2 license:gpl3))))
3376 (define-public r-truncnorm
3378 (name "r-truncnorm")
3383 (uri (cran-uri "truncnorm" version))
3386 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3387 (build-system r-build-system)
3388 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3389 (synopsis "Truncated normal distribution")
3390 (description "This package provides functions for the truncated normal
3391 distribution with mean equal to @code{mean} and standard deviation equal to
3392 @code{sd}. It includes density, distribution, quantile, and expected value
3393 functions, as well as a random generation function.")
3394 (license license:gpl2)))
3396 (define-public r-rsolnp
3403 (uri (cran-uri "Rsolnp" version))
3406 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3407 (properties `((upstream-name . "Rsolnp")))
3408 (build-system r-build-system)
3410 `(("r-truncnorm" ,r-truncnorm)))
3411 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3412 (synopsis "General non-linear optimization")
3413 (description "The Rsolnp package implements a general non-linear augmented
3414 Lagrange multiplier method solver, a @dfn{sequential quadratic
3415 programming} (SQP) based solver).")
3416 ;; Any version of the GPL.
3417 (license license:gpl2+)))
3419 (define-public r-hardyweinberg
3421 (name "r-hardyweinberg")
3426 (uri (cran-uri "HardyWeinberg" version))
3429 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3430 (properties `((upstream-name . "HardyWeinberg")))
3431 (build-system r-build-system)
3433 `(("r-mice" ,r-mice)
3435 ("r-rsolnp" ,r-rsolnp)))
3436 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3437 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3439 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3440 diallelic genetic marker data. All classical tests (chi-square, exact,
3441 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3442 included in the package, as well as functions for power computation and for
3443 the simulation of marker data under equilibrium and disequilibrium. Routines
3444 for dealing with markers on the X-chromosome are included. Functions for
3445 testing equilibrium in the presence of missing data by using multiple
3446 imputation are also provided. Implements several graphics for exploring the
3447 equilibrium status of a large set of diallelic markers: ternary plots with
3448 acceptance regions, log-ratio plots and Q-Q plots.")
3449 (license license:gpl2+)))
3458 (uri (cran-uri "sm" version))
3461 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3462 (build-system r-build-system)
3463 (native-inputs `(("gfortran" ,gfortran)))
3464 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3465 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3467 "This is software accompanying the book 'Applied Smoothing Techniques for
3468 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3469 University Press. It provides smoothing methods for nonparametric regression
3470 and density estimation")
3471 (license license:gpl2+)))
3473 (define-public r-venndiagram
3475 (name "r-venndiagram")
3479 (uri (cran-uri "VennDiagram" version))
3482 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3483 (properties `((upstream-name . "VennDiagram")))
3484 (build-system r-build-system)
3486 `(("r-futile-logger" ,r-futile-logger)))
3487 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3488 (synopsis "Generate High-Resolution Venn and Euler Plots")
3490 "This package provides a set of functions to generate high-resolution
3491 Venn and Euler plots. It includes handling for several special cases,
3492 including two-case scaling, and extensive customization of plot shape and
3494 (license license:gpl2+)))
3496 (define-public r-vioplot
3503 (uri (cran-uri "vioplot" version))
3506 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3507 (build-system r-build-system)
3511 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3512 (synopsis "Violin plot")
3514 "This package provides a violin plot, which is a combination of a box
3515 plot and a kernel density plot.")
3516 (license license:bsd-3)))
3518 (define-public r-rsofia
3524 ;; This package has been removed from CRAN, so we can
3525 ;; only fetch it from the archives.
3526 (uri (string-append "https://cran.r-project.org/src/"
3527 "contrib/Archive/RSofia/RSofia_"
3531 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3532 (properties `((upstream-name . "RSofia")))
3533 (build-system r-build-system)
3535 `(("r-rcpp" ,r-rcpp)))
3536 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3537 (synopsis "Port of sofia-ml to R")
3538 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3539 suite of fast incremental algorithms for machine learning that can be used for
3540 training models for classification or ranking.")
3541 (license license:asl2.0)))
3543 (define-public r-xts
3550 (uri (cran-uri "xts" version))
3553 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3554 (build-system r-build-system)
3555 (propagated-inputs `(("r-zoo" ,r-zoo)))
3556 (home-page "https://github.com/joshuaulrich/xts")
3557 (synopsis "Extensible time series")
3559 "This package provides for uniform handling of R's different time-based
3560 data classes by extending @code{zoo}, maximizing native format information
3561 preservation and allowing for user-level customization and extension, while
3562 simplifying cross-class interoperability.")
3563 (license license:gpl2+)))
3565 (define-public r-performanceanalytics
3567 (name "r-performanceanalytics")
3572 (uri (cran-uri "PerformanceAnalytics" version))
3575 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3577 `((upstream-name . "PerformanceAnalytics")))
3578 (build-system r-build-system)
3580 `(("r-quadprog" ,r-quadprog)
3583 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3584 (synopsis "Econometric tools for performance and risk analysis")
3585 (description "This is a collection of econometric functions for
3586 performance and risk analysis. This package aims to aid practitioners and
3587 researchers in utilizing the latest research in analysis of non-normal return
3588 streams. In general, it is most tested on return (rather than price) data on
3589 a regular scale, but most functions will work with irregular return data as
3590 well, and increasing numbers of functions will work with P&L or price data
3592 ;; Either version may be picked.
3593 (license (list license:gpl2 license:gpl3))))
3595 (define-public r-laeken
3602 (uri (cran-uri "laeken" version))
3605 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3606 (build-system r-build-system)
3608 `(("r-boot" ,r-boot)
3609 ("r-mass" ,r-mass)))
3610 (home-page "https://cran.r-project.org/web/packages/laeken/")
3611 (synopsis "Estimation of indicators on social exclusion and poverty")
3612 (description "This package provides tools for the estimation of indicators
3613 on social exclusion and poverty, as well as an implementation of Pareto tail
3614 modeling for empirical income distributions.")
3615 (license license:gpl2+)))
3617 (define-public r-vcd
3624 (uri (cran-uri "vcd" version))
3627 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3628 (build-system r-build-system)
3630 `(("r-colorspace" ,r-colorspace)
3631 ("r-lmtest" ,r-lmtest)
3632 ("r-mass" ,r-mass)))
3633 (home-page "https://cran.r-project.org/web/packages/vcd/")
3634 (synopsis "Visualizing categorical data")
3635 (description "This package provides visualization techniques, data sets,
3636 summary and inference procedures aimed particularly at categorical data.
3637 Special emphasis is given to highly extensible grid graphics. The package was
3638 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3639 Friendly and is now the main support package for a new book, \"Discrete Data
3640 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3641 (license license:gpl2)))
3643 (define-public r-ica
3650 (uri (cran-uri "ica" version))
3653 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3654 (build-system r-build-system)
3655 (home-page "https://cran.r-project.org/web/packages/ica/")
3656 (synopsis "Independent component analysis")
3657 (description "This package provides tools for @dfn{Independent Component
3658 Analysis} (ICA) using various algorithms: FastICA,
3659 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3660 of Eigenmatrices} (JADE).")
3661 (license license:gpl2+)))
3663 (define-public r-dtw
3670 (uri (cran-uri "dtw" version))
3673 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3674 (build-system r-build-system)
3675 (propagated-inputs `(("r-proxy" ,r-proxy)))
3676 (home-page "http://dtw.r-forge.r-project.org/")
3677 (synopsis "Dynamic Time Warping Algorithms")
3678 (description "This package provides a comprehensive implementation of
3679 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3680 optimal (least cumulative distance) alignment between points of two time
3681 series. Common DTW variants covered include local (slope) and global (window)
3682 constraints, subsequence matches, arbitrary distance definitions,
3683 normalizations, minimum variance matching, and so on.")
3684 (license license:gpl2+)))
3686 (define-public r-sdmtools
3689 (version "1.1-221.2")
3693 (uri (cran-uri "SDMTools" version))
3696 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3697 (properties `((upstream-name . "SDMTools")))
3698 (build-system r-build-system)
3699 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3700 (home-page "http://www.rforge.net/SDMTools/")
3701 (synopsis "Species distribution modelling tools")
3702 (description "This package provides a set of tools for post processing
3703 the outcomes of species distribution modeling exercises. It includes novel
3704 methods for comparing models and tracking changes in distributions through
3705 time. It further includes methods for visualizing outcomes, selecting
3706 thresholds, calculating measures of accuracy and landscape fragmentation
3708 (license license:gpl3+)))
3710 (define-public r-scatterplot3d
3712 (name "r-scatterplot3d")
3717 (uri (cran-uri "scatterplot3d" version))
3720 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3721 (build-system r-build-system)
3722 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3723 (synopsis "3D scatter plot")
3724 (description "This package provides an implementation of scatter plots for
3725 plotting. a three dimensional point cloud.")
3726 (license license:gpl2)))
3728 (define-public r-ggridges
3735 (uri (cran-uri "ggridges" version))
3738 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3739 (build-system r-build-system)
3741 `(("r-ggplot2" ,r-ggplot2)
3743 ("r-scales" ,r-scales)
3744 ("r-withr" ,r-withr)))
3745 (home-page "https://github.com/clauswilke/ggridges")
3746 (synopsis "Ridgeline plots in ggplot2")
3748 "Ridgeline plots provide a convenient way of visualizing changes in
3749 distributions over time or space. This package enables the creation of such
3750 plots in @code{ggplot2}.")
3751 (license license:gpl2)))
3753 (define-public r-ggjoy
3760 (uri (cran-uri "ggjoy" version))
3763 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3764 (build-system r-build-system)
3766 `(("r-ggplot2" ,r-ggplot2)
3767 ("r-ggridges" ,r-ggridges)))
3768 (home-page "https://github.com/clauswilke/ggjoy")
3769 (synopsis "Joyplots in ggplot2")
3770 (description "Joyplots provide a convenient way of visualizing changes in
3771 distributions over time or space. This package enables the creation of such
3772 plots in @code{ggplot2}.")
3773 (license license:gpl2)))
3775 (define-public r-cli
3782 (uri (cran-uri "cli" version))
3785 "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki"))))
3786 (build-system r-build-system)
3788 `(("r-assertthat" ,r-assertthat)
3789 ("r-crayon" ,r-crayon)
3790 ("r-fansi" ,r-fansi)
3791 ("r-glue" ,r-glue)))
3792 (home-page "https://github.com/r-lib/cli#readme")
3793 (synopsis "Helpers for developing command line interfaces")
3794 (description "This package provides a suite of tools designed to build
3795 attractive command line interfaces (CLIs). It includes tools for drawing
3796 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3797 (license license:expat)))
3799 (define-public r-argparser
3801 (name "r-argparser")
3806 (uri (cran-uri "argparser" version))
3809 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3810 (build-system r-build-system)
3811 (home-page "https://bitbucket.org/djhshih/argparser")
3812 (synopsis "Command-line argument parser")
3814 "This package provides a cross-platform command-line argument parser
3815 written purely in R with no external dependencies. It is useful with the
3816 Rscript front-end and facilitates turning an R script into an executable
3818 (license license:gpl3+)))
3820 (define-public r-debugme
3827 (uri (cran-uri "debugme" version))
3830 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3831 (build-system r-build-system)
3832 (propagated-inputs `(("r-crayon" ,r-crayon)))
3833 (home-page "https://github.com/r-lib/debugme#readme")
3834 (synopsis "Debug R packages")
3836 "This package allows the user to specify debug messages as special string
3837 constants, and control debugging of packages via environment variables.")
3838 (license license:expat)))
3840 (define-public r-processx
3847 (uri (cran-uri "processx" version))
3850 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3851 (build-system r-build-system)
3855 (home-page "https://github.com/r-lib/processx3")
3856 (synopsis "Execute and control system processes")
3858 "This package provides portable tools to run system processes in the
3859 background. It can check if a background process is running; wait on a
3860 background process to finish; get the exit status of finished processes; kill
3861 background processes and their children; restart processes. It can read the
3862 standard output and error of the processes, using non-blocking connections.
3863 @code{processx} can poll a process for standard output or error, with a
3864 timeout. It can also poll several processes at once.")
3865 (license license:expat)))
3867 (define-public r-tsp
3874 (uri (cran-uri "TSP" version))
3877 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3878 (properties `((upstream-name . "TSP")))
3879 (build-system r-build-system)
3880 (propagated-inputs `(("r-foreach" ,r-foreach)))
3881 (home-page "https://cran.r-project.org/web/packages/TSP/")
3882 (synopsis "Traveling salesperson problem (TSP)")
3883 (description "This package provides basic infrastructure and some
3884 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3885 traveling salesman problem).")
3886 (license license:gpl3)))
3888 (define-public r-qap
3895 (uri (cran-uri "qap" version))
3898 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3899 (build-system r-build-system)
3900 (native-inputs `(("gfortran" ,gfortran)))
3901 (home-page "https://cran.r-project.org/web/packages/qap/")
3902 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3903 (description "This package implements heuristics for the @dfn{quadratic
3904 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3906 (license license:gpl3)))
3908 (define-public r-gclus
3915 (uri (cran-uri "gclus" version))
3918 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3919 (build-system r-build-system)
3920 (propagated-inputs `(("r-cluster" ,r-cluster)))
3921 (home-page "https://cran.r-project.org/web/packages/gclus/")
3922 (synopsis "Clustering graphics")
3923 (description "This package orders panels in scatterplot matrices and
3924 parallel coordinate displays by some merit index. It contains various indices
3925 of merit, ordering functions, and enhanced versions of @code{pairs} and
3926 @code{parcoord} which color panels according to their merit level.")
3927 (license license:gpl2+)))
3929 (define-public r-webshot
3936 (uri (cran-uri "webshot" version))
3939 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3940 (build-system r-build-system)
3942 `(("r-callr" ,r-callr)
3943 ("r-jsonlite" ,r-jsonlite)
3944 ("r-magrittr" ,r-magrittr)))
3945 (home-page "https://github.com/wch/webshot/")
3946 (synopsis "Take screenshots of web pages")
3948 "Webshot makes it easy to take screenshots of web pages from within R.
3949 It can also run Shiny applications locally and take screenshots of the
3950 application; and it can render and screenshot static as well as interactive R
3951 Markdown documents.")
3952 (license license:gpl2)))
3954 (define-public r-seriation
3956 (name "r-seriation")
3961 (uri (cran-uri "seriation" version))
3964 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3965 (build-system r-build-system)
3967 `(("r-cluster" ,r-cluster)
3968 ("r-colorspace" ,r-colorspace)
3969 ("r-dendextend" ,r-dendextend)
3970 ("r-gclus" ,r-gclus)
3971 ("r-gplots" ,r-gplots)
3974 ("r-registry" ,r-registry)
3976 (native-inputs `(("gfortran" ,gfortran)))
3977 (home-page "http://s2.smu.edu/IDA/seriation/")
3978 (synopsis "Infrastructure for ordering objects using seriation")
3980 "This package provides infrastructure for seriation with an
3981 implementation of several seriation/sequencing techniques to reorder matrices,
3982 dissimilarity matrices, and dendrograms. It also provides (optimally)
3983 reordered heatmaps, color images and clustering visualizations like
3984 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3986 (license license:gpl3)))
3988 (define-public r-xfun
3995 (uri (cran-uri "xfun" version))
3997 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
3998 (build-system r-build-system)
3999 (home-page "https://github.com/yihui/xfun")
4000 (synopsis "Miscellaneous functions")
4002 "This package provides miscellaneous functions commonly used in other
4003 packages maintained by Yihui Xie.")
4004 (license license:expat)))
4006 (define-public r-utf8
4013 (uri (cran-uri "utf8" version))
4016 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4017 (build-system r-build-system)
4018 (home-page "https://github.com/patperry/r-utf8")
4019 (synopsis "Unicode text processing")
4021 "This package provides tools to process and print UTF-8 encoded
4022 international text (Unicode). Input, validate, normalize, encode, format, and
4024 (license license:asl2.0)))
4026 (define-public r-zeallot
4033 (uri (cran-uri "zeallot" version))
4036 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4037 (build-system r-build-system)
4038 (home-page "https://github.com/nteetor/zeallot")
4039 (synopsis "Multiple, unpacking, and destructuring assignment")
4041 "This package provides a @code{%<-%} operator to perform multiple,
4042 unpacking, and destructuring assignment in R. The operator unpacks the
4043 right-hand side of an assignment into multiple values and assigns these values
4044 to variables on the left-hand side of the assignment.")
4045 (license license:expat)))
4047 (define-public r-vctrs
4054 (uri (cran-uri "vctrs" version))
4057 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
4058 (build-system r-build-system)
4060 `(("r-backports" ,r-backports)
4061 ("r-digest" ,r-digest)
4062 ("r-ellipsis" ,r-ellipsis)
4064 ("r-rlang" ,r-rlang)
4065 ("r-zeallot" ,r-zeallot)))
4066 (home-page "https://github.com/r-lib/vctrs")
4067 (synopsis "Vector helpers")
4069 "There are three main goals to the @code{vctrs} package:
4072 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4073 @code{length()} and @code{class()}. These definitions are paired with a
4074 framework for type-coercion and size-recycling.
4075 @item To define type- and size-stability as desirable function properties, use
4076 them to analyse existing base function, and to propose better alternatives.
4077 This work has been particularly motivated by thinking about the ideal
4078 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4079 @item To provide a new @code{vctr} base class that makes it easy to create new
4080 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4081 a few new @code{vctrs} generics, making implementation considerably simpler
4084 (license license:gpl3)))
4086 (define-public r-pillar
4093 (uri (cran-uri "pillar" version))
4096 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
4097 (build-system r-build-system)
4100 ("r-crayon" ,r-crayon)
4101 ("r-fansi" ,r-fansi)
4102 ("r-rlang" ,r-rlang)
4104 ("r-vctrs" ,r-vctrs)))
4105 (home-page "https://github.com/r-lib/pillar")
4106 (synopsis "Coloured formatting for columns")
4108 "This package provides a @code{pillar} generic designed for formatting
4109 columns of data using the full range of colours provided by modern
4111 (license license:gpl3)))
4113 (define-public r-uuid
4120 (uri (cran-uri "uuid" version))
4123 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4124 (build-system r-build-system)
4125 (home-page "http://www.rforge.net/uuid")
4126 (synopsis "Tools for generating and handling of UUIDs")
4128 "This package provides tools for generating and handling of
4129 @dfn{Universally Unique Identifiers} (UUIDs).")
4130 (license license:expat)))
4132 (define-public r-tinytex
4139 (uri (cran-uri "tinytex" version))
4142 "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
4143 (build-system r-build-system)
4145 `(("r-xfun" ,r-xfun)))
4146 (home-page "https://github.com/yihui/tinytex")
4147 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4149 "This package provides helper functions to install and maintain the LaTeX
4150 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4151 easy-to-maintain version of TeX Live. This package also contains helper
4152 functions to compile LaTeX documents, and install missing LaTeX packages
4154 (license license:expat)))
4156 (define-public r-network
4163 (uri (cran-uri "network" version))
4166 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4167 (build-system r-build-system)
4169 `(("r-magrittr" ,r-magrittr)
4170 ("r-tibble" ,r-tibble)))
4171 (home-page "https://statnet.org/")
4172 (synopsis "Classes for relational data")
4174 "This package provides tools to create and modify network objects. The
4175 @code{network} class can represent a range of relational data types, and
4176 supports arbitrary vertex/edge/graph attributes.")
4177 (license license:gpl2+)))
4179 (define-public r-statnet-common
4181 (name "r-statnet-common")
4186 (uri (cran-uri "statnet.common" version))
4189 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4191 `((upstream-name . "statnet.common")))
4192 (build-system r-build-system)
4194 `(("r-coda" ,r-coda)))
4195 (home-page "https://statnet.org")
4196 (synopsis "R scripts and utilities used by the Statnet software")
4197 (description "This package provides non-statistical utilities used by the
4198 software developed by the Statnet Project.")
4199 (license license:gpl3)))
4201 (define-public r-statcheck
4203 (name "r-statcheck")
4208 (uri (cran-uri "statcheck" version))
4211 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4212 (build-system r-build-system)
4214 `(("r-ggplot2" ,r-ggplot2)
4216 ("r-rmarkdown" ,r-rmarkdown)))
4217 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4218 (synopsis "Extract statistics from articles and recompute p-values")
4219 (description "This package can automatically extract statistical
4220 null-hypothesis significant testing (NHST) results from articles and recompute
4221 the p-values based on the reported test statistic and degrees of freedom to
4222 detect possible inconsistencies.")
4223 (license license:gpl2)))
4225 (define-public r-sna
4232 (uri (cran-uri "sna" version))
4235 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4236 (build-system r-build-system)
4238 `(("r-network" ,r-network)
4239 ("r-statnet-common" ,r-statnet-common)))
4240 (home-page "https://statnet.org")
4241 (synopsis "Tools for social network analysis")
4243 "This package provides a range of tools for social network analysis,
4244 including node and graph-level indices, structural distance and covariance
4245 methods, structural equivalence detection, network regression, random graph
4246 generation, and 2D/3D network visualization.")
4247 (license license:gpl2+)))
4249 (define-public r-tfisher
4256 (uri (cran-uri "TFisher" version))
4259 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4260 (properties `((upstream-name . "TFisher")))
4261 (build-system r-build-system)
4263 `(("r-matrix" ,r-matrix)
4264 ("r-mvtnorm" ,r-mvtnorm)
4266 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4267 (synopsis "Optimal thresholding Fisher's p-value combination method")
4269 "This package provides the @dfn{cumulative distribution function} (CDF),
4270 quantile, and statistical power calculator for a collection of thresholding
4271 Fisher's p-value combination methods, including Fisher's p-value combination
4272 method, truncated product method and, in particular, soft-thresholding
4273 Fisher's p-value combination method which is proven to be optimal in some
4274 context of signal detection. The p-value calculator for the omnibus version
4275 of these tests are also included.")
4276 (license license:gpl2)))
4278 (define-public r-ttr
4285 (uri (cran-uri "TTR" version))
4288 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
4289 (properties `((upstream-name . "TTR")))
4290 (build-system r-build-system)
4292 `(("r-curl" ,r-curl)
4295 (home-page "https://github.com/joshuaulrich/TTR")
4296 (synopsis "Technical trading rules")
4298 "This package provides functions and data to construct technical trading
4300 (license license:gpl2)))
4302 (define-public r-leaps
4309 (uri (cran-uri "leaps" version))
4312 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4313 (build-system r-build-system)
4314 (native-inputs `(("gfortran" ,gfortran)))
4315 (home-page "https://cran.r-project.org/web/packages/leaps/")
4316 (synopsis "Regression subset selection")
4318 "This package provides tools for regression subset selection, including
4319 exhaustive search.")
4320 (license license:gpl2+)))
4322 (define-public r-splus2r
4329 (uri (cran-uri "splus2R" version))
4332 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4333 (properties `((upstream-name . "splus2R")))
4334 (build-system r-build-system)
4335 (native-inputs `(("gfortran" ,gfortran)))
4336 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4337 (synopsis "Supplemental S-PLUS functionality in R")
4339 "Currently there are many functions in S-PLUS that are missing in R. To
4340 facilitate the conversion of S-PLUS packages to R packages, this package
4341 provides some missing S-PLUS functionality in R.")
4342 (license license:gpl2)))
4344 (define-public r-ifultools
4346 (name "r-ifultools")
4351 (uri (cran-uri "ifultools" version))
4354 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4355 (build-system r-build-system)
4357 `(("r-mass" ,r-mass)
4358 ("r-splus2r" ,r-splus2r)))
4359 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4360 (synopsis "Insightful research tools")
4361 (description "This package provides C code used by the wmtsa, fractal, and
4363 (license license:gpl2)))
4365 (define-public r-sapa
4372 (uri (cran-uri "sapa" version))
4375 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4376 (build-system r-build-system)
4378 `(("r-ifultools" ,r-ifultools)
4379 ("r-splus2r" ,r-splus2r)))
4380 (home-page "https://cran.r-project.org/web/packages/sapa/")
4381 (synopsis "Spectral analysis for physical applications")
4382 (description "This package provides software for the book Spectral
4383 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4384 Cambridge University Press, 1993.")
4385 (license license:gpl2)))
4387 (define-public r-aggregation
4389 (name "r-aggregation")
4394 (uri (cran-uri "aggregation" version))
4397 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4398 (build-system r-build-system)
4399 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4400 (synopsis "Methods for p-value aggregation")
4402 "This package contains functionality for performing the following methods
4403 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4404 Fisher's method), and Sidak correction.")
4405 (license license:gpl3)))
4407 (define-public r-quantmod
4414 (uri (cran-uri "quantmod" version))
4417 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4418 (build-system r-build-system)
4420 `(("r-curl" ,r-curl)
4424 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4425 (synopsis "Quantitative financial modelling framework")
4426 (description "This package provides a quantitative financial modelling
4427 framework to allow users to specify, build, trade, and analyse quantitative
4428 financial trading strategies.")
4429 (license license:gpl3)))
4431 (define-public r-tseries
4438 (uri (cran-uri "tseries" version))
4441 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4442 (build-system r-build-system)
4444 `(("r-quadprog" ,r-quadprog)
4445 ("r-quantmod" ,r-quantmod)
4448 `(("gfortran" ,gfortran)))
4449 (home-page "https://cran.r-project.org/web/packages/tseries/")
4450 (synopsis "Time series analysis and computational finance")
4452 "This package provides functions relating to time series analysis and
4453 computational finance.")
4454 (license license:gpl2)))
4456 (define-public r-wmtsa
4463 (uri (cran-uri "wmtsa" version))
4466 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4467 (build-system r-build-system)
4469 `(("r-ifultools" ,r-ifultools)
4471 ("r-splus2r" ,r-splus2r)))
4472 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4473 (synopsis "Wavelet methods for time series analysis")
4475 "This package provides software to accompany the book \"Wavelet Methods
4476 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4477 University Press, 2000.")
4478 (license license:gpl2)))
4480 (define-public r-tsa
4487 (uri (cran-uri "TSA" version))
4490 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4491 (properties `((upstream-name . "TSA")))
4492 (build-system r-build-system)
4494 `(("r-leaps" ,r-leaps)
4495 ("r-locfit" ,r-locfit)
4496 ("r-mgcv" ,r-mgcv)))
4497 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4498 (synopsis "Time series analysis")
4500 "This package contains R functions and datasets detailed in the book
4501 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4502 Cryer and Kung-Sik Chan.")
4503 (license license:gpl2+)))
4505 (define-public r-extradistr
4507 (name "r-extradistr")
4512 (uri (cran-uri "extraDistr" version))
4515 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4516 (properties `((upstream-name . "extraDistr")))
4517 (build-system r-build-system)
4519 `(("r-rcpp" ,r-rcpp)))
4520 (home-page "https://github.com/twolodzko/extraDistr")
4521 (synopsis "Additional univariate and multivariate distributions")
4523 "This package implements density, distribution functions, quantile
4524 functions and random generation functions for a large number of univariate and
4525 multivariate distributions.")
4526 (license license:gpl2)))
4528 (define-public r-fractal
4535 (uri (cran-uri "fractal" version))
4538 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4539 (build-system r-build-system)
4541 `(("r-ifultools" ,r-ifultools)
4544 ("r-scatterplot3d" ,r-scatterplot3d)
4545 ("r-splus2r" ,r-splus2r)
4546 ("r-wmtsa" ,r-wmtsa)))
4547 (home-page "https://cran.r-project.org/web/packages/fractal/")
4548 (synopsis "Fractal time series modeling and analysis")
4550 "This package provides tools for stochastic fractal and deterministic
4551 chaotic time series analysis.")
4552 (license license:gpl2)))
4554 (define-public r-urca
4561 (uri (cran-uri "urca" version))
4564 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4565 (build-system r-build-system)
4566 (propagated-inputs `(("r-nlme" ,r-nlme)))
4567 (native-inputs `(("gfortran" ,gfortran)))
4568 (home-page "https://cran.r-project.org/web/packages/urca/")
4569 (synopsis "Unit root and cointegration tests for time series data")
4571 "This package provides unit root and cointegration tests encountered in
4572 applied econometric analysis.")
4573 (license license:gpl2+)))
4575 (define-public r-cubature
4582 (uri (cran-uri "cubature" version))
4585 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4586 (build-system r-build-system)
4588 `(("r-rcpp" ,r-rcpp)))
4589 (home-page "https://github.com/bnaras/cubature")
4590 (synopsis "Adaptive multivariate integration over hypercubes")
4592 "This package is an R wrapper around the cubature C library for adaptive
4593 multivariate integration over hypercubes. This version provides both
4594 @code{hcubature} and @code{pcubature} routines in addition to a vector
4596 ;; The included cubature C library is released under GPLv2+, but the
4597 ;; wrapper declares the license to be GPLv3+.
4598 (license (list license:gpl2+ license:gpl3+))))
4600 (define-public r-trend
4607 (uri (cran-uri "trend" version))
4610 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4611 (build-system r-build-system)
4613 `(("r-extradistr" ,r-extradistr)))
4615 `(("gfortran" ,gfortran)))
4616 (home-page "https://cran.r-project.org/web/packages/trend/")
4617 (synopsis "Non-parametric trend tests and change-point detection")
4619 "The analysis of environmental data often requires the detection of
4620 trends and change-points. This package includes tests for trend
4621 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4622 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4623 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4624 correlation trend test), change-point detection (Lanzante's test procedures,
4625 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4626 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4627 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4628 sample Robust Rank-Order Distributional Test.")
4629 (license license:gpl3)))
4631 (define-public r-expm
4638 (uri (cran-uri "expm" version))
4641 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4642 (build-system r-build-system)
4643 (propagated-inputs `(("r-matrix" ,r-matrix)))
4644 (native-inputs `(("gfortran" ,gfortran)))
4645 (home-page "https://r-forge.r-project.org/projects/expm/")
4646 (synopsis "Tools for matrix exponentials and related quantities")
4648 "This package provides tools for the computation of the matrix
4649 exponential, logarithm, square root, and related quantities.")
4650 (license license:gpl2+)))
4652 (define-public r-complexplus
4654 (name "r-complexplus")
4659 (uri (cran-uri "complexplus" version))
4662 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4663 (build-system r-build-system)
4665 `(("r-expm" ,r-expm)
4666 ("r-matrix" ,r-matrix)))
4667 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4668 (synopsis "Functions of complex or real variables")
4670 "This package extends several functions to the complex domain, including
4671 the matrix exponential and logarithm, and the determinant.")
4672 (license license:gpl2)))
4674 (define-public r-phontools
4676 (name "r-phontools")
4681 (uri (cran-uri "phonTools" version))
4684 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4685 (properties `((upstream-name . "phonTools")))
4686 (build-system r-build-system)
4687 (home-page "http://www.santiagobarreda.com/rscripts.html")
4688 (synopsis "Tools for phonetic and acoustic analyses")
4690 "This package contains tools for the organization, display, and analysis
4691 of the sorts of data frequently encountered in phonetics research and
4692 experimentation, including the easy creation of IPA vowel plots, and the
4693 creation and manipulation of WAVE audio files.")
4694 (license license:bsd-2)))
4703 (uri (cran-uri "np" version))
4706 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4707 (build-system r-build-system)
4709 `(("r-boot" ,r-boot)
4710 ("r-cubature" ,r-cubature)
4711 ("r-quadprog" ,r-quadprog)
4712 ("r-quantreg" ,r-quantreg)))
4713 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4714 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4715 (description "This package provides non-parametric (and semi-parametric)
4716 kernel methods that seamlessly handle a mix of continuous, unordered, and
4717 ordered factor data types.")
4718 ;; Any version of the GPL.
4719 (license license:gpl3+)))
4721 (define-public r-powerplus
4723 (name "r-powerplus")
4728 (uri (cran-uri "powerplus" version))
4731 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4732 (build-system r-build-system)
4734 `(("r-complexplus" ,r-complexplus)
4737 ("r-matrix" ,r-matrix)
4738 ("r-phontools" ,r-phontools)))
4739 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4740 (synopsis "Exponentiation operations")
4742 "This package provides tools for the computation of matrix and scalar
4744 (license license:gpl2)))
4746 (define-public r-egg
4753 (uri (cran-uri "egg" version))
4756 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4757 (properties `((upstream-name . "egg")))
4758 (build-system r-build-system)
4760 `(("r-ggplot2" ,r-ggplot2)
4761 ("r-gridextra" ,r-gridextra)
4762 ("r-gtable" ,r-gtable)))
4763 (home-page "https://cran.r-project.org/web/packages/egg")
4764 (synopsis "Extensions for ggplot2")
4766 "This package provides miscellaneous functions to help customize ggplot2
4767 objects. High-level functions are provided to post-process ggplot2 layouts
4768 and allow alignment between plot panels, as well as setting panel sizes to
4769 fixed values. Other functions include a custom @code{geom}, and helper
4770 functions to enforce symmetric scales or add tags to facetted plots.")
4771 (license license:gpl3)))
4773 (define-public r-heatmaply
4775 (name "r-heatmaply")
4780 (uri (cran-uri "heatmaply" version))
4783 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4784 (build-system r-build-system)
4786 `(("r-assertthat" ,r-assertthat)
4787 ("r-colorspace" ,r-colorspace)
4788 ("r-dendextend" ,r-dendextend)
4790 ("r-ggplot2" ,r-ggplot2)
4791 ("r-htmlwidgets" ,r-htmlwidgets)
4792 ("r-magrittr" ,r-magrittr)
4793 ("r-plotly" ,r-plotly)
4794 ("r-rcolorbrewer" ,r-rcolorbrewer)
4795 ("r-reshape2" ,r-reshape2)
4796 ("r-scales" ,r-scales)
4797 ("r-seriation" ,r-seriation)
4798 ("r-viridis" ,r-viridis)
4799 ("r-webshot" ,r-webshot)))
4800 (home-page "https://cran.r-project.org/package=heatmaply")
4801 (synopsis "Interactive cluster heat maps using plotly")
4803 "This package enables you to create interactive cluster heatmaps that can
4804 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4805 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4806 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4807 a popular graphical method for visualizing high-dimensional data, in which a
4808 table of numbers is encoded as a grid of colored cells. The rows and columns
4809 of the matrix are ordered to highlight patterns and are often accompanied by
4811 ;; Either version of the license.
4812 (license (list license:gpl2 license:gpl3))))
4821 (uri (cran-uri "h5" version))
4824 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4825 (build-system r-build-system)
4830 `(("which" ,which)))
4832 `(("r-rcpp" ,r-rcpp)))
4833 (home-page "https://github.com/mannau/h5")
4834 (synopsis "Interface to the HDF5 Library")
4836 "This package provides an S4 interface to the HDF5 library supporting
4837 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4838 binary files in a language independent format. The HDF5 format can therefore
4839 be used as an alternative to R's save/load mechanism. Since h5 is able to
4840 access only subsets of stored data it can also handle data sets which do not
4842 (license license:bsd-2)))
4844 (define-public r-cgdsr
4851 (uri (cran-uri "cgdsr" version))
4854 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4855 (build-system r-build-system)
4857 `(("r-httr" ,r-httr)
4858 ("r-r-methodss3" ,r-r-methodss3)
4859 ("r-r-oo" ,r-r-oo)))
4860 (home-page "https://github.com/cBioPortal/cgdsr")
4861 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4863 "This package provides a basic set of R functions for querying the Cancer
4864 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4865 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4866 (license license:lgpl3)))
4868 (define-public r-import
4875 (uri (cran-uri "import" version))
4878 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4879 (build-system r-build-system)
4880 (home-page "https://github.com/smbache/import")
4881 (synopsis "Import mechanism for R")
4883 "This is an alternative mechanism for importing objects from packages.
4884 The syntax allows for importing multiple objects from a package with a single
4885 command in an expressive way. The import package bridges some of the gap
4886 between using @code{library} (or @code{require}) and direct (single-object)
4887 imports. Furthermore the imported objects are not placed in the current
4888 environment. It is also possible to import objects from stand-alone @code{.R}
4890 (license license:expat)))
4892 (define-public r-shinyace
4899 (uri (cran-uri "shinyAce" version))
4902 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4903 (properties `((upstream-name . "shinyAce")))
4904 (build-system r-build-system)
4906 `(("r-shiny" ,r-shiny)
4907 ("r-jsonlite" ,r-jsonlite)))
4908 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4909 (synopsis "Ace editor bindings for Shiny")
4911 "This package provides Ace editor bindings to enable a rich text editing
4912 environment within Shiny.")
4913 (license license:expat)))
4915 (define-public r-base64url
4917 (name "r-base64url")
4922 (uri (cran-uri "base64url" version))
4925 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4926 (build-system r-build-system)
4928 `(("r-backports" ,r-backports)))
4929 (home-page "https://github.com/mllg/base64url")
4930 (synopsis "Fast and URL-safe base64 encoder and decoder")
4932 "This package provides a URL-safe base64 encoder and decoder. In
4933 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4934 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4935 encoder does not fill the string with trailing @code{=}. The resulting
4936 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4937 and thus are safe to use in URLs or for file names. The package also comes
4938 with a simple base32 encoder/decoder suited for case insensitive file
4940 (license license:gpl3)))
4942 (define-public r-radiant-data
4944 (name "r-radiant-data")
4949 (uri (cran-uri "radiant.data" version))
4952 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4953 (modules '((guix build utils)))
4956 ;; Delete files that are under CC-NC-SA.
4957 (delete-file-recursively "inst/app/tools/help")
4959 (properties `((upstream-name . "radiant.data")))
4960 (build-system r-build-system)
4962 `(("r-base64enc" ,r-base64enc)
4963 ("r-broom" ,r-broom)
4966 ("r-dplyr" ,r-dplyr)
4969 ("r-ggplot2" ,r-ggplot2)
4970 ("r-gridextra" ,r-gridextra)
4971 ("r-import" ,r-import)
4972 ("r-jsonlite" ,r-jsonlite)
4973 ("r-knitr" ,r-knitr)
4974 ("r-lubridate" ,r-lubridate)
4975 ("r-magrittr" ,r-magrittr)
4976 ("r-markdown" ,r-markdown)
4977 ("r-plotly" ,r-plotly)
4978 ("r-psych" ,r-psych)
4979 ("r-readr" ,r-readr)
4980 ("r-readxl" ,r-readxl)
4981 ("r-rlang" ,r-rlang)
4982 ("r-rmarkdown" ,r-rmarkdown)
4983 ("r-rstudioapi" ,r-rstudioapi)
4984 ("r-scales" ,r-scales)
4985 ("r-shiny" ,r-shiny)
4986 ("r-shinyfiles" ,r-shinyfiles)
4987 ("r-shinyace" ,r-shinyace)
4988 ("r-stringi" ,r-stringi)
4989 ("r-tibble" ,r-tibble)
4990 ("r-tidyr" ,r-tidyr)
4991 ("r-writexl" ,r-writexl)))
4992 (home-page "https://github.com/radiant-rstats/radiant.data")
4993 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4995 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4996 visualizing, summarizing, transforming, and combining data. It also contains
4997 functionality to generate reproducible reports of the analyses conducted in
4999 (license license:agpl3)))
5001 (define-public r-algdesign
5003 (name "r-algdesign")
5008 (uri (cran-uri "AlgDesign" version))
5010 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5011 (properties `((upstream-name . "AlgDesign")))
5012 (build-system r-build-system)
5013 (home-page "https://github.com/jvbraun/AlgDesign")
5014 (synopsis "Algorithmic experimental design")
5016 "This package provides tools to calculate exact and approximate theory
5017 experimental designs for D, A, and I criteria. Very large designs may be
5018 created. Experimental designs may be blocked or blocked designs created from
5019 a candidate list, using several criteria. The blocking can be done when whole
5020 and within plot factors interact.")
5021 (license license:gpl2+)))
5023 (define-public r-signal
5030 (uri (cran-uri "signal" version))
5033 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5034 (build-system r-build-system)
5035 (propagated-inputs `(("r-mass" ,r-mass)))
5036 (native-inputs `(("gfortran" ,gfortran)))
5037 (home-page "https://cran.r-project.org/web/packages/signal/")
5038 (synopsis "Signal processing")
5040 "This package provides a set of signal processing functions originally
5041 written for Matlab and GNU Octave. It includes filter generation utilities,
5042 filtering functions, resampling routines, and visualization of filter models.
5043 It also includes interpolation functions.")
5044 (license license:gpl2)))
5046 (define-public r-gsubfn
5053 (uri (cran-uri "gsubfn" version))
5056 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5057 (build-system r-build-system)
5058 (propagated-inputs `(("r-proto" ,r-proto)))
5059 (home-page "http://gsubfn.googlecode.com")
5060 (synopsis "Utilities for strings and function arguments.")
5062 "This package provides @code{gsubfn} which is like @code{gsub} but can
5063 take a replacement function or certain other objects instead of the
5064 replacement string. Matches and back references are input to the replacement
5065 function and replaced by the function output. @code{gsubfn} can be used to
5066 split strings based on content rather than delimiters and for quasi-perl-style
5067 string interpolation. The package also has facilities for translating
5068 formulas to functions and allowing such formulas in function calls instead of
5070 (license license:gpl2+)))
5072 (define-public r-sqldf
5079 (uri (cran-uri "sqldf" version))
5082 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5083 (build-system r-build-system)
5085 `(("r-chron" ,r-chron)
5087 ("r-gsubfn" ,r-gsubfn)
5088 ("r-proto" ,r-proto)
5089 ("r-rsqlite" ,r-rsqlite)))
5090 (home-page "https://github.com/ggrothendieck/sqldf")
5091 (synopsis "Manipulate R data frames using SQL")
5093 "The @code{sqldf} function is typically passed a single argument which is
5094 an SQL select statement where the table names are ordinary R data frame names.
5095 @code{sqldf} transparently sets up a database, imports the data frames into
5096 that database, performs the SQL statement and returns the result using a
5097 heuristic to determine which class to assign to each column of the returned
5098 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5099 used to read filtered files into R even if the original files are larger than
5100 R itself can handle.")
5101 (license license:gpl2)))
5103 (define-public r-abind
5110 (uri (cran-uri "abind" version))
5113 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5114 (build-system r-build-system)
5115 (home-page "https://cran.r-project.org/web/packages/abind/")
5116 (synopsis "Combine multidimensional arrays")
5118 "This package provides tools to combine multidimensional arrays into a
5119 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5120 works with vectors, matrices, and higher-dimensional arrays. It also provides
5121 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5122 extracting and replacing data in arrays.")
5123 (license license:lgpl2.0+)))
5125 (define-public r-prroc
5132 (uri (cran-uri "PRROC" version))
5135 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5136 (properties `((upstream-name . "PRROC")))
5137 (build-system r-build-system)
5138 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5139 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5141 "This package computes the areas under the @dfn{precision-recall} (PR)
5142 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5143 contrast to other implementations, the interpolation between points of the PR
5144 curve is done by a non-linear piecewise function. In addition to the areas
5145 under the curves, the curves themselves can also be computed and plotted by a
5146 specific S3-method.")
5147 (license license:gpl3)))
5149 (define-public r-vim
5156 (uri (cran-uri "VIM" version))
5159 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5160 (properties `((upstream-name . "VIM")))
5161 (build-system r-build-system)
5164 ("r-colorspace" ,r-colorspace)
5165 ("r-data-table" ,r-data-table)
5166 ("r-e1071" ,r-e1071)
5167 ("r-laeken" ,r-laeken)
5170 ("r-ranger" ,r-ranger)
5172 ("r-robustbase" ,r-robustbase)
5175 (home-page "https://github.com/alexkowa/VIM")
5176 (synopsis "Visualization and imputation of missing values")
5178 "This package provides tools for the visualization of missing and/or
5179 imputed values are introduced, which can be used for exploring the data and
5180 the structure of the missing and/or imputed values. Depending on this
5181 structure of the missing values, the corresponding methods may help to
5182 identify the mechanism generating the missing values and allows to explore the
5183 data including missing values. In addition, the quality of imputation can be
5184 visually explored using various univariate, bivariate, multiple and
5185 multivariate plot methods.")
5186 (license license:gpl2+)))
5188 (define-public r-fnn
5195 (uri (cran-uri "FNN" version))
5198 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5199 (properties `((upstream-name . "FNN")))
5200 (build-system r-build-system)
5201 (home-page "https://cran.r-project.org/web/packages/FNN")
5202 (synopsis "Fast nearest neighbor search algorithms and applications")
5204 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5205 search algorithms. Related applications including KNN classification,
5206 regression and information measures are implemented.")
5207 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5208 ;; later can be used.
5209 (license license:gpl2+)))
5211 (define-public r-smoother
5218 (uri (cran-uri "smoother" version))
5221 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5222 (build-system r-build-system)
5224 `(("r-ttr" ,r-ttr)))
5225 (home-page "http://cran.r-project.org/web/packages/smoother")
5226 (synopsis "Functions relating to the smoothing of numerical data")
5228 "This package provides a collection of methods for smoothing numerical
5229 data, commencing with a port of the Matlab gaussian window smoothing function.
5230 In addition, several functions typically used in smoothing of financial data
5232 (license license:gpl2)))
5234 (define-public r-riverplot
5236 (name "r-riverplot")
5241 (uri (cran-uri "riverplot" version))
5244 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5245 (build-system r-build-system)
5246 (home-page "https://logfc.wordpress.com")
5247 (synopsis "Sankey or ribbon plots")
5249 "Sankey plots are a type of diagram that is convenient to illustrate how
5250 flow of information, resources etc. separates and joins, much like observing
5251 how rivers split and merge. For example, they can be used to compare
5252 different clusterings. This package provides an implementation of Sankey
5254 (license license:gpl2+)))
5256 (define-public r-dyn
5263 (uri (cran-uri "dyn" version))
5266 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5267 (build-system r-build-system)
5269 `(("r-zoo" ,r-zoo)))
5270 (home-page "https://cran.r-project.org/web/packages/dyn")
5271 (synopsis "Time series regression")
5273 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5274 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5275 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5276 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5277 @code{randomForest::randomForest()} and other regression functions, allowing
5278 those functions to be used with time series including specifications that may
5279 contain lags, diffs and missing values.")
5281 (license license:gpl2+)))
5283 (define-public r-catdap
5290 (uri (cran-uri "catdap" version))
5293 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5294 (build-system r-build-system)
5296 `(("gfortran" ,gfortran)))
5297 (home-page "https://cran.r-project.org/web/packages/catdap/")
5298 (synopsis "Tools for categorical data analysis")
5300 "This package provides functions for analyzing multivariate data.
5301 Dependencies of the distribution of the specified variable (response
5302 variable) to other variables (explanatory variables) are derived and
5303 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5304 (license license:gpl2+)))
5306 (define-public r-arules
5313 (uri (cran-uri "arules" version))
5316 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5317 (build-system r-build-system)
5319 `(("r-matrix" ,r-matrix)))
5320 (home-page "https://github.com/mhahsler/arules")
5321 (synopsis "Mining association rules and frequent itemsets")
5323 "This package provides an infrastructure for representing, manipulating
5324 and analyzing transaction data and patterns (frequent itemsets and association rules).
5325 It also provides C implementations of the association mining algorithms Apriori
5327 (license license:gpl3)))
5329 (define-public r-parsedate
5331 (name "r-parsedate")
5336 (uri (cran-uri "parsedate" version))
5339 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5340 (build-system r-build-system)
5342 `(("r-rematch2" ,r-rematch2)))
5343 (home-page "https://github.com/gaborcsardi/parsedate")
5345 "Recognize and parse dates in various formats")
5347 "This package provides three functions for dealing with dates:
5348 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5349 time formats, @code{parse_date} parses dates in unspecified formats,
5350 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5351 (license license:gpl2)))
5353 (define-public r-abc-data
5360 (uri (cran-uri "abc.data" version))
5363 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5364 (properties `((upstream-name . "abc.data")))
5365 (build-system r-build-system)
5366 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5367 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5369 "This package contains data which are used by functions of the abc
5370 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5371 algorithms for performing parameter estimation, model selection, and
5373 (license license:gpl3+)))
5375 (define-public r-abc
5382 (uri (cran-uri "abc" version))
5385 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5386 (build-system r-build-system)
5388 `(("r-abc-data" ,r-abc-data)
5389 ("r-locfit" ,r-locfit)
5392 ("r-quantreg" ,r-quantreg)))
5393 (home-page "https://cran.r-project.org/web/packages/abc/")
5394 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5396 "This package implements several @dfn{Approximate Bayesian
5397 Computation} (ABC) algorithms for performing parameter estimation, model
5398 selection, and goodness-of-fit. Cross-validation tools are also available for
5399 measuring the accuracy of ABC estimates, and to calculate the
5400 misclassification probabilities of different models.")
5401 (license license:gpl3+)))
5403 (define-public r-zip
5410 (uri (cran-uri "zip" version))
5413 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5414 (build-system r-build-system)
5415 (home-page "https://github.com/gaborcsardi/zip")
5416 (synopsis "Cross-platform Zip compression")
5418 "This package provides a cross-platform Zip compression library for R.
5419 It is a replacement for the @code{zip} function, that does not require any
5420 additional external tools on any platform.")
5421 (license license:cc0)))
5423 (define-public r-openxlsx
5430 (uri (cran-uri "openxlsx" version))
5433 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5434 (build-system r-build-system)
5436 `(("r-rcpp" ,r-rcpp)
5437 ("r-stringi" ,r-stringi)
5439 (home-page "https://github.com/awalker89/openxlsx")
5440 (synopsis "Read, write and edit XLSX files")
5442 "This package simplifies the creation of Excel @code{.xlsx} files by
5443 providing a high level interface to writing, styling and editing worksheets.
5444 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5445 and @code{XLConnect} packages with the added benefit of removing the
5446 dependency on Java.")
5447 (license license:gpl3)))
5449 (define-public r-rio
5456 (uri (cran-uri "rio" version))
5459 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5460 (build-system r-build-system)
5462 `(("r-curl" ,r-curl)
5463 ("r-data-table" ,r-data-table)
5464 ("r-foreign" ,r-foreign)
5465 ("r-haven" ,r-haven)
5466 ("r-openxlsx" ,r-openxlsx)
5467 ("r-readxl" ,r-readxl)
5468 ("r-tibble" ,r-tibble)))
5469 (home-page "https://github.com/leeper/rio")
5470 (synopsis "Swiss-army knife for data I/O")
5472 "This package provides streamlined data import and export infrastructure
5473 by making assumptions that the user is probably willing to make: @code{import}
5474 and @code{export} determine the data structure from the file extension,
5475 reasonable defaults are used for data import and export (e.g.,
5476 @code{stringsAsFactors=FALSE}), web-based import is natively
5477 supported (including from SSL/HTTPS), compressed files can be read directly
5478 without explicit decompression, and fast import packages are used where
5479 appropriate. An additional convenience function, @code{convert}, provides a
5480 simple method for converting between file types.")
5481 (license license:gpl2)))
5483 (define-public r-maptools
5490 (uri (cran-uri "maptools" version))
5493 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5494 (build-system r-build-system)
5496 `(("r-foreign" ,r-foreign)
5497 ("r-lattice" ,r-lattice)
5499 (home-page "http://r-forge.r-project.org/projects/maptools/")
5500 (synopsis "Tools for reading and handling spatial objects")
5502 "This package provides a set of tools for manipulating and reading
5503 geographic data, in particular ESRI Shapefiles. It includes binary access to
5504 GSHHG shoreline files. The package also provides interface wrappers for
5505 exchanging spatial objects with other R packages.")
5506 ;; The C source files from shapelib are released under the Expat license.
5507 ;; The R code is released under GPL version 2 or later.
5508 (license (list license:gpl2+
5511 (define-public r-later
5518 (uri (cran-uri "later" version))
5521 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5522 (build-system r-build-system)
5526 ("r-rlang" ,r-rlang)))
5527 (home-page "https://github.com/r-lib/later")
5528 (synopsis "Utilities for delaying function execution")
5530 "This package provides tools to execute arbitrary R or C functions some
5531 time after the current time, after the R execution stack has emptied.")
5532 (license license:gpl2+)))
5534 (define-public r-promises
5541 (uri (cran-uri "promises" version))
5544 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5545 (build-system r-build-system)
5547 `(("r-later" ,r-later)
5548 ("r-magrittr" ,r-magrittr)
5551 ("r-rlang" ,r-rlang)))
5552 (home-page "https://rstudio.github.io/promises")
5553 (synopsis "Abstractions for promise-based asynchronous programming")
5555 "This package provides fundamental abstractions for doing asynchronous
5556 programming in R using promises. Asynchronous programming is useful for
5557 allowing a single R process to orchestrate multiple tasks in the background
5558 while also attending to something else. Semantics are similar to JavaScript
5559 promises, but with a syntax that is idiomatic R.")
5560 (license license:expat)))
5562 (define-public r-dosnow
5569 (uri (cran-uri "doSNOW" version))
5572 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5573 (properties `((upstream-name . "doSNOW")))
5574 (build-system r-build-system)
5576 `(("r-foreach" ,r-foreach)
5577 ("r-iterators" ,r-iterators)
5578 ("r-snow" ,r-snow)))
5579 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5580 (synopsis "Foreach parallel adaptor for the snow package")
5582 "This package provides a parallel backend for the @code{%dopar%} function
5583 using the @code{snow} package.")
5584 (license license:gpl2)))
5586 (define-public r-snowfall
5589 (version "1.84-6.1")
5592 (uri (cran-uri "snowfall" version))
5594 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5595 (build-system r-build-system)
5597 `(("r-snow" ,r-snow)))
5598 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5599 (synopsis "Easier cluster computing")
5600 (description "This package is a usability wrapper around snow for easier
5601 development of parallel R programs. This package offers e.g. extended error
5602 checks, and additional functions. All functions work in sequential mode, too,
5603 if no cluster is present or wished. The package is also designed as connector
5604 to the cluster management tool @code{sfCluster}, but can also used without
5606 (license license:gpl2+)))
5608 (define-public r-rappdirs
5615 (uri (cran-uri "rappdirs" version))
5618 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5619 (build-system r-build-system)
5620 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5621 (synopsis "Determine where to save data, caches, and logs")
5623 "This package provides an easy way to determine which directories on the
5624 user's computer should be used to save data, caches and logs. It is a port of
5625 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5626 (license license:expat)))
5628 (define-public r-renv
5635 (uri (cran-uri "renv" version))
5638 "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm"))))
5639 (properties `((upstream-name . "renv")))
5640 (build-system r-build-system)
5641 (home-page "https://rstudio.github.io/renv")
5642 (synopsis "Project environments")
5644 "This package provides a dependency management toolkit for R. Using
5645 renv, you can create and manage project-local R libraries, save the state of
5646 these libraries to a lockfile, and later restore your library as required.
5647 Together, these tools can help make your projects more isolated, portable, and
5649 (license license:expat)))
5651 (define-public r-learnr
5658 (uri (cran-uri "learnr" version))
5661 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5662 (build-system r-build-system)
5664 `(("r-checkmate" ,r-checkmate)
5665 ("r-ellipsis" ,r-ellipsis)
5666 ("r-evaluate" ,r-evaluate)
5667 ("r-htmltools" ,r-htmltools)
5668 ("r-htmlwidgets" ,r-htmlwidgets)
5669 ("r-jsonlite" ,r-jsonlite)
5670 ("r-knitr" ,r-knitr)
5671 ("r-markdown" ,r-markdown)
5672 ("r-rappdirs" ,r-rappdirs)
5674 ("r-rmarkdown" ,r-rmarkdown)
5675 ("r-rprojroot" ,r-rprojroot)
5676 ("r-shiny" ,r-shiny)
5677 ("r-withr" ,r-withr)))
5678 (home-page "https://rstudio.github.io/learnr/")
5679 (synopsis "Interactive tutorials for R")
5681 "This package provides tools to create interactive tutorials using R
5682 Markdown. Use a combination of narrative, figures, videos, exercises, and
5683 quizzes to create self-paced tutorials for learning about R and R packages.")
5684 (license license:asl2.0)))
5686 (define-public r-analytics
5688 (name "r-analytics")
5693 (uri (cran-uri "analytics" version))
5696 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5697 (build-system r-build-system)
5700 ("r-cluster" ,r-cluster)
5701 ("r-fractal" ,r-fractal)
5702 ("r-lmtest" ,r-lmtest)
5705 ("r-powerplus" ,r-powerplus)
5706 ("r-robust" ,r-robust)
5707 ("r-trend" ,r-trend)
5711 (home-page "https://cran.r-project.org/web/packages/analytics/")
5712 (synopsis "Collection of data analysis tools")
5714 "This package is a collection of data analysis tools. It includes tools
5715 for regression outlier detection in a fitted linear model, stationary
5716 bootstrap using a truncated geometric distribution, a comprehensive test for
5717 weak stationarity, column means by group, weighted biplots, and a heuristic to
5718 obtain a better initial configuration in non-metric MDS.")
5719 (license license:gpl2)))
5721 (define-public r-reticulate
5723 (name "r-reticulate")
5728 (uri (cran-uri "reticulate" version))
5731 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5732 (build-system r-build-system)
5733 (inputs `(("python" ,python)))
5735 `(("r-jsonlite" ,r-jsonlite)
5736 ("r-matrix" ,r-matrix)
5737 ("r-rcpp" ,r-rcpp)))
5738 (home-page "https://github.com/rstudio/reticulate")
5739 (synopsis "R interface to Python")
5741 "This package provides an interface from R to Python modules, classes,
5742 and functions. When calling into Python, R data types are automatically
5743 converted to their equivalent Python types. When values are returned from
5744 Python to R they are converted back to R types.")
5745 (license license:asl2.0)))
5747 (define-public r-bibtex
5754 (uri (cran-uri "bibtex" version))
5757 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5758 (build-system r-build-system)
5759 (propagated-inputs `(("r-stringr" ,r-stringr)))
5760 (home-page "https://github.com/romainfrancois/bibtex")
5761 (synopsis "Bibtex parser")
5762 (description "This package provides a utility for R to parse a bibtex
5764 (license license:gpl2+)))
5766 (define-public r-ggseqlogo
5768 (name "r-ggseqlogo")
5773 (uri (cran-uri "ggseqlogo" version))
5776 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5777 (build-system r-build-system)
5778 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5779 (home-page "https://github.com/omarwagih/ggseqlogo")
5780 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5782 "The range of functions provided by this package makes it possible to
5783 draw highly versatile genomic sequence logos. Features include, but are not
5784 limited to, modifying colour schemes and fonts used to draw the logo,
5785 generating multiple logo plots, and aiding the visualisation with annotations.
5786 Sequence logos can easily be combined with other ggplot2 plots.")
5787 ;; Unspecified version of the LGPL.
5788 (license license:lgpl3+)))
5790 (define-public r-ggsci
5797 (uri (cran-uri "ggsci" version))
5800 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5801 (build-system r-build-system)
5803 `(("r-ggplot2" ,r-ggplot2)
5804 ("r-scales" ,r-scales)))
5805 (home-page "https://nanx.me/ggsci/")
5806 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5808 "This package provides a collection of ggplot2 color palettes inspired by
5809 plots in scientific journals, data visualization libraries, science fiction
5810 movies, and TV shows.")
5811 (license license:gpl3)))
5813 (define-public r-ggsignif
5820 (uri (cran-uri "ggsignif" version))
5823 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5824 (build-system r-build-system)
5826 `(("r-ggplot2" ,r-ggplot2)))
5827 (home-page "https://github.com/const-ae/ggsignif")
5828 (synopsis "Significance brackets for ggplot2")
5830 "Enrich your ggplots with group-wise comparisons. This package provides
5831 an easy way to indicate if two groups are significantly different. Commonly
5832 this is shown by a bracket on top connecting the groups of interest which
5833 itself is annotated with the level of significance. The package provides a
5834 single layer that takes the groups for comparison and the test as arguments
5835 and adds the annotation to the plot.")
5836 (license license:gpl3)))
5838 (define-public r-ggpubr
5845 (uri (cran-uri "ggpubr" version))
5848 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5849 (build-system r-build-system)
5851 `(("r-cowplot" ,r-cowplot)
5852 ("r-dplyr" ,r-dplyr)
5853 ("r-ggplot2" ,r-ggplot2)
5854 ("r-ggrepel" ,r-ggrepel)
5855 ("r-ggsci" ,r-ggsci)
5856 ("r-ggsignif" ,r-ggsignif)
5858 ("r-gridextra" ,r-gridextra)
5859 ("r-magrittr" ,r-magrittr)
5860 ("r-polynom" ,r-polynom)
5861 ("r-purrr" ,r-purrr)
5862 ("r-rlang" ,r-rlang)
5863 ("r-scales" ,r-scales)
5864 ("r-tidyr" ,r-tidyr)))
5865 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5866 (synopsis "ggplot2-based publication-ready plots")
5868 "The ggplot2 package is an excellent and flexible package for elegant
5869 data visualization in R. However the default generated plots require some
5870 formatting before we can send them for publication. The ggpubr package
5871 provides some easy-to-use functions for creating and customizing ggplot2-based
5872 publication-ready plots.")
5873 (license license:gpl2)))
5875 (define-public r-ellipse
5882 (uri (cran-uri "ellipse" version))
5885 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5886 (build-system r-build-system)
5887 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5888 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5890 "This package contains various routines for drawing ellipses and
5891 ellipse-like confidence regions, implementing the plots described in Murdoch
5892 and Chow (1996), A graphical display of large correlation matrices, The
5893 American Statistician 50, 178-180. There are also routines implementing the
5894 profile plots described in Bates and Watts (1988), Nonlinear Regression
5895 Analysis and its Applications.")
5896 (license license:gpl2+)))
5898 (define-public r-flashclust
5900 (name "r-flashclust")
5905 (uri (cran-uri "flashClust" version))
5908 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5909 (properties `((upstream-name . "flashClust")))
5910 (build-system r-build-system)
5911 (native-inputs `(("gfortran" ,gfortran)))
5912 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5913 (synopsis "Implementation of optimal hierarchical clustering")
5915 "This package provides a fast implementation of hierarchical
5917 (license license:gpl2+)))
5919 (define-public r-factominer
5921 (name "r-factominer")
5926 (uri (cran-uri "FactoMineR" version))
5929 "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
5930 (properties `((upstream-name . "FactoMineR")))
5931 (build-system r-build-system)
5934 ("r-cluster" ,r-cluster)
5935 ("r-ellipse" ,r-ellipse)
5936 ("r-flashclust" ,r-flashclust)
5937 ("r-ggplot2" ,r-ggplot2)
5938 ("r-ggrepel" ,r-ggrepel)
5939 ("r-lattice" ,r-lattice)
5940 ("r-leaps" ,r-leaps)
5942 ("r-scatterplot3d" ,r-scatterplot3d)))
5943 (home-page "http://factominer.free.fr")
5944 (synopsis "Multivariate exploratory data analysis and data mining")
5946 "This package provides exploratory data analysis methods to summarize,
5947 visualize and describe datasets. The main principal component methods are
5948 available, those with the largest potential in terms of applications:
5949 principal component analysis (PCA) when variables are quantitative,
5950 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5951 variables are categorical, Multiple Factor Analysis when variables are
5952 structured in groups, etc. and hierarchical cluster analysis.")
5953 (license license:gpl2+)))
5955 (define-public r-factoextra
5957 (name "r-factoextra")
5962 (uri (cran-uri "factoextra" version))
5965 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5966 (build-system r-build-system)
5968 `(("r-abind" ,r-abind)
5969 ("r-cluster" ,r-cluster)
5970 ("r-dendextend" ,r-dendextend)
5971 ("r-factominer" ,r-factominer)
5972 ("r-ggplot2" ,r-ggplot2)
5973 ("r-ggpubr" ,r-ggpubr)
5974 ("r-ggrepel" ,r-ggrepel)
5975 ("r-reshape2" ,r-reshape2)
5976 ("r-tidyr" ,r-tidyr)))
5977 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5978 (synopsis "Extract and visualize the results of multivariate data analyses")
5980 "This package provides some easy-to-use functions to extract and
5981 visualize the output of multivariate data analyses, including
5982 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5983 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5984 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5985 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5986 packages. It contains also functions for simplifying some clustering analysis
5987 steps and provides ggplot2-based elegant data visualization.")
5988 (license license:gpl2)))
5990 (define-public r-fansi
5997 (uri (cran-uri "fansi" version))
6000 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
6001 (build-system r-build-system)
6003 `(("r-knitr" ,r-knitr))) ; for vignettes
6004 (home-page "https://github.com/brodieG/fansi")
6005 (synopsis "ANSI control sequence aware string functions")
6007 "This package provides counterparts to R string manipulation functions
6008 that account for the effects of ANSI text formatting control sequences.")
6009 (license license:gpl2+)))
6011 (define-public r-nbclust
6018 (uri (cran-uri "NbClust" version))
6021 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6022 (properties `((upstream-name . "NbClust")))
6023 (build-system r-build-system)
6024 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6025 (synopsis "Determine the best number of clusters in a data set")
6027 "NbClust provides 30 indexes for determining the optimal number of
6028 clusters in a data set and offers the best clustering scheme from different
6029 results to the user.")
6030 (license license:gpl2)))
6032 (define-public r-hdf5r
6039 (uri (cran-uri "hdf5r" version))
6042 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
6043 (build-system r-build-system)
6048 `(("r-bit64" ,r-bit64)
6050 (home-page "https://hhoeflin.github.io/hdf5r")
6051 (synopsis "Interface to the HDF5 binary data format")
6053 "HDF5 is a data model, library and file format for storing and managing
6054 large amounts of data. This package provides a nearly feature complete,
6055 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6056 functionality is added so that HDF5 objects behave very similar to their
6057 corresponding R counterparts.")
6058 (license license:asl2.0)))
6060 (define-public r-itertools
6062 (name "r-itertools")
6067 (uri (cran-uri "itertools" version))
6070 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6071 (build-system r-build-system)
6073 `(("r-iterators" ,r-iterators)))
6074 (home-page "https://cran.r-project.org/web/packages/itertools/")
6075 (synopsis "Iterator tools")
6077 "This package provides various tools for creating iterators, many
6078 patterned after functions in the Python @code{itertools} module, and others
6079 patterned after functions in the snow package.")
6080 (license license:gpl2)))
6082 (define-public r-polynom
6089 (uri (cran-uri "polynom" version))
6092 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6093 (build-system r-build-system)
6094 (home-page "https://cran.r-project.org/web/packages/polynom/")
6095 (synopsis "Functions for univariate polynomial manipulations")
6097 "This package provides a collection of functions to implement a class for
6098 univariate polynomial manipulations.")
6099 (license license:gpl2)))
6101 (define-public r-gbrd
6108 (uri (cran-uri "gbRd" version))
6111 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6112 (properties `((upstream-name . "gbRd")))
6113 (build-system r-build-system)
6114 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6115 (synopsis "Utilities for processing Rd objects and files")
6117 "This package provides utilities for processing Rd objects and files.
6118 Extract argument descriptions and other parts of the help pages of
6120 (license license:gpl2+)))
6122 (define-public r-rjags
6129 (uri (cran-uri "rjags" version))
6132 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6133 (build-system r-build-system)
6135 `(("r-coda" ,r-coda)))
6139 `(("pkg-config" ,pkg-config)))
6140 (home-page "http://mcmc-jags.sourceforge.net")
6141 (synopsis "Bayesian graphical models using MCMC")
6143 "This package provides an R interface to the JAGS MCMC library. JAGS is
6144 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6145 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6146 (license license:gpl2)))
6148 (define-public r-rdpack
6155 (uri (cran-uri "Rdpack" version))
6158 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
6159 (properties `((upstream-name . "Rdpack")))
6160 (build-system r-build-system)
6162 `(("r-bibtex" ,r-bibtex)
6163 ("r-gbrd" ,r-gbrd)))
6164 (home-page "https://github.com/GeoBosh/Rdpack")
6165 (synopsis "Update and manipulate Rd documentation objects")
6167 "This package provides functions for manipulation of R documentation
6168 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6169 updating Rd documentation for functions, methods and classes; it also includes
6170 Rd macros for citations and import of references from bibtex files for use in
6171 Rd files and roxygen2 comments, as well as many functions for manipulation of
6172 references and Rd files.")
6173 (license license:gpl2+)))
6175 (define-public r-officer
6182 (uri (cran-uri "officer" version))
6185 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6186 (build-system r-build-system)
6188 `(("r-base64enc" ,r-base64enc)
6189 ("r-digest" ,r-digest)
6190 ("r-htmltools" ,r-htmltools)
6191 ("r-magrittr" ,r-magrittr)
6194 ("r-rlang" ,r-rlang)
6198 (home-page "https://davidgohel.github.io/officer")
6199 (synopsis "Manipulation of Word and PowerPoint documents")
6201 "This package provides tools to access and manipulate Word and PowerPoint
6202 documents from R. The package focuses on tabular and graphical reporting from
6203 R; it also provides two functions that let users get document content into
6204 data objects. A set of functions lets add and remove images, tables and
6205 paragraphs of text in new or existing documents. When working with PowerPoint
6206 presentations, slides can be added or removed; shapes inside slides can also
6207 be added or removed. When working with Word documents, a cursor can be used
6208 to help insert or delete content at a specific location in the document.")
6209 (license license:gpl3)))
6211 (define-public r-abn
6218 (uri (cran-uri "abn" version))
6221 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6222 (build-system r-build-system)
6226 `(("r-lme4" ,r-lme4)
6230 ("r-rcpparmadillo" ,r-rcpparmadillo)
6231 ("r-rjags" ,r-rjags)))
6232 (home-page "http://www.r-bayesian-networks.org")
6233 (synopsis "Modelling multivariate data with additive bayesian networks")
6235 "Bayesian network analysis is a form of probabilistic graphical models
6236 which derives from empirical data a directed acyclic graph, DAG, describing
6237 the dependency structure between random variables. An additive Bayesian
6238 network model consists of a form of a DAG where each node comprises a
6239 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6240 equivalent to Bayesian multivariate regression using graphical modelling, they
6241 generalises the usual multivariable regression, GLM, to multiple dependent
6242 variables. This package provides routines to help determine optimal Bayesian
6243 network models for a given data set, where these models are used to identify
6244 statistical dependencies in messy, complex data.")
6245 (license license:gpl2+)))
6247 (define-public r-acd
6254 (uri (cran-uri "ACD" version))
6257 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6258 (properties `((upstream-name . "ACD")))
6259 (build-system r-build-system)
6260 (home-page "https://cran.r-project.org/web/packages/ACD/")
6261 (synopsis "Categorical data analysis with complete or missing responses")
6263 "This package provides tools for categorical data analysis with complete
6264 or missing responses.")
6265 (license license:gpl2+)))
6267 (define-public r-acdm
6274 (uri (cran-uri "ACDm" version))
6277 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6278 (properties `((upstream-name . "ACDm")))
6279 (build-system r-build-system)
6281 `(("r-dplyr" ,r-dplyr)
6282 ("r-ggplot2" ,r-ggplot2)
6284 ("r-rsolnp" ,r-rsolnp)
6286 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6287 (synopsis "Tools for Autoregressive Conditional Duration Models")
6289 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6290 and Russell, 1998) models. It creates trade, price or volume durations from
6291 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6293 (license license:gpl2+)))
6295 (define-public r-overlap
6302 (uri (cran-uri "overlap" version))
6305 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6306 (build-system r-build-system)
6307 (home-page "https://cran.r-project.org/web/packages/overlap/")
6308 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6310 "This package provides functions to fit kernel density functions to data
6311 on temporal activity patterns of animals; estimate coefficients of overlapping
6312 of densities for two species; and calculate bootstrap estimates of confidence
6314 (license license:gpl3+)))
6316 (define-public r-snakecase
6318 (name "r-snakecase")
6323 (uri (cran-uri "snakecase" version))
6326 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6327 (build-system r-build-system)
6329 `(("r-stringi" ,r-stringi)
6330 ("r-stringr" ,r-stringr)))
6331 (home-page "https://github.com/Tazinho/snakecase")
6332 (synopsis "Convert strings into any case")
6334 "This package provides a consistent, flexible and easy to use tool to
6335 parse and convert strings into cases like snake or camel among others.")
6336 (license license:gpl3)))
6338 (define-public r-prediction
6340 (name "r-prediction")
6345 (uri (cran-uri "prediction" version))
6348 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6349 (build-system r-build-system)
6351 `(("r-data-table" ,r-data-table)))
6352 (home-page "https://github.com/leeper/prediction")
6353 (synopsis "Tidy, type-safe prediction methods")
6355 "This package provides the @code{prediction()} function, a type-safe
6356 alternative to @code{predict()} that always returns a data frame. The package
6357 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6358 from the @code{stats} package, as well as numerous other model classes from
6359 other add-on packages.")
6360 (license license:expat)))
6362 (define-public r-insight
6369 (uri (cran-uri "insight" version))
6372 "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad"))))
6373 (build-system r-build-system)
6374 (home-page "https://easystats.github.io/insight/")
6375 (synopsis "Easy access to model information for various model objects")
6377 "This package provides a tool to provide an easy, intuitive and
6378 consistent access to information contained in various R models, like model
6379 formulas, model terms, information about random effects, data that was used to
6380 fit the model or data from response variables. The package mainly revolves
6381 around two types of functions: Functions that find (the names of) information,
6382 starting with @code{find_}, and functions that get the underlying data,
6383 starting with @code{get_}. The package has a consistent syntax and works with
6384 many different model objects, where otherwise functions to access these
6385 information are missing.")
6386 (license license:gpl3)))
6388 (define-public r-sjlabelled
6390 (name "r-sjlabelled")
6395 (uri (cran-uri "sjlabelled" version))
6398 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6399 (build-system r-build-system)
6401 `(("r-haven" ,r-haven)
6402 ("r-insight" ,r-insight)
6403 ("r-magrittr" ,r-magrittr)
6404 ("r-purrr" ,r-purrr)
6405 ("r-rlang" ,r-rlang)
6406 ("r-tidyselect" ,r-tidyselect)))
6407 (home-page "https://github.com/strengejacke/sjlabelled")
6408 (synopsis "Labelled data utility functions")
6410 "This package provides a collection of functions dealing with labelled
6411 data, like reading and writing data between R and other statistical software
6412 packages. This includes easy ways to get, set or change value and variable
6413 label attributes, to convert labelled vectors into factors or numeric (and
6414 vice versa), or to deal with multiple declared missing values.")
6415 (license license:gpl3)))
6417 (define-public r-sjmisc
6424 (uri (cran-uri "sjmisc" version))
6427 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6428 (build-system r-build-system)
6430 `(("r-dplyr" ,r-dplyr)
6431 ("r-insight" ,r-insight)
6432 ("r-magrittr" ,r-magrittr)
6433 ("r-purrr" ,r-purrr)
6434 ("r-rlang" ,r-rlang)
6435 ("r-sjlabelled" ,r-sjlabelled)
6436 ("r-tidyselect" ,r-tidyselect)))
6437 (home-page "https://github.com/strengejacke/sjmisc")
6438 (synopsis "Data and variable transformation functions")
6440 "This package is a collection of miscellaneous utility functions,
6441 supporting data transformation tasks like recoding, dichotomizing or grouping
6442 variables, setting and replacing missing values. The data transformation
6443 functions also support labelled data, and all integrate seamlessly into a
6444 tidyverse workflow.")
6445 (license license:gpl3)))
6447 (define-public r-nortest
6454 (uri (cran-uri "nortest" version))
6457 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6458 (build-system r-build-system)
6459 (home-page "https://cran.r-project.org/web/packages/nortest/")
6460 (synopsis "Tests for normality")
6462 "This package provides five omnibus tests for testing the composite
6463 hypothesis of normality.")
6464 (license license:gpl2+)))
6466 (define-public r-moonbook
6473 (uri (cran-uri "moonBook" version))
6476 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6477 (properties `((upstream-name . "moonBook")))
6478 (build-system r-build-system)
6480 `(("r-magrittr" ,r-magrittr)
6481 ("r-nortest" ,r-nortest)
6482 ("r-purrr" ,r-purrr)
6483 ("r-sjmisc" ,r-sjmisc)
6484 ("r-stringr" ,r-stringr)
6485 ("r-survival" ,r-survival)))
6486 (home-page "https://github.com/cardiomoon/moonBook")
6487 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6489 "This package provides several analysis-related functions for the book
6490 entitled \"R statistics and graph for medical articles\" (written in Korean),
6491 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6493 (license license:gpl2)))
6495 (define-public r-flextable
6497 (name "r-flextable")
6502 (uri (cran-uri "flextable" version))
6505 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6506 (build-system r-build-system)
6508 `(("r-base64enc" ,r-base64enc)
6509 ("r-data-table" ,r-data-table)
6510 ("r-gdtools" ,r-gdtools)
6511 ("r-htmltools" ,r-htmltools)
6512 ("r-knitr" ,r-knitr)
6513 ("r-officer" ,r-officer)
6514 ("r-rlang" ,r-rlang)
6515 ("r-rmarkdown" ,r-rmarkdown)
6516 ("r-xml2" ,r-xml2)))
6517 (home-page "https://davidgohel.github.io/flextable")
6518 (synopsis "Functions for tabular reporting")
6520 "This package provides tools to create pretty tables for HTML documents
6521 and other formats. Functions are provided to let users create tables, modify
6522 and format their content. It extends the @code{officer} package and can be
6523 used within R markdown documents when rendering to HTML and to Word
6525 (license license:gpl3)))
6527 (define-public r-writexl
6534 (uri (cran-uri "writexl" version))
6537 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6538 (build-system r-build-system)
6539 (inputs `(("zlib" ,zlib)))
6540 (home-page "https://github.com/ropensci/writexl")
6541 (synopsis "Export data frames to xlsx format")
6543 "This package provides a data frame to xlsx exporter based on
6545 (license license:bsd-2)))
6547 (define-public r-biasedurn
6549 (name "r-biasedurn")
6554 (uri (cran-uri "BiasedUrn" version))
6557 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6558 (properties `((upstream-name . "BiasedUrn")))
6559 (build-system r-build-system)
6560 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6561 (synopsis "Biased Urn model distributions")
6563 "This package provides statistical models of biased sampling in the form
6564 of univariate and multivariate noncentral hypergeometric distributions,
6565 including Wallenius' noncentral hypergeometric distribution and Fisher's
6566 noncentral hypergeometric distribution (also called extended hypergeometric
6568 (license license:gpl3)))
6570 (define-public r-goplot
6577 (uri (cran-uri "GOplot" version))
6580 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6581 (properties `((upstream-name . "GOplot")))
6582 (build-system r-build-system)
6584 `(("r-ggdendro" ,r-ggdendro)
6585 ("r-ggplot2" ,r-ggplot2)
6586 ("r-gridextra" ,r-gridextra)
6587 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6588 (home-page "https://github.com/wencke/wencke.github.io")
6589 (synopsis "Visualization of functional analysis data")
6591 "This package provides an implementation of multilayered visualizations
6592 for enhanced graphical representation of functional analysis data. It
6593 combines and integrates omics data derived from expression and functional
6594 annotation enrichment analyses. Its plotting functions have been developed
6595 with an hierarchical structure in mind: starting from a general overview to
6596 identify the most enriched categories (modified bar plot, bubble plot) to a
6597 more detailed one displaying different types of relevant information for the
6598 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6599 Venn diagram, heatmap).")
6600 (license license:gpl2)))
6602 (define-public r-getopt
6609 (uri (cran-uri "getopt" version))
6612 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6613 (build-system r-build-system)
6614 (home-page "https://github.com/trevorld/getopt")
6615 (synopsis "Command-line option processor for R")
6617 "This package is designed to be used with Rscript to write shebang
6618 scripts that accept short and long options. Many users will prefer to
6619 use the packages @code{optparse} or @code{argparse} which add extra
6620 features like automatically generated help options and usage texts,
6621 support for default values, positional argument support, etc.")
6622 (license license:gpl2+)))
6624 (define-public r-findpython
6626 (name "r-findpython")
6631 (uri (cran-uri "findpython" version))
6634 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6635 (build-system r-build-system)
6636 (home-page "https://github.com/trevorld/findpython")
6637 (synopsis "Functions to find an acceptable Python binary")
6639 "This package was designed to find an acceptable Python binary that
6640 matches version and feature constraints.")
6641 (license license:expat)))
6643 ;; This in not the same as "r-argparser"
6644 (define-public r-argparse
6651 (uri (cran-uri "argparse" version))
6654 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6655 (build-system r-build-system)
6656 (inputs `(("python" ,python)))
6658 `(("r-findpython" ,r-findpython)
6659 ("r-jsonlite" ,r-jsonlite)
6661 (home-page "https://github.com/trevorld/argparse")
6662 (synopsis "Command line optional and positional argument parser")
6664 "This package provides a command line parser to be used with Rscript to
6665 write shebang scripts that gracefully accept positional and optional arguments
6666 and automatically generate usage notices.")
6667 (license license:gpl2+)))
6669 (define-public r-hash
6676 (uri (cran-uri "hash" version))
6679 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6680 (build-system r-build-system)
6681 (home-page "https://cran.r-project.org/web/packages/hash/")
6682 (synopsis "Implementation of hash/associated arrays/dictionaries")
6684 "This package implements a data structure similar to hashes in Perl and
6685 dictionaries in Python but with a purposefully R flavor. For objects of
6686 appreciable size, access using hashes outperforms native named lists and
6688 (license license:gpl2+)))
6690 (define-public r-orddom
6697 (uri (cran-uri "orddom" version))
6700 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6701 (build-system r-build-system)
6702 (propagated-inputs `(("r-psych" ,r-psych)))
6703 (home-page "https://cran.r-project.org/web/packages/orddom/")
6704 (synopsis "Ordinal dominance statistics")
6706 "This package provides tools to compute ordinal, statistics and effect
6707 sizes as an alternative to mean comparison: Cliff's delta or success rate
6708 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6709 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6710 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6711 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6712 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6713 Group (Non-)Overlap considerations.")
6714 (license license:gpl2)))
6716 (define-public r-deriv
6723 (uri (cran-uri "Deriv" version))
6726 "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
6727 (properties `((upstream-name . "Deriv")))
6728 (build-system r-build-system)
6729 (home-page "https://cran.r-project.org/web/packages/Deriv")
6730 (synopsis "Symbolic differentiation")
6732 "This package provides an R-based solution for symbolic differentiation.
6733 It admits user-defined functions as well as function substitution in arguments
6734 of functions to be differentiated. Some symbolic simplification is part of
6736 (license license:gpl3+)))
6738 (define-public r-doby
6745 (uri (cran-uri "doBy" version))
6748 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6749 (properties `((upstream-name . "doBy")))
6750 (build-system r-build-system)
6752 `(("r-broom" ,r-broom)
6753 ("r-deriv" ,r-deriv)
6754 ("r-dplyr" ,r-dplyr)
6755 ("r-magrittr" ,r-magrittr)
6757 ("r-matrix" ,r-matrix)
6759 ("r-pbkrtest" ,r-pbkrtest)
6760 ("r-tibble" ,r-tibble)))
6761 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6762 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6764 "This package contains:
6767 @item facilities for working with grouped data: @code{do}
6768 something to data stratified @code{by} some variables.
6769 @item implementations of least-squares means, general linear contrasts, and
6770 @item miscellaneous other utilities.
6772 (license license:gpl2+)))
6774 (define-public r-refgenome
6776 (name "r-refgenome")
6781 (uri (cran-uri "refGenome" version))
6784 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6785 (properties `((upstream-name . "refGenome")))
6786 (build-system r-build-system)
6790 ("r-rsqlite" ,r-rsqlite)))
6791 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6793 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6795 "This package contains functionality for importing and managing of
6796 downloaded genome annotation data from the Ensembl genome browser (European
6797 Bioinformatics Institute) and from the UCSC genome browser (University of
6798 California, Santa Cruz) and annotation routines for genomic positions and
6799 splice site positions.")
6800 (license license:gpl2)))
6802 (define-public r-basix
6809 (uri (cran-uri "BASIX" version))
6812 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6813 (properties `((upstream-name . "BASIX")))
6814 (build-system r-build-system)
6815 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6816 (synopsis "Efficient C/C++ toolset for R")
6818 "BASIX provides some efficient C/C++ implementations of native R
6819 procedures to speed up calculations in R.")
6820 (license license:gpl2)))
6822 (define-public r-blockfest
6824 (name "r-blockfest")
6829 (uri (cran-uri "BlockFeST" version))
6832 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6833 (properties `((upstream-name . "BlockFeST")))
6834 (build-system r-build-system)
6835 (propagated-inputs `(("r-basix" ,r-basix)))
6836 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6837 (synopsis "Bayesian calculation of region-specific fixation index")
6839 "This package provides an R implementation of an extension of the
6840 BayeScan software for codominant markers, adding the option to group
6841 individual SNPs into pre-defined blocks. A typical application of this new
6842 approach is the identification of genomic regions, genes, or gene sets
6843 containing one or more SNPs that evolved under directional selection.")
6844 (license license:gpl2)))
6846 (define-public r-proc
6853 (uri (cran-uri "pROC" version))
6856 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6857 (properties `((upstream-name . "pROC")))
6858 (build-system r-build-system)
6860 `(("r-plyr" ,r-plyr)
6861 ("r-rcpp" ,r-rcpp)))
6862 (home-page "http://expasy.org/tools/pROC/")
6863 (synopsis "Display and analyze ROC curves")
6865 "This package provides tools for visualizing, smoothing and comparing
6866 receiver operating characteristic (ROC curves). The area under the
6867 curve (AUC) can be compared with statistical tests based on U-statistics or
6868 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6869 (license license:gpl3+)))
6871 (define-public r-rootsolve
6873 (name "r-rootsolve")
6878 (uri (cran-uri "rootSolve" version))
6881 "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx"))))
6882 (properties `((upstream-name . "rootSolve")))
6883 (build-system r-build-system)
6884 (native-inputs `(("gfortran" ,gfortran)))
6885 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6886 (synopsis "Tools for the analysis of ordinary differential equations")
6888 "This package provides routines to find the root of nonlinear functions,
6889 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6890 differential equations} (ODE). It includes routines that:
6893 @item generate gradient and jacobian matrices (full and banded),
6894 @item find roots of non-linear equations by the Newton-Raphson method,
6895 @item estimate steady-state conditions of a system of (differential) equations
6896 in full, banded or sparse form, using the Newton-Raphson method, or by
6897 dynamically running,
6898 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6899 and 3-D partial differential equations, that have been converted to ordinary
6900 differential equations by numerical differencing (using the method-of-lines
6903 (license license:gpl2+)))
6905 (define-public r-abcanalysis
6907 (name "r-abcanalysis")
6912 (uri (cran-uri "ABCanalysis" version))
6914 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6915 (properties `((upstream-name . "ABCanalysis")))
6916 (build-system r-build-system)
6917 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6918 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6919 (synopsis "Computed ABC Analysis")
6921 "Multivariate data sets often differ in several factors or derived statistical
6922 parameters, which have to be selected for a valid interpretation. Basing this
6923 selection on traditional statistical limits leads occasionally to the perception
6924 of losing information from a data set. This package provides tools to calculate
6925 these limits on the basis of the mathematical properties of the distribution of
6926 the analyzed items.")
6927 (license license:gpl3)))
6929 (define-public r-slam
6936 (uri (cran-uri "slam" version))
6938 (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
6939 (build-system r-build-system)
6940 (home-page "https://cran.r-project.org/web/packages/slam/")
6941 (synopsis "Sparse lightweight arrays and matrices")
6943 "This package contains data structures and algorithms for sparse arrays and matrices,
6944 based on index arrays and simple triplet representations, respectively.")
6945 (license license:gpl2)))
6947 (define-public r-manipulatewidget
6949 (name "r-manipulatewidget")
6954 (uri (cran-uri "manipulateWidget" version))
6956 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6958 `((upstream-name . "manipulateWidget")))
6959 (build-system r-build-system)
6961 `(("r-base64enc" ,r-base64enc)
6962 ("r-codetools" ,r-codetools)
6963 ("r-htmltools" ,r-htmltools)
6964 ("r-htmlwidgets" ,r-htmlwidgets)
6965 ("r-knitr" ,r-knitr)
6966 ("r-miniui" ,r-miniui)
6967 ("r-shiny" ,r-shiny)
6968 ("r-webshot" ,r-webshot)))
6969 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6970 (synopsis "Add even more interactivity to interactive charts")
6972 "This package lets you create in just a few lines of R code a nice user interface to
6973 modify the data or the graphical parameters of one or multiple interactive
6974 charts. It is useful to quickly explore visually some data or for package
6975 developers to generate user interfaces easy to maintain.")
6976 (license license:gpl2+)))
6985 (uri (cran-uri "A3" version))
6987 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6988 (properties `((upstream-name . "A3")))
6989 (build-system r-build-system)
6991 `(("r-pbapply" ,r-pbapply)
6992 ("r-xtable" ,r-xtable)))
6993 (home-page "https://cran.r-project.org/web/packages/A3/")
6994 (synopsis "Error metrics for predictive models")
6996 "This package supplies tools for tabulating and analyzing the results of predictive
6997 models. The methods employed are applicable to virtually any predictive model
6998 and make comparisons between different methodologies straightforward.")
6999 (license license:gpl2+)))
7001 (define-public r-infotheo
7008 (uri (cran-uri "infotheo" version))
7011 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7012 (build-system r-build-system)
7013 (home-page "http://homepage.meyerp.com/software")
7014 (synopsis "Information-theoretic measures")
7016 "This package implements various measures of information theory based on
7017 several entropy estimators.")
7018 (license license:gpl3+)))
7020 (define-public r-abcoptim
7027 (uri (cran-uri "ABCoptim" version))
7029 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7030 (properties `((upstream-name . "ABCoptim")))
7031 (build-system r-build-system)
7032 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7033 (home-page "https://github.com/gvegayon/ABCoptim/")
7034 (synopsis "Optimization of Artificial Bee Colony algorithm")
7036 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7037 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7038 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7039 algorithms, and uses only common control parameters such as colony size and
7040 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7041 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7042 This version is a work-in-progress and is written in R code.")
7043 (license license:expat)))
7045 (define-public r-abcp2
7052 (uri (cran-uri "ABCp2" version))
7054 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7055 (properties `((upstream-name . "ABCp2")))
7056 (build-system r-build-system)
7057 (propagated-inputs `(("r-mass" ,r-mass)))
7058 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7059 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7061 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7062 Poisson, and Gamma distribution and estimates the proportional paternity of the
7063 second male (P2) based on the best fit distribution.")
7064 (license license:gpl2)))
7066 (define-public r-abcrf
7073 (uri (cran-uri "abcrf" version))
7075 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7076 (build-system r-build-system)
7078 `(("r-doparallel" ,r-doparallel)
7079 ("r-foreach" ,r-foreach)
7081 ("r-matrixstats" ,r-matrixstats)
7082 ("r-ranger" ,r-ranger)
7084 ("r-rcpparmadillo" ,r-rcpparmadillo)
7085 ("r-readr" ,r-readr)
7086 ("r-stringr" ,r-stringr)))
7087 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7088 (synopsis "Approximate bayesian computation via random forests")
7090 "This package performs approximate bayesian computation (ABC) model choice and
7091 parameter inference via random forests. This machine learning tool named random
7092 forests (RF) can conduct selection among the highly complex models covered by
7094 (license license:gpl2+)))
7096 (define-public r-abctools
7103 (uri (cran-uri "abctools" version))
7105 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7106 (build-system r-build-system)
7109 ("r-abind" ,r-abind)
7110 ("r-hmisc" ,r-hmisc)
7111 ("r-plyr" ,r-plyr)))
7112 (home-page "https://github.com/dennisprangle/abctools/")
7113 (synopsis "Tools for ABC analyses")
7115 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7116 including summary statistic selection and assessing coverage. This includes
7117 recent dimension reduction algorithms to tune the choice of summary statistics,
7118 and coverage methods to tune the choice of threshold.")
7119 (license license:gpl2+)))
7121 (define-public r-ggstance
7128 (uri (cran-uri "ggstance" version))
7130 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7131 (build-system r-build-system)
7133 `(("r-ggplot2" ,r-ggplot2)
7135 ("r-rlang" ,r-rlang)
7136 ("r-withr" ,r-withr)))
7137 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7138 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7140 "This package is a @code{r-ggplot2} extension that provides flipped components:
7142 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7143 @item vertical versions of @code{r-ggplot2} positions.
7145 (license license:gpl3)))
7147 (define-public r-mosaiccore
7149 (name "r-mosaiccore")
7154 (uri (cran-uri "mosaicCore" version))
7156 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7157 (properties `((upstream-name . "mosaicCore")))
7158 (build-system r-build-system)
7160 `(("r-dplyr" ,r-dplyr)
7161 ("r-lazyeval" ,r-lazyeval)
7163 ("r-rlang" ,r-rlang)
7164 ("r-tidyr" ,r-tidyr)))
7165 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7166 (synopsis "Common utilities for mosaic family packages")
7168 "Common utilities used in other Mosaic family packages are collected here.")
7169 (license license:gpl2+)))
7171 (define-public r-ggformula
7173 (name "r-ggformula")
7178 (uri (cran-uri "ggformula" version))
7180 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7181 (build-system r-build-system)
7183 `(("r-ggplot2" ,r-ggplot2)
7184 ("r-ggstance" ,r-ggstance)
7185 ("r-magrittr" ,r-magrittr)
7186 ("r-mosaiccore" ,r-mosaiccore)
7187 ("r-rlang" ,r-rlang)
7188 ("r-stringr" ,r-stringr)
7189 ("r-tibble" ,r-tibble)
7190 ("r-tidyr" ,r-tidyr)))
7191 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7192 (synopsis "Formula interface for the @code{r-ggplot2}")
7194 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7195 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7196 and extends the excellent simplicity of the lattice-graphics formula interface,
7197 while providing the intuitive capabilities of @code{r-ggplot2}.")
7198 (license license:expat)))
7200 (define-public r-mosaicdata
7202 (name "r-mosaicdata")
7207 (uri (cran-uri "mosaicData" version))
7209 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7210 (properties `((upstream-name . "mosaicData")))
7211 (build-system r-build-system)
7212 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7213 (synopsis "Data sets for project Mosaic")
7215 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7216 used to teach mathematics, statistics, computation and modeling.")
7217 (license license:gpl2+)))
7219 (define-public r-raster
7226 (uri (cran-uri "raster" version))
7229 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7230 (build-system r-build-system)
7232 `(("r-rcpp" ,r-rcpp)
7234 (home-page "https://www.rspatial.org/")
7235 (synopsis "Geographic data analysis and modeling")
7237 "The package implements basic and high-level functions for reading,
7238 writing, manipulating, analyzing and modeling of gridded spatial data.
7239 Processing of very large files is supported.")
7240 (license license:gpl3+)))
7242 (define-public r-mosaic
7249 (uri (cran-uri "mosaic" version))
7251 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7252 (build-system r-build-system)
7254 `(("r-broom" ,r-broom)
7255 ("r-dplyr" ,r-dplyr)
7256 ("r-ggdendro" ,r-ggdendro)
7257 ("r-ggformula" ,r-ggformula)
7258 ("r-ggplot2" ,r-ggplot2)
7259 ("r-ggrepel" ,r-ggrepel)
7261 ("r-gridextra" ,r-gridextra)
7262 ("r-lattice" ,r-lattice)
7263 ("r-latticeextra" ,r-latticeextra)
7264 ("r-lazyeval" ,r-lazyeval)
7266 ("r-matrix" ,r-matrix)
7267 ("r-mosaiccore" ,r-mosaiccore)
7268 ("r-mosaicdata" ,r-mosaicdata)
7269 ("r-readr" ,r-readr)
7270 ("r-tidyr" ,r-tidyr)))
7271 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7272 (synopsis "Mathematics, statistics, and computation teaching utilities")
7274 "This package contain data sets and utilities from
7275 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7276 statistics, computation and modeling. Project MOSAIC is a community of
7277 educators working to tie together aspects of quantitative work that students
7278 in science, technology, engineering and mathematics will need in their
7279 professional lives, but which are usually taught in isolation, if at all.")
7280 (license license:gpl2+)))
7282 (define-public r-abd
7289 (uri (cran-uri "abd" version))
7291 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7292 (build-system r-build-system)
7294 `(("r-lattice" ,r-lattice)
7295 ("r-mosaic" ,r-mosaic)
7296 ("r-nlme" ,r-nlme)))
7297 (home-page "https://cran.r-project.org/web/packages/abd/")
7298 (synopsis "Analysis of biological data")
7300 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7301 biological data by Michael Whitlock and Dolph Schluter.")
7302 (license license:gpl2)))
7304 (define-public r-svgui
7311 (uri (cran-uri "svGUI" version))
7313 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7314 (properties `((upstream-name . "svGUI")))
7315 (build-system r-build-system)
7316 (home-page "https://github.com/SciViews/svGUI/")
7317 (synopsis "Functions for managing GUI clients in R")
7319 "The SciViews @code{svGUI} package eases the management of Graphical User
7320 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7321 centralizes info about GUI elements currently used, and it dispatches GUI
7322 calls to the particular toolkits in use in function of the context.")
7323 (license license:gpl2)))
7325 (define-public r-svdialogs
7327 (name "r-svdialogs")
7332 (uri (cran-uri "svDialogs" version))
7334 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7335 (properties `((upstream-name . "svDialogs")))
7336 (build-system r-build-system)
7339 ("zenity" ,zenity)))
7341 `(("r-rstudioapi" ,r-rstudioapi)
7342 ("r-svgui" ,r-svgui)))
7343 (home-page "https://github.com/SciViews/svDialogs/")
7344 (synopsis "Portable dialog boxes")
7346 "This package helps to construct standard dialog boxes for your GUI, including
7347 message boxes, input boxes, list, file or directory selection, and others. In
7348 case R cannot display GUI dialog boxes, a simpler command line version of these
7349 interactive elements is also provided as a fallback solution.")
7350 (license license:gpl2)))
7352 (define-public r-abe
7359 (uri (cran-uri "abe" version))
7362 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7363 (build-system r-build-system)
7364 (home-page "https://cran.r-project.org/web/packages/abe/")
7365 (synopsis "Augmented backward elimination")
7367 "This package performs augmented backward elimination and checks the
7368 stability of the obtained model. Augmented backward elimination combines
7369 significance or information based criteria with the change in estimate to
7370 either select the optimal model for prediction purposes or to serve as a tool
7371 to obtain a practically sound, highly interpretable model.")
7372 (license license:gpl2+)))
7374 (define-public r-abf2
7381 (uri (cran-uri "abf2" version))
7383 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7384 (build-system r-build-system)
7385 (home-page "https://cran.r-project.org/web/packages/abf2/")
7386 (synopsis "Load gap-free axon @code{r-abf2} files")
7388 "This package loads electrophysiology data from ABF2 files, as created by
7389 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7390 mode are currently supported.")
7391 (license license:artistic2.0)))
7393 (define-public r-abhgenotyper
7395 (name "r-abhgenotyper")
7400 (uri (cran-uri "ABHgenotypeR" version))
7402 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7403 (properties `((upstream-name . "ABHgenotypeR")))
7404 (build-system r-build-system)
7406 `(("r-ggplot2" ,r-ggplot2)
7407 ("r-reshape2" ,r-reshape2)))
7408 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7409 (synopsis "Visualize and manipulate ABH genotypes")
7411 "The @code{r-abhgenotyper} package provides simple imputation,
7412 error-correction and plotting capacities for genotype data. The package is
7413 supposed to serve as an intermediate but independent analysis tool between the
7414 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7415 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7416 genotypes as \"graphical genotypes\".")
7417 (license license:gpl3)))
7419 (define-public r-furrr
7426 (uri (cran-uri "furrr" version))
7429 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7430 (build-system r-build-system)
7432 `(("r-future" ,r-future)
7433 ("r-globals" ,r-globals)
7434 ("r-purrr" ,r-purrr)
7435 ("r-rlang" ,r-rlang)))
7436 (home-page "https://github.com/DavisVaughan/furrr")
7437 (synopsis "Apply mapping functions in parallel using futures")
7439 "This package provides implementations of the family of @code{map()}
7440 functions from the @code{purrr} package that can be resolved using any
7441 @code{future}-supported backend, e.g. parallel on the local machine or
7442 distributed on a compute cluster.")
7443 (license license:lgpl2.1+)))
7445 (define-public r-abjutils
7452 (uri (cran-uri "abjutils" version))
7454 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7455 (build-system r-build-system)
7457 `(("r-devtools" ,r-devtools)
7458 ("r-dplyr" ,r-dplyr)
7459 ("r-furrr" ,r-furrr)
7460 ("r-future" ,r-future)
7463 ("r-magrittr" ,r-magrittr)
7464 ("r-progress" ,r-progress)
7465 ("r-purrr" ,r-purrr)
7466 ("r-readr" ,r-readr)
7467 ("r-rlang" ,r-rlang)
7468 ("r-rstudioapi" ,r-rstudioapi)
7469 ("r-scales" ,r-scales)
7470 ("r-stringi" ,r-stringi)
7471 ("r-stringr" ,r-stringr)
7472 ("r-tibble" ,r-tibble)
7473 ("r-tidyr" ,r-tidyr)))
7474 (home-page "https://github.com/abjur/abjutils/")
7475 (synopsis "Collection of tools for jurimetrical analysis")
7477 "This package implements general purpose tools, such as functions for
7478 sampling and basic manipulation of Brazilian lawsuits identification number.
7479 It also implements functions for text cleaning, such as accentuation
7481 (license license:expat)))
7483 (define-public r-abnormality
7485 (name "r-abnormality")
7490 (uri (cran-uri "abnormality" version))
7492 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7493 (build-system r-build-system)
7495 `(("r-mass" ,r-mass)
7496 ("r-matrix" ,r-matrix)))
7497 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7498 (synopsis "Measure a subject's abnormality with respect to a reference population")
7500 "This package contains functions to implement the methodology and
7501 considerations laid out by Marks et al. in the article \"Measuring abnormality
7502 in high dimensional spaces: applications in biomechanical gait analysis\".
7503 Using high-dimensional datasets to measure a subject's overall level of
7504 abnormality as compared to a reference population is often needed in outcomes
7506 (license license:expat)))
7508 (define-public r-abodoutlier
7510 (name "r-abodoutlier")
7515 (uri (cran-uri "abodOutlier" version))
7517 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7518 (properties `((upstream-name . "abodOutlier")))
7519 (build-system r-build-system)
7521 `(("r-cluster" ,r-cluster)))
7522 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7523 (synopsis "Angle-based outlier detection")
7525 "This package performs angle-based outlier detection on a given data
7526 frame. It offers three methods to process data:
7528 @item full but slow implementation using all the data that has cubic
7530 @item a fully randomized method;
7531 @item a method using k-nearest neighbours.
7533 These algorithms are well suited for high dimensional data outlier
7535 (license license:expat)))
7537 (define-public r-abps
7544 (uri (cran-uri "ABPS" version))
7546 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7547 (properties `((upstream-name . "ABPS")))
7548 (build-system r-build-system)
7549 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7550 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7551 (synopsis "Abnormal blood profile score to detect blood doping")
7553 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7554 The ABPS is a part of the Athlete biological passport program of the World
7555 anti-doping agency, which combines several blood parameters into a single
7556 score in order to detect blood doping. The package also contains functions to
7557 calculate other scores used in anti-doping programs, such as the ratio of
7558 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7559 (license license:gpl2+)))
7561 (define-public r-parmigene
7563 (name "r-parmigene")
7568 (uri (cran-uri "parmigene" version))
7571 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7572 (build-system r-build-system)
7573 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7574 (synopsis "Mutual information estimation for gene network reconstruction")
7576 "This package provides a parallel estimation of the mutual information
7577 based on entropy estimates from k-nearest neighbors distances and algorithms
7578 for the reconstruction of gene regulatory networks.")
7579 (license license:agpl3+)))
7581 (define-public r-pscl
7588 (uri (cran-uri "pscl" version))
7590 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7591 (build-system r-build-system)
7593 `(("r-mass" ,r-mass)))
7594 (home-page "https://github.com/atahk/pscl/")
7595 (synopsis "Political science computational laboratory")
7597 "The @code{pscl} is an R package providing classes and methods for:
7599 @item Bayesian analysis of roll call data (item-response models);
7600 @item elementary Bayesian statistics;
7601 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7603 @item utility functions.
7605 (license license:gpl2)))
7607 (define-public r-accelmissing
7609 (name "r-accelmissing")
7614 (uri (cran-uri "accelmissing" version))
7616 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7617 (build-system r-build-system)
7619 `(("r-mice" ,r-mice)
7620 ("r-pscl" ,r-pscl)))
7621 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7622 (synopsis "Missing value imputation for accelerometer data")
7624 "This package provides a statistical method to impute the missing values in
7625 accelerometer data. The methodology includes both parametric and
7626 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7627 model. It also provides multiple functions to preprocess the accelerometer data
7628 previous to the missing data imputation. These include detecting the wearing
7629 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7630 (license license:gpl2+)))
7632 (define-public r-mhsmm
7639 (uri (cran-uri "mhsmm" version))
7641 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7642 (build-system r-build-system)
7643 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7644 (home-page "https://github.com/jaredo/mhsmm/")
7645 (synopsis "Inference for hidden Markov and semi-Markov models")
7647 "The @code{r-mhsmm} package implements estimation and prediction methods for
7648 hidden Markov and semi-Markov models for multiple observation sequences. Such
7649 techniques are of interest when observed data is thought to be dependent on some
7650 unobserved (or hidden) state. Also, this package is suitable for equidistant
7651 time series data, with multivariate and/or missing data. Allows user defined
7652 emission distributions.")
7653 (license license:gpl2+)))
7655 (define-public r-nleqslv
7662 (uri (cran-uri "nleqslv" version))
7664 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7665 (build-system r-build-system)
7666 (native-inputs `(("gfortran" ,gfortran)))
7667 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7668 (synopsis "Solve systems of nonlinear equations")
7670 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7671 Broyden or a Newton method with a choice of global strategies such as line
7672 search and trust region. There are options for using a numerical or user
7673 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7674 singular or ill-conditioned Jacobian.")
7675 (license license:gpl2+)))
7677 (define-public r-physicalactivity
7679 (name "r-physicalactivity")
7684 (uri (cran-uri "PhysicalActivity" version))
7686 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7688 `((upstream-name . "PhysicalActivity")))
7689 (build-system r-build-system)
7690 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7691 (synopsis "Procesing accelerometer data for physical activity measurement")
7693 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7694 for classification of monitor wear and nonwear time intervals in accelerometer
7695 data collected to assess physical activity. The package also contains functions
7696 for making plots of accelerometer data and obtaining the summary of various
7697 information including daily monitor wear time and the mean monitor wear time
7698 during valid days. The revised package version 0.2-1 improved the functions
7699 regarding speed, robustness and add better support for time zones and daylight
7700 saving. In addition, several functions were added:
7702 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7703 @item the @code{markPAI} can categorize physical activity intensity level based
7704 on user-defined cut-points of accelerometer counts.
7706 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7707 @code{queryActigraph} functions.")
7708 (license license:gpl3+)))
7710 (define-public r-acc
7717 (uri (cran-uri "acc" version))
7719 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7720 (build-system r-build-system)
7722 `(("r-circlize" ,r-circlize)
7724 ("r-ggplot2" ,r-ggplot2)
7725 ("r-iterators" ,r-iterators)
7726 ("r-mhsmm" ,r-mhsmm)
7727 ("r-nleqslv" ,r-nleqslv)
7728 ("r-physicalactivity" ,r-physicalactivity)
7730 ("r-r-utils" ,r-r-utils)
7732 ("r-rcpparmadillo" ,r-rcpparmadillo)
7733 ("r-rsqlite" ,r-rsqlite)
7735 (home-page "https://cran.r-project.org/web/packages/acc/")
7736 (synopsis "Exploring accelerometer data")
7738 "This package processes accelerometer data from uni-axial and tri-axial devices
7739 and generates data summaries. Also, includes functions to plot, analyze, and
7740 simulate accelerometer data.")
7741 (license license:gpl2+)))
7743 (define-public r-rbenchmark
7745 (name "r-rbenchmark")
7750 (uri (cran-uri "rbenchmark" version))
7752 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7753 (build-system r-build-system)
7754 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7755 (synopsis "Benchmarking routine for R")
7757 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7758 and is intended to facilitate benchmarking of arbitrary R code. The library
7759 consists of just one function, benchmark, which is a simple wrapper around
7760 system.time. Given a specification of the benchmarking process (counts of
7761 replications, evaluation environment) and an arbitrary number of expressions,
7762 benchmark evaluates each of the expressions in the specified environment,
7763 replicating the evaluation as many times as specified, and returning the results
7764 conveniently wrapped into a data frame.")
7765 (license license:gpl2+)))
7767 (define-public r-mitools
7774 (uri (cran-uri "mitools" version))
7777 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7778 (build-system r-build-system)
7779 (propagated-inputs `(("r-dbi" ,r-dbi)))
7780 (home-page "https://cran.r-project.org/web/packages/mitools/")
7781 (synopsis "Tools for multiple imputation of missing data")
7783 "This package provides tools to perform analyses and combine results from
7784 multiple-imputation datasets.")
7785 (license license:gpl2)))
7787 (define-public r-magick
7794 (uri (cran-uri "magick" version))
7797 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7798 (build-system r-build-system)
7800 `(("imagemagick" ,imagemagick)
7803 `(("r-curl" ,r-curl)
7804 ("r-magrittr" ,r-magrittr)
7805 ("r-rcpp" ,r-rcpp)))
7807 `(("pkg-config" ,pkg-config)))
7808 (home-page "https://github.com/ropensci/magick")
7809 (synopsis "Advanced graphics and image-processing in R")
7811 "This package provides bindings to ImageMagick, a comprehensive image
7812 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7813 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7814 operations are vectorized via the Magick++ STL meaning they operate either on
7815 a single frame or a series of frames for working with layers, collages, or
7816 animation. In RStudio, images are automatically previewed when printed to the
7817 console, resulting in an interactive editing environment.")
7818 (license license:expat)))
7820 (define-public r-survey
7827 (uri (cran-uri "survey" version))
7830 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7831 (build-system r-build-system)
7833 `(("r-lattice" ,r-lattice)
7834 ("r-matrix" ,r-matrix)
7835 ("r-minqa" ,r-minqa)
7836 ("r-mitools" ,r-mitools)
7837 ("r-numderiv" ,r-numderiv)
7838 ("r-survival" ,r-survival)))
7839 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7840 (synopsis "Analysis of complex survey samples")
7842 "This package provides tools for the analysis of complex survey samples.
7843 The provided features include: summary statistics, two-sample tests, rank
7844 tests, generalised linear models, cumulative link models, Cox models,
7845 loglinear models, and general maximum pseudolikelihood estimation for
7846 multistage stratified, cluster-sampled, unequally weighted survey samples;
7847 variances by Taylor series linearisation or replicate weights;
7848 post-stratification, calibration, and raking; two-phase subsampling designs;
7849 graphics; PPS sampling without replacement; principal components, and factor
7851 ;; Either version of the GPL.
7852 (license (list license:gpl2 license:gpl3))))
7854 (define-public r-dvmisc
7861 (uri (cran-uri "dvmisc" version))
7863 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7864 (build-system r-build-system)
7866 `(("r-cubature" ,r-cubature)
7867 ("r-data-table" ,r-data-table)
7868 ("r-dplyr" ,r-dplyr)
7869 ("r-ggplot2" ,r-ggplot2)
7871 ("r-mvtnorm" ,r-mvtnorm)
7872 ("r-pracma" ,r-pracma)
7873 ("r-purrr" ,r-purrr)
7874 ("r-rbenchmark" ,r-rbenchmark)
7876 ("r-survey" ,r-survey)))
7877 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7878 (synopsis "Faster computation of common statistics and miscellaneous functions")
7880 "This package implements faster versions of base R functions (e.g. mean, standard
7881 deviation, covariance, weighted mean), mostly written in C++, along with
7882 miscellaneous functions for various purposes (e.g. create the histogram with
7883 fitted probability density function or probability mass function curve, create
7884 the body mass index groups, assess the linearity assumption in logistic
7886 (license license:gpl2)))
7888 (define-public r-accelerometry
7890 (name "r-accelerometry")
7895 (uri (cran-uri "accelerometry" version))
7897 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7898 (build-system r-build-system)
7900 `(("r-dvmisc" ,r-dvmisc)
7901 ("r-rcpp" ,r-rcpp)))
7902 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7903 (synopsis "Functions for processing accelerometer data")
7905 "This package provides a collection of functions that perform operations on
7906 time-series accelerometer data, such as identify the non-wear time, flag minutes
7907 that are part of an activity bout, and find the maximum 10-minute average count
7908 value. The functions are generally very flexible, allowing for a variety of
7909 algorithms to be implemented.")
7910 (license license:gpl3)))
7912 (define-public r-absim
7919 (uri (cran-uri "AbSim" version))
7921 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7922 (properties `((upstream-name . "AbSim")))
7923 (build-system r-build-system)
7926 ("r-powerlaw" ,r-powerlaw)))
7927 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7928 (synopsis "Time resolved simulations of antibody repertoires")
7930 "This package provides simulation methods for the evolution of antibody repertoires.
7931 The heavy and light chain variable region of both human and C57BL/6 mice can
7932 be simulated in a time-dependent fashion. Both single lineages using one set of
7933 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7934 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7935 Upon completion, the main loop of the algorithm begins, with each iteration
7936 representing one simulated time step. Various mutation events are possible at
7937 each time step, contributing to a diverse final repertoire.")
7938 (license license:gpl2)))
7940 (define-public r-quic
7947 (uri (cran-uri "QUIC" version))
7949 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7950 (properties `((upstream-name . "QUIC")))
7951 (build-system r-build-system)
7952 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7953 (synopsis "Regularized sparse inverse covariance matrix estimation")
7955 "This package implements the regularized Gaussian maximum likelihood
7956 estimation of the inverse of a covariance matrix. It uses Newton's method and
7957 coordinate descent to solve the regularized inverse covariance matrix
7958 estimation problem.")
7959 ;; The project home page states that the release is under GPLv3 or later.
7960 ;; The CRAN page only says GPL-3.
7961 (license license:gpl3+)))
7963 (define-public r-abundant
7970 (uri (cran-uri "abundant" version))
7972 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7973 (build-system r-build-system)
7975 `(("r-quic" ,r-quic)))
7976 (home-page "https://cran.r-project.org/web/packages/abundant/")
7977 (synopsis "Abundant regression and high-dimensional principal fitted components")
7979 "This package provides tools to fit and predict with the high-dimensional
7980 principal fitted components model. This model is described by Cook, Forzani,
7981 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7982 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7983 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7984 (license license:gpl2+)))
7986 (define-public r-ac3net
7993 (uri (cran-uri "Ac3net" version))
7995 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7996 (properties `((upstream-name . "Ac3net")))
7997 (build-system r-build-system)
7999 `(("r-data-table" ,r-data-table)))
8000 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8001 (synopsis "Inferring directional conservative causal core gene networks")
8002 (description "This package infers directional Conservative causal core
8003 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8004 directional network.")
8005 (license license:gpl3+)))
8007 (define-public r-aca
8014 (uri (cran-uri "ACA" version))
8016 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8017 (properties `((upstream-name . "ACA")))
8018 (build-system r-build-system)
8019 (home-page "https://cran.r-project.org/web/packages/ACA/")
8020 (synopsis "Abrupt change-point or aberration detection in point series")
8022 "This package offers an interactive function for the detection of breakpoints in
8024 ;; Any version of the GPL
8025 (license (list license:gpl2+ license:gpl3+))))
8027 (define-public r-acceptancesampling
8029 (name "r-acceptancesampling")
8034 (uri (cran-uri "AcceptanceSampling" version))
8036 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8038 `((upstream-name . "AcceptanceSampling")))
8039 (build-system r-build-system)
8040 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8041 (synopsis "Creation and evaluation of acceptance sampling plans")
8043 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8044 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8045 in quality control and improvement. International standards of acceptance
8046 sampling provide sampling plans for specific circumstances. The aim of this
8047 package is to provide an easy-to-use interface to visualize single, double or
8048 multiple sampling plans. In addition, methods have been provided to enable the
8049 user to assess sampling plans against pre-specified levels of performance, as
8050 measured by the probability of acceptance for a given level of quality in the
8052 (license license:gpl3+)))
8054 (define-public r-acclma
8061 (uri (cran-uri "ACCLMA" version))
8063 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8064 (properties `((upstream-name . "ACCLMA")))
8065 (build-system r-build-system)
8066 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8067 (synopsis "ACC & LMA graph plotting")
8069 "This package contains a function that imports data from a @acronym{CSV,
8070 Comma-Separated Values} file, or uses manually entered data from the format (x,
8071 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8072 Curve} vs @acronym{LOI, Line of Independence} graph and
8073 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8074 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8075 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8076 string) was passed, a manual data entry window is opened. The header parameter
8077 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8078 a header row or not. The dataset should contain only one independent variable
8079 (x) and one dependent variable (y) and can contain a weight for each
8081 (license license:gpl2)))
8083 (define-public r-aspi
8090 (uri (cran-uri "aspi" version))
8092 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8093 (build-system r-build-system)
8095 "https://cran.r-project.org/web/packages/aspi/")
8097 "Analysis of symmetry of parasitic infections")
8099 "This package provides tools for the analysis and visualization of bilateral
8100 asymmetry in parasitic infections.")
8101 (license license:gpl3+)))
8103 (define-public r-sandwich
8110 (uri (cran-uri "sandwich" version))
8113 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8114 (build-system r-build-system)
8116 `(("r-zoo" ,r-zoo)))
8117 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8118 (synopsis "Robust Covariance Matrix Estimators")
8120 "This package provides model-robust standard error estimators for
8121 cross-sectional, time series, clustered, panel, and longitudinal data.")
8122 ;; Either version of the license.
8123 (license (list license:gpl2 license:gpl3))))
8125 (define-public r-th-data
8132 (uri (cran-uri "TH.data" version))
8135 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8136 (properties `((upstream-name . "TH.data")))
8137 (build-system r-build-system)
8139 `(("r-mass" ,r-mass)
8140 ("r-survival" ,r-survival)))
8141 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8142 (synopsis "Shared data sets")
8144 "This package contains supporting data sets that are used in other
8145 packages maintained by Torsten Hothorn.")
8146 (license license:gpl3)))
8148 (define-public r-multcomp
8155 (uri (cran-uri "multcomp" version))
8158 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
8159 (build-system r-build-system)
8161 `(("r-codetools" ,r-codetools)
8162 ("r-mvtnorm" ,r-mvtnorm)
8163 ("r-sandwich" ,r-sandwich)
8164 ("r-survival" ,r-survival)
8165 ("r-th-data" ,r-th-data)))
8166 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8167 (synopsis "Simultaneous inference in general parametric models")
8169 "Simultaneous tests and confidence intervals for general linear
8170 hypotheses in parametric models, including linear, generalized linear, linear
8171 mixed effects, and survival models. The package includes demos reproducing
8172 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8173 Hothorn, Westfall, 2010, CRC Press).")
8174 (license license:gpl2)))
8176 (define-public r-emmeans
8179 (version "1.4.3.01")
8183 (uri (cran-uri "emmeans" version))
8186 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8187 (build-system r-build-system)
8189 `(("r-estimability" ,r-estimability)
8190 ("r-mvtnorm" ,r-mvtnorm)
8191 ("r-numderiv" ,r-numderiv)
8193 ("r-xtable" ,r-xtable)))
8194 (home-page "https://github.com/rvlenth/emmeans")
8195 (synopsis "Estimated marginal means, aka least-squares means")
8197 "This package provides tools to obtain @dfn{estimated marginal
8198 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8199 be used to compute contrasts or linear functions of EMMs, trends, and
8200 comparisons of slopes.")
8201 ;; Either version of the license.
8202 (license (list license:gpl2 license:gpl3))))
8204 (define-public r-pwr
8211 (uri (cran-uri "pwr" version))
8214 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8215 (build-system r-build-system)
8217 `(("r-knitr" ,r-knitr)))
8218 (home-page "https://github.com/heliosdrm/pwr")
8219 (synopsis "Basic functions for power analysis")
8221 "This package provides power analysis functions along the lines of
8223 (license license:gpl3+)))
8225 (define-public r-libcoin
8232 (uri (cran-uri "libcoin" version))
8235 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8236 (build-system r-build-system)
8237 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8238 (home-page "https://cran.r-project.org/web/packages/libcoin")
8239 (synopsis "Linear test statistics for permutation inference")
8241 "This package provides basic infrastructure for linear test statistics
8242 and permutation inference in the framework of Strasser and Weber (1999).")
8243 (license license:gpl2)))
8245 (define-public r-coin
8252 (uri (cran-uri "coin" version))
8255 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8256 (build-system r-build-system)
8258 `(("r-libcoin" ,r-libcoin)
8259 ("r-matrixstats" ,r-matrixstats)
8260 ("r-modeltools" ,r-modeltools)
8261 ("r-multcomp" ,r-multcomp)
8262 ("r-mvtnorm" ,r-mvtnorm)
8263 ("r-survival" ,r-survival)))
8264 (home-page "http://coin.r-forge.r-project.org")
8265 (synopsis "Conditional inference procedures in a permutation test framework")
8267 "This package provides conditional inference procedures for the general
8268 independence problem including two-sample, K-sample (non-parametric ANOVA),
8269 correlation, censored, ordered and multivariate problems.")
8270 (license license:gpl2)))
8272 (define-public r-bayesplot
8274 (name "r-bayesplot")
8279 (uri (cran-uri "bayesplot" version))
8282 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8283 (build-system r-build-system)
8285 `(("pandoc" ,ghc-pandoc)
8286 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8288 `(("r-dplyr" ,r-dplyr)
8289 ("r-ggplot2" ,r-ggplot2)
8290 ("r-ggridges" ,r-ggridges)
8292 ("r-reshape2" ,r-reshape2)
8293 ("r-rlang" ,r-rlang)
8294 ("r-tibble" ,r-tibble)
8295 ("r-tidyselect" ,r-tidyselect)))
8296 (home-page "http://mc-stan.org/bayesplot")
8297 (synopsis "Plotting for Bayesian models")
8299 "This package provides plotting functions for posterior analysis, model
8300 checking, and MCMC diagnostics. The package is designed not only to provide
8301 convenient functionality for users, but also a common set of functions that
8302 can be easily used by developers working on a variety of R packages for
8303 Bayesian modeling.")
8304 (license license:gpl3+)))
8306 (define-public r-tmb
8313 (uri (cran-uri "TMB" version))
8316 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8317 (properties `((upstream-name . "TMB")))
8318 (build-system r-build-system)
8320 `(("r-matrix" ,r-matrix)
8321 ("r-rcppeigen" ,r-rcppeigen)))
8322 (home-page "http://tmb-project.org")
8323 (synopsis "Template model builder: a general random effect tool")
8325 "With this tool, a user should be able to quickly implement complex
8326 random effect models through simple C++ templates. The package combines
8327 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8328 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8329 from R) to obtain an efficient implementation of the applied Laplace
8330 approximation with exact derivatives. Key features are: Automatic sparseness
8331 detection, parallelism through BLAS and parallel user templates.")
8332 (license license:gpl2)))
8334 (define-public r-sjstats
8341 (uri (cran-uri "sjstats" version))
8343 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8344 (build-system r-build-system)
8346 `(("r-bayestestr" ,r-bayestestr)
8347 ("r-broom" ,r-broom)
8348 ("r-dplyr" ,r-dplyr)
8349 ("r-emmeans" ,r-emmeans)
8350 ("r-insight" ,r-insight)
8352 ("r-magrittr" ,r-magrittr)
8354 ("r-modelr" ,r-modelr)
8355 ("r-parameters" ,r-parameters)
8356 ("r-performance" ,r-performance)
8357 ("r-purrr" ,r-purrr)
8358 ("r-rlang" ,r-rlang)
8359 ("r-sjlabelled" ,r-sjlabelled)
8360 ("r-sjmisc" ,r-sjmisc)
8361 ("r-tidyr" ,r-tidyr)))
8362 (home-page "https://github.com/strengejacke/sjstats")
8363 (synopsis "Functions for common statistical computations")
8365 "This package provides a collection of convenient functions for common
8366 statistical computations, which are not directly provided by R's @code{base}
8367 or @code{stats} packages. This package aims at providing, first, shortcuts
8368 for statistical measures, which otherwise could only be calculated with
8369 additional effort. Second, these shortcut functions are generic, and can be
8370 applied not only to vectors, but also to other objects as well. The focus of
8371 most functions lies on summary statistics or fit measures for regression
8372 models, including generalized linear models, mixed effects models and Bayesian
8374 (license license:gpl3)))
8376 (define-public r-glmmtmb
8383 (uri (cran-uri "glmmTMB" version))
8386 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8387 (properties `((upstream-name . "glmmTMB")))
8388 (build-system r-build-system)
8390 `(("r-lme4" ,r-lme4)
8391 ("r-matrix" ,r-matrix)
8393 ("r-rcppeigen" ,r-rcppeigen)
8396 `(("r-knitr" ,r-knitr))) ; for vignettes
8397 (home-page "https://github.com/glmmTMB")
8398 (synopsis "Generalized linear mixed models")
8400 "Fit linear and generalized linear mixed models with various extensions,
8401 including zero-inflation. The models are fitted using maximum likelihood
8402 estimation via the Template Model Builder. Random effects are assumed to be
8403 Gaussian on the scale of the linear predictor and are integrated out using the
8404 Laplace approximation. Gradients are calculated using automatic
8406 (license license:agpl3+)))
8408 (define-public r-bayestestr
8410 (name "r-bayestestr")
8415 (uri (cran-uri "bayestestR" version))
8418 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8419 (properties `((upstream-name . "bayestestR")))
8420 (build-system r-build-system)
8422 `(("r-insight" ,r-insight)))
8423 (home-page "https://github.com/easystats/bayestestR")
8424 (synopsis "Describe Bayesian models and posterior distributions")
8426 "This package provides utilities to understand and describe posterior
8427 distributions and Bayesian models. It includes point-estimates such as
8428 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8429 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8430 ROPE percentage and pd).")
8431 (license license:gpl3)))
8433 (define-public r-performance
8435 (name "r-performance")
8440 (uri (cran-uri "performance" version))
8443 "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
8444 (build-system r-build-system)
8446 `(("r-bayestestr" ,r-bayestestr)
8447 ("r-insight" ,r-insight)))
8448 (home-page "https://easystats.github.io/performance/")
8449 (synopsis "Assessment of regression models performance")
8451 "This package provides utilities for computing measures to assess model
8452 quality, which are not directly provided by R's @code{base} or @code{stats}
8453 packages. These include e.g. measures like r-squared, intraclass correlation
8454 coefficient, root mean squared error or functions to check models for
8455 overdispersion, singularity or zero-inflation and more. Functions apply to a
8456 large variety of regression models, including generalized linear models, mixed
8457 effects models and Bayesian models.")
8458 (license license:gpl3)))
8460 (define-public r-ggeffects
8462 (name "r-ggeffects")
8467 (uri (cran-uri "ggeffects" version))
8470 "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
8471 (build-system r-build-system)
8473 `(("r-dplyr" ,r-dplyr)
8474 ("r-insight" ,r-insight)
8475 ("r-magrittr" ,r-magrittr)
8477 ("r-purrr" ,r-purrr)
8478 ("r-rlang" ,r-rlang)
8479 ("r-sjlabelled" ,r-sjlabelled)
8480 ("r-sjmisc" ,r-sjmisc)))
8481 (home-page "https://github.com/strengejacke/ggeffects")
8482 (synopsis "Create tidy data frames of marginal effects for ggplot")
8484 "This package provides tools to compute marginal effects from statistical
8485 models and return the result as tidy data frames. These data frames are ready
8486 to use with the @code{ggplot2} package. Marginal effects can be calculated
8487 for many different models. Interaction terms, splines and polynomial terms
8488 are also supported. The two main functions are @code{ggpredict()} and
8489 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8490 results using @code{ggplot2}.")
8491 (license license:gpl3)))
8493 (define-public r-effectsize
8495 (name "r-effectsize")
8500 (uri (cran-uri "effectsize" version))
8503 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8504 (properties `((upstream-name . "effectsize")))
8505 (build-system r-build-system)
8507 `(("r-bayestestr" ,r-bayestestr)
8508 ("r-insight" ,r-insight)
8509 ("r-parameters" ,r-parameters)))
8510 (home-page "https://github.com/easystats/effectsize")
8511 (synopsis "Indices of effect size and standardized parameters")
8513 "This package provides utilities to work with indices of effect size and
8514 standardized parameters for a wide variety of models, allowing computation and
8515 conversion of indices such as Cohen's d, r, odds, etc.")
8516 (license license:gpl3)))
8518 (define-public r-sjplot
8525 (uri (cran-uri "sjPlot" version))
8527 (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
8528 (properties `((upstream-name . "sjPlot")))
8529 (build-system r-build-system)
8531 `(("r-bayestestr" ,r-bayestestr)
8532 ("r-dplyr" ,r-dplyr)
8533 ("r-effectsize" ,r-effectsize)
8534 ("r-forcats" ,r-forcats)
8535 ("r-ggeffects" ,r-ggeffects)
8536 ("r-ggplot2" ,r-ggplot2)
8537 ("r-ggrepel" ,r-ggrepel)
8538 ("r-glmmtmb" ,r-glmmtmb)
8539 ("r-insight" ,r-insight)
8540 ("r-knitr" ,r-knitr)
8542 ("r-magrittr" ,r-magrittr)
8544 ("r-modelr" ,r-modelr)
8545 ("r-parameters" ,r-parameters)
8546 ("r-performance" ,r-performance)
8547 ("r-psych" ,r-psych)
8548 ("r-purrr" ,r-purrr)
8549 ("r-rlang" ,r-rlang)
8550 ("r-scales" ,r-scales)
8551 ("r-sjlabelled" ,r-sjlabelled)
8552 ("r-sjmisc" ,r-sjmisc)
8553 ("r-sjstats" ,r-sjstats)
8554 ("r-tidyr" ,r-tidyr)))
8555 (home-page "https://strengejacke.github.io/sjPlot/")
8556 (synopsis "Data visualization for statistics in social science")
8558 "This package represents a collection of plotting and table output
8559 functions for data visualization. Results of various statistical
8560 analyses (that are commonly used in social sciences) can be visualized using
8561 this package, including simple and cross tabulated frequencies, histograms,
8562 box plots, (generalized) linear models, mixed effects models, principal
8563 component analysis and correlation matrices, cluster analyses, scatter plots,
8564 stacked scales, effects plots of regression models (including interaction
8565 terms) and much more. This package supports labelled data.")
8566 (license license:gpl3)))
8568 (define-public r-ini
8575 (uri (cran-uri "ini" version))
8578 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8579 (build-system r-build-system)
8580 (home-page "https://github.com/dvdscripter/ini")
8581 (synopsis "Read and write configuration files")
8583 "This package provides tools to parse simple @code{.ini} configuration
8584 files to an structured list. Users can manipulate this resulting list with
8585 @code{lapply()} functions. This same structured list can be used to write
8586 back to file after modifications.")
8587 (license license:gpl3)))
8596 (uri (cran-uri "gh" version))
8599 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8600 (build-system r-build-system)
8602 `(("r-httr" ,r-httr)
8604 ("r-jsonlite" ,r-jsonlite)))
8605 (home-page "https://github.com/r-lib/gh#readme")
8606 (synopsis "Access the GitHub API via R")
8608 "This package provides a minimal R client to access the GitHub API.")
8609 (license license:expat)))
8618 (uri (cran-uri "fs" version))
8621 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8622 (build-system r-build-system)
8624 `(("r-rcpp" ,r-rcpp)))
8626 `(("pkg-config" ,pkg-config)))
8627 (home-page "http://fs.r-lib.org")
8628 (synopsis "Cross-platform file system operations based on libuv")
8630 "This package provides a cross-platform interface to file system
8631 operations, built on top of the libuv C library.")
8632 (license license:gpl3)))
8634 (define-public r-clisymbols
8636 (name "r-clisymbols")
8641 (uri (cran-uri "clisymbols" version))
8644 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8645 (build-system r-build-system)
8646 (home-page "https://github.com/gaborcsardi/clisymbols")
8647 (synopsis "Unicode symbols at the R prompt")
8649 "This package provides a small subset of Unicode symbols, that are useful
8650 when building command line applications. They fall back to alternatives on
8651 terminals that do not support Unicode.")
8652 (license license:expat)))
8654 (define-public r-usethis
8661 (uri (cran-uri "usethis" version))
8664 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8665 (build-system r-build-system)
8667 `(("r-clipr" ,r-clipr)
8668 ("r-clisymbols" ,r-clisymbols)
8669 ("r-crayon" ,r-crayon)
8674 ("r-git2r" ,r-git2r)
8676 ("r-purrr" ,r-purrr)
8677 ("r-rlang" ,r-rlang)
8678 ("r-rprojroot" ,r-rprojroot)
8679 ("r-rstudioapi" ,r-rstudioapi)
8680 ("r-whisker" ,r-whisker)
8681 ("r-withr" ,r-withr)
8682 ("r-yaml" ,r-yaml)))
8683 (home-page "https://github.com/r-lib/usethis")
8684 (synopsis "Automate R package and project setup")
8686 "This package helps you to automate R package and project setup tasks
8687 that are otherwise performed manually. This includes setting up unit testing,
8688 test coverage, continuous integration, Git, GitHub integration, licenses,
8689 Rcpp, RStudio projects, and more.")
8690 (license license:gpl3)))
8692 (define-public r-sessioninfo
8694 (name "r-sessioninfo")
8699 (uri (cran-uri "sessioninfo" version))
8702 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8703 (build-system r-build-system)
8706 ("r-withr" ,r-withr)))
8707 (home-page "https://github.com/r-lib/sessioninfo#readme")
8708 (synopsis "R session information")
8710 "This package provides tools to query and print information about the
8711 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8712 more information about packages, and where they were installed from.")
8713 (license license:gpl2)))
8715 (define-public r-remotes
8722 (uri (cran-uri "remotes" version))
8725 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8726 (build-system r-build-system)
8727 (home-page "https://github.com/r-lib/remotes#readme")
8728 (synopsis "R package installation from remote repositories")
8730 "Download and install R packages stored in GitHub, BitBucket, or plain
8731 subversion or git repositories. This package is a lightweight replacement of
8732 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8733 the code was copied over from @code{devtools}.")
8734 (license license:gpl2+)))
8736 (define-public r-xopen
8743 (uri (cran-uri "xopen" version))
8746 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8747 (build-system r-build-system)
8749 `(("r-processx" ,r-processx)))
8750 (home-page "https://github.com/r-lib/xopen#readme")
8751 (synopsis "Open system files, URLs, anything")
8753 "This package provides a cross-platform solution to open files,
8754 directories or URLs with their associated programs.")
8755 (license license:expat)))
8757 (define-public r-rcmdcheck
8759 (name "r-rcmdcheck")
8764 (uri (cran-uri "rcmdcheck" version))
8767 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8768 (build-system r-build-system)
8770 `(("r-callr" ,r-callr)
8772 ("r-crayon" ,r-crayon)
8774 ("r-digest" ,r-digest)
8775 ("r-pkgbuild" ,r-pkgbuild)
8776 ("r-prettyunits" ,r-prettyunits)
8778 ("r-rprojroot" ,r-rprojroot)
8779 ("r-sessioninfo" ,r-sessioninfo)
8780 ("r-withr" ,r-withr)
8781 ("r-xopen" ,r-xopen)))
8782 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8783 (synopsis "Run R CMD check from R and capture results")
8785 "Run @code{R CMD check} from R programmatically, and capture the results
8786 of the individual checks.")
8787 (license license:expat)))
8789 (define-public r-rapportools
8791 (name "r-rapportools")
8796 (uri (cran-uri "rapportools" version))
8799 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8800 (build-system r-build-system)
8802 `(("r-pander" ,r-pander)
8804 ("r-reshape" ,r-reshape)))
8805 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8806 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8808 "This package provides helper functions that act as wrappers to more
8809 advanced statistical methods with the advantage of having sane defaults for
8811 (license license:agpl3+)))
8813 (define-public r-pander
8820 (uri (cran-uri "pander" version))
8823 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8824 (build-system r-build-system)
8826 `(("r-digest" ,r-digest)
8827 ("r-rcpp" ,r-rcpp)))
8828 (home-page "https://rapporter.github.io/pander")
8829 (synopsis "Render R objects into Pandoc's markdown")
8831 "The main aim of the pander R package is to provide a minimal and easy
8832 tool for rendering R objects into Pandoc's markdown. The package is also
8833 capable of exporting/converting complex Pandoc documents (reports) in various
8835 ;; This package is licensed under either the AGPLv3+ or the very rarely
8837 (license license:agpl3+)))
8839 (define-public r-summarytools
8841 (name "r-summarytools")
8846 (uri (cran-uri "summarytools" version))
8849 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8850 (build-system r-build-system)
8852 `(("r-checkmate" ,r-checkmate)
8853 ("r-dplyr" ,r-dplyr)
8854 ("r-htmltools" ,r-htmltools)
8855 ("r-lubridate" ,r-lubridate)
8856 ("r-magick" ,r-magick)
8857 ("r-matrixstats" ,r-matrixstats)
8858 ("r-pander" ,r-pander)
8860 ("r-rapportools" ,r-rapportools)
8861 ("r-rcurl" ,r-rcurl)
8862 ("r-tibble" ,r-tibble)
8863 ("r-tidyr" ,r-tidyr)))
8864 (home-page "https://github.com/dcomtois/summarytools")
8865 (synopsis "Tools to quickly and neatly summarize data")
8867 "This package provides tools for data frame summaries, cross-tabulations,
8868 weight-enabled frequency tables and common univariate statistics in concise
8869 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8870 good point-of-entry for exploring data, both for experienced and new R
8872 (license license:gpl2)))
8874 (define-public r-lsei
8881 (uri (cran-uri "lsei" version))
8884 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8885 (build-system r-build-system)
8887 `(("gfortran" ,gfortran)))
8888 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8889 (synopsis "Solve regression problems under equality/inequality constraints")
8891 "It contains functions that solve least squares linear regression
8892 problems under linear equality/inequality constraints. Functions for solving
8893 quadratic programming problems are also available, which transform such
8894 problems into least squares ones first.")
8895 (license license:gpl2+)))
8897 (define-public r-npsurv
8904 (uri (cran-uri "npsurv" version))
8907 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8908 (build-system r-build-system)
8910 `(("r-lsei" ,r-lsei)))
8911 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8912 (synopsis "Nonparametric survival analysis")
8914 "This package contains functions for non-parametric survival analysis of
8915 exact and interval-censored observations.")
8916 (license license:gpl2+)))
8918 (define-public r-clusteval
8920 (name "r-clusteval")
8925 (uri (cran-uri "clusteval" version))
8928 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8929 (build-system r-build-system)
8931 `(("r-mvtnorm" ,r-mvtnorm)
8932 ("r-rcpp" ,r-rcpp)))
8933 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8934 (synopsis "Evaluation of clustering algorithms")
8936 "This R package provides a suite of tools to evaluate clustering
8937 algorithms, clusterings, and individual clusters.")
8938 (license license:expat)))
8940 (define-public r-tweedie
8947 (uri (cran-uri "tweedie" version))
8950 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8951 (build-system r-build-system)
8952 (native-inputs `(("gfortran" ,gfortran)))
8953 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8954 (synopsis "Evaluation of Tweedie exponential family models")
8956 "Maximum likelihood computations for Tweedie families, including the
8957 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8958 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8959 and related methods.")
8960 (license license:gpl2+)))
8962 (define-public r-rcppgsl
8969 (uri (cran-uri "RcppGSL" version))
8971 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
8972 (properties `((upstream-name . "RcppGSL")))
8973 (build-system r-build-system)
8975 `(("r-rcpp" ,r-rcpp)
8978 `(("r-knitr" ,r-knitr))) ; for vignettes
8979 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8980 (synopsis "Rcpp integration for GSL vectors and matrices")
8982 "The GNU Scientific Library (or GSL) is a collection of numerical
8983 routines for scientific computing. It is particularly useful for C and C++
8984 programs as it provides a standard C interface to a wide range of mathematical
8985 routines. There are over 1000 functions in total with an extensive test
8986 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8987 structures and R using concepts from Rcpp which is itself a package that eases
8988 the interfaces between R and C++.")
8989 (license license:gpl2+)))
8991 (define-public r-mvabund
8998 (uri (cran-uri "mvabund" version))
9001 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
9002 (build-system r-build-system)
9004 `(("r-mass" ,r-mass)
9006 ("r-rcppgsl" ,r-rcppgsl)
9007 ("r-statmod" ,r-statmod)
9008 ("r-tweedie" ,r-tweedie)))
9009 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9010 (synopsis "Statistical methods for analysing multivariate abundance data")
9012 "This package provides a set of tools for displaying, modeling and
9013 analysing multivariate abundance data in community ecology.")
9014 (license license:lgpl2.1+)))
9016 (define-public r-afex
9023 (uri (cran-uri "afex" version))
9026 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
9027 (build-system r-build-system)
9031 ("r-lmertest" ,r-lmertest)
9032 ("r-pbkrtest" ,r-pbkrtest)
9033 ("r-reshape2" ,r-reshape2)))
9034 (home-page "https://afex.singmann.science/")
9035 (synopsis "Analysis of factorial experiments")
9037 "This package provides convenience functions for analyzing factorial
9038 experiments using ANOVA or mixed models.")
9039 (license license:gpl2+)))
9041 (define-public r-lmertest
9048 (uri (cran-uri "lmerTest" version))
9051 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
9052 (properties `((upstream-name . "lmerTest")))
9053 (build-system r-build-system)
9055 `(("r-ggplot2" ,r-ggplot2)
9058 ("r-numderiv" ,r-numderiv)))
9059 (home-page "https://github.com/runehaubo/lmerTestR")
9060 (synopsis "Tests in linear mixed effects models")
9062 "This package provides p-values in type I, II or III anova and summary
9063 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9064 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9065 package. Model selection methods include step, drop1 and anova-like tables
9066 for random effects (ranova). Methods for Least-Square means (LS-means) and
9067 tests of linear contrasts of fixed effects are also available.")
9068 (license license:gpl2+)))
9070 (define-public r-r2glmm
9077 (uri (cran-uri "r2glmm" version))
9080 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9081 (build-system r-build-system)
9083 `(("r-afex" ,r-afex)
9084 ("r-data-table" ,r-data-table)
9085 ("r-dplyr" ,r-dplyr)
9086 ("r-ggplot2" ,r-ggplot2)
9087 ("r-gridextra" ,r-gridextra)
9088 ("r-lmertest" ,r-lmertest)
9090 ("r-matrix" ,r-matrix)
9092 ("r-pbkrtest" ,r-pbkrtest)))
9093 (home-page "https://github.com/bcjaeger/r2glmm")
9094 (synopsis "Compute R squared for mixed (multilevel) models")
9096 "This package computes model and semi partial R squared with confidence
9097 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9098 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9099 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9101 (license license:gpl2)))
9103 (define-public r-weights
9110 (uri (cran-uri "weights" version))
9113 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9114 (build-system r-build-system)
9116 `(("r-gdata" ,r-gdata)
9117 ("r-hmisc" ,r-hmisc)
9118 ("r-mice" ,r-mice)))
9120 "https://cran.r-project.org/web/packages/weights/")
9121 (synopsis "Weighting and weighted statistics")
9122 (description "This package Provides a variety of functions for producing
9123 simple weighted statistics, such as weighted Pearson's correlations, partial
9124 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9125 includes some software for quickly recoding survey data and plotting point
9126 estimates from interaction terms in regressions (and multiply imputed
9127 regressions). NOTE: Weighted partial correlation calculations pulled to
9129 (license license:gpl2+)))
9131 (define-public r-rcppannoy
9133 (name "r-rcppannoy")
9138 (uri (cran-uri "RcppAnnoy" version))
9141 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9142 (properties `((upstream-name . "RcppAnnoy")))
9143 (build-system r-build-system)
9145 `(("r-rcpp" ,r-rcpp)))
9147 `(("r-knitr" ,r-knitr))) ; for vignettes
9148 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9149 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9151 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9152 for efficient memory usage as well an ability to load from and save to disk.
9153 This package provides an R interface.")
9154 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9156 (license (list license:gpl2+ license:asl2.0))))
9158 (define-public r-rcpphnsw
9165 (uri (cran-uri "RcppHNSW" version))
9168 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9169 (properties `((upstream-name . "RcppHNSW")))
9170 (build-system r-build-system)
9171 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9172 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9173 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9175 "Hnswlib is a C++ library for approximate nearest neighbors. This
9176 package provides a minimal R interface by relying on the Rcpp package.")
9177 ;; hnswlib is released under Version 2.0 of the Apache License.
9178 (license (list license:gpl3 license:asl2.0))))
9180 (define-public r-rcppparallel
9182 (name "r-rcppparallel")
9187 (uri (cran-uri "RcppParallel" version))
9190 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9191 (properties `((upstream-name . "RcppParallel")))
9192 (build-system r-build-system)
9193 (home-page "http://rcppcore.github.io/RcppParallel")
9194 (synopsis "Parallel programming tools for Rcpp")
9196 "This package provides high level functions for parallel programming with
9197 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9198 the work of a standard serial @code{for} loop into a parallel one and the
9199 @code{parallelReduce()} function can be used for accumulating aggregates or
9201 (license license:gpl2)))
9203 (define-public r-ncdf4
9210 (uri (cran-uri "ncdf4" version))
9213 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9214 (build-system r-build-system)
9216 `(("netcdf" ,netcdf)
9218 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9219 (synopsis "R interface to Unidata netCDF format data files")
9221 "This package provides a high-level R interface to data files written
9222 using Unidata's netCDF library (version 4 or earlier), which are binary data
9223 files that are portable across platforms and include metadata information in
9224 addition to the data sets. Using this package, netCDF files can be opened and
9225 data sets read in easily. It is also easy to create new netCDF dimensions,
9226 variables, and files, in either version 3 or 4 format, and manipulate existing
9228 (license license:gpl3+)))
9230 (define-public r-biocmanager
9232 (name "r-biocmanager")
9237 (uri (cran-uri "BiocManager" version))
9239 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9240 (properties `((upstream-name . "BiocManager")))
9241 (build-system r-build-system)
9242 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9243 (synopsis "Access the Bioconductor project package repository")
9245 "This package provides a convenient tool to install and update
9246 Bioconductor packages.")
9247 (license license:artistic2.0)))
9249 (define-public r-rgl
9252 (version "0.100.30")
9256 (uri (cran-uri "rgl" version))
9259 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9260 (build-system r-build-system)
9262 `(("pkg-config" ,pkg-config)))
9264 `(("freetype" ,freetype)
9268 ("ghc-pandoc" ,ghc-pandoc)
9271 `(("r-crosstalk" ,r-crosstalk)
9272 ("r-htmltools" ,r-htmltools)
9273 ("r-htmlwidgets" ,r-htmlwidgets)
9274 ("r-jsonlite" ,r-jsonlite)
9275 ("r-knitr" ,r-knitr)
9276 ("r-magrittr" ,r-magrittr)
9277 ("r-manipulatewidget" ,r-manipulatewidget)
9278 ("r-shiny" ,r-shiny)))
9279 (home-page "https://r-forge.r-project.org/projects/rgl/")
9280 (synopsis "3D visualization using OpenGL")
9282 "This package provides medium to high level functions for 3D interactive graphics,
9283 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9284 as functions for constructing representations of geometric
9285 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9286 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9287 image formats, including PNG, Postscript, SVG, PGF.")
9288 ;; Any version of the GPL.
9289 (license (list license:gpl2+ license:gpl3+))))
9291 (define-public r-multicool
9293 (name "r-multicool")
9298 (uri (cran-uri "multicool" version))
9301 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9302 (build-system r-build-system)
9303 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9304 (home-page "https://cran.r-project.org/web/packages/multicool/")
9305 (synopsis "Permutations of multisets in cool-lex order")
9307 "This package provides a set of tools to permute multisets without loops
9308 or hash tables and to generate integer partitions. Cool-lex order is similar
9309 to colexicographical order.")
9310 (license license:gpl2)))
9312 (define-public r-misc3d
9319 (uri (cran-uri "misc3d" version))
9322 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9323 (build-system r-build-system)
9324 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9325 (synopsis "Miscellaneous 3D Plots")
9327 "This package provides a collection of miscellaneous 3d plots, including
9329 ;; Any version of the GPL.
9330 (license (list license:gpl2+ license:gpl3+))))
9339 (uri (cran-uri "ks" version))
9341 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9342 (build-system r-build-system)
9345 ("r-kernlab" ,r-kernlab)
9346 ("r-kernsmooth" ,r-kernsmooth)
9347 ("r-matrix" ,r-matrix)
9348 ("r-mclust" ,r-mclust)
9350 ("r-multicool" ,r-multicool)
9351 ("r-mvtnorm" ,r-mvtnorm)))
9352 (home-page "http://www.mvstat.net/tduong/")
9353 (synopsis "Kernel smoothing")
9355 "This package provides kernel smoothers for univariate and multivariate
9356 data, including density functions, density derivatives, cumulative
9357 distributions, modal clustering, discriminant analysis, and two-sample
9358 hypothesis testing.")
9359 ;; Either version of the GPL.
9360 (license (list license:gpl2 license:gpl3))))
9362 (define-public r-feature
9369 (uri (cran-uri "feature" version))
9372 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9373 (build-system r-build-system)
9376 ("r-misc3d" ,r-misc3d)
9378 (home-page "http://www.mvstat.net/tduong/")
9379 (synopsis "Inferential feature significance for kernel density estimation")
9381 "The feature package contains functions to display and compute kernel
9382 density estimates, significant gradient and significant curvature regions.
9383 Significant gradient and/or curvature regions often correspond to significant
9384 features (e.g. local modes).")
9385 ;; Either version of the GPL.
9386 (license (list license:gpl2 license:gpl3))))
9388 (define-public r-arm
9395 (uri (cran-uri "arm" version))
9398 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9399 (build-system r-build-system)
9401 `(("r-abind" ,r-abind)
9405 ("r-matrix" ,r-matrix)
9406 ("r-nlme" ,r-nlme)))
9407 (home-page "https://cran.r-project.org/web/packages/arm/")
9408 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9410 "This package provides functions to accompany A. Gelman and J. Hill,
9411 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9412 University Press, 2007.")
9413 (license license:gpl3+)))
9415 (define-public r-circular
9422 (uri (cran-uri "circular" version))
9425 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9426 (build-system r-build-system)
9428 `(("r-boot" ,r-boot)
9429 ("r-mvtnorm" ,r-mvtnorm)))
9431 `(("gfortran" ,gfortran)))
9432 (home-page "https://cran.r-project.org/web/packages/circular/")
9433 (synopsis "Circular statistics")
9435 "This package provides tools for circular statistics, from \"Topics in
9436 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9438 (license license:gpl2+)))
9440 (define-public r-activity
9447 (uri (cran-uri "activity" version))
9450 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9451 (build-system r-build-system)
9453 `(("r-circular" ,r-circular)
9454 ("r-insol" ,r-insol)
9455 ("r-pbapply" ,r-pbapply)))
9456 (home-page "https://cran.r-project.org/web/packages/activity/")
9457 (synopsis "Animal activity statistics")
9459 "This package provides functions to fit kernel density functions to
9460 animal activity time data; plot activity distributions; quantify overall
9461 levels of activity; statistically compare activity metrics through
9462 bootstrapping; and evaluate variation in linear variables with time (or other
9463 circular variables).")
9464 (license license:gpl3)))
9466 (define-public r-ouch
9473 (uri (cran-uri "ouch" version))
9476 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9477 (build-system r-build-system)
9478 (propagated-inputs `(("r-subplex" ,r-subplex)))
9479 (home-page "http://kingaa.github.io/ouch/")
9480 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9482 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9483 for evolution along a phylogenetic tree.")
9484 (license license:gpl2+)))
9486 (define-public r-fmsb
9493 (uri (cran-uri "fmsb" version))
9496 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9497 (build-system r-build-system)
9498 (home-page "http://minato.sip21c.org/msb/")
9499 (synopsis "Functions for medical statistics book with demographic data")
9501 "This package provides several utility functions for the book entitled
9502 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9503 Japan, 2007) with Japanese demographic data and some demographic analysis
9504 related functions.")
9505 (license license:gpl2+)))
9507 (define-public r-stabledist
9509 (name "r-stabledist")
9514 (uri (cran-uri "stabledist" version))
9517 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9518 (build-system r-build-system)
9519 (home-page "http://www.rmetrics.org")
9520 (synopsis "Stable distribution functions")
9522 "This package provides density, probability and quantile functions, and
9523 random number generation for (skew) stable distributions, using the
9524 parametrizations of Nolan.")
9525 (license license:gpl2+)))
9527 (define-public r-gsl
9534 (uri (cran-uri "gsl" version))
9537 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9538 (build-system r-build-system)
9541 (home-page "https://cran.r-project.org/web/packages/gsl")
9542 (synopsis "Wrapper for the GNU Scientific Library")
9544 "This package provides an R wrapper for the special functions and quasi
9545 random number generators of the GNU Scientific Library.")
9546 (license license:gpl2+)))
9548 (define-public r-adgoftest
9550 (name "r-adgoftest")
9555 (uri (cran-uri "ADGofTest" version))
9558 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9559 (properties `((upstream-name . "ADGofTest")))
9560 (build-system r-build-system)
9561 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9562 (synopsis "Anderson-Darling GoF test")
9564 "This package provides an implementation of the Anderson-Darling GoF test
9565 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9566 Anderson-Darling Distribution\".")
9567 ;; Any version of the GPL.
9568 (license license:gpl3+)))
9570 (define-public r-softimpute
9572 (name "r-softimpute")
9577 (uri (cran-uri "softImpute" version))
9580 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9581 (properties `((upstream-name . "softImpute")))
9582 (build-system r-build-system)
9584 `(("r-matrix" ,r-matrix)))
9586 `(("gfortran" ,gfortran)))
9587 (home-page "https://cran.r-project.org/web/packages/softImpute")
9588 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9590 "This package provides iterative methods for matrix completion that use
9591 nuclear-norm regularization. The package includes procedures for centering
9592 and scaling rows, columns or both, and for computing low-rank @dfn{single
9593 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9595 (license license:gpl2)))
9597 (define-public r-fftwtools
9599 (name "r-fftwtools")
9604 (uri (cran-uri "fftwtools" version))
9607 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9608 (build-system r-build-system)
9609 (inputs `(("fftw" ,fftw)))
9610 (home-page "https://github.com/krahim/fftwtools")
9611 (synopsis "Wrapper for FFTW3")
9613 "This package provides a wrapper for several FFTW functions. It provides
9614 access to the two-dimensional FFT, the multivariate FFT, and the
9615 one-dimensional real to complex FFT using the FFTW3 library. The package
9616 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9617 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9618 The FFT functions have a parameter that allows them to not return the
9619 redundant complex conjugate when the input is real data.")
9620 (license license:gpl2+)))
9622 (define-public r-tiff
9629 (uri (cran-uri "tiff" version))
9632 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9633 (build-system r-build-system)
9635 `(("libtiff" ,libtiff)
9636 ("libjpeg" ,libjpeg)
9638 (home-page "http://www.rforge.net/tiff/")
9639 (synopsis "Read and write TIFF images")
9641 "This package provides an easy and simple way to read, write and display
9642 bitmap images stored in the TIFF format. It can read and write both files and
9643 in-memory raw vectors.")
9644 ;; Either of these two license versions.
9645 (license (list license:gpl2 license:gpl3))))
9647 (define-public r-nlp
9654 (uri (cran-uri "NLP" version))
9657 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9658 (properties `((upstream-name . "NLP")))
9659 (build-system r-build-system)
9660 (home-page "https://cran.r-project.org/web/packages/NLP/")
9661 (synopsis "Natural language processing infrastructure")
9663 "This package provides basic classes and methods for Natural Language
9665 (license license:gpl3)))
9674 (uri (cran-uri "tm" version))
9677 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
9678 (properties `((upstream-name . "tm")))
9679 (build-system r-build-system)
9685 ("r-xml2" ,r-xml2)))
9686 (home-page "http://tm.r-forge.r-project.org/")
9687 (synopsis "Text mining package")
9689 "This package provides a framework for text mining applications within R.")
9690 (license license:gpl3)))
9692 (define-public r-waveslim
9699 (uri (cran-uri "waveslim" version))
9702 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9703 (build-system r-build-system)
9705 `(("gfortran" ,gfortran)))
9706 (home-page "http://waveslim.blogspot.com")
9707 (synopsis "Basic wavelet routines for signal processing")
9709 "This package provides basic wavelet routines for time series (1D),
9710 image (2D) and array (3D) analysis. The code provided here is based on
9711 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9712 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9713 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9714 pairs (Selesnick 2001, 2002).")
9715 (license license:bsd-3)))
9717 (define-public r-wordcloud
9719 (name "r-wordcloud")
9724 (uri (cran-uri "wordcloud" version))
9727 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9728 (build-system r-build-system)
9730 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9732 ;; The "tm" package is only "suggested" according to CRAN, but the
9733 ;; wordcloud package cannot be loaded without it.
9735 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9736 (synopsis "Word clouds")
9738 "This package provides functionality to create pretty word clouds,
9739 visualize differences and similarity between documents, and avoid
9740 over-plotting in scatter plots with text.")
9741 (license license:lgpl2.1)))
9743 (define-public r-colorramps
9745 (name "r-colorramps")
9750 (uri (cran-uri "colorRamps" version))
9753 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9754 (properties `((upstream-name . "colorRamps")))
9755 (build-system r-build-system)
9756 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9757 (synopsis "Build color tables")
9758 (description "This package provides features to build gradient color
9760 ;; Any version of the GPL
9761 (license license:gpl3+)))
9763 (define-public r-tidytree
9770 (uri (cran-uri "tidytree" version))
9772 (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
9773 (build-system r-build-system)
9776 ("r-dplyr" ,r-dplyr)
9777 ("r-lazyeval" ,r-lazyeval)
9778 ("r-magrittr" ,r-magrittr)
9779 ("r-rlang" ,r-rlang)
9780 ("r-tibble" ,r-tibble)))
9781 (home-page "https://github.com/GuangchuangYu/tidytree")
9782 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9784 "Phylogenetic trees generally contain multiple components including nodes,
9785 edges, branches and associated data. This package provides an approach to
9786 convert tree objects to tidy data frames. It also provides tidy interfaces to
9787 manipulate tree data.")
9788 (license license:artistic2.0)))
9790 (define-public r-rvcheck
9797 (uri (cran-uri "rvcheck" version))
9799 (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
9800 (build-system r-build-system)
9802 `(("r-biocmanager" ,r-biocmanager)
9803 ("r-rlang" ,r-rlang)))
9804 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9805 (synopsis "R package version check")
9807 "This package provides tools to check the latest release version of R and
9808 R packages (on CRAN, Bioconductor or Github).")
9809 (license license:artistic2.0)))
9811 (define-public r-docopt
9818 (uri (cran-uri "docopt" version))
9821 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9822 (build-system r-build-system)
9823 (home-page "https://github.com/docopt/docopt.R")
9824 (synopsis "Command-line interface specification language")
9826 "This package enables you to define a command-line interface by just
9827 giving it a description in the specific format.")
9828 (license license:expat)))
9830 (define-public r-sparsesvd
9832 (name "r-sparsesvd")
9837 (uri (cran-uri "sparsesvd" version))
9840 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9841 (build-system r-build-system)
9842 (propagated-inputs `(("r-matrix" ,r-matrix)))
9843 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9844 (synopsis "Sparse truncated singular value decomposition")
9846 "This package provides a Wrapper around the SVDLIBC library
9847 for (truncated) singular value decomposition of a sparse matrix. Currently,
9848 only sparse real matrices in Matrix package format are supported.")
9849 ;; SVDLIBC is released under BSD-2. The R interface is released under
9851 (license (list license:bsd-3 license:bsd-2))))
9853 (define-public r-speedglm
9860 (uri (cran-uri "speedglm" version))
9863 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9864 (build-system r-build-system)
9866 `(("r-mass" ,r-mass)
9867 ("r-matrix" ,r-matrix)))
9868 (home-page "https://cran.r-project.org/web/packages/speedglm")
9869 (synopsis "Fit linear and generalized linear models to large data sets")
9871 "This package provides tools for fitting linear models and generalized
9872 linear models to large data sets by updating algorithms.")
9873 ;; Any version of the GPL
9874 (license license:gpl2+)))
9876 (define-public r-densityclust
9878 (name "r-densityclust")
9883 (uri (cran-uri "densityClust" version))
9886 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9887 (properties `((upstream-name . "densityClust")))
9888 (build-system r-build-system)
9891 ("r-ggplot2" ,r-ggplot2)
9892 ("r-ggrepel" ,r-ggrepel)
9893 ("r-gridextra" ,r-gridextra)
9894 ("r-rcolorbrewer" ,r-rcolorbrewer)
9896 ("r-rtsne" ,r-rtsne)))
9897 (home-page "https://cran.r-project.org/web/packages/densityClust")
9898 (synopsis "Clustering by fast search and find of density peaks")
9900 "This package provides an improved implementation (based on k-nearest
9901 neighbors) of the density peak clustering algorithm, originally described by
9902 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9903 large datasets (> 100,000 samples) very efficiently.")
9904 (license license:gpl2+)))
9906 (define-public r-combinat
9913 (uri (cran-uri "combinat" version))
9916 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9917 (build-system r-build-system)
9918 (home-page "https://cran.r-project.org/web/packages/combinat")
9919 (synopsis "Combinatorics utilities")
9920 (description "This package provides assorted routines for combinatorics.")
9921 (license license:gpl2)))
9923 (define-public r-qlcmatrix
9925 (name "r-qlcmatrix")
9930 (uri (cran-uri "qlcMatrix" version))
9933 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9934 (properties `((upstream-name . "qlcMatrix")))
9935 (build-system r-build-system)
9937 `(("r-docopt" ,r-docopt)
9938 ("r-matrix" ,r-matrix)
9940 ("r-sparsesvd" ,r-sparsesvd)))
9941 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9942 (synopsis "Sparse matrix functions for quantitative language comparison")
9944 "This package provides an extension of the functionality of the Matrix
9945 package for using sparse matrices. Some of the functions are very general,
9946 while other are highly specific for the special data format used for
9947 @dfn{quantitative language comparison} (QLC).")
9948 (license license:gpl3)))
9950 (define-public r-ddrtree
9957 (uri (cran-uri "DDRTree" version))
9960 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9961 (properties `((upstream-name . "DDRTree")))
9962 (build-system r-build-system)
9965 ("r-irlba" ,r-irlba)
9967 ("r-rcppeigen" ,r-rcppeigen)))
9968 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9969 (synopsis "Learning principal graphs with DDRTree")
9971 "This package provides an implementation of the framework of
9972 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9973 dimensional space while constructs a principal tree which passes through the
9974 middle of the data simultaneously. DDRTree shows superiority to
9975 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9976 intrinsic structure of single cell genomics data. In general, it could be
9977 used to reconstruct the temporal progression as well as the bifurcation
9978 structure of any data type.")
9979 (license license:asl2.0)))
9981 (define-public r-corpcor
9988 (uri (cran-uri "corpcor" version))
9991 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9992 (build-system r-build-system)
9993 (home-page "http://strimmerlab.org/software/corpcor/")
9994 (synopsis "Efficient estimation of covariance and (partial) correlation")
9996 "This package implements a James-Stein-type shrinkage estimator for the
9997 covariance matrix, with separate shrinkage for variances and correlations.
9998 Furthermore, functions are available for fast singular value decomposition,
9999 for computing the pseudoinverse, and for checking the rank and positive
10000 definiteness of a matrix.")
10001 (license license:gpl3+)))
10003 (define-public r-rspectra
10005 (name "r-rspectra")
10010 (uri (cran-uri "RSpectra" version))
10013 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10014 (properties `((upstream-name . "RSpectra")))
10015 (build-system r-build-system)
10017 `(("r-matrix" ,r-matrix)
10019 ("r-rcppeigen" ,r-rcppeigen)))
10020 (home-page "https://github.com/yixuan/RSpectra")
10021 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10023 "This package provides an R interface to the Spectra library for
10024 large-scale eigenvalue and SVD problems. It is typically used to compute a
10025 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10026 which is usually more efficient than @code{eigen()} if k << n.")
10028 (license license:mpl2.0)))
10030 (define-public r-vbsr
10037 (uri (cran-uri "vbsr" version))
10040 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10041 (build-system r-build-system)
10042 (home-page "https://cran.r-project.org/web/packages/vbsr")
10043 (synopsis "Variational Bayes spike regression regularized linear models")
10045 "This package provides an efficient algorithm for solving ultra-sparse
10046 regularized regression models using a variational Bayes algorithm with a spike
10047 prior. The algorithm is solved on a path, with coordinate updates, and is
10048 capable of generating very sparse models. Very general model
10049 diagnostics for controlling type-1 errors are also provided.")
10050 (license license:gpl2)))
10052 (define-public r-flare
10055 (version "1.6.0.2")
10059 (uri (cran-uri "flare" version))
10062 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10063 (build-system r-build-system)
10065 `(("r-igraph" ,r-igraph)
10066 ("r-lattice" ,r-lattice)
10068 ("r-matrix" ,r-matrix)))
10069 (home-page "https://cran.r-project.org/web/packages/flare")
10070 (synopsis "Family of Lasso regression implementations")
10072 "This package provides implementations of a family of Lasso variants
10073 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10074 high dimensional sparse linear models.")
10075 (license license:gpl2)))
10077 (define-public r-lassopv
10084 (uri (cran-uri "lassopv" version))
10087 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10088 (build-system r-build-system)
10089 (propagated-inputs `(("r-lars" ,r-lars)))
10090 (home-page "https://github.com/lingfeiwang/lassopv")
10091 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10093 "This package enables you to estimate the p-values for predictors x
10094 against target variable y in Lasso regression, using the regularization
10095 strength when each predictor enters the active set of regularization path for
10096 the first time as the statistic.")
10097 (license license:gpl3)))
10099 (define-public r-splitstackshape
10101 (name "r-splitstackshape")
10106 (uri (cran-uri "splitstackshape" version))
10109 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10110 (build-system r-build-system)
10112 `(("r-data-table" ,r-data-table)))
10113 (home-page "https://github.com/mrdwab/splitstackshape")
10114 (synopsis "Stack and reshape datasets after splitting concatenated values")
10116 "Online data collection tools like Google Forms often export
10117 multiple-response questions with data concatenated in cells. The
10118 @code{concat.split} (cSplit) family of functions provided by this package
10119 splits such data into separate cells. This package also includes functions to
10120 stack groups of columns and to reshape wide data, even when the data are
10121 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10122 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10124 (license license:gpl3)))
10126 (define-public r-tfmpvalue
10128 (name "r-tfmpvalue")
10133 (uri (cran-uri "TFMPvalue" version))
10136 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10137 (properties `((upstream-name . "TFMPvalue")))
10138 (build-system r-build-system)
10139 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10140 (home-page "https://github.com/ge11232002/TFMPvalue")
10141 (synopsis "P-value computation for position weight matrices")
10143 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10144 identification from sequence/alignments, we are interested in the significance
10145 of certain match scores. TFMPvalue provides the accurate calculation of a
10146 p-value with a score threshold for position weight matrices, or the score with
10147 a given p-value. It is an interface to code originally made available by
10148 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10149 Touzet and Varre (2007).")
10150 (license license:gpl2)))
10152 (define-public r-rnifti
10159 (uri (cran-uri "RNifti" version))
10162 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10163 (properties `((upstream-name . "RNifti")))
10164 (build-system r-build-system)
10165 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10166 (home-page "https://github.com/jonclayden/RNifti")
10167 (synopsis "Fast R and C++ access to NIfTI images")
10169 "This package provides very fast read and write access to images stored
10170 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10171 compiled C and interpreted R code. It also provides a C/C++ API that can be
10172 used by other packages.")
10173 (license license:gpl2)))
10175 (define-public r-shades
10182 (uri (cran-uri "shades" version))
10185 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10186 (build-system r-build-system)
10187 (home-page "https://github.com/jonclayden/shades")
10188 (synopsis "Simple color manipulation")
10190 "This package provides functions for easily manipulating colors,
10191 creating color scales and calculating color distances.")
10192 (license license:bsd-3)))
10194 (define-public r-ore
10201 (uri (cran-uri "ore" version))
10203 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10204 (build-system r-build-system)
10205 (home-page "https://github.com/jonclayden/ore")
10206 (synopsis "R interface to the Onigmo regular expression library")
10208 "This package provides an alternative to R's built-in functionality for
10209 handling regular expressions, based on the Onigmo library. It offers
10210 first-class compiled regex objects, partial matching and function-based
10211 substitutions, amongst other features.")
10212 (license license:bsd-3)))
10214 (define-public r-reportr
10221 (uri (cran-uri "reportr" version))
10224 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10225 (build-system r-build-system)
10226 (propagated-inputs `(("r-ore" ,r-ore)))
10227 (home-page "https://github.com/jonclayden/reportr")
10228 (synopsis "General message and error reporting system")
10230 "This package provides a system for reporting messages, which offers
10231 certain useful features over the standard R system, such as the incorporation
10232 of output consolidation, message filtering, assertions, expression
10233 substitution, automatic generation of stack traces for debugging, and
10234 conditional reporting based on the current \"output level\".")
10235 (license license:gpl2)))
10237 (define-public r-tractor-base
10239 (name "r-tractor-base")
10244 (uri (cran-uri "tractor.base" version))
10247 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10248 (properties `((upstream-name . "tractor.base")))
10249 (build-system r-build-system)
10252 ("r-reportr" ,r-reportr)
10253 ("r-rnifti" ,r-rnifti)
10254 ("r-shades" ,r-shades)))
10255 (home-page "http://www.tractor-mri.org.uk")
10256 (synopsis "Read, manipulate and visualize magnetic resonance images")
10258 "This package provides functions for working with magnetic resonance
10259 images. It supports reading and writing of popular file formats (DICOM,
10260 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10261 visualization; flexible image manipulation; metadata and sparse image
10263 (license license:gpl2)))
10265 (define-public r-grimport
10267 (name "r-grimport")
10272 (uri (cran-uri "grImport" version))
10275 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10276 (properties `((upstream-name . "grImport")))
10277 (build-system r-build-system)
10279 `(("ghostscript" ,ghostscript)))
10281 `(("r-xml" ,r-xml)))
10282 (home-page "https://cran.r-project.org/web/packages/grImport")
10283 (synopsis "Convert, import, and draw PostScript pictures")
10285 "This package provides functions for converting, importing, and drawing
10286 PostScript pictures in R plots.")
10287 (license license:gpl2+)))
10289 (define-public r-grimport2
10291 (name "r-grimport2")
10296 (uri (cran-uri "grImport2" version))
10299 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10300 (properties `((upstream-name . "grImport2")))
10301 (build-system r-build-system)
10303 `(("r-base64enc" ,r-base64enc)
10307 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10308 (synopsis "Import SVG graphics")
10310 "This package provides functions for importing external vector images and
10311 drawing them as part of R plots. This package is different from the
10312 @code{grImport} package because, where that package imports PostScript format
10313 images, this package imports SVG format images. Furthermore, this package
10314 imports a specific subset of SVG, so external images must be preprocessed
10315 using a package like @code{rsvg} to produce SVG that this package can import.
10316 SVG features that are not supported by R graphics, such as gradient fills, can
10317 be imported and then exported via the @code{gridSVG} package.")
10318 (license license:gpl2+)))
10320 (define-public r-kohonen
10327 (uri (cran-uri "kohonen" version))
10330 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10331 (build-system r-build-system)
10333 `(("r-rcpp" ,r-rcpp)))
10334 (home-page "https://cran.r-project.org/web/packages/kohonen")
10335 (synopsis "Supervised and unsupervised self-organising maps")
10337 "This package provides functions to train @dfn{self-organising
10338 maps} (SOMs). Also interrogation of the maps and prediction using trained
10339 maps are supported. The name of the package refers to Teuvo Kohonen, the
10340 inventor of the SOM.")
10341 (license license:gpl2+)))
10343 (define-public r-nnls
10350 (uri (cran-uri "nnls" version))
10353 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10354 (build-system r-build-system)
10355 (native-inputs `(("gfortran" ,gfortran)))
10356 (home-page "https://cran.r-project.org/web/packages/nnls")
10357 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10359 "This package provides an R interface to the Lawson-Hanson implementation
10360 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10361 the combination of non-negative and non-positive constraints.")
10362 (license license:gpl2+)))
10364 (define-public r-iso
10371 (uri (cran-uri "Iso" version))
10374 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10375 (properties `((upstream-name . "Iso")))
10376 (build-system r-build-system)
10377 (native-inputs `(("gfortran" ,gfortran)))
10378 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10379 (synopsis "Functions to perform isotonic regression")
10381 "This package provides support for linear order and unimodal
10382 order (univariate) isotonic regression and bivariate isotonic regression with
10383 linear order on both variables.")
10384 (license license:gpl2+)))
10386 (define-public r-chemometricswithr
10388 (name "r-chemometricswithr")
10393 (uri (cran-uri "ChemometricsWithR" version))
10396 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10398 `((upstream-name . "ChemometricsWithR")))
10399 (build-system r-build-system)
10401 `(("r-devtools" ,r-devtools)
10402 ("r-kohonen" ,r-kohonen)
10405 (home-page "https://github.com/rwehrens/CWR")
10406 (synopsis "Chemometrics with R")
10408 "This package provides functions and scripts used in the book
10409 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10410 Life Sciences\" by Ron Wehrens, Springer (2011).")
10411 (license license:gpl2+)))
10413 (define-public r-als
10420 (uri (cran-uri "ALS" version))
10423 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10424 (properties `((upstream-name . "ALS")))
10425 (build-system r-build-system)
10428 ("r-nnls" ,r-nnls)))
10429 (home-page "https://cran.r-project.org/web/packages/ALS")
10430 (synopsis "Multivariate curve resolution alternating least squares")
10432 "Alternating least squares is often used to resolve components
10433 contributing to data with a bilinear structure; the basic technique may be
10434 extended to alternating constrained least squares. This package provides an
10435 implementation of @dfn{multivariate curve resolution alternating least
10436 squares} (MCR-ALS).
10438 Commonly applied constraints include unimodality, non-negativity, and
10439 normalization of components. Several data matrices may be decomposed
10440 simultaneously by assuming that one of the two matrices in the bilinear
10441 decomposition is shared between datasets.")
10442 (license license:gpl2+)))
10444 (define-public r-strucchange
10446 (name "r-strucchange")
10451 (uri (cran-uri "strucchange" version))
10454 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10455 (build-system r-build-system)
10457 `(("r-sandwich" ,r-sandwich)
10459 (home-page "https://cran.r-project.org/web/packages/strucchange")
10460 (synopsis "Testing, monitoring, and dating structural changes")
10462 "This package provides tools for testing, monitoring and dating
10463 structural changes in (linear) regression models. It features tests/methods
10464 from the generalized fluctuation test framework as well as from the F
10465 test (Chow test) framework. This includes methods to fit, plot and test
10466 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10467 statistics, respectively. It is possible to monitor incoming data online
10468 using fluctuation processes. Finally, the breakpoints in regression models
10469 with structural changes can be estimated together with confidence intervals.
10470 Emphasis is always given to methods for visualizing the data.")
10471 ;; Either of these two GPL versions
10472 (license (list license:gpl2 license:gpl3))))
10474 (define-public r-pixmap
10481 (uri (cran-uri "pixmap" version))
10484 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10485 (build-system r-build-system)
10486 (home-page "https://cran.r-project.org/web/packages/pixmap")
10487 (synopsis "Tools for bitmap images")
10489 "This package provides functions for importing, exporting, plotting and
10490 other manipulations of bitmapped images.")
10491 (license license:gpl2)))
10493 (define-public r-rapidjsonr
10495 (name "r-rapidjsonr")
10500 (uri (cran-uri "rapidjsonr" version))
10503 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10504 (build-system r-build-system)
10505 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10506 (synopsis "JSON parser")
10508 "This package provides JSON parsing capability through the Rapidjson
10510 (license license:expat)))
10512 (define-public r-ontologyindex
10514 (name "r-ontologyindex")
10519 (uri (cran-uri "ontologyIndex" version))
10522 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10523 (properties `((upstream-name . "ontologyIndex")))
10524 (build-system r-build-system)
10525 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10526 (synopsis "Functions for processing ontologies in R")
10528 "This package provides functions for reading ontologies into R as lists
10529 and manipulating sets of ontological terms.")
10530 (license license:gpl2+)))
10532 (define-public r-gargle
10539 (uri (cran-uri "gargle" version))
10542 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10543 (build-system r-build-system)
10548 ("r-jsonlite" ,r-jsonlite)
10549 ("r-rlang" ,r-rlang)
10550 ("r-withr" ,r-withr)))
10551 (home-page "https://gargle.r-lib.org")
10552 (synopsis "Utilities for working with Google APIs")
10554 "This package provides utilities for working with Google APIs. This
10555 includes functions and classes for handling common credential types and for
10556 preparing, executing, and processing HTTP requests.")
10557 (license license:expat)))
10559 (define-public r-bigrquery
10561 (name "r-bigrquery")
10566 (uri (cran-uri "bigrquery" version))
10569 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10570 (build-system r-build-system)
10572 `(("r-assertthat" ,r-assertthat)
10573 ("r-bit64" ,r-bit64)
10576 ("r-gargle" ,r-gargle)
10579 ("r-jsonlite" ,r-jsonlite)
10580 ("r-prettyunits" ,r-prettyunits)
10581 ("r-progress" ,r-progress)
10582 ("r-rapidjsonr" ,r-rapidjsonr)
10584 ("r-rlang" ,r-rlang)
10585 ("r-tibble" ,r-tibble)))
10586 (home-page "https://github.com/rstats-db/bigrquery")
10587 (synopsis "R interface to Google's BigQuery API")
10589 "This package provides an R interface to Google's BigQuery database.")
10590 (license license:gpl3)))
10592 (define-public r-gmp
10595 (version "0.5-13.5")
10599 (uri (cran-uri "gmp" version))
10602 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10603 (build-system r-build-system)
10606 (modify-phases %standard-phases
10607 (add-after 'unpack 'set-CC
10608 (lambda _ (setenv "CC" "gcc") #t)))))
10609 (inputs `(("gmp" ,gmp)))
10610 (home-page "https://cran.r-project.org/web/packages/gmp")
10611 (synopsis "Multiple precision arithmetic")
10613 "This package supports multiple precision arithmetic (big integers and
10614 rationals, prime number tests, matrix computation), \"arithmetic without
10615 limitations\" using the GNU Multiple Precision library.")
10616 ;; Any version of the GPL.
10617 (license license:gpl3+)))
10619 (define-public r-rmpfr
10626 (uri (cran-uri "Rmpfr" version))
10629 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10630 (properties `((upstream-name . "Rmpfr")))
10631 (build-system r-build-system)
10635 `(("r-gmp" ,r-gmp)))
10636 (home-page "http://rmpfr.r-forge.r-project.org/")
10637 (synopsis "R bindings to the MPFR library")
10639 "This package supports arithmetic (via S4 classes and methods) for
10640 arbitrary precision floating point numbers, including transcendental
10641 functions. To this end, the package interfaces with the @dfn{Multiple
10642 Precision Floating-Point Reliable} (MPFR) library.")
10643 (license license:gpl2+)))
10645 (define-public r-assertive-base
10647 (name "r-assertive-base")
10652 (uri (cran-uri "assertive.base" version))
10655 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10657 `((upstream-name . "assertive.base")))
10658 (build-system r-build-system)
10659 (home-page "https://bitbucket.org/richierocks/assertive.base")
10660 (synopsis "Core of the assertive package")
10662 "This package provides a minimal set of predicates and assertions used by
10663 the assertive package. This is mainly for use by other package developers who
10664 want to include run-time testing features in their own packages.")
10665 (license license:gpl3+)))
10667 (define-public r-assertive-properties
10669 (name "r-assertive-properties")
10674 (uri (cran-uri "assertive.properties" version))
10677 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10679 `((upstream-name . "assertive.properties")))
10680 (build-system r-build-system)
10682 `(("r-assertive-base" ,r-assertive-base)))
10683 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10684 (synopsis "Assertions to check properties of variables")
10686 "This package provides a set of predicates and assertions for checking
10687 the properties of variables, such as length, names and attributes. This is
10688 mainly for use by other package developers who want to include run-time
10689 testing features in their own packages.")
10690 (license license:gpl3+)))
10692 (define-public r-assertive-numbers
10694 (name "r-assertive-numbers")
10699 (uri (cran-uri "assertive.numbers" version))
10702 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10704 `((upstream-name . "assertive.numbers")))
10705 (build-system r-build-system)
10707 `(("r-assertive-base" ,r-assertive-base)))
10708 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10709 (synopsis "Assertions to check properties of numbers")
10711 "This package provides a set of predicates and assertions for checking
10712 the properties of numbers. This is mainly for use by other package developers
10713 who want to include run-time testing features in their own packages.")
10714 (license license:gpl3+)))
10716 (define-public r-assertive-sets
10718 (name "r-assertive-sets")
10723 (uri (cran-uri "assertive.sets" version))
10726 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10728 `((upstream-name . "assertive.sets")))
10729 (build-system r-build-system)
10731 `(("r-assertive-base" ,r-assertive-base)))
10732 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10733 (synopsis "Assertions to check properties of sets")
10735 "This package provides a set of predicates and assertions for checking
10736 the properties of sets. This is mainly for use by other package developers
10737 who want to include run-time testing features in their own packages.")
10738 (license license:gpl3+)))
10740 (define-public r-assertive-matrices
10742 (name "r-assertive-matrices")
10747 (uri (cran-uri "assertive.matrices" version))
10750 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10752 `((upstream-name . "assertive.matrices")))
10753 (build-system r-build-system)
10755 `(("r-assertive-base" ,r-assertive-base)))
10756 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10757 (synopsis "Assertions to check properties of matrices")
10759 "This package provides a set of predicates and assertions for checking
10760 the properties of matrices. This is mainly for use by other package
10761 developers who want to include run-time testing features in their own
10763 (license license:gpl3+)))
10765 (define-public r-assertive-models
10767 (name "r-assertive-models")
10772 (uri (cran-uri "assertive.models" version))
10775 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10777 `((upstream-name . "assertive.models")))
10778 (build-system r-build-system)
10780 `(("r-assertive-base" ,r-assertive-base)))
10781 (home-page "https://bitbucket.org/richierocks/assertive.models")
10782 (synopsis "Assertions to check properties of models")
10784 "This package provides a set of predicates and assertions for checking
10785 the properties of models. This is mainly for use by other package developers
10786 who want to include run-time testing features in their own packages.")
10787 (license license:gpl3+)))
10789 (define-public r-assertive-reflection
10791 (name "r-assertive-reflection")
10796 (uri (cran-uri "assertive.reflection" version))
10799 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10801 `((upstream-name . "assertive.reflection")))
10802 (build-system r-build-system)
10804 `(("r-assertive-base" ,r-assertive-base)))
10805 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10806 (synopsis "Assertions for checking the state of R")
10808 "This package provides a set of predicates and assertions for checking
10809 the state and capabilities of R, the operating system it is running on, and
10810 the IDE being used. This is mainly for use by other package developers who
10811 want to include run-time testing features in their own packages.")
10812 (license license:gpl3+)))
10814 (define-public r-assertive-types
10816 (name "r-assertive-types")
10821 (uri (cran-uri "assertive.types" version))
10824 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10826 `((upstream-name . "assertive.types")))
10827 (build-system r-build-system)
10829 `(("r-assertive-base" ,r-assertive-base)
10830 ("r-assertive-properties" ,r-assertive-properties)
10831 ("r-codetools" ,r-codetools)))
10832 (home-page "https://bitbucket.org/richierocks/assertive.types")
10833 (synopsis "Assertions to check types of variables")
10835 "This package provides a set of predicates and assertions for checking
10836 the types of variables. This is mainly for use by other package developers
10837 who want to include run-time testing features in their own packages.")
10838 (license license:gpl3+)))
10840 (define-public r-assertive-files
10842 (name "r-assertive-files")
10847 (uri (cran-uri "assertive.files" version))
10850 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10852 `((upstream-name . "assertive.files")))
10853 (build-system r-build-system)
10855 `(("r-assertive-base" ,r-assertive-base)
10856 ("r-assertive-numbers" ,r-assertive-numbers)))
10857 (home-page "https://bitbucket.org/richierocks/assertive.files")
10858 (synopsis "Assertions to check properties of files")
10860 "This package provides a set of predicates and assertions for checking
10861 the properties of files and connections. This is mainly for use by other
10862 package developers who want to include run-time testing features in their own
10864 (license license:gpl3+)))
10866 (define-public r-assertive-code
10868 (name "r-assertive-code")
10873 (uri (cran-uri "assertive.code" version))
10876 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10878 `((upstream-name . "assertive.code")))
10879 (build-system r-build-system)
10881 `(("r-assertive-base" ,r-assertive-base)
10882 ("r-assertive-properties" ,r-assertive-properties)
10883 ("r-assertive-types" ,r-assertive-types)))
10884 (home-page "https://bitbucket.org/richierocks/assertive.code")
10885 (synopsis "Assertions to check properties of code")
10887 "This package provides a set of predicates and assertions for checking
10888 the properties of code. This is mainly for use by other package developers
10889 who want to include run-time testing features in their own packages.")
10890 (license license:gpl3+)))
10892 (define-public r-assertive-datetimes
10894 (name "r-assertive-datetimes")
10899 (uri (cran-uri "assertive.datetimes" version))
10902 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10904 `((upstream-name . "assertive.datetimes")))
10905 (build-system r-build-system)
10907 `(("r-assertive-base" ,r-assertive-base)
10908 ("r-assertive-types" ,r-assertive-types)))
10909 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10910 (synopsis "Assertions to check properties of dates and times")
10912 "This package provides a set of predicates and assertions for checking
10913 the properties of dates and times. This is mainly for use by other package
10914 developers who want to include run-time testing features in their own
10916 (license license:gpl3+)))
10918 (define-public r-assertive-strings
10920 (name "r-assertive-strings")
10925 (uri (cran-uri "assertive.strings" version))
10928 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10930 `((upstream-name . "assertive.strings")))
10931 (build-system r-build-system)
10933 `(("r-assertive-base" ,r-assertive-base)
10934 ("r-assertive-types" ,r-assertive-types)
10935 ("r-stringi" ,r-stringi)))
10936 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10937 (synopsis "Assertions to check properties of strings")
10939 "This package provides a set of predicates and assertions for checking
10940 the properties of strings. This is mainly for use by other package developers
10941 who want to include run-time testing features in their own packages.")
10942 (license license:gpl3+)))
10944 (define-public r-assertive-data-us
10946 (name "r-assertive-data-us")
10951 (uri (cran-uri "assertive.data.us" version))
10954 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10956 `((upstream-name . "assertive.data.us")))
10957 (build-system r-build-system)
10959 `(("r-assertive-base" ,r-assertive-base)
10960 ("r-assertive-strings" ,r-assertive-strings)))
10961 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10962 (synopsis "Assertions to check properties of strings")
10964 "This package provides a set of predicates and assertions for checking
10965 the properties of US-specific complex data types. This is mainly for use by
10966 other package developers who want to include run-time testing features in
10967 their own packages.")
10968 (license license:gpl3+)))
10970 (define-public r-assertive-data-uk
10972 (name "r-assertive-data-uk")
10977 (uri (cran-uri "assertive.data.uk" version))
10980 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10982 `((upstream-name . "assertive.data.uk")))
10983 (build-system r-build-system)
10985 `(("r-assertive-base" ,r-assertive-base)
10986 ("r-assertive-strings" ,r-assertive-strings)))
10987 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10988 (synopsis "Assertions to check properties of strings")
10990 "This package provides a set of predicates and assertions for checking
10991 the properties of UK-specific complex data types. This is mainly for use by
10992 other package developers who want to include run-time testing features in
10993 their own packages.")
10994 (license license:gpl3+)))
10996 (define-public r-assertive-data
10998 (name "r-assertive-data")
11003 (uri (cran-uri "assertive.data" version))
11006 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11008 `((upstream-name . "assertive.data")))
11009 (build-system r-build-system)
11011 `(("r-assertive-base" ,r-assertive-base)
11012 ("r-assertive-strings" ,r-assertive-strings)))
11013 (home-page "https://bitbucket.org/richierocks/assertive.data")
11014 (synopsis "Assertions to check properties of data")
11016 "This package provides a set of predicates and assertions for checking
11017 the properties of (country independent) complex data types. This is mainly
11018 for use by other package developers who want to include run-time testing
11019 features in their own packages.")
11020 (license license:gpl3+)))
11022 (define-public r-assertive
11024 (name "r-assertive")
11029 (uri (cran-uri "assertive" version))
11032 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11033 (build-system r-build-system)
11035 `(("r-assertive-base" ,r-assertive-base)
11036 ("r-assertive-code" ,r-assertive-code)
11037 ("r-assertive-data" ,r-assertive-data)
11038 ("r-assertive-data-uk" ,r-assertive-data-uk)
11039 ("r-assertive-data-us" ,r-assertive-data-us)
11040 ("r-assertive-datetimes" ,r-assertive-datetimes)
11041 ("r-assertive-files" ,r-assertive-files)
11042 ("r-assertive-matrices" ,r-assertive-matrices)
11043 ("r-assertive-models" ,r-assertive-models)
11044 ("r-assertive-numbers" ,r-assertive-numbers)
11045 ("r-assertive-properties" ,r-assertive-properties)
11046 ("r-assertive-reflection" ,r-assertive-reflection)
11047 ("r-assertive-sets" ,r-assertive-sets)
11048 ("r-assertive-strings" ,r-assertive-strings)
11049 ("r-assertive-types" ,r-assertive-types)
11050 ("r-knitr" ,r-knitr)))
11051 (home-page "https://bitbucket.org/richierocks/assertive")
11052 (synopsis "Readable check functions to ensure code integrity")
11054 "This package provides lots of predicates (@code{is_*} functions) to
11055 check the state of your variables, and assertions (@code{assert_*} functions)
11056 to throw errors if they aren't in the right form.")
11057 (license license:gpl3+)))
11059 (define-public r-dotcall64
11061 (name "r-dotcall64")
11066 (uri (cran-uri "dotCall64" version))
11069 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11070 (properties `((upstream-name . "dotCall64")))
11071 (build-system r-build-system)
11072 (native-inputs `(("gfortran" ,gfortran)))
11073 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11074 (synopsis "Enhanced foreign function interface supporting long vectors")
11076 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11077 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11078 supports long vectors, arguments of type 64-bit integer, and provides a
11079 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11080 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11081 (license license:gpl2+)))
11083 (define-public r-spam
11090 (uri (cran-uri "spam" version))
11092 (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2"))))
11093 (build-system r-build-system)
11095 `(("r-dotcall64" ,r-dotcall64)))
11096 (native-inputs `(("gfortran" ,gfortran)))
11097 (home-page "https://www.math.uzh.ch/pages/spam/")
11098 (synopsis "Sparse matrix algebra")
11100 "This package provides a set of functions for sparse matrix algebra.
11101 Differences with other sparse matrix packages are:
11104 @item it only supports (essentially) one sparse matrix format;
11105 @item it is based on transparent and simple structure(s);
11106 @item it is tailored for MCMC calculations within G(M)RF;
11107 @item and it is fast and scalable (with the extension package @code{spam64}).
11109 ;; Either of these licenses
11110 (license (list license:bsd-3 license:lgpl2.0))))
11112 (define-public r-fields
11119 (uri (cran-uri "fields" version))
11121 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11122 (build-system r-build-system)
11124 `(("r-maps" ,r-maps)
11125 ("r-spam" ,r-spam)))
11127 `(("gfortran" ,gfortran)))
11128 (home-page "https://www.image.ucar.edu/fields")
11129 (synopsis "Tools for spatial data")
11131 "This is a package for curve, surface and function fitting with an
11132 emphasis on splines, spatial data and spatial statistics. The major methods
11133 include cubic, and thin plate splines, Kriging, and compactly supported
11134 covariance functions for large data sets.")
11135 (license license:gpl2+)))
11137 (define-public r-spatialextremes
11139 (name "r-spatialextremes")
11140 (version "2.0-7.2")
11144 (uri (cran-uri "SpatialExtremes" version))
11147 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11149 `((upstream-name . "SpatialExtremes")))
11150 (build-system r-build-system)
11152 `(("r-fields" ,r-fields)
11153 ("r-maps" ,r-maps)))
11154 (home-page "http://spatialextremes.r-forge.r-project.org/")
11155 (synopsis "Modelling spatial extremes")
11157 "This package provides tools for the statistical modelling of spatial
11158 extremes using max-stable processes, copula or Bayesian hierarchical models.
11159 More precisely, this package allows (conditional) simulations from various
11160 parametric max-stable models, analysis of the extremal spatial dependence, the
11161 fitting of such processes using composite likelihoods or least square (simple
11162 max-stable processes only), model checking and selection and prediction.")
11163 (license license:gpl2+)))
11165 (define-public r-drc
11172 (uri (cran-uri "drc" version))
11175 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11176 (build-system r-build-system)
11179 ("r-gtools" ,r-gtools)
11181 ("r-multcomp" ,r-multcomp)
11182 ("r-plotrix" ,r-plotrix)
11183 ("r-scales" ,r-scales)))
11184 (home-page "https://cran.r-project.org/web/packages/drc")
11185 (synopsis "Analysis of dose-response curves")
11187 "This package provides a suite of flexible and versatile model fitting
11188 and after-fitting functions for the analysis of dose-response data.")
11189 (license license:gpl2+)))
11191 (define-public r-rmeta
11198 (uri (cran-uri "rmeta" version))
11201 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11202 (build-system r-build-system)
11203 (home-page "https://cran.r-project.org/web/packages/rmeta")
11204 (synopsis "Tools for meta-analysis")
11206 "This package provides functions for simple fixed and random effects
11207 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11208 draws standard summary plots, funnel plots, and computes summaries and tests
11209 for association and heterogeneity.")
11210 (license license:gpl2)))
11212 (define-public r-bootstrap
11214 (name "r-bootstrap")
11219 (uri (cran-uri "bootstrap" version))
11222 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11223 (build-system r-build-system)
11224 (native-inputs `(("gfortran" ,gfortran)))
11225 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11226 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11228 "This package provides software and data for the book \"An Introduction
11229 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11230 This package is primarily provided for projects already based on it, and for
11231 support of the book. New projects should preferentially use the recommended
11232 package \"boot\".")
11233 (license license:bsd-3)))
11235 (define-public r-survivalroc
11237 (name "r-survivalroc")
11242 (uri (cran-uri "survivalROC" version))
11245 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11246 (properties `((upstream-name . "survivalROC")))
11247 (build-system r-build-system)
11248 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11249 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11251 "Compute time-dependent ROC curve from censored survival data using
11252 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11253 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11254 (license license:gpl2+)))
11256 (define-public r-longitudinal
11258 (name "r-longitudinal")
11263 (uri (cran-uri "longitudinal" version))
11266 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11267 (build-system r-build-system)
11268 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11269 (home-page "http://strimmerlab.org/software/longitudinal/")
11270 (synopsis "Analysis of multiple time course data")
11272 "This package contains general data structures and functions for
11273 longitudinal data with multiple variables, repeated measurements, and
11274 irregularly spaced time points. It also implements a shrinkage estimator of
11275 dynamical correlation and dynamical covariance.")
11276 (license license:gpl3+)))
11278 (define-public r-genenet
11285 (uri (cran-uri "GeneNet" version))
11288 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11289 (properties `((upstream-name . "GeneNet")))
11290 (build-system r-build-system)
11292 `(("r-corpcor" ,r-corpcor)
11293 ("r-fdrtool" ,r-fdrtool)
11294 ("r-longitudinal" ,r-longitudinal)))
11295 (home-page "http://strimmerlab.org/software/genenet/")
11296 (synopsis "Modeling and inferring gene networks")
11298 "This package analyzes gene expression (time series) data with focus on
11299 the inference of gene networks. In particular, GeneNet implements the methods
11300 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11301 for learning large-scale gene association networks (including assignment of
11302 putative directions).")
11303 (license license:gpl3+)))
11305 (define-public r-rbamtools
11307 (name "r-rbamtools")
11308 (version "2.16.17")
11312 (uri (cran-uri "rbamtools" version))
11315 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11316 (build-system r-build-system)
11317 (inputs `(("zlib" ,zlib)))
11319 `(("r-refgenome" ,r-refgenome)))
11320 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11321 (synopsis "Read and write BAM (binary alignment) files")
11323 "This package provides an R interface to functions of the SAMtools
11325 (license license:artistic2.0)))
11327 (define-public r-protviz
11334 (uri (cran-uri "protViz" version))
11337 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11338 (properties `((upstream-name . "protViz")))
11339 (build-system r-build-system)
11340 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11341 (home-page "https://github.com/protViz/protViz/")
11342 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11344 "This package helps with quality checks, visualizations and analysis of
11345 mass spectrometry data, coming from proteomics experiments. The package is
11346 developed, tested and used at the Functional Genomics Center Zurich, where it
11347 is used mainly for prototyping, teaching, and having fun with proteomics data.
11348 But it can also be used to do data analysis for small scale data sets.")
11349 (license license:gpl3)))
11351 (define-public r-cmprsk
11358 (uri (cran-uri "cmprsk" version))
11360 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11361 (build-system r-build-system)
11363 `(("r-survival" ,r-survival)))
11365 `(("gfortran" ,gfortran)))
11366 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11367 (synopsis "Subdistribution analysis of competing risks")
11369 "This package provides tool for estimation, testing and regression
11370 modeling of subdistribution functions in competing risks, as described in
11371 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11372 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11373 A proportional hazards model for the subdistribution of a competing risk,
11374 JASA, 94:496-509.")
11375 (license license:gpl2+)))
11377 (define-public r-etm
11384 (uri (cran-uri "etm" version))
11387 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11388 (build-system r-build-system)
11390 `(("r-data-table" ,r-data-table)
11391 ("r-lattice" ,r-lattice)
11393 ("r-rcpparmadillo" ,r-rcpparmadillo)
11394 ("r-survival" ,r-survival)))
11395 (home-page "https://cran.r-project.org/web/packages/etm")
11396 (synopsis "Empirical transition matrix")
11398 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11399 the matrix of transition probabilities for any time-inhomogeneous multistate
11400 model with finite state space using the Aalen-Johansen estimator.")
11401 (license license:expat)))
11403 (define-public r-epi
11410 (uri (cran-uri "Epi" version))
11413 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11414 (properties `((upstream-name . "Epi")))
11415 (build-system r-build-system)
11417 `(("r-cmprsk" ,r-cmprsk)
11418 ("r-data-table" ,r-data-table)
11421 ("r-matrix" ,r-matrix)
11423 ("r-numderiv" ,r-numderiv)
11425 ("r-survival" ,r-survival)
11427 (home-page "http://BendixCarstensen.com/Epi/")
11428 (synopsis "Statistical analysis in epidemiology")
11430 "This package provides functions for demographic and epidemiological
11431 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11432 particular representation, manipulation and simulation of multistate data -
11433 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11434 @code{etm} and @code{cmprsk} packages. It also contains functions for
11435 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11436 data and some useful functions for tabulation and plotting, as well as a
11437 number of epidemiological data sets.")
11438 (license license:gpl2)))
11440 (define-public r-ppls
11443 (version "1.6-1.1")
11447 (uri (cran-uri "ppls" version))
11450 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11451 (build-system r-build-system)
11452 (propagated-inputs `(("r-mass" ,r-mass)))
11453 (home-page "https://cran.r-project.org/web/packages/ppls")
11454 (synopsis "Penalized partial least squares")
11456 "This package contains linear and nonlinear regression methods based on
11457 partial least squares and penalization techniques. Model parameters are
11458 selected via cross-validation, and confidence intervals ans tests for the
11459 regression coefficients can be conducted via jackknifing.")
11460 (license license:gpl2+)))
11462 (define-public r-huge
11469 (uri (cran-uri "huge" version))
11471 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11472 (build-system r-build-system)
11474 `(("r-igraph" ,r-igraph)
11476 ("r-matrix" ,r-matrix)
11478 ("r-rcppeigen" ,r-rcppeigen)))
11479 (home-page "https://cran.r-project.org/web/packages/huge")
11480 (synopsis "High-dimensional undirected graph estimation")
11482 "This package provides a general framework for high-dimensional
11483 undirected graph estimation. It integrates data preprocessing, neighborhood
11484 screening, graph estimation, and model selection techniques into a pipeline.")
11485 (license license:gpl2)))
11487 (define-public r-parcor
11494 (uri (cran-uri "parcor" version))
11497 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11498 (build-system r-build-system)
11501 ("r-genenet" ,r-genenet)
11502 ("r-glmnet" ,r-glmnet)
11504 ("r-ppls" ,r-ppls)))
11505 (home-page "https://cran.r-project.org/web/packages/parcor")
11506 (synopsis "Regularized estimation of partial correlation matrices")
11508 "This package estimates the matrix of partial correlations based on
11509 different regularized regression methods: lasso, adaptive lasso, PLS, and
11510 Ridge Regression. In addition, the package provides model selection for
11511 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11512 (license license:gpl2+)))
11514 (define-public r-mcmc
11521 (uri (cran-uri "mcmc" version))
11524 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11525 (build-system r-build-system)
11526 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11527 (synopsis "Markov chain Monte Carlo")
11529 "This package simulates continuous distributions of random vectors using
11530 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11531 function that evaluates the log unnormalized density. Algorithms are random
11532 walk Metropolis algorithm (function @code{metrop}), simulated
11533 tempering (function @code{temper}), and morphometric random walk
11534 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11535 by change of variable.")
11536 (license license:expat)))
11538 (define-public r-listenv
11545 (uri (cran-uri "listenv" version))
11548 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11549 (build-system r-build-system)
11551 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11552 (home-page "https://github.com/HenrikBengtsson/listenv")
11553 (synopsis "Environments behaving (almost) as lists")
11555 "This package implements list environments. List environments are
11556 environments that have list-like properties. For instance, the elements of a
11557 list environment are ordered and can be accessed and iterated over using index
11559 (license license:lgpl2.1+)))
11561 (define-public r-globals
11568 (uri (cran-uri "globals" version))
11571 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11572 (build-system r-build-system)
11574 `(("r-codetools" ,r-codetools)))
11575 (home-page "https://github.com/HenrikBengtsson/globals")
11576 (synopsis "Identify global objects in R expressions")
11578 "This package provides tools to identify global (\"unknown\" or \"free\")
11579 objects in R expressions by code inspection using various strategies, e.g.
11580 conservative or liberal. The objective of this package is to make it as
11581 simple as possible to identify global objects for the purpose of exporting
11582 them in distributed compute environments.")
11583 (license license:lgpl2.1+)))
11585 (define-public r-future
11592 (uri (cran-uri "future" version))
11595 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11596 (build-system r-build-system)
11598 `(("r-digest" ,r-digest)
11599 ("r-globals" ,r-globals)
11600 ("r-listenv" ,r-listenv)))
11602 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11603 (home-page "https://github.com/HenrikBengtsson/future")
11604 (synopsis "Unified parallel and distributed processing in R")
11606 "The purpose of this package is to provide a lightweight and unified
11607 Future API for sequential and parallel processing of R expression via futures.
11608 This package implements sequential, multicore, multisession, and cluster
11609 futures. With these, R expressions can be evaluated on the local machine, in
11610 parallel a set of local machines, or distributed on a mix of local and remote
11611 machines. Extensions to this package implement additional backends for
11612 processing futures via compute cluster schedulers etc. Because of its unified
11613 API, there is no need to modify any code in order to switch from sequential on
11614 the local machine to, say, distributed processing on a remote compute cluster.")
11615 (license license:lgpl2.1+)))
11617 (define-public r-future-apply
11619 (name "r-future-apply")
11624 (uri (cran-uri "future.apply" version))
11627 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11628 (properties `((upstream-name . "future.apply")))
11629 (build-system r-build-system)
11631 `(("r-future" ,r-future)
11632 ("r-globals" ,r-globals)))
11634 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11635 (home-page "https://github.com/HenrikBengtsson/future.apply")
11636 (synopsis "Apply function to elements in parallel using futures")
11638 "This package provides implementations of @code{apply()},
11639 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11640 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11641 can be resolved using any future-supported backend, e.g. parallel on the local
11642 machine or distributed on a compute cluster.")
11643 (license license:gpl2+)))
11645 (define-public r-rsvd
11652 (uri (cran-uri "rsvd" version))
11655 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11656 (build-system r-build-system)
11658 `(("r-matrix" ,r-matrix)))
11659 (home-page "https://github.com/erichson/rSVD")
11660 (synopsis "Randomized singular value decomposition")
11662 "Low-rank matrix decompositions are fundamental tools and widely used for
11663 data analysis, dimension reduction, and data compression. Classically, highly
11664 accurate deterministic matrix algorithms are used for this task. However, the
11665 emergence of large-scale data has severely challenged our computational
11666 ability to analyze big data. The concept of randomness has been demonstrated
11667 as an effective strategy to quickly produce approximate answers to familiar
11668 problems such as the @dfn{singular value decomposition} (SVD). This package
11669 provides several randomized matrix algorithms such as the randomized singular
11670 value decomposition (@code{rsvd}), randomized principal component
11671 analysis (@code{rpca}), randomized robust principal component
11672 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11673 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11674 functions are provided.")
11675 (license license:gpl3+)))
11677 (define-public r-sloop
11684 (uri (cran-uri "sloop" version))
11687 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11688 (build-system r-build-system)
11690 `(("r-codetools" ,r-codetools)
11691 ("r-crayon" ,r-crayon)
11692 ("r-purrr" ,r-purrr)
11693 ("r-rlang" ,r-rlang)
11694 ("r-tibble" ,r-tibble)))
11695 (home-page "https://github.com/r-lib/sloop")
11696 (synopsis "Helpers for object-oriented programming in R")
11698 "This package provides a collection of helper functions designed to
11699 help you to better understand object oriented programming in R, particularly
11701 (license license:gpl3)))
11703 (define-public r-capushe
11710 (uri (cran-uri "capushe" version))
11713 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11714 (build-system r-build-system)
11715 (propagated-inputs `(("r-mass" ,r-mass)))
11716 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11717 (synopsis "Calibrating penalties using slope heuristics")
11719 "This package provides tools for the calibration of penalized criteria
11720 for model selection. The calibration methods available are based on the slope
11722 (license license:gpl2+)))
11724 (define-public r-dorng
11731 (uri (cran-uri "doRNG" version))
11734 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11735 (properties `((upstream-name . "doRNG")))
11736 (build-system r-build-system)
11738 `(("r-foreach" ,r-foreach)
11739 ("r-iterators" ,r-iterators)
11740 ("r-pkgmaker" ,r-pkgmaker)
11741 ("r-rngtools" ,r-rngtools)))
11742 (home-page "https://renozao.github.io/doRNG/")
11743 (synopsis "Generic reproducible parallel backend for foreach loops")
11745 "This package provides functions to perform reproducible parallel
11746 @code{foreach} loops, using independent random streams as generated by
11747 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11748 convert standard @code{%dopar%} loops into fully reproducible loops,
11749 independently of the number of workers, the task scheduling strategy, or the
11750 chosen parallel environment and associated foreach backend.")
11751 (license license:gpl2+)))
11753 (define-public r-blockmodeling
11755 (name "r-blockmodeling")
11760 (uri (cran-uri "blockmodeling" version))
11763 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11764 (build-system r-build-system)
11766 `(("r-doparallel" ,r-doparallel)
11767 ("r-dorng" ,r-dorng)
11768 ("r-foreach" ,r-foreach)
11769 ("r-matrix" ,r-matrix)))
11770 (native-inputs `(("gfortran" ,gfortran)))
11771 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11772 (synopsis "Generalized and classical blockmodeling of valued networks")
11774 "This package is primarily meant as an implementation of generalized
11775 blockmodeling for valued networks. In addition, measures of similarity or
11776 dissimilarity based on structural equivalence and regular equivalence (REGE
11777 algorithms) can be computed and partitioned matrices can be plotted.")
11778 (license license:gpl2+)))
11780 (define-public r-upsetr
11787 (uri (cran-uri "UpSetR" version))
11790 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11791 (properties `((upstream-name . "UpSetR")))
11792 (build-system r-build-system)
11794 `(("r-ggplot2" ,r-ggplot2)
11795 ("r-gridextra" ,r-gridextra)
11797 ("r-scales" ,r-scales)))
11798 (home-page "https://github.com/hms-dbmi/UpSetR")
11799 (synopsis "Visualize intersecting sets")
11801 "This package provides a more scalable alternative to Venn and Euler
11802 diagrams for visualizing intersecting sets. Create visualizations of
11803 intersecting sets using a novel matrix design, along with visualizations of
11804 several common set, element and attribute related tasks.")
11805 (license license:expat)))
11807 ;; This package includes a JavaScript file, which is not minified. When
11808 ;; upgrading please check that there are no new minified JavaScript files.
11809 (define-public r-shinybs
11816 (uri (cran-uri "shinyBS" version))
11819 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11820 (properties `((upstream-name . "shinyBS")))
11821 (build-system r-build-system)
11822 ;; The tests spawn Shiny browser apps. They cannot be run
11823 ;; non-interactively.
11824 (arguments '(#:tests? #f))
11826 `(("r-htmltools" ,r-htmltools)
11827 ("r-shiny" ,r-shiny)))
11828 (home-page "https://ebailey78.github.io/shinyBS/")
11829 (synopsis "Twitter Bootstrap components for Shiny")
11831 "This package adds additional Twitter Bootstrap components to Shiny.")
11832 (license license:gpl3)))
11834 (define-public r-outliers
11836 (name "r-outliers")
11841 (uri (cran-uri "outliers" version))
11844 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11845 (build-system r-build-system)
11846 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11847 (synopsis "Tests for outliers")
11849 "This package provides a collection of some tests commonly used for
11850 identifying outliers.")
11851 (license license:gpl2+)))
11853 (define-public r-bayesm
11860 (uri (cran-uri "bayesm" version))
11862 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11863 (build-system r-build-system)
11865 `(("r-rcpp" ,r-rcpp)
11866 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11867 (home-page "http://www.perossi.org/home/bsm-1")
11868 (synopsis "Bayesian inference for marketing/micro-econometrics")
11870 "This package covers many important models used in marketing and
11871 micro-econometrics applications, including Bayes Regression (univariate or
11872 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11873 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11874 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11875 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11876 Estimation with normal base, Hierarchical Linear Models with normal prior and
11877 covariates, Hierarchical Linear Models with a mixture of normals prior and
11878 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11879 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11880 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11881 analysis of choice-based conjoint data, Bayesian treatment of linear
11882 instrumental variables models, Analysis of Multivariate Ordinal survey data
11883 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11884 Coefficient Logit Models.")
11885 (license license:gpl2+)))
11887 (define-public r-tensora
11894 (uri (cran-uri "tensorA" version))
11897 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11898 (properties `((upstream-name . "tensorA")))
11899 (build-system r-build-system)
11900 (home-page "http://www.stat.boogaart.de/tensorA")
11901 (synopsis "Advanced tensor arithmetic with named indices")
11903 "This package provides convenience functions for advanced linear algebra
11904 with tensors and computation with datasets of tensors on a higher level
11905 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11906 co- and contravariate indices, and parallel computations on sequences of
11908 (license license:gpl2+)))
11910 (define-public r-rarpack
11917 (uri (cran-uri "rARPACK" version))
11920 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11921 (properties `((upstream-name . "rARPACK")))
11922 (build-system r-build-system)
11923 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11924 (home-page "https://github.com/yixuan/rARPACK")
11925 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11927 "This package was previously an R wrapper of the ARPACK library, and now
11928 a shell of the R package RSpectra, an R interface to the Spectra library for
11929 solving large scale eigenvalue/vector problems. The current version of
11930 rARPACK simply imports and exports the functions provided by RSpectra. New
11931 users of rARPACK are advised to switch to the RSpectra package.")
11932 (license license:bsd-3)))
11934 (define-public r-compositions
11936 (name "r-compositions")
11941 (uri (cran-uri "compositions" version))
11944 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
11945 (build-system r-build-system)
11947 `(("r-bayesm" ,r-bayesm)
11948 ("r-robustbase" ,r-robustbase)
11949 ("r-tensora" ,r-tensora)))
11950 (home-page "http://www.stat.boogaart.de/compositions")
11951 (synopsis "Compositional data analysis")
11953 "This package provides functions for the consistent analysis of
11954 compositional data (e.g. portions of substances) and positive
11955 numbers (e.g. concentrations).")
11956 (license license:gpl2+)))
11958 (define-public r-cobs
11965 (uri (cran-uri "cobs" version))
11968 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11969 (build-system r-build-system)
11971 `(("r-quantreg" ,r-quantreg)
11972 ("r-sparsem" ,r-sparsem)))
11973 (home-page "https://cran.r-project.org/web/packages/cobs")
11974 (synopsis "Constrained B-Splines (sparse matrix based)")
11976 "This package provides qualitatively constrained (regression) smoothing
11977 splines via linear programming and sparse matrices.")
11978 (license license:gpl2+)))
11980 (define-public r-drimpute
11982 (name "r-drimpute")
11987 (uri (cran-uri "DrImpute" version))
11990 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11991 (properties `((upstream-name . "DrImpute")))
11992 (build-system r-build-system)
11994 `(("r-rcpp" ,r-rcpp)
11995 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11996 (home-page "https://github.com/ikwak2/DrImpute")
11997 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11999 "This is an R package for imputing dropout events. Many statistical
12000 methods in cell type identification, visualization and lineage reconstruction
12001 do not account for dropout events. DrImpute can improve the performance of
12002 such software by imputing dropout events.")
12003 (license license:gpl3)))
12005 (define-public r-gamlss-dist
12007 (name "r-gamlss-dist")
12012 (uri (cran-uri "gamlss.dist" version))
12014 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
12015 (properties `((upstream-name . "gamlss.dist")))
12016 (build-system r-build-system)
12017 (propagated-inputs `(("r-mass" ,r-mass)))
12018 (home-page "http://www.gamlss.org/")
12019 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12021 "This package provides a set of distributions which can be used for
12022 modelling the response variables in Generalized Additive Models for Location
12023 Scale and Shape. The distributions can be continuous, discrete or mixed
12024 distributions. Extra distributions can be created, by transforming, any
12025 continuous distribution defined on the real line, to a distribution defined on
12026 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12027 transformation, respectively.")
12028 ;; Either version of the GPL.
12029 (license (list license:gpl2 license:gpl3))))
12031 ;; This package includes JavaScript files, which are not minified. When
12032 ;; upgrading please check that there are no new minified JavaScript files.
12033 (define-public r-shinyjs
12040 (uri (cran-uri "shinyjs" version))
12043 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
12044 (build-system r-build-system)
12046 `(("r-digest" ,r-digest)
12047 ("r-htmltools" ,r-htmltools)
12048 ("r-jsonlite" ,r-jsonlite)
12049 ("r-shiny" ,r-shiny)))
12050 (home-page "https://deanattali.com/shinyjs")
12051 (synopsis "Improve the user experience of your Shiny apps")
12053 "Perform common useful JavaScript operations in Shiny apps that will
12054 greatly improve your apps without having to know any JavaScript. Examples
12055 include: hiding an element, disabling an input, resetting an input back to its
12056 original value, delaying code execution by a few seconds, and many more useful
12057 functions for both the end user and the developer. Shinyjs can also be used
12058 to easily call your own custom JavaScript functions from R.")
12059 (license license:agpl3+)))
12061 ;; This package includes minified JavaScript files. When upgrading please
12062 ;; check that there are no new minified JavaScript files.
12063 (define-public r-colourpicker
12065 (name "r-colourpicker")
12070 (uri (cran-uri "colourpicker" version))
12073 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12074 (build-system r-build-system)
12076 `(#:modules ((guix build utils)
12077 (guix build r-build-system)
12081 (modify-phases %standard-phases
12082 (add-after 'unpack 'process-javascript
12083 (lambda* (#:key inputs #:allow-other-keys)
12084 (with-directory-excursion "inst"
12088 `((,(assoc-ref inputs "js-salvattore")
12089 "examples/colourInput/www/salvattore.min.js")
12090 (,(assoc-ref inputs "js-jquery")
12091 "htmlwidgets/lib/jquery/jquery.min.js")
12092 ("www/shared/colourpicker/js/colourpicker.js"
12093 "www/shared/colourpicker/js/colourpicker.min.js"))))
12094 (lambda (sources targets)
12095 (for-each (lambda (source target)
12096 (format #t "Processing ~a --> ~a~%"
12098 (delete-file target)
12099 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12100 (call-with-output-file target
12102 (dump-port minified port)))))
12103 sources targets))))
12106 `(("r-ggplot2" ,r-ggplot2)
12107 ("r-htmltools" ,r-htmltools)
12108 ("r-htmlwidgets" ,r-htmlwidgets)
12109 ("r-jsonlite" ,r-jsonlite)
12110 ("r-miniui" ,r-miniui)
12111 ("r-shiny" ,r-shiny)
12112 ("r-shinyjs" ,r-shinyjs)))
12114 `(("uglify-js" ,uglify-js)
12118 (uri "https://code.jquery.com/jquery-3.3.1.js")
12121 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12125 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12128 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12129 (home-page "https://github.com/daattali/colourpicker")
12130 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12132 "This package provides a color picker that can be used as an input in
12133 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12134 custom color palettes, and many more options. A plot color helper tool is
12135 available as an RStudio Addin, which helps you pick colors to use in your
12136 plots. A more generic color picker RStudio Addin is also provided to let you
12137 select colors to use in your R code.")
12138 (license license:expat)))
12140 (define-public r-ggextra
12147 (uri (cran-uri "ggExtra" version))
12150 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12151 (properties `((upstream-name . "ggExtra")))
12152 (build-system r-build-system)
12154 `(("r-colourpicker" ,r-colourpicker)
12155 ("r-ggplot2" ,r-ggplot2)
12156 ("r-gtable" ,r-gtable)
12157 ("r-miniui" ,r-miniui)
12159 ("r-scales" ,r-scales)
12160 ("r-shiny" ,r-shiny)
12161 ("r-shinyjs" ,r-shinyjs)))
12162 (home-page "https://github.com/daattali/ggExtra")
12163 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12165 "This package is a collection of functions and layers to enhance ggplot2.
12166 The flagship function is @code{ggMarginal()}, which can be used to add
12167 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12168 (license license:expat)))
12170 (define-public r-minpack-lm
12172 (name "r-minpack-lm")
12177 (uri (cran-uri "minpack.lm" version))
12180 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12181 (properties `((upstream-name . "minpack.lm")))
12182 (build-system r-build-system)
12183 (native-inputs `(("gfortran" ,gfortran)))
12184 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12185 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12187 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12188 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12189 problems by a modification of the Levenberg-Marquardt algorithm, with support
12190 for lower and upper parameter bounds. The implementation can be used via
12191 @code{nls}-like calls using the @code{nlsLM} function.")
12192 (license license:gpl3)))
12194 (define-public r-moments
12201 (uri (cran-uri "moments" version))
12204 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12205 (build-system r-build-system)
12206 (home-page "https://cran.r-project.org/web/packages/moments")
12207 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12209 "This package provides functions to calculate: moments, Pearson's
12210 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12211 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12212 (license license:gpl2+)))
12214 (define-public r-msir
12221 (uri (cran-uri "msir" version))
12224 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12225 (build-system r-build-system)
12227 `(("r-mclust" ,r-mclust)))
12228 (home-page "https://cran.r-project.org/web/packages/msir")
12229 (synopsis "Model-based sliced inverse regression")
12231 "This is an R package for dimension reduction based on finite Gaussian
12232 mixture modeling of inverse regression.")
12233 (license license:gpl2+)))
12235 (define-public r-pbivnorm
12237 (name "r-pbivnorm")
12242 (uri (cran-uri "pbivnorm" version))
12245 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12246 (build-system r-build-system)
12247 (native-inputs `(("gfortran" ,gfortran)))
12248 (home-page "https://github.com/brentonk/pbivnorm")
12249 (synopsis "Vectorized bivariate normal CDF")
12251 "This package provides a vectorized R function for calculating
12252 probabilities from a standard bivariate normal CDF.")
12253 (license license:gpl2+)))
12255 (define-public r-lavaan
12262 (uri (cran-uri "lavaan" version))
12265 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12266 (build-system r-build-system)
12268 `(("r-mass" ,r-mass)
12269 ("r-mnormt" ,r-mnormt)
12270 ("r-numderiv" ,r-numderiv)
12271 ("r-pbivnorm" ,r-pbivnorm)))
12272 (home-page "http://lavaan.ugent.be")
12273 (synopsis "Latent variable analysis")
12275 "This package provides tools to fit a variety of latent variable models,
12276 including confirmatory factor analysis, structural equation modeling and
12277 latent growth curve models.")
12278 (license license:gpl2+)))
12280 (define-public r-nonnest2
12282 (name "r-nonnest2")
12287 (uri (cran-uri "nonnest2" version))
12290 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12291 (build-system r-build-system)
12293 `(("r-compquadform" ,r-compquadform)
12294 ("r-lavaan" ,r-lavaan)
12295 ("r-mvtnorm" ,r-mvtnorm)
12296 ("r-sandwich" ,r-sandwich)))
12297 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12298 (synopsis "Tests of non-nested models")
12300 "This package allows for testing of non-nested models. It includes tests
12301 of model distinguishability and of model fit that can be applied to both
12302 nested and non-nested models. The package also includes functionality to
12303 obtain confidence intervals associated with AIC and BIC.")
12304 ;; Either version of the GPL.
12305 (license (list license:gpl2 license:gpl3))))
12307 (define-public r-penalized
12309 (name "r-penalized")
12314 (uri (cran-uri "penalized" version))
12317 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12318 (build-system r-build-system)
12320 `(("r-rcpp" ,r-rcpp)
12321 ("r-rcpparmadillo" ,r-rcpparmadillo)
12322 ("r-survival" ,r-survival)))
12323 (home-page "https://cran.r-project.org/web/packages/penalized/")
12324 (synopsis "Penalized estimation in GLMs and in the Cox model")
12326 "This package provides tools for fitting possibly high dimensional
12327 penalized regression models. The penalty structure can be any combination of
12328 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12329 constraint on the regression coefficients. The supported regression models
12330 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12331 model. Cross-validation routines allow optimization of the tuning
12333 (license license:gpl2+)))
12335 (define-public r-zim
12342 (uri (cran-uri "ZIM" version))
12345 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12346 (properties `((upstream-name . "ZIM")))
12347 (build-system r-build-system)
12348 (propagated-inputs `(("r-mass" ,r-mass)))
12349 (home-page "https://github.com/biostatstudio/ZIM")
12350 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12352 "Analyze count time series with excess zeros. Two types of statistical
12353 models are supported: Markov regression and state-space models. They are also
12354 known as observation-driven and parameter-driven models respectively in the
12355 time series literature. The functions used for Markov regression or
12356 observation-driven models can also be used to fit ordinary regression models
12357 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12358 negative binomial (ZINB) assumption. The package also contains miscellaneous
12359 functions to compute density, distribution, quantile, and generate random
12360 numbers from ZIP and ZINB distributions.")
12361 (license license:gpl3)))
12363 (define-public r-nor1mix
12370 (uri (cran-uri "nor1mix" version))
12373 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12374 (build-system r-build-system)
12375 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12376 (synopsis "Normal (1-d) mixture models")
12378 "This package provides S3 classes and methods for one-dimensional normal
12379 mixture models, for, e.g., density estimation or clustering algorithms
12380 research and teaching; it provides the widely used Marron-Wand densities. It
12381 also provides tools for efficient random number generation and graphics.")
12382 (license license:gpl2+)))
12384 (define-public r-beanplot
12386 (name "r-beanplot")
12391 (uri (cran-uri "beanplot" version))
12394 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12395 (build-system r-build-system)
12396 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12397 (synopsis "Visualization via beanplots")
12399 "This package provides beanplots, an alternative to
12400 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12402 (license license:gpl2)))
12404 (define-public r-pbdzmq
12411 (uri (cran-uri "pbdZMQ" version))
12414 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12415 (properties `((upstream-name . "pbdZMQ")))
12416 (build-system r-build-system)
12418 `(("zeromq" ,zeromq)
12421 `(("pkg-config" ,pkg-config)))
12422 (home-page "https://pbdr.org/")
12423 (synopsis "R interface to ZeroMQ")
12425 "ZeroMQ is a well-known library for high-performance asynchronous
12426 messaging in scalable, distributed applications. This package provides high
12427 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12428 interactive client/server programming frameworks. A few wrapper functions
12429 compatible with @code{rzmq} are also provided.")
12430 (license license:gpl3)))
12432 (define-public r-repr
12439 (uri (cran-uri "repr" version))
12442 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12443 (build-system r-build-system)
12445 `(("r-base64enc" ,r-base64enc)
12446 ("r-htmltools" ,r-htmltools)
12447 ("r-jsonlite" ,r-jsonlite)
12448 ("r-pillar" ,r-pillar)))
12449 (home-page "https://cran.r-project.org/web/packages/repr/")
12450 (synopsis "Serializable representations")
12452 "This package provides string and binary representations of objects for
12453 several formats and MIME types.")
12454 (license license:gpl3)))
12456 (define-public r-irdisplay
12458 (name "r-irdisplay")
12463 (uri (cran-uri "IRdisplay" version))
12466 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12467 (properties `((upstream-name . "IRdisplay")))
12468 (build-system r-build-system)
12470 `(("r-repr" ,r-repr)))
12471 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12472 (synopsis "Jupyter display machinery")
12474 "This package provides an interface to the rich display capabilities of
12475 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12476 running IRkernel session.")
12477 (license license:expat)))
12479 (define-public r-irkernel
12481 (name "r-irkernel")
12486 (uri (cran-uri "IRkernel" version))
12489 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12490 (properties `((upstream-name . "IRkernel")))
12491 (build-system r-build-system)
12494 (modify-phases %standard-phases
12495 (add-after 'install 'install-kernelspec
12496 (lambda* (#:key outputs #:allow-other-keys)
12497 (let ((out (assoc-ref outputs "out")))
12498 (setenv "HOME" "/tmp")
12499 (invoke "jupyter" "kernelspec" "install"
12502 (string-append out "/site-library/IRkernel/kernelspec"))
12505 `(("jupyter" ,jupyter)))
12507 `(("r-crayon" ,r-crayon)
12508 ("r-digest" ,r-digest)
12509 ("r-evaluate" ,r-evaluate)
12510 ("r-irdisplay" ,r-irdisplay)
12511 ("r-jsonlite" ,r-jsonlite)
12512 ("r-pbdzmq" ,r-pbdzmq)
12514 ("r-uuid" ,r-uuid)))
12515 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12516 (synopsis "Native R kernel for Jupyter")
12518 "The R kernel for the Jupyter environment executes R code which the
12519 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12521 (license license:expat)))
12523 (define-public r-gmodels
12530 (uri (cran-uri "gmodels" version))
12533 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12534 (build-system r-build-system)
12536 `(("r-gdata" ,r-gdata)
12537 ("r-mass" ,r-mass)))
12538 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12539 (synopsis "Various R programming tools for model fitting")
12541 "This package provides various R programming tools for model fitting.")
12542 (license license:gpl2)))
12544 (define-public r-apcluster
12546 (name "r-apcluster")
12551 (uri (cran-uri "apcluster" version))
12554 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12555 (build-system r-build-system)
12557 `(("r-matrix" ,r-matrix)
12558 ("r-rcpp" ,r-rcpp)))
12559 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12560 (synopsis "Affinity propagation clustering")
12562 "This package implements affinity propagation clustering introduced by
12563 Frey and Dueck (2007). The package further provides leveraged affinity
12564 propagation and an algorithm for exemplar-based agglomerative clustering that
12565 can also be used to join clusters obtained from affinity propagation. Various
12566 plotting functions are available for analyzing clustering results.")
12567 (license license:gpl2+)))
12569 (define-public r-valr
12576 (uri (cran-uri "valr" version))
12579 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12580 (build-system r-build-system)
12582 `(("r-broom" ,r-broom)
12583 ("r-dplyr" ,r-dplyr)
12584 ("r-ggplot2" ,r-ggplot2)
12586 ("r-readr" ,r-readr)
12587 ("r-rlang" ,r-rlang)
12588 ("r-stringr" ,r-stringr)
12589 ("r-tibble" ,r-tibble)))
12590 (home-page "http://github.com/rnabioco/valr")
12591 (synopsis "Genome interval arithmetic in R")
12593 "This package enables you to read and manipulate genome intervals and
12594 signals. It provides functionality similar to command-line tool suites within
12595 R, enabling interactive analysis and visualization of genome-scale data.")
12596 (license license:expat)))
12598 (define-public r-rematch2
12600 (name "r-rematch2")
12605 (uri (cran-uri "rematch2" version))
12608 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12609 (build-system r-build-system)
12611 `(("r-tibble" ,r-tibble)))
12612 (home-page "https://github.com/r-lib/rematch2")
12613 (synopsis "Tidy output from regular expression matching")
12615 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12616 return the match results in tidy data frames.")
12617 (license license:expat)))
12619 (define-public r-picante
12626 (uri (cran-uri "picante" version))
12629 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12630 (build-system r-build-system)
12634 ("r-vegan" ,r-vegan)))
12635 (home-page "https://cran.r-project.org/web/packages/picante/")
12636 (synopsis "Integrating phylogenies and ecology")
12638 "This package provides functions for phylocom integration, community
12639 analyses, null-models, traits and evolution. It implements numerous
12640 ecophylogenetic approaches including measures of community phylogenetic and
12641 trait diversity, phylogenetic signal, estimation of trait values for
12642 unobserved taxa, null models for community and phylogeny randomizations, and
12643 utility functions for data input/output and phylogeny plotting. A full
12644 description of package functionality and methods are provided by Kembel et
12646 (license license:gpl2)))
12648 (define-public r-reinforcelearn
12650 (name "r-reinforcelearn")
12655 (uri (cran-uri "reinforcelearn" version))
12658 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12659 (build-system r-build-system)
12661 `(("r-checkmate" ,r-checkmate)
12663 ("r-purrr" ,r-purrr)
12665 (home-page "https://markusdumke.github.io/reinforcelearn")
12666 (synopsis "Reinforcement learning")
12668 "This package implements reinforcement learning environments and
12669 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12670 can be used with function approximation, eligibility traces (Singh & Sutton,
12671 1996) and experience replay (Mnih et al., 2013).")
12672 (license license:expat)))
12674 (define-public r-lemon
12681 (uri (cran-uri "lemon" version))
12684 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12685 (build-system r-build-system)
12687 `(("r-ggplot2" ,r-ggplot2)
12688 ("r-gridextra" ,r-gridextra)
12689 ("r-gtable" ,r-gtable)
12690 ("r-knitr" ,r-knitr)
12691 ("r-lattice" ,r-lattice)
12693 ("r-scales" ,r-scales)))
12694 (home-page "https://github.com/stefanedwards/lemon")
12695 (synopsis "Freshen up your ggplot2 plots")
12697 "This package provides functions for working with legends and axis lines
12698 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12700 (license license:gpl3)))
12702 (define-public r-wgaim
12709 (uri (cran-uri "wgaim" version))
12711 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12712 (build-system r-build-system)
12714 `(("r-ggplot2" ,r-ggplot2)
12716 (home-page "https://cran.r-project.org/web/packages/wgaim")
12717 (synopsis "Whole genome average interval mapping for QTL detection")
12719 "This package integrates sophisticated mixed modelling methods with a
12720 whole genome approach to detecting significant QTL in linkage maps.")
12721 (license license:gpl2+)))
12723 (define-public r-bedr
12730 (uri (cran-uri "bedr" version))
12733 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12734 (build-system r-build-system)
12736 `(("r-data-table" ,r-data-table)
12737 ("r-r-utils" ,r-r-utils)
12738 ("r-testthat" ,r-testthat)
12739 ("r-venndiagram" ,r-venndiagram)
12742 ("bedtools" ,bedtools)
12743 ("htslib" ,htslib))) ; for tabix
12745 `(("r-knitr" ,r-knitr))) ; for vignettes
12746 (home-page "https://cran.r-project.org/web/packages/bedr")
12747 (synopsis "Genomic region processing")
12749 "This package is for genomic regions processing using command line tools
12750 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12751 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12752 The bedr package's API enhances access to these tools as well as offers
12753 additional utilities for genomic regions processing.")
12754 (license license:gpl2)))
12756 (define-public r-sets
12763 (uri (cran-uri "sets" version))
12766 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12767 (properties `((upstream-name . "sets")))
12768 (build-system r-build-system)
12769 (home-page "https://cran.r-project.org/web/packages/sets")
12770 (synopsis "Sets, generalized sets, customizable sets and intervals")
12772 "This package provides data structures and basic operations for ordinary
12773 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12774 customizable sets, and intervals.")
12775 (license license:gpl2)))
12777 (define-public r-partitions
12779 (name "r-partitions")
12784 (uri (cran-uri "partitions" version))
12787 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12788 (build-system r-build-system)
12791 ("r-polynom" ,r-polynom)
12792 ("r-sets" ,r-sets)))
12793 (home-page "https://cran.r-project.org/web/packages/partitions")
12794 (synopsis "Additive partitions of integers")
12796 "This package provides tools to enumerates the partitions, unequal
12797 partitions, and restricted partitions of an integer; the three corresponding
12798 partition functions are also given.")
12799 ;; Any version of the GPL
12800 (license license:gpl2+)))
12802 (define-public r-brobdingnag
12804 (name "r-brobdingnag")
12809 (uri (cran-uri "Brobdingnag" version))
12812 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12813 (properties `((upstream-name . "Brobdingnag")))
12814 (build-system r-build-system)
12815 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12816 (synopsis "Very large numbers in R")
12818 "This package handles very large numbers in R. Real numbers are held
12819 using their natural logarithms, plus a logical flag indicating sign. The
12820 package includes a vignette that gives a step-by-step introduction to using S4
12822 ;; Any version of the GPL
12823 (license license:gpl2+)))
12825 (define-public r-untb
12832 (uri (cran-uri "untb" version))
12835 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12836 (build-system r-build-system)
12838 `(("r-brobdingnag" ,r-brobdingnag)
12839 ("r-partitions" ,r-partitions)
12840 ("r-polynom" ,r-polynom)))
12841 (home-page "https://github.com/RobinHankin/untb.git")
12842 (synopsis "Ecological drift under the UNTB")
12844 "This package provides numerical simulations, and visualizations, of
12845 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12846 (license license:gpl2+)))
12848 (define-public r-stepwise
12850 (name "r-stepwise")
12855 (uri (cran-uri "stepwise" version))
12858 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12859 (build-system r-build-system)
12860 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12861 (synopsis "Stepwise detection of recombination breakpoints")
12863 "This package provides a stepwise approach to identifying recombination
12864 breakpoints in a genomic sequence alignment.")
12865 (license license:gpl2+)))
12867 (define-public r-snpmaxsel
12869 (name "r-snpmaxsel")
12874 (uri (cran-uri "SNPmaxsel" version))
12877 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12878 (properties `((upstream-name . "SNPmaxsel")))
12879 (build-system r-build-system)
12881 `(("r-combinat" ,r-combinat)
12882 ("r-mvtnorm" ,r-mvtnorm)))
12883 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12884 (synopsis "Maximally selected statistics for SNP data")
12886 "This package implements asymptotic methods related to maximally selected
12887 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12889 (license license:gpl2+)))
12891 (define-public r-acsnminer
12893 (name "r-acsnminer")
12894 (version "0.16.8.25")
12897 (uri (cran-uri "ACSNMineR" version))
12900 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12901 (properties `((upstream-name . "ACSNMineR")))
12902 (build-system r-build-system)
12904 `(("r-ggplot2" ,r-ggplot2)
12905 ("r-gridextra" ,r-gridextra)))
12906 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12907 (synopsis "Gene enrichment analysis")
12909 "This package provides tools to compute and represent gene set enrichment
12910 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12911 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12912 enrichment can be run with hypergeometric test or Fisher exact test, and can
12913 use multiple corrections. Visualization of data can be done either by
12914 barplots or heatmaps.")
12915 (license license:gpl2+)))
12917 (define-public r-seqinr
12924 (uri (cran-uri "seqinr" version))
12927 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12928 (build-system r-build-system)
12930 `(("r-ade4" ,r-ade4)
12931 ("r-segmented" ,r-segmented)))
12934 (home-page "http://seqinr.r-forge.r-project.org/")
12935 (synopsis "Biological sequences retrieval and analysis")
12937 "This package provides tools for exploratory data analysis and data
12938 visualization of biological sequence (DNA and protein) data. It also includes
12939 utilities for sequence data management under the ACNUC system.")
12940 (license license:gpl2+)))
12942 (define-public r-units
12949 (uri (cran-uri "units" version))
12952 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
12953 (build-system r-build-system)
12955 `(("udunits" ,udunits)))
12957 `(("r-rcpp" ,r-rcpp)))
12958 (home-page "https://github.com/r-quantities/units/")
12959 (synopsis "Measurement Units for R Vectors")
12961 "This package provides support for measurement units in R vectors,
12962 matrices and arrays: automatic propagation, conversion, derivation and
12963 simplification of units; raising errors in case of unit incompatibility. It
12964 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12966 (license license:gpl2)))
12968 (define-public r-classint
12970 (name "r-classint")
12975 (uri (cran-uri "classInt" version))
12978 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
12979 (properties `((upstream-name . "classInt")))
12980 (build-system r-build-system)
12982 `(("r-class" ,r-class)
12983 ("r-e1071" ,r-e1071)
12984 ("r-kernsmooth" ,r-kernsmooth)))
12985 (native-inputs `(("gfortran" ,gfortran)))
12986 (home-page "https://github.com/r-spatial/classInt/")
12987 (synopsis "Choose univariate class intervals")
12989 "This package provides selected commonly used methods for choosing
12990 univariate class intervals for mapping or other graphics purposes.")
12991 (license license:gpl2+)))
12993 (define-public r-spdata
13000 (uri (cran-uri "spData" version))
13003 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
13004 (properties `((upstream-name . "spData")))
13005 (build-system r-build-system)
13006 (home-page "https://github.com/Nowosad/spData")
13007 (synopsis "Datasets for spatial analysis")
13009 "This a package containing diverse spatial datasets for demonstrating,
13010 benchmarking and teaching spatial data analysis. It includes R data of class
13011 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13012 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13013 of the datasets are designed to illustrate specific analysis techniques.
13014 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13015 illustrate point pattern analysis techniques.")
13016 (license license:cc0)))
13018 (define-public r-learnbayes
13020 (name "r-learnbayes")
13025 (uri (cran-uri "LearnBayes" version))
13028 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13029 (properties `((upstream-name . "LearnBayes")))
13030 (build-system r-build-system)
13031 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13032 (synopsis "Functions for learning Bayesian inference")
13034 "This package provides a collection of functions helpful in learning the
13035 basic tenets of Bayesian statistical inference. It contains functions for
13036 summarizing basic one and two parameter posterior distributions and predictive
13037 distributions. It contains MCMC algorithms for summarizing posterior
13038 distributions defined by the user. It also contains functions for regression
13039 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13041 (license license:gpl2+)))
13043 (define-public r-deldir
13050 (uri (cran-uri "deldir" version))
13053 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
13054 (build-system r-build-system)
13055 (native-inputs `(("gfortran" ,gfortran)))
13056 (home-page "https://cran.r-project.org/web/packages/deldir")
13057 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13059 "This package provides tools for calculating the Delaunay triangulation
13060 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13061 of a planar point set. It plots triangulations and tessellations in various
13062 ways, clips tessellations to sub-windows, calculates perimeters of
13063 tessellations, and summarizes information about the tiles of the
13065 (license license:gpl2+)))
13067 (define-public r-sf
13074 (uri (cran-uri "sf" version))
13077 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
13078 (build-system r-build-system)
13085 `(("r-classint" ,r-classint)
13087 ("r-magrittr" ,r-magrittr)
13089 ("r-units" ,r-units)))
13090 (native-inputs `(("pkg-config" ,pkg-config)))
13091 (home-page "https://github.com/r-spatial/sf/")
13092 (synopsis "Simple features for R")
13094 "This package provides support for simple features, a standardized way to
13095 encode spatial vector data. It binds to GDAL for reading and writing data, to
13096 GEOS for geometrical operations, and to PROJ for projection conversions and
13097 datum transformations.")
13098 ;; Either of these licenses
13099 (license (list license:gpl2 license:expat))))
13101 (define-public r-spdep
13108 (uri (cran-uri "spdep" version))
13111 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13112 (build-system r-build-system)
13114 `(("r-boot" ,r-boot)
13116 ("r-deldir" ,r-deldir)
13118 ("r-gmodels" ,r-gmodels)
13119 ("r-learnbayes" ,r-learnbayes)
13121 ("r-matrix" ,r-matrix)
13125 ("r-spdata" ,r-spdata)))
13126 (home-page "https://github.com/r-spatial/spdep/")
13127 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13129 "This package provides a collection of functions to create spatial
13130 weights matrix objects from polygon contiguities, from point patterns by
13131 distance and tessellations, for summarizing these objects, and for permitting
13132 their use in spatial data analysis, including regional aggregation by minimum
13134 (license license:gpl2+)))
13136 (define-public r-adegenet
13138 (name "r-adegenet")
13143 (uri (cran-uri "adegenet" version))
13146 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13147 (build-system r-build-system)
13149 `(("r-ade4" ,r-ade4)
13152 ("r-dplyr" ,r-dplyr)
13153 ("r-ggplot2" ,r-ggplot2)
13154 ("r-igraph" ,r-igraph)
13156 ("r-reshape2" ,r-reshape2)
13157 ("r-seqinr" ,r-seqinr)
13158 ("r-shiny" ,r-shiny)
13159 ("r-spdep" ,r-spdep)
13160 ("r-vegan" ,r-vegan)))
13161 (home-page "https://github.com/thibautjombart/adegenet")
13162 (synopsis "Exploratory analysis of genetic and genomic data")
13164 "This package provides a toolset for the exploration of genetic and
13165 genomic data. Adegenet provides formal (S4) classes for storing and handling
13166 various genetic data, including genetic markers with varying ploidy and
13167 hierarchical population structure (@code{genind} class), alleles counts by
13168 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13169 also implements original multivariate methods (DAPC, sPCA), graphics,
13170 statistical tests, simulation tools, distance and similarity measures, and
13171 several spatial methods. A range of both empirical and simulated datasets is
13172 also provided to illustrate various methods.")
13173 (license license:gpl2+)))
13175 (define-public r-pegas
13182 (uri (cran-uri "pegas" version))
13184 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13185 (build-system r-build-system)
13187 `(("r-adegenet" ,r-adegenet)
13189 (home-page "http://ape-package.ird.fr/pegas.html")
13190 (synopsis "Population and evolutionary genetics analysis system")
13192 "This package provides functions for reading, writing, plotting,
13193 analysing, and manipulating allelic and haplotypic data, including from VCF
13194 files, and for the analysis of population nucleotide sequences and
13195 micro-satellites including coalescent analyses, linkage disequilibrium,
13196 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13197 minimum spanning tree and network, and median-joining networks.")
13198 (license license:gpl2+)))
13200 (define-public r-rmetasim
13202 (name "r-rmetasim")
13207 (uri (cran-uri "rmetasim" version))
13210 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13211 (build-system r-build-system)
13213 `(("r-ade4" ,r-ade4)
13214 ("r-adegenet" ,r-adegenet)
13215 ("r-gtools" ,r-gtools)
13216 ("r-pegas" ,r-pegas)))
13217 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13218 (synopsis "Individual-based population genetic simulation environment")
13220 "This package provides an interface between R and the metasim simulation
13221 engine. The simulation environment is documented in: Strand, A.(2002),
13222 Metasim 1.0: an individual-based environment for simulating population
13223 genetics of complex population dynamics.")
13225 (license license:gpl2+)))
13227 (define-public r-genetics
13229 (name "r-genetics")
13230 (version "1.3.8.1.2")
13234 (uri (cran-uri "genetics" version))
13237 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13238 (build-system r-build-system)
13240 `(("r-combinat" ,r-combinat)
13241 ("r-gdata" ,r-gdata)
13242 ("r-gtools" ,r-gtools)
13244 ("r-mvtnorm" ,r-mvtnorm)))
13245 (home-page "https://cran.r-project.org/web/packages/genetics/")
13246 (synopsis "Population genetics")
13248 "This package provides classes and methods for handling genetic data.
13249 It includes classes to represent genotypes and haplotypes at single markers up
13250 to multiple markers on multiple chromosomes. Function include allele
13251 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13252 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13253 and testing for linkage disequilibrium, ...")
13254 ;; Any GPL version.
13255 (license license:gpl2+)))
13257 (define-public r-snp-plotter
13259 (name "r-snp-plotter")
13264 (uri (cran-uri "snp.plotter" version))
13267 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13268 (properties `((upstream-name . "snp.plotter")))
13269 (build-system r-build-system)
13270 (propagated-inputs `(("r-genetics" ,r-genetics)))
13271 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13272 (synopsis "Plot p-values using single SNP and/or haplotype data")
13274 "This package helps you create plots of p-values using single SNP and/or
13275 haplotype data. Main features of the package include options to display a
13276 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13277 datasets simultaneously. Plots can be created using global and/or individual
13278 haplotype p-values along with single SNP p-values. Images are created as
13279 either PDF/EPS files.")
13280 (license license:gpl2+)))
13282 (define-public r-polspline
13284 (name "r-polspline")
13289 (uri (cran-uri "polspline" version))
13291 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13292 (build-system r-build-system)
13293 (native-inputs `(("gfortran" ,gfortran)))
13294 (home-page "https://cran.r-project.org/web/packages/polspline/")
13295 (synopsis "Polynomial spline routines")
13297 "This package provides routines for the polynomial spline fitting
13298 routines hazard regression, hazard estimation with flexible tails, logspline,
13299 lspec, polyclass, and polymars.")
13300 (license license:gpl2+)))
13302 (define-public r-rms
13309 (uri (cran-uri "rms" version))
13311 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13312 (build-system r-build-system)
13314 `(("r-ggplot2" ,r-ggplot2)
13315 ("r-hmisc" ,r-hmisc)
13316 ("r-htmltable" ,r-htmltable)
13317 ("r-htmltools" ,r-htmltools)
13318 ("r-lattice" ,r-lattice)
13319 ("r-multcomp" ,r-multcomp)
13321 ("r-polspline" ,r-polspline)
13322 ("r-quantreg" ,r-quantreg)
13323 ("r-rpart" ,r-rpart)
13324 ("r-sparsem" ,r-sparsem)
13325 ("r-survival" ,r-survival)))
13326 (native-inputs `(("gfortran" ,gfortran)))
13327 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13328 (synopsis "Regression modeling strategies")
13330 "This is a package for regression modeling, testing, estimation,
13331 validation, graphics, prediction, and typesetting by storing enhanced model
13332 design attributes in the fit. The rms package is a collection of functions
13333 that assist with and streamline modeling. It also contains functions for
13334 binary and ordinal logistic regression models, ordinal models for continuous Y
13335 with a variety of distribution families, and the Buckley-James multiple
13336 regression model for right-censored responses, and implements penalized
13337 maximum likelihood estimation for logistic and ordinary linear models. The
13338 package works with almost any regression model, but it was especially written
13339 to work with binary or ordinal regression models, Cox regression, accelerated
13340 failure time models, ordinary linear models, the Buckley-James model,
13341 generalized least squares for serially or spatially correlated observations,
13342 generalized linear models, and quantile regression.")
13343 (license license:gpl2+)))
13345 (define-public r-haplo-stats
13347 (name "r-haplo-stats")
13352 (uri (cran-uri "haplo.stats" version))
13355 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13356 (properties `((upstream-name . "haplo.stats")))
13357 (build-system r-build-system)
13359 `(("r-rms" ,r-rms)))
13361 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13362 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13363 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13365 "This package provides routines for the analysis of indirectly measured
13366 haplotypes. The statistical methods assume that all subjects are unrelated
13367 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13368 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13369 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13370 examples in the vignette.")
13371 (license license:gpl2+)))
13373 (define-public r-bqtl
13380 (uri (cran-uri "bqtl" version))
13383 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13384 (build-system r-build-system)
13385 (native-inputs `(("gfortran" ,gfortran)))
13386 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13387 (synopsis "Bayesian QTL mapping toolkit")
13389 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13390 lines. It includes maximum likelihood and Bayesian tools.")
13391 (license license:gpl2+)))
13393 (define-public r-ibdreg
13400 (uri (cran-uri "ibdreg" version))
13403 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13404 (build-system r-build-system)
13405 (home-page "https://www.mayo.edu/research/labs/\
13406 statistical-genetics-genetic-epidemiology/software")
13407 (synopsis "Regression methods for IBD linkage with covariates")
13409 "This package provides a method to test genetic linkage with covariates
13410 by regression methods with response IBD sharing for relative pairs. Account
13411 for correlations of IBD statistics and covariates for relative pairs within
13412 the same pedigree.")
13413 (license license:gpl2+)))
13415 (define-public r-dlmap
13422 (uri (cran-uri "dlmap" version))
13425 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13426 (build-system r-build-system)
13428 `(("r-ibdreg" ,r-ibdreg)
13432 ("r-wgaim" ,r-wgaim)))
13433 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13434 (synopsis "Detection localization mapping for QTL")
13436 "This is package for QTL mapping in a mixed model framework with separate
13437 detection and localization stages. The first stage detects the number of QTL
13438 on each chromosome based on the genetic variation due to grouped markers on
13439 the chromosome; the second stage uses this information to determine the most
13440 likely QTL positions. The mixed model can accommodate general fixed and
13441 random effects, including spatial effects in field trials and pedigree
13442 effects. It is applicable to backcrosses, doubled haploids, recombinant
13443 inbred lines, F2 intercrosses, and association mapping populations.")
13444 (license license:gpl2)))
13446 (define-public r-ldheatmap
13448 (name "r-ldheatmap")
13453 (uri (cran-uri "LDheatmap" version))
13456 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13457 (properties `((upstream-name . "LDheatmap")))
13458 (build-system r-build-system)
13460 `(("r-genetics" ,r-genetics)
13462 ("r-snpstats" ,r-snpstats)))
13463 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13464 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13466 "This package provides tools to produce a graphical display, as a heat
13467 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13468 optionally include the physical locations or genetic map distances of each SNP
13470 (license license:gpl3)))
13472 (define-public r-hwde
13479 (uri (cran-uri "hwde" version))
13482 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13483 (build-system r-build-system)
13484 (home-page "https://cran.r-project.org/web/packages/hwde/")
13485 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13487 "This package fits models for genotypic disequilibria, as described in
13488 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13489 terms are available that account for first order interactions between loci.
13490 It also implements, for a single locus in a single population, a conditional
13491 exact test for Hardy-Weinberg equilibrium.")
13492 (license license:gpl2+)))
13494 (define-public r-tdthap
13501 (uri (cran-uri "tdthap" version))
13504 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13505 (build-system r-build-system)
13506 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13507 (synopsis "TDT tests for extended haplotypes")
13509 "Functions and examples are provided for transmission/disequilibrium
13510 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13511 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13512 (license license:artistic2.0)))
13514 (define-public r-sparql
13520 (uri (cran-uri "SPARQL" version))
13523 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13524 (properties `((upstream-name . "SPARQL")))
13525 (build-system r-build-system)
13527 `(("r-rcurl" ,r-rcurl)
13529 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13530 (synopsis "SPARQL client for R")
13531 (description "This package provides an interface to use SPARQL to pose
13532 SELECT or UPDATE queries to an end-point.")
13533 ;; The only license indication is found in the DESCRIPTION file,
13534 ;; which states GPL-3. So we cannot assume GPLv3+.
13535 (license license:gpl3)))
13537 (define-public r-bookdown
13539 (name "r-bookdown")
13543 (uri (cran-uri "bookdown" version))
13546 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13547 (build-system r-build-system)
13549 `(("r-htmltools" ,r-htmltools)
13550 ("r-knitr" ,r-knitr)
13551 ("r-rmarkdown" ,r-rmarkdown)
13552 ("r-tinytex" ,r-tinytex)
13554 ("pandoc" ,ghc-pandoc)))
13555 (home-page "https://github.com/rstudio/bookdown")
13556 (synopsis "Authoring books and technical documents with R markdown")
13557 (description "This package provides output formats and utilities for
13558 authoring books and technical documents with R Markdown.")
13559 (license license:gpl3)))
13561 (define-public r-optparse
13563 (name "r-optparse")
13568 (uri (cran-uri "optparse" version))
13571 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13572 (build-system r-build-system)
13574 `(("r-getopt" ,r-getopt)))
13575 (home-page "https://github.com/trevorld/optparse")
13576 (synopsis "Command line option parser")
13578 "This package provides a command line parser inspired by Python's
13579 @code{optparse} library to be used with Rscript to write shebang scripts
13580 that accept short and long options.")
13581 (license license:gpl2+)))
13583 (define-public r-wgcna
13590 (uri (cran-uri "WGCNA" version))
13593 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13594 (properties `((upstream-name . "WGCNA")))
13595 (build-system r-build-system)
13597 `(("r-annotationdbi" ,r-annotationdbi)
13598 ("r-doparallel" ,r-doparallel)
13599 ("r-dynamictreecut" ,r-dynamictreecut)
13600 ("r-fastcluster" ,r-fastcluster)
13601 ("r-foreach" ,r-foreach)
13602 ("r-go-db" ,r-go-db)
13603 ("r-hmisc" ,r-hmisc)
13604 ("r-impute" ,r-impute)
13606 ("r-robust" ,r-robust)
13607 ("r-survival" ,r-survival)
13608 ("r-matrixstats" ,r-matrixstats)
13609 ("r-preprocesscore" ,r-preprocesscore)))
13611 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13612 (synopsis "Weighted correlation network analysis")
13614 "This package provides functions necessary to perform Weighted
13615 Correlation Network Analysis on high-dimensional data. It includes functions
13616 for rudimentary data cleaning, construction and summarization of correlation
13617 networks, module identification and functions for relating both variables and
13618 modules to sample traits. It also includes a number of utility functions for
13619 data manipulation and visualization.")
13620 (license license:gpl2+)))
13622 (define-public r-kernlab
13629 (uri (cran-uri "kernlab" version))
13631 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13632 (build-system r-build-system)
13633 (home-page "https://cran.r-project.org/web/packages/kernlab")
13634 (synopsis "Kernel-based machine learning tools")
13636 "This package provides kernel-based machine learning methods for
13637 classification, regression, clustering, novelty detection, quantile regression
13638 and dimensionality reduction. Among other methods @code{kernlab} includes
13639 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13641 (license license:gpl2)))
13643 (define-public r-hierfstat
13645 (name "r-hierfstat")
13646 (version "0.04-22")
13650 (uri (cran-uri "hierfstat" version))
13653 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13654 (build-system r-build-system)
13656 `(("r-ade4" ,r-ade4)
13657 ("r-adegenet" ,r-adegenet)
13658 ("r-gtools" ,r-gtools)))
13659 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13660 (synopsis "Estimation and tests of hierarchical F-statistics")
13662 "This package allows the estimation of hierarchical F-statistics from
13663 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13664 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13665 are also given to test via randomisations the significance of each F and
13666 variance components, using the likelihood-ratio statistics G.")
13667 (license license:gpl2+)))
13669 (define-public r-hapassoc
13671 (name "r-hapassoc")
13676 (uri (cran-uri "hapassoc" version))
13679 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13680 (build-system r-build-system)
13681 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13682 (synopsis "Inference of trait associations with SNP haplotypes")
13684 "Hapassoc performs likelihood inference of trait associations with
13685 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13686 functions are developed primarily for data collected in cohort or
13687 cross-sectional studies. They can accommodate uncertain haplotype phase and
13688 handle missing genotypes at some SNPs.")
13689 (license license:gpl2)))
13691 (define-public r-sampling
13693 (name "r-sampling")
13698 (uri (cran-uri "sampling" version))
13701 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13702 (build-system r-build-system)
13704 `(("r-lpsolve" ,r-lpsolve)
13705 ("r-mass" ,r-mass)))
13706 (home-page "https://cran.r-project.org/web/packages/sampling/")
13707 (synopsis "Survey sampling")
13709 "This package provides functions for drawing and calibrating samples.")
13710 (license license:gpl2+)))
13712 (define-public r-r2html
13719 (uri (cran-uri "R2HTML" version))
13722 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13723 (properties `((upstream-name . "R2HTML")))
13724 (build-system r-build-system)
13725 (home-page "https://github.com/nalimilan/R2HTML")
13726 (synopsis "HTML export for R objects")
13728 "This package includes HTML functions and methods to write in an HTML
13729 file. Thus, making HTML reports is easy. It includes a function that allows
13730 redirection on the fly, which appears to be very useful for teaching purposes,
13731 as the student can keep a copy of the produced output to keep all that they
13732 did during the course. The package comes with a vignette describing how to
13733 write HTML reports for statistical analysis. Finally, a driver for Sweave
13734 allows to parse HTML flat files containing R code and to automatically write
13735 the corresponding outputs (tables and graphs).")
13736 (license license:gpl2+)))
13738 (define-public r-rjava
13745 (uri (cran-uri "rJava" version))
13748 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13749 (properties `((upstream-name . "rJava")))
13750 (build-system r-build-system)
13752 `(#:modules ((guix build utils)
13753 (guix build r-build-system)
13756 (modify-phases %standard-phases
13757 (add-after 'unpack 'set-JAVA_HOME
13758 (lambda* (#:key inputs #:allow-other-keys)
13759 (let ((jdk (assoc-ref inputs "jdk")))
13760 (setenv "JAVA_HOME" jdk)
13761 (setenv "JAVA" (which "java"))
13762 (setenv "JAR" (which "jar"))
13763 (setenv "JAVAC" (which "javac"))
13764 (setenv "JAVAH" (which "javah"))
13765 (setenv "JAVA_CPPFLAGS"
13766 (string-append "-I" jdk "/include "
13767 "-I" jdk "/include/linux"))
13768 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13769 ((lib) (setenv "JAVA_LIBS" lib))
13770 (_ (error "Could not find libjvm.so"))))
13774 ("jdk" ,icedtea-8 "jdk")
13777 (home-page "http://www.rforge.net/rJava/")
13778 (synopsis "Low-Level R to Java interface")
13780 "This package provides a low-level interface to the Java VM very much
13781 like .C/.Call and friends. It allows the creation of objects, calling methods
13782 and accessing fields.")
13783 (license license:gpl2)))
13785 (define-public r-svmisc
13792 (uri (cran-uri "svMisc" version))
13795 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13796 (properties `((upstream-name . "svMisc")))
13797 (build-system r-build-system)
13798 (home-page "https://github.com/SciViews/svMisc")
13799 (synopsis "Miscellaneous functions for SciViews")
13801 "This package provides miscellaneous functions for SciViews or general
13802 use, including tools to manage a temporary environment attached to the search
13803 path for temporary variables you do not want to @code{save()} or
13804 @code{load()}; test the current platform; showing progress bars, etc.")
13805 (license license:gpl2)))
13807 (define-public r-xyz
13814 (uri (cran-uri "xyz" version))
13817 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13818 (build-system r-build-system)
13820 `(("r-rcpp" ,r-rcpp)))
13821 (home-page "https://cran.r-project.org/web/packages/xyz/")
13822 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13824 "High dimensional interaction search by brute force requires a quadratic
13825 computational cost in the number of variables. The xyz algorithm provably
13826 finds strong interactions in almost linear time. For details of the algorithm
13827 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13828 interaction search in high-dimensional data.")
13829 ;; Any version of the GPL.
13830 (license license:gpl2+)))
13832 (define-public r-rttf2pt1
13834 (name "r-rttf2pt1")
13839 (uri (cran-uri "Rttf2pt1" version))
13842 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13843 (properties `((upstream-name . "Rttf2pt1")))
13844 (build-system r-build-system)
13845 (home-page "https://github.com/wch/Rttf2pt1")
13846 (synopsis "Font conversion utility")
13848 "This package contains the program @code{ttf2pt1}, for use with the
13849 @code{extrafont} package.")
13850 ;; Most of the files are covered under the Expat license. Some files are
13851 ;; covered under BSD-3. Deviations for individual files are recorded in
13852 ;; the LICENSE file.
13853 (license (list license:bsd-3 license:expat
13854 (license:non-copyleft "file://LICENSE")))))
13856 (define-public r-extrafontdb
13858 (name "r-extrafontdb")
13863 (uri (cran-uri "extrafontdb" version))
13866 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13867 (build-system r-build-system)
13868 (home-page "https://github.com/wch/extrafontdb")
13869 (synopsis "Database for the extrafont package")
13871 "This package holds the database for the @code{extrafont} package.")
13872 (license license:gpl2)))
13874 (define-public r-extrafont
13876 (name "r-extrafont")
13881 (uri (cran-uri "extrafont" version))
13884 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13885 (build-system r-build-system)
13887 `(("r-extrafontdb" ,r-extrafontdb)
13888 ("r-rttf2pt1" ,r-rttf2pt1)))
13889 (home-page "https://github.com/wch/extrafont")
13890 (synopsis "Tools for using fonts in R")
13892 "The extrafont package makes it easier to use fonts other than the basic
13893 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13894 used with PDF or PostScript output files. There are two hurdles for using
13895 fonts in PDF (or Postscript) output files:
13898 @item Making R aware of the font and the dimensions of the characters.
13899 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13900 properly on a device that doesn't have the font. This is usually needed if
13901 you want to print the PDF file or share it with others.
13904 The extrafont package makes both of these things easier.")
13905 (license license:gpl2)))
13907 (define-public r-xkcd
13914 (uri (cran-uri "xkcd" version))
13917 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13918 (build-system r-build-system)
13920 `(("r-extrafont" ,r-extrafont)
13921 ("r-ggplot2" ,r-ggplot2)
13922 ("r-hmisc" ,r-hmisc)))
13923 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13924 (synopsis "Plot ggplot2 graphics in the XKCD style")
13926 "This package provides the means to plot ggplot2 graphs in the style of
13927 the XKCD web comic.")
13928 (license license:gpl3)))
13930 (define-public r-msigdbr
13937 (uri (cran-uri "msigdbr" version))
13940 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
13941 (build-system r-build-system)
13943 `(("r-dplyr" ,r-dplyr)
13944 ("r-magrittr" ,r-magrittr)
13945 ("r-rlang" ,r-rlang)
13946 ("r-tibble" ,r-tibble)))
13947 (home-page "https://github.com/igordot/msigdbr")
13948 (synopsis "MSigDB gene sets for multiple organisms")
13950 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13951 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13952 software in a standard R data frame with key-value pairs. Included are the
13953 original human gene symbols and Entrez IDs as well as the equivalents for
13954 various frequently studied model organisms such as mouse, rat, pig, fly, and
13956 ;; The package is covered under the Expat license, but the upstream MSigDB
13957 ;; files are made available under the Creative Commons Attribution 4.0
13958 ;; International license.
13959 (license (list license:expat license:cc-by4.0))))
13961 (define-public r-gridgraphics
13963 (name "r-gridgraphics")
13968 (uri (cran-uri "gridGraphics" version))
13971 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13972 (properties `((upstream-name . "gridGraphics")))
13973 (build-system r-build-system)
13974 (home-page "https://github.com/pmur002/gridgraphics")
13975 (synopsis "Redraw base graphics using @code{grid} graphics")
13977 "This package provides functions to convert a page of plots drawn with
13978 the @code{graphics} package into identical output drawn with the @code{grid}
13979 package. The result looks like the original @code{graphics}-based plot, but
13980 consists of @code{grid} grobs and viewports that can then be manipulated with
13981 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13982 (license license:gpl2+)))
13984 (define-public r-farver
13991 (uri (cran-uri "farver" version))
13994 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
13995 (build-system r-build-system)
13996 (home-page "https://github.com/thomasp85/farver")
13997 (synopsis "Vectorized color conversion and comparison")
13999 "The encoding of color can be handled in many different ways, using
14000 different color spaces. As different color spaces have different uses,
14001 efficient conversion between these representations are important. This
14002 package provides a set of functions that gives access to very fast color space
14003 conversion and comparisons implemented in C++, and offers 100-fold speed
14004 improvements over the @code{convertColor} function in the @code{grDevices}
14006 (license license:expat)))
14008 (define-public r-ggplotify
14010 (name "r-ggplotify")
14015 (uri (cran-uri "ggplotify" version))
14018 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
14019 (build-system r-build-system)
14021 `(("r-ggplot2" ,r-ggplot2)
14022 ("r-gridgraphics" ,r-gridgraphics)
14023 ("r-rvcheck" ,r-rvcheck)))
14024 (home-page "https://github.com/GuangchuangYu/ggplotify")
14025 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14027 "This package provides tools to convert plot function calls (using
14028 expression or formula) to @code{grob} or @code{ggplot} objects that are
14029 compatible with the @code{grid} and @code{ggplot2} environment. With this
14030 package, we are able to e.g. use @code{cowplot} to align plots produced by
14031 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14032 converting them to @code{ggplot} objects.")
14033 (license license:artistic2.0)))
14035 (define-public r-triebeard
14037 (name "r-triebeard")
14042 (uri (cran-uri "triebeard" version))
14045 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14046 (build-system r-build-system)
14047 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14048 (home-page "https://github.com/Ironholds/triebeard/")
14049 (synopsis "Radix trees in Rcpp")
14051 "Radix trees, or tries, are key-value data structures optimized for
14052 efficient lookups, similar in purpose to hash tables. This package provides
14053 an implementation of radix trees for use in R programming and in developing
14054 packages with Rcpp.")
14055 (license license:expat)))
14057 (define-public r-tweenr
14064 (uri (cran-uri "tweenr" version))
14067 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14068 (build-system r-build-system)
14070 `(("r-farver" ,r-farver)
14071 ("r-magrittr" ,r-magrittr)
14073 ("r-rlang" ,r-rlang)))
14074 (home-page "https://github.com/thomasp85/tweenr")
14075 (synopsis "Interpolate data for smooth animations")
14077 "In order to create smooth animation between states of data, tweening is
14078 necessary. This package provides a range of functions for creating tweened
14079 data that can be used as basis for animation. Furthermore it adds a number of
14080 vectorized interpolaters for common R data types such as numeric, date and
14082 (license license:expat)))
14084 (define-public r-polyclip
14086 (name "r-polyclip")
14091 (uri (cran-uri "polyclip" version))
14094 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14095 (build-system r-build-system)
14096 (native-inputs `(("pkg-config" ,pkg-config)))
14097 (home-page "http://www.angusj.com/delphi/clipper.php")
14098 (synopsis "Polygon clipping")
14100 "This package provides an R port of the library Clipper. It performs
14101 polygon clipping operations (intersection, union, set minus, set difference)
14102 for polygonal regions of arbitrary complexity, including holes. It computes
14103 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14104 dilations) for polygonal regions and polygonal lines. It computes the
14105 Minkowski Sum of general polygons. There is a function for removing
14106 self-intersections from polygon data.")
14107 (license license:boost1.0)))
14109 (define-public r-urltools
14111 (name "r-urltools")
14116 (uri (cran-uri "urltools" version))
14119 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14120 (build-system r-build-system)
14122 `(("r-rcpp" ,r-rcpp)
14123 ("r-triebeard" ,r-triebeard)))
14124 (home-page "https://github.com/Ironholds/urltools/")
14125 (synopsis "Vectorized tools for URL handling and parsing")
14127 "This package provides a toolkit for all URL-handling needs, including
14128 encoding and decoding, parsing, parameter extraction and modification. All
14129 functions are designed to be both fast and entirely vectorized. It is
14130 intended to be useful for people dealing with web-related datasets, such as
14131 server-side logs, although may be useful for other situations involving large
14133 (license license:expat)))
14135 (define-public r-ggforce
14142 (uri (cran-uri "ggforce" version))
14145 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14146 (build-system r-build-system)
14148 `(("r-ggplot2" ,r-ggplot2)
14149 ("r-gtable" ,r-gtable)
14151 ("r-polyclip" ,r-polyclip)
14153 ("r-rcppeigen" ,r-rcppeigen)
14154 ("r-rlang" ,r-rlang)
14155 ("r-scales" ,r-scales)
14156 ("r-tidyselect" ,r-tidyselect)
14157 ("r-tweenr" ,r-tweenr)
14158 ("r-withr" ,r-withr)))
14159 (home-page "https://ggforce.data-imaginist.com")
14160 (synopsis "Accelerating ggplot2")
14162 "The aim of the ggplot2 package is to aid in visual data investigations.
14163 This focus has led to a lack of facilities for composing specialized plots.
14164 Thi package aims to be a collection of mainly new statistics and geometries
14165 that fills this gap.")
14166 (license license:expat)))
14168 (define-public r-europepmc
14170 (name "r-europepmc")
14175 (uri (cran-uri "europepmc" version))
14178 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14179 (build-system r-build-system)
14181 `(("r-dplyr" ,r-dplyr)
14183 ("r-jsonlite" ,r-jsonlite)
14185 ("r-progress" ,r-progress)
14186 ("r-purrr" ,r-purrr)
14187 ("r-urltools" ,r-urltools)
14188 ("r-xml2" ,r-xml2)))
14189 (home-page "https://github.com/ropensci/europepmc/")
14190 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14192 "This package provides an R Client for the
14193 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14194 Service}. It gives access to both metadata on life science literature and
14195 open access full texts. Europe PMC indexes all PubMed content and other
14196 literature sources including Agricola, a bibliographic database of citations
14197 to the agricultural literature, or Biological Patents. In addition to
14198 bibliographic metadata, the client allows users to fetch citations and
14199 reference lists. Links between life-science literature and other EBI
14200 databases, including ENA, PDB or ChEMBL are also accessible.")
14201 (license license:gpl3)))
14203 (define-public r-ggraph
14210 (uri (cran-uri "ggraph" version))
14213 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14214 (build-system r-build-system)
14216 `(("r-digest" ,r-digest)
14217 ("r-dplyr" ,r-dplyr)
14218 ("r-ggforce" ,r-ggforce)
14219 ("r-ggplot2" ,r-ggplot2)
14220 ("r-ggrepel" ,r-ggrepel)
14221 ("r-graphlayouts" ,r-graphlayouts)
14222 ("r-gtable" ,r-gtable)
14223 ("r-igraph" ,r-igraph)
14226 ("r-rlang" ,r-rlang)
14227 ("r-scales" ,r-scales)
14228 ("r-tidygraph" ,r-tidygraph)
14229 ("r-viridis" ,r-viridis)))
14230 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14231 (synopsis "Implementation of grammar of graphics for graphs and networks")
14233 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14234 graph and network visualizations due to its reliance on tabular data input.
14235 The ggraph package is an extension of the ggplot2 API tailored to graph
14236 visualizations and provides the same flexible approach to building up plots
14238 (license license:gpl3)))
14240 (define-public r-varselrf
14242 (name "r-varselrf")
14247 (uri (cran-uri "varSelRF" version))
14250 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14251 (properties `((upstream-name . "varSelRF")))
14252 (build-system r-build-system)
14254 `(("r-randomforest" ,r-randomforest)))
14255 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14256 (synopsis "Variable selection using random forests")
14258 "This package provides tools for the variable selection from random
14259 forests using both backwards variable elimination (for the selection of small
14260 sets of non-redundant variables) and selection based on the importance
14261 spectrum (somewhat similar to scree plots; for the selection of large,
14262 potentially highly-correlated variables). The main applications are in
14263 high-dimensional data (e.g., microarray data, and other genomics and
14264 proteomics applications).")
14265 (license license:gpl2+)))
14267 (define-public r-pamr
14274 (uri (cran-uri "pamr" version))
14277 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14278 (build-system r-build-system)
14280 `(("r-cluster" ,r-cluster)
14281 ("r-survival" ,r-survival)))
14282 (native-inputs `(("gfortran" ,gfortran)))
14283 (home-page "https://cran.r-project.org/web/packages/pamr/")
14284 (synopsis "Prediction Analysis for Microarrays")
14286 "This package provides some functions for sample classification in
14288 (license license:gpl2)))
14290 (define-public r-rda
14293 (version "1.0.2-2.1")
14297 (uri (cran-uri "rda" version))
14300 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14301 (build-system r-build-system)
14302 (home-page "https://cran.r-project.org/web/packages/rda/")
14303 (synopsis "Shrunken centroids regularized discriminant analysis")
14305 "This package provides tools for shrunken centroids regularized
14306 discriminant analysis for the purpose of classifying high dimensional data.")
14307 (license license:gpl2+)))
14309 (define-public r-ggvis
14316 (uri (cran-uri "ggvis" version))
14319 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14320 (build-system r-build-system)
14322 `(("r-assertthat" ,r-assertthat)
14323 ("r-dplyr" ,r-dplyr)
14324 ("r-htmltools" ,r-htmltools)
14325 ("r-jsonlite" ,r-jsonlite)
14326 ("r-lazyeval" ,r-lazyeval)
14327 ("r-magrittr" ,r-magrittr)
14328 ("r-shiny" ,r-shiny)))
14329 (home-page "https://ggvis.rstudio.com/")
14330 (synopsis "Interactive grammar of graphics")
14332 "This package is a data visualization package for R providing an
14333 implementation of an interactive grammar of graphics, taking the best parts of
14334 ggplot2, combining them with the reactive framework of Shiny and drawing web
14335 graphics using Vega.")
14336 (license license:gpl2)))
14338 (define-public r-gbm
14345 (uri (cran-uri "gbm" version))
14348 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14349 (build-system r-build-system)
14351 `(("r-gridextra" ,r-gridextra)
14352 ("r-lattice" ,r-lattice)
14353 ("r-survival" ,r-survival)))
14354 (home-page "https://github.com/gbm-developers/gbm")
14355 (synopsis "Generalized boosted regression models")
14357 "This package is an implementation of extensions to Freund and Schapire's
14358 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14359 regression methods for least squares, absolute loss, t-distribution loss,
14360 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14361 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14362 and Learning to Rank measures (LambdaMart).")
14363 (license license:gpl2+)))
14365 (define-public r-threejs
14372 (uri (cran-uri "threejs" version))
14375 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14376 (build-system r-build-system)
14378 `(#:modules ((guix build utils)
14379 (guix build r-build-system)
14383 (modify-phases %standard-phases
14384 (add-after 'unpack 'process-javascript
14385 (lambda* (#:key inputs #:allow-other-keys)
14386 (with-directory-excursion "inst"
14390 `((,(assoc-ref inputs "js-jquery")
14391 "htmlwidgets/lib/jquery/jquery.min.js")
14392 (,(assoc-ref inputs "js-threejs-85")
14393 "htmlwidgets/lib/threejs-85/three.min.js"))))
14394 (lambda (sources targets)
14395 (for-each (lambda (source target)
14396 (format #t "Processing ~a --> ~a~%"
14398 (delete-file target)
14399 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14400 (call-with-output-file target
14402 (dump-port minified port)))))
14403 sources targets))))
14406 `(("r-base64enc" ,r-base64enc)
14407 ("r-crosstalk" ,r-crosstalk)
14408 ("r-htmlwidgets" ,r-htmlwidgets)
14409 ("r-igraph" ,r-igraph)))
14411 `(("uglify-js" ,uglify-js)
14415 (uri "https://code.jquery.com/jquery-3.3.1.js")
14418 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14422 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14425 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14426 (home-page "https://bwlewis.github.io/rthreejs")
14427 (synopsis "Interactive 3D scatter plots, networks and globes")
14429 "Create interactive 3D scatter plots, network plots, and globes in R
14430 using the three.js visualization library.")
14431 (license license:expat)))
14433 (define-public r-mlbench
14440 (uri (cran-uri "mlbench" version))
14443 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14444 (build-system r-build-system)
14445 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14446 (synopsis "Machine learning benchmark problems")
14448 "This package provides a collection of artificial and real-world machine
14449 learning benchmark problems, including, e.g., several data sets from the UCI
14451 (license license:gpl2)))
14453 (define-public r-mpm
14460 (uri (cran-uri "mpm" version))
14463 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14464 (build-system r-build-system)
14466 `(("r-kernsmooth" ,r-kernsmooth)
14467 ("r-mass" ,r-mass)))
14468 (home-page "http://mpm.r-forge.r-project.org")
14469 (synopsis "Multivariate projection methods")
14471 "This is a package for exploratory graphical analysis of multivariate
14472 data, specifically gene expression data with different projection methods:
14473 principal component analysis, correspondence analysis, spectral map
14475 (license license:gpl2+)))
14477 (define-public r-png
14483 (uri (cran-uri "png" version))
14486 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14487 (build-system r-build-system)
14489 `(("libpng" ,libpng)
14491 (home-page "http://www.rforge.net/png/")
14492 (synopsis "Read and write PNG images")
14494 "This package provides an easy and simple way to read, write and display
14495 bitmap images stored in the PNG format. It can read and write both files and
14496 in-memory raw vectors.")
14497 ;; Any of these GPL versions.
14498 (license (list license:gpl2 license:gpl3))))
14500 (define-public r-ggcorrplot
14502 (name "r-ggcorrplot")
14507 (uri (cran-uri "ggcorrplot" version))
14510 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14511 (build-system r-build-system)
14513 `(("r-ggplot2" ,r-ggplot2)
14514 ("r-reshape2" ,r-reshape2)))
14515 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14516 (synopsis "Visualization of a correlation matrix using ggplot2")
14518 "The ggcorrplot package can be used to visualize easily a correlation
14519 matrix using ggplot2. It provides a solution for reordering the correlation
14520 matrix and displays the significance level on the plot. It also includes a
14521 function for computing a matrix of correlation p-values.")
14522 (license license:gpl2)))
14524 (define-public r-flexdashboard
14526 (name "r-flexdashboard")
14527 (version "0.5.1.1")
14531 (uri (cran-uri "flexdashboard" version))
14534 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14535 (build-system r-build-system)
14537 `(#:modules ((guix build utils)
14538 (guix build r-build-system)
14542 (ice-9 textual-ports))
14544 (modify-phases %standard-phases
14545 (add-after 'unpack 'process-javascript
14546 (lambda* (#:key inputs #:allow-other-keys)
14547 (with-directory-excursion "inst"
14548 ;; Concatenate all components of prism.js
14549 (let ((contents (string-join
14550 (map (lambda (name)
14551 (call-with-input-file
14552 (assoc-ref inputs name)
14556 "js-prism-line-numbers"))
14558 (call-with-output-file "prism-src.js"
14559 (cut display contents <>)))
14563 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14564 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14566 "www/sly/sly.min.js")
14568 "www/prism/prism.js")
14569 (,(assoc-ref inputs "js-raphael")
14570 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14571 (,(assoc-ref inputs "js-featherlight")
14572 "www/featherlight/featherlight.min.js"))))
14573 (lambda (sources targets)
14574 (for-each (lambda (source target)
14575 (format #t "Processing ~a --> ~a~%"
14577 (delete-file target)
14578 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14579 (call-with-output-file target
14581 (dump-port minified port)))))
14582 sources targets))))
14585 `(("r-htmltools" ,r-htmltools)
14586 ("r-htmlwidgets" ,r-htmlwidgets)
14587 ("r-jsonlite" ,r-jsonlite)
14588 ("r-knitr" ,r-knitr)
14589 ("r-rmarkdown" ,r-rmarkdown)
14590 ("r-shiny" ,r-shiny)))
14592 `(("uglify-js" ,uglify-js)
14596 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14599 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14603 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14606 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14610 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14613 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14614 ("js-prism-line-numbers"
14617 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14620 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14624 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14627 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14628 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14629 (synopsis "R Markdown format for flexible dashboards")
14631 "This package provides an R Markdown format for converting an R Markdown
14632 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14633 of its components to the containing web page.")
14634 (license license:expat)))
14636 (define-public r-preseqr
14643 (uri (cran-uri "preseqR" version))
14646 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14647 (properties `((upstream-name . "preseqR")))
14648 (build-system r-build-system)
14650 `(("r-polynom" ,r-polynom)))
14651 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14652 (synopsis "Predicting species accumulation curves")
14654 "This package can be used to predict the r-species accumulation
14655 curve (r-SAC), which is the number of species represented at least r times as
14656 a function of the sampling effort. When r = 1, the curve is known as the
14657 species accumulation curve, or the library complexity curve in high-throughput
14658 genomic sequencing. The package includes both parametric and nonparametric
14659 methods, as described by Deng C, et al. (2018).")
14660 (license license:gpl3)))
14662 (define-public r-mapplots
14664 (name "r-mapplots")
14669 (uri (cran-uri "mapplots" version))
14672 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14673 (build-system r-build-system)
14674 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14675 (synopsis "Data visualization on maps")
14677 "This package helps you create simple maps; add sub-plots like pie plots
14678 to a map or any other plot; format, plot and export gridded data. The package
14679 was developed for displaying fisheries data but most functions can be used for
14680 more generic data visualisation.")
14681 (license license:gpl2+)))
14683 (define-public r-pmcmr
14690 (uri (cran-uri "PMCMR" version))
14693 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14694 (properties `((upstream-name . "PMCMR")))
14695 (build-system r-build-system)
14696 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14697 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14699 "This is a deprecated package for calculating pairwise multiple
14700 comparisons of mean rank sums. This package is superseded by the novel
14701 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14702 compatibility of dependent packages for some time.")
14703 (license license:gpl3+)))
14705 (define-public r-downloader
14707 (name "r-downloader")
14712 (uri (cran-uri "downloader" version))
14715 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14716 (build-system r-build-system)
14718 `(("r-digest" ,r-digest)))
14719 (home-page "https://github.com/wch/downloader")
14720 (synopsis "Download files over HTTP and HTTPS")
14722 "This package provides a wrapper for the @code{download.file} function,
14723 making it possible to download files over HTTPS across platforms. The
14724 @code{RCurl} package provides this functionality (and much more) but has
14725 external dependencies. This package has is implemented purely in R.")
14726 (license license:gpl2)))
14728 (define-public r-rex
14735 (uri (cran-uri "rex" version))
14738 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14739 (build-system r-build-system)
14741 `(("r-lazyeval" ,r-lazyeval)
14742 ("r-magrittr" ,r-magrittr)))
14743 (home-page "https://github.com/kevinushey/rex")
14744 (synopsis "Friendly regular expressions")
14746 "This package provides a friendly interface for the construction of
14747 regular expressions. Regular expressions are a very powerful feature, however
14748 they are often difficult to interpret. Rex allows you to build complex
14749 regular expressions from human readable expressions")
14750 (license license:expat)))
14752 (define-public r-xmlparsedata
14754 (name "r-xmlparsedata")
14759 (uri (cran-uri "xmlparsedata" version))
14762 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14763 (properties `((upstream-name . "xmlparsedata")))
14764 (build-system r-build-system)
14765 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14766 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14768 "This package provides tools to convert the output of
14769 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14770 @code{XPath}, and is easier to manipulate in general.")
14771 (license license:expat)))
14773 (define-public r-cyclocomp
14775 (name "r-cyclocomp")
14780 (uri (cran-uri "cyclocomp" version))
14783 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14784 (properties `((upstream-name . "cyclocomp")))
14785 (build-system r-build-system)
14787 `(("r-callr" ,r-callr)
14788 ("r-crayon" ,r-crayon)
14790 ("r-remotes" ,r-remotes)
14791 ("r-withr" ,r-withr)))
14792 (home-page "https://github.com/MangoTheCat/cyclocomp")
14793 (synopsis "Cyclomatic complexity of R code")
14795 "Cyclomatic complexity is a software metric, used to indicate the
14796 complexity of a program. It is a quantitative measure of the number of
14797 linearly independent paths through a program's source code. This package
14798 provides tools to compute this metric.")
14799 (license license:expat)))
14801 (define-public r-lintr
14808 (uri (cran-uri "lintr" version))
14811 "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb"))))
14812 (properties `((upstream-name . "lintr")))
14813 (build-system r-build-system)
14815 `(("r-codetools" ,r-codetools)
14816 ("r-crayon" ,r-crayon)
14817 ("r-cyclocomp" ,r-cyclocomp)
14818 ("r-digest" ,r-digest)
14820 ("r-jsonlite" ,r-jsonlite)
14821 ("r-knitr" ,r-knitr)
14823 ("r-rstudioapi" ,r-rstudioapi)
14824 ("r-stringdist" ,r-stringdist)
14825 ("r-testthat" ,r-testthat)
14827 ("r-xmlparsedata" ,r-xmlparsedata)))
14828 (home-page "https://github.com/jimhester/lintr")
14829 (synopsis "Linter for R code")
14830 (description "This package checks adherence to a given style, syntax
14831 errors and possible semantic issues. It supports on the fly checking of R
14832 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14833 (license license:expat)))
14835 (define-public r-sctransform
14837 (name "r-sctransform")
14842 (uri (cran-uri "sctransform" version))
14845 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14846 (build-system r-build-system)
14848 `(("r-future" ,r-future)
14849 ("r-future-apply" ,r-future-apply)
14850 ("r-ggplot2" ,r-ggplot2)
14851 ("r-gridextra" ,r-gridextra)
14853 ("r-matrix" ,r-matrix)
14855 ("r-rcppeigen" ,r-rcppeigen)
14856 ("r-reshape2" ,r-reshape2)))
14857 (home-page "https://github.com/ChristophH/sctransform")
14858 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14860 "This package provides a normalization method for single-cell UMI count
14861 data using a variance stabilizing transformation. The transformation is based
14862 on a negative binomial regression model with regularized parameters. As part
14863 of the same regression framework, this package also provides functions for
14864 batch correction, and data correction.")
14865 (license license:gpl3)))
14867 (define-public r-styler
14874 (uri (cran-uri "styler" version))
14877 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14878 (build-system r-build-system)
14880 `(("r-backports" ,r-backports)
14882 ("r-magrittr" ,r-magrittr)
14883 ("r-purrr" ,r-purrr)
14884 ("r-rematch2" ,r-rematch2)
14885 ("r-rlang" ,r-rlang)
14886 ("r-rprojroot" ,r-rprojroot)
14887 ("r-tibble" ,r-tibble)
14888 ("r-withr" ,r-withr)
14889 ("r-xfun" ,r-xfun)))
14890 (home-page "https://github.com/r-lib/styler")
14891 (synopsis "Non-invasive pretty printing of R code")
14893 "This is a package for pretty-printing R code without changing the user's
14894 formatting intent.")
14895 (license license:gpl3)))
14897 (define-public r-scrime
14904 (uri (cran-uri "scrime" version))
14907 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14908 (build-system r-build-system)
14909 (home-page "https://cran.r-project.org/web/packages/scrime/")
14910 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14912 "This package provides tools for the analysis of high-dimensional data
14913 developed/implemented at the group \"Statistical Complexity Reduction In
14914 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14915 the functions can also be applied to other types of categorical data.")
14916 (license license:gpl2)))
14918 (define-public r-pbmcapply
14920 (name "r-pbmcapply")
14925 (uri (cran-uri "pbmcapply" version))
14928 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14929 (build-system r-build-system)
14930 (home-page "https://github.com/kvnkuang/pbmcapply")
14931 (synopsis "Track the progress of apply procedures with a progress bar")
14933 "This light-weight package helps you track and visualize the progress of
14934 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14935 (license license:expat)))
14937 (define-public r-blme
14944 (uri (cran-uri "blme" version))
14947 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14948 (build-system r-build-system)
14949 (propagated-inputs `(("r-lme4" ,r-lme4)))
14950 (home-page "https://github.com/vdorie/blme")
14951 (synopsis "Bayesian linear mixed-effects models")
14953 "This package provides tools for maximum a posteriori estimation for
14954 linear and generalized linear mixed-effects models in a Bayesian setting. It
14955 extends the lme4 package.")
14956 (license license:gpl2+)))
14958 (define-public r-batchtools
14960 (name "r-batchtools")
14965 (uri (cran-uri "batchtools" version))
14968 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14969 (build-system r-build-system)
14971 `(("r-backports" ,r-backports)
14972 ("r-base64url" ,r-base64url)
14974 ("r-checkmate" ,r-checkmate)
14975 ("r-data-table" ,r-data-table)
14976 ("r-digest" ,r-digest)
14978 ("r-progress" ,r-progress)
14980 ("r-rappdirs" ,r-rappdirs)
14981 ("r-stringi" ,r-stringi)
14982 ("r-withr" ,r-withr)))
14983 (home-page "https://github.com/mllg/batchtools")
14984 (synopsis "Tools for computation on batch systems")
14986 "As a successor of the packages BatchJobs and BatchExperiments, this
14987 package provides a parallel implementation of the Map function for high
14988 performance computing systems managed by various schedulers. A multicore and
14989 socket mode allow the parallelization on a local machines, and multiple
14990 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14991 the package provides an abstraction mechanism to define large-scale computer
14992 experiments in a well-organized and reproducible way.")
14993 (license license:lgpl3)))
14995 (define-public r-clue
15002 (uri (cran-uri "clue" version))
15005 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15006 (build-system r-build-system)
15007 (propagated-inputs `(("r-cluster" ,r-cluster)))
15008 (home-page "https://cran.r-project.org/web/packages/clue/")
15009 (synopsis "Tools for analyzing cluster ensembles")
15010 (description "Cluster ensembles are collections of individual solutions to
15011 a given clustering problem which are useful or necessary to consider in a wide
15012 range of applications. This R package provides an extensible computational
15013 environment for creating and analyzing cluster ensembles, with basic data
15014 structures for representing partitions and hierarchies, and facilities for
15015 computing on them, including methods for measuring proximity and obtaining
15016 consensus and secondary clusterings.")
15017 (license license:gpl2)))
15019 (define-public r-sitmo
15026 (uri (cran-uri "sitmo" version))
15029 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15030 (build-system r-build-system)
15031 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15032 (home-page "https://github.com/coatless/sitmo/")
15033 (synopsis "Parallel pseudo random number generator header files")
15035 "This package provides two high quality and fast PPRNGs that may be used
15036 in an OpenMP parallel environment. In addition, there is a generator for one
15037 dimensional low-discrepancy sequence.")
15038 (license license:expat)))
15040 (define-public r-dqrng
15047 (uri (cran-uri "dqrng" version))
15050 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15051 (build-system r-build-system)
15055 ("r-sitmo" ,r-sitmo)))
15056 (home-page "https://www.daqana.org/dqrng")
15057 (synopsis "Fast pseudo random number generators")
15059 "Several fast random number generators are provided as C++ header-only
15060 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15061 Additionally, fast functions for generating random numbers according to a
15062 uniform, normal and exponential distribution are included. The latter two use
15063 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15064 functions are exported to R and as a C++ interface and are enabled for use
15065 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15066 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15067 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15068 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15069 ;; whole is distributed under the terms of the AGPL 3.
15070 (license license:agpl3)))
15072 (define-public r-dalex
15079 (uri (cran-uri "DALEX" version))
15082 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
15083 (properties `((upstream-name . "DALEX")))
15084 (build-system r-build-system)
15085 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15086 (home-page "https://pbiecek.github.io/DALEX/")
15087 (synopsis "Descriptive machine learning explanations")
15089 "Machine Learning models are widely used and have various applications in
15090 classification or regression. Models created with boosting, bagging, stacking
15091 or similar techniques are often used due to their high performance, but such
15092 black-box models usually lack interpretability. The DALEX package contains
15093 various explainers that help to understand the link between input variables
15094 and model output.")
15095 ;; Any version of the GPL
15096 (license license:gpl3+)))
15098 (define-public r-enrichr
15105 (uri (cran-uri "enrichR" version))
15108 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15109 (properties `((upstream-name . "enrichR")))
15110 (build-system r-build-system)
15112 `(("r-httr" ,r-httr)
15113 ("r-rjson" ,r-rjson)))
15114 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15115 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15117 "This package provides an R interface to all Enrichr databases, a
15118 web-based tool for analyzing gene sets and returns any enrichment of common
15119 annotated biological functions.")
15120 (license license:gpl2+)))
15122 (define-public r-plot3d
15129 (uri (cran-uri "plot3D" version))
15132 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
15133 (properties `((upstream-name . "plot3D")))
15134 (build-system r-build-system)
15135 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15136 (home-page "https://cran.r-project.org/web/packages/plot3D")
15137 (synopsis "Plot multi-dimensional data")
15139 "This package provides functions for viewing 2D and 3D data, including
15140 perspective plots, slice plots, surface plots, scatter plots, etc. It
15141 includes data sets from oceanography.")
15142 (license license:gpl3+)))
15144 (define-public r-ggfortify
15146 (name "r-ggfortify")
15151 (uri (cran-uri "ggfortify" version))
15154 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15155 (build-system r-build-system)
15157 `(("r-dplyr" ,r-dplyr)
15158 ("r-ggplot2" ,r-ggplot2)
15159 ("r-gridextra" ,r-gridextra)
15160 ("r-scales" ,r-scales)
15161 ("r-stringr" ,r-stringr)
15162 ("r-tibble" ,r-tibble)
15163 ("r-tidyr" ,r-tidyr)))
15164 (home-page "https://github.com/sinhrks/ggfortify")
15165 (synopsis "Data visualization tools for statistical analysis results")
15167 "This package provides unified plotting tools for statistics commonly
15168 used, such as GLM, time series, PCA families, clustering and survival
15169 analysis. The package offers a single plotting interface for these analysis
15170 results and plots in a unified style using the @code{ggplot2} package.")
15171 (license license:gpl2)))
15173 (define-public r-refmanager
15175 (name "r-refmanager")
15180 (uri (cran-uri "RefManageR" version))
15183 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15184 (properties `((upstream-name . "RefManageR")))
15185 (build-system r-build-system)
15187 `(("r-bibtex" ,r-bibtex)
15189 ("r-jsonlite" ,r-jsonlite)
15190 ("r-lubridate" ,r-lubridate)
15192 ("r-stringr" ,r-stringr)
15193 ("r-xml2" ,r-xml2)))
15194 (home-page "https://github.com/ropensci/RefManageR/")
15195 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15197 "This package provides tools for importing and working with bibliographic
15198 references. It greatly enhances the @code{bibentry} class by providing a
15199 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15200 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15201 by various formats for name lists (author by last names, translator by full
15202 names, etc.). Entries can be updated, combined, sorted, printed in a number
15203 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15204 into R and converted to @code{BibEntry} objects.")
15205 ;; Any of these licenses may be picked.
15206 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15208 (define-public r-citr
15215 (uri (cran-uri "citr" version))
15218 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15219 (build-system r-build-system)
15221 `(("r-assertthat" ,r-assertthat)
15224 ("r-miniui" ,r-miniui)
15225 ("r-refmanager" ,r-refmanager)
15226 ("r-rstudioapi" ,r-rstudioapi)
15227 ("r-shiny" ,r-shiny)
15228 ("r-shinyjs" ,r-shinyjs)
15229 ("r-yaml" ,r-yaml)))
15230 (home-page "https://github.com/crsh/citr")
15231 (synopsis "RStudio add-in to insert Markdown citations")
15233 "This package provides functions and an RStudio add-in that search a
15234 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15235 the current document.")
15236 (license license:expat)))
15238 (define-public r-xgboost
15241 (version "0.90.0.2")
15245 (uri (cran-uri "xgboost" version))
15248 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15249 (build-system r-build-system)
15251 `(("r-data-table" ,r-data-table)
15252 ("r-magrittr" ,r-magrittr)
15253 ("r-matrix" ,r-matrix)
15254 ("r-stringi" ,r-stringi)))
15255 (home-page "https://github.com/dmlc/xgboost")
15256 (synopsis "Extreme gradient boosting")
15258 "This package provides an R interface to Extreme Gradient Boosting, which
15259 is an efficient implementation of the gradient boosting framework from Chen
15260 and Guestrin (2016). The package includes efficient linear model solver and
15261 tree learning algorithms. The package can automatically do parallel
15262 computation on a single machine. It supports various objective functions,
15263 including regression, classification and ranking. The package is made to be
15264 extensible, so that users are also allowed to define their own objectives
15266 (license license:asl2.0)))
15268 (define-public r-umap
15271 (version "0.2.4.0")
15275 (uri (cran-uri "umap" version))
15278 "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch"))))
15279 (build-system r-build-system)
15281 `(("r-openssl" ,r-openssl)
15283 ("r-reticulate" ,r-reticulate)
15284 ("r-rspectra" ,r-rspectra)))
15285 (home-page "https://github.com/tkonopka/umap")
15286 (synopsis "Uniform manifold approximation and projection")
15288 "Uniform manifold approximation and projection is a technique for
15289 dimension reduction. This package provides an interface to the UMAP algorithm
15290 in R, including a translation of the original algorithm into R.")
15291 (license license:expat)))
15293 (define-public r-uwot
15300 (uri (cran-uri "uwot" version))
15303 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15304 (build-system r-build-system)
15306 `(("r-dqrng" ,r-dqrng)
15308 ("r-irlba" ,r-irlba)
15309 ("r-matrix" ,r-matrix)
15311 ("r-rcppannoy" ,r-rcppannoy)
15312 ("r-rcppparallel" ,r-rcppparallel)
15313 ("r-rcppprogress" ,r-rcppprogress)
15314 ("r-rspectra" ,r-rspectra)))
15315 (home-page "https://github.com/jlmelville/uwot")
15316 (synopsis "Uniform manifold approximation and projection")
15318 "This package provides an implementation of the Uniform Manifold
15319 Approximation and Projection dimensionality reduction by McInnes et
15320 al. (2018). It also provides means to transform new data and to carry out
15321 supervised dimensionality reduction. An implementation of the related
15322 LargeVis method of Tang et al. (2016) is also provided.")
15323 (license license:gpl3)))
15325 (define-public r-kableextra
15327 (name "r-kableextra")
15332 (uri (cran-uri "kableExtra" version))
15335 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15336 (properties `((upstream-name . "kableExtra")))
15337 (build-system r-build-system)
15339 `(("r-digest" ,r-digest)
15341 ("r-htmltools" ,r-htmltools)
15342 ("r-knitr" ,r-knitr)
15343 ("r-magrittr" ,r-magrittr)
15344 ("r-readr" ,r-readr)
15345 ("r-rmarkdown" ,r-rmarkdown)
15346 ("r-rstudioapi" ,r-rstudioapi)
15347 ("r-rvest" ,r-rvest)
15348 ("r-scales" ,r-scales)
15349 ("r-stringr" ,r-stringr)
15350 ("r-viridislite" ,r-viridislite)
15351 ("r-webshot" ,r-webshot)
15352 ("r-xml2" ,r-xml2)))
15353 (home-page "https://haozhu233.github.io/kableExtra/")
15354 (synopsis "Construct complex tables with pipe syntax")
15356 "Build complex HTML or LaTeX tables using @code{kable()} from
15357 @code{knitr} and the piping syntax from @code{magrittr}. The function
15358 @code{kable()} is a light weight table generator coming from @code{knitr}.
15359 This package simplifies the way to manipulate the HTML or LaTeX codes
15360 generated by @code{kable()} and allows users to construct complex tables and
15361 customize styles using a readable syntax.")
15362 (license license:expat)))
15364 (define-public r-glasso
15371 (uri (cran-uri "glasso" version))
15373 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15374 (build-system r-build-system)
15375 (native-inputs `(("gfortran" ,gfortran)))
15376 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15377 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15379 "This is a package for estimation of a sparse inverse covariance matrix
15380 using a lasso (L1) penalty. Facilities are provided for estimates along a
15381 path of values for the regularization parameter.")
15382 (license license:gpl2)))
15384 (define-public r-rhpcblasctl
15386 (name "r-rhpcblasctl")
15387 (version "0.18-205")
15391 (uri (cran-uri "RhpcBLASctl" version))
15394 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15395 (properties `((upstream-name . "RhpcBLASctl")))
15396 (build-system r-build-system)
15397 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15398 (synopsis "Control the number of threads on BLAS")
15400 "This package allows you to control the number of threads the BLAS
15401 library uses. It is also possible to control the number of threads in
15403 (license license:agpl3+)))
15405 (define-public r-lda
15412 (uri (cran-uri "lda" version))
15415 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15416 (build-system r-build-system)
15417 (home-page "https://cran.r-project.org/web/packages/lda/")
15418 (synopsis "Collapsed Gibbs sampling methods for topic models")
15420 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15421 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15422 mixed-membership stochastic blockmodel. Inference for all of these models is
15423 implemented via a fast collapsed Gibbs sampler written in C. Utility
15424 functions for reading/writing data typically used in topic models, as well as
15425 tools for examining posterior distributions are also included.")
15426 ;; Any version of the LGPL
15427 (license license:lgpl3+)))
15429 (define-public r-rann-l1
15436 (uri (cran-uri "RANN.L1" version))
15439 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15440 (properties `((upstream-name . "RANN.L1")))
15441 (build-system r-build-system)
15442 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15443 (synopsis "Fast nearest neighbour search using L1 metric")
15445 "This package provides tools to find the k nearest neighbours for every
15446 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15447 library. There is support for approximate as well as exact searches, fixed
15448 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15449 computed using the L1 (Manhattan, taxicab) metric.")
15450 (license license:gpl3+)))
15452 (define-public r-leiden
15459 (uri (cran-uri "leiden" version))
15462 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15463 (properties `((upstream-name . "leiden")))
15464 (build-system r-build-system)
15466 `(("r-igraph" ,r-igraph)
15467 ("r-matrix" ,r-matrix)
15468 ("r-reticulate" ,r-reticulate)))
15469 (home-page "https://github.com/TomKellyGenetics/leiden")
15470 (synopsis "R implementation of Leiden clustering algorithm")
15472 "This package implements the Python @code{leidenalg} module to be called
15473 in R. It enables clustering using the Leiden algorithm for partitioning a
15474 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15475 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15476 (license license:gpl3)))
15478 (define-public r-patchwork
15479 ;; There has been no public release yet.
15480 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15483 (name "r-patchwork")
15484 (version (git-version "0.0.1" revision commit))
15488 (uri (git-reference
15489 (url "https://github.com/thomasp85/patchwork.git")
15491 (file-name (git-file-name name version))
15494 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15495 (build-system r-build-system)
15497 `(("r-ggplot2" ,r-ggplot2)
15498 ("r-gtable" ,r-gtable)))
15499 (home-page "https://github.com/thomasp85/patchwork")
15500 (synopsis "Compose ggplot2 plots")
15502 "The @code{ggplot2} package provides a strong API for sequentially
15503 building up a plot, but does not concern itself with composition of multiple
15504 plots. Patchwork is a package that expands the API to allow for arbitrarily
15505 complex composition of plots by providing mathmatical operators for combining
15507 (license license:expat))))
15509 (define-public r-liger
15516 (uri (git-reference
15517 (url "https://github.com/MacoskoLab/liger.git")
15518 (commit (string-append "v" version))))
15519 (file-name (git-file-name name version))
15522 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15523 (modules '((guix build utils)))
15526 (delete-file "inst/java/ModularityOptimizer.jar")
15528 (build-system r-build-system)
15531 (modify-phases %standard-phases
15532 (add-after 'unpack 'build-java-part
15533 (lambda* (#:key inputs #:allow-other-keys)
15534 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15535 (for-each (lambda (file) (invoke "javac" file))
15536 (find-files "." "\\.java$"))
15537 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15538 (find-files "." "\\.class$"))
15541 `(("r-cowplot" ,r-cowplot)
15542 ("r-dosnow" ,r-dosnow)
15543 ("r-dplyr" ,r-dplyr)
15545 ("r-foreach" ,r-foreach)
15546 ("r-ggplot2" ,r-ggplot2)
15547 ("r-ggrepel" ,r-ggrepel)
15548 ("r-hmisc" ,r-hmisc)
15550 ("r-irlba" ,r-irlba)
15551 ("r-matrix" ,r-matrix)
15552 ("r-mclust" ,r-mclust)
15553 ("r-patchwork" ,r-patchwork)
15555 ("r-rann-l1" ,r-rann-l1)
15557 ("r-rcpparmadillo" ,r-rcpparmadillo)
15558 ("r-riverplot" ,r-riverplot)
15559 ("r-rtsne" ,r-rtsne)
15560 ("r-snow" ,r-snow)))
15562 `(("jdk" ,icedtea "jdk")
15563 ;; See https://github.com/MacoskoLab/liger/issues/96
15564 ;; The optimizer is released under the Expat license.
15568 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15571 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15573 ("r-knitr" ,r-knitr))) ; for vignettes
15574 (home-page "https://github.com/MacoskoLab/liger")
15575 (synopsis "Integrate and analyze multiple single-cell datasets")
15577 "LIGER is a package for integrating and analyzing multiple single-cell
15578 datasets, developed and maintained by the Macosko lab. It relies on
15579 integrative non-negative matrix factorization to identify shared and
15580 dataset-specific factors.")
15581 (license license:gpl3)))
15583 (define-public r-harmony
15584 ;; There are no tagged commits
15585 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15589 (version (git-version "1.0" revision commit))
15593 (uri (git-reference
15594 (url "https://github.com/immunogenomics/harmony")
15596 (file-name (git-file-name name version))
15599 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15600 (build-system r-build-system)
15602 `(("r-cowplot" ,r-cowplot)
15603 ("r-dplyr" ,r-dplyr)
15604 ("r-ggplot2" ,r-ggplot2)
15605 ("r-irlba" ,r-irlba)
15606 ("r-matrix" ,r-matrix)
15608 ("r-rcpparmadillo" ,r-rcpparmadillo)
15609 ("r-rcppprogress" ,r-rcppprogress)
15610 ("r-rlang" ,r-rlang)
15611 ("r-tibble" ,r-tibble)
15612 ("r-tidyr" ,r-tidyr)))
15613 (home-page "https://github.com/immunogenomics/harmony")
15614 (synopsis "Integration of single cell sequencing data")
15616 "This package provides an implementation of the Harmony algorithm for
15617 single cell integration, described in Korsunsky et al
15618 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15619 function and interfaces to external frameworks.")
15620 (license license:gpl3))))
15622 (define-public r-covr
15629 (uri (cran-uri "covr" version))
15631 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15632 (properties `((upstream-name . "covr")))
15633 (build-system r-build-system)
15635 `(("r-crayon" ,r-crayon)
15636 ("r-digest" ,r-digest)
15638 ("r-jsonlite" ,r-jsonlite)
15640 ("r-withr" ,r-withr)
15641 ("r-yaml" ,r-yaml)))
15642 (home-page "https://github.com/r-lib/covr")
15643 (synopsis "Test coverage for R packages")
15645 "Thisp package enables you to track and report code coverage for your
15646 package and (optionally) upload the results to a coverage service. Code
15647 coverage is a measure of the amount of code being exercised by a set of tests.
15648 It is an indirect measure of test quality and completeness. This package is
15649 compatible with any testing methodology or framework and tracks coverage of
15650 both R code and compiled C/C++/FORTRAN code.")
15651 (license license:gpl3)))
15653 (define-public r-systemfonts
15655 (name "r-systemfonts")
15660 (uri (cran-uri "systemfonts" version))
15663 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15664 (properties `((upstream-name . "systemfonts")))
15665 (build-system r-build-system)
15667 `(("fontconfig" ,fontconfig)
15668 ("freetype" ,freetype)
15671 `(("pkg-config" ,pkg-config)))
15672 (home-page "https://github.com/r-lib/systemfonts")
15673 (synopsis "System native font finding")
15675 "This package provides system native access to the font catalogue. As
15676 font handling varies between systems it is difficult to correctly locate
15677 installed fonts across different operating systems. The 'systemfonts' package
15678 provides bindings to the native libraries for finding font files that can then
15679 be used further by e.g. graphic devices.")
15680 (license license:expat)))
15682 (define-public r-graphlayouts
15684 (name "r-graphlayouts")
15689 (uri (cran-uri "graphlayouts" version))
15692 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15693 (properties `((upstream-name . "graphlayouts")))
15694 (build-system r-build-system)
15696 `(("r-igraph" ,r-igraph)
15698 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15699 (home-page "https://github.com/schochastics/graphlayouts")
15700 (synopsis "Additional layout algorithms for network visualizations")
15702 "This package provides several layout algorithms to visualize networks
15703 which are not part of the igraph library. Most are based on the concept of
15704 stress majorization by Gansner et al. (2004)
15705 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15706 emphasize hidden group structures in networks or focus on specific nodes.")
15707 (license license:expat)))
15709 (define-public r-tidygraph
15711 (name "r-tidygraph")
15716 (uri (cran-uri "tidygraph" version))
15719 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15720 (properties `((upstream-name . "tidygraph")))
15721 (build-system r-build-system)
15723 `(("r-dplyr" ,r-dplyr)
15724 ("r-igraph" ,r-igraph)
15725 ("r-magrittr" ,r-magrittr)
15726 ("r-pillar" ,r-pillar)
15729 ("r-rlang" ,r-rlang)
15730 ("r-tibble" ,r-tibble)
15731 ("r-tidyr" ,r-tidyr)))
15732 (home-page "https://github.com/thomasp85/tidygraph")
15733 (synopsis "Tidy API for graph manipulation")
15735 "This package provides a graph implementation that can be thought of as
15736 two tidy data frames describing node and edge data respectively. It provides
15737 an approach to manipulate these two virtual data frames using the API defined
15738 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15739 common graph algorithms.")
15740 (license license:expat)))
15742 (define-public r-soupx
15743 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15747 (version (git-version "0.3.1" revision commit))
15751 (uri (git-reference
15752 (url "https://github.com/constantAmateur/SoupX")
15754 (file-name (git-file-name name version))
15757 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15758 (properties `((upstream-name . "SoupX")))
15759 (build-system r-build-system)
15761 `(("r-ggplot2" ,r-ggplot2)
15762 ("r-matrix" ,r-matrix)
15763 ("r-seurat" ,r-seurat)))
15764 (home-page "https://github.com/constantAmateur/SoupX")
15765 (synopsis "Single cell mRNA Soup eXterminator")
15767 "This package provides a package for quantifying, profiling and
15768 removing cell free mRNA contamination (the \"soup\") from droplet based single
15769 cell RNA-seq experiments.")
15770 (license license:gpl2))))
15772 (define-public r-assertr
15779 (uri (cran-uri "assertr" version))
15782 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15783 (build-system r-build-system)
15785 `(("r-dplyr" ,r-dplyr)
15787 ("r-rlang" ,r-rlang)))
15789 `(("r-knitr" ,r-knitr))) ; needed for vignette
15790 (home-page "https://github.com/ropensci/assertr")
15791 (synopsis "Assertive programming for R analysis pipelines")
15793 "This package provides functionality to assert conditions that have to be
15794 met so that errors in data used in analysis pipelines can fail quickly. It is
15795 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15797 (license license:expat)))
15799 (define-public r-parameters
15801 (name "r-parameters")
15806 (uri (cran-uri "parameters" version))
15809 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15810 (properties `((upstream-name . "parameters")))
15811 (build-system r-build-system)
15813 `(("r-bayestestr" ,r-bayestestr)
15814 ("r-insight" ,r-insight)))
15815 (home-page "https://cran.r-project.org/web/packages/parameters")
15816 (synopsis "Processing of model parameters")
15818 "This package provides utilities for processing the parameters of various
15819 statistical models. Beyond computing p values, CIs, and other indices for a
15820 wide variety of models, this package implements features like standardization
15821 or bootstrapping of parameters and models, feature reduction (feature
15822 extraction and variable selection) as well as conversion between indices of
15824 (license license:gpl3)))
15826 (define-public r-rgdal
15833 (uri (cran-uri "rgdal" version))
15835 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15836 (properties `((upstream-name . "rgdal")))
15837 (build-system r-build-system)
15845 `(("pkg-config" ,pkg-config)))
15846 (home-page "http://rgdal.r-forge.r-project.org")
15847 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15849 "This package provides bindings to the Geospatial Data Abstraction
15850 Library (GDAL) and access to projection/transformation operations from the
15852 (license license:gpl2+)))
15854 (define-public r-insol
15861 (uri (cran-uri "insol" version))
15864 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
15865 (properties `((upstream-name . "insol")))
15866 (build-system r-build-system)
15868 `(("r-raster" ,r-raster)
15869 ("r-rgdal" ,r-rgdal)))
15871 `(("gfortran" ,gfortran)))
15872 (home-page "https://meteoexploration.com/R/insol/index.html")
15873 (synopsis "Tools for calculating solar radiation")
15875 "This package provides functions to compute insolation on tilted
15876 surfaces, computes atmospheric transmittance and related parameters such as:
15877 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15878 time, vector in the direction of the sun, vector normal to surface, and some
15879 atmospheric physics.")
15880 (license license:gpl2+)))
15882 (define-public r-lifecycle
15884 (name "r-lifecycle")
15889 (uri (cran-uri "lifecycle" version))
15892 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15893 (properties `((upstream-name . "lifecycle")))
15894 (build-system r-build-system)
15896 `(("r-glue" ,r-glue)
15897 ("r-rlang" ,r-rlang)))
15898 (home-page "https://github.com/r-lib/lifecycle")
15899 (synopsis "Manage the life cycle of your package functions")
15901 "Manage the life cycle of your exported functions with shared
15902 conventions, documentation badges, and non-invasive deprecation warnings. The
15903 lifecycle package defines four development stages (experimental, maturing,
15904 stable, and questioning) and three deprecation stages (soft-deprecated,
15905 deprecated, and defunct). It makes it easy to insert badges corresponding to
15906 these stages in your documentation. Usage of deprecated functions are
15907 signalled with increasing levels of non-invasive verbosity.")
15908 (license license:gpl3)))
15910 (define-public r-assertable
15912 (name "r-assertable")
15917 (uri (cran-uri "assertable" version))
15920 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15921 (build-system r-build-system)
15923 `(("r-data-table" ,r-data-table)))
15924 (home-page "https://cran.r-project.org/web/packages/assertable/")
15925 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15926 (description "This package provides simple, flexible assertions on
15927 data.frame or data.table objects with verbose output for vetting. While other
15928 assertion packages apply towards more general use-cases, @code{assertable} is
15929 tailored towards tabular data. It includes functions to check variable names
15930 and values, whether the dataset contains all combinations of a given set of
15931 unique identifiers, and whether it is a certain length. In addition,
15932 @code{assertable} includes utility functions to check the existence of target
15933 files and to efficiently import multiple tabular data files into one
15935 (license license:gpl3)))
15937 (define-public r-quadprog
15939 (name "r-quadprog")
15944 (uri (cran-uri "quadprog" version))
15946 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
15947 (build-system r-build-system)
15949 `(("gfortran" ,gfortran)))
15950 (home-page "https://cran.r-project.org/web/packages/quadprog")
15951 (synopsis "Functions to solve quadratic programming problems")
15953 "This package contains routines and documentation for solving quadratic
15954 programming problems.")
15955 (license license:gpl3+)))
15957 (define-public r-desolve
15964 (uri (cran-uri "deSolve" version))
15966 (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
15967 (properties `((upstream-name . "deSolve")))
15968 (build-system r-build-system)
15970 `(("gfortran" ,gfortran)))
15971 (home-page "https://desolve.r-forge.r-project.org/")
15972 (synopsis "Solvers for initial value problems of differential equations")
15973 (description "This package provides functions that solve initial value
15974 problems of a system of first-order @dfn{ordinary differential
15975 equations} (ODE), of @dfn{partial differential equations} (PDE), of
15976 @dfn{differential algebraic equations} (DAE), and of delay differential
15977 equations. The functions provide an interface to the FORTRAN functions
15978 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
15979 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
15980 C-implementation of solvers of the Runge-Kutta family with fixed or variable
15981 time steps. The package contains routines designed for solving ODEs resulting
15982 from 1-D, 2-D and 3-D partial differential equations that have been converted
15983 to ODEs by numerical differencing.")
15984 (license license:gpl2+)))
15986 (define-public r-pracma
15992 (uri (cran-uri "pracma" version))
15994 (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
15995 (build-system r-build-system)
15996 (home-page "https://cran.r-project.org/web/packages/pracma/")
15997 (synopsis "Practical numerical math functions")
15998 (description "This package provides functions for numerical analysis and
15999 linear algebra, numerical optimization, differential equations, plus some
16000 special functions. It uses Matlab function names where appropriate to simplify
16002 (license license:gpl3+)))
16004 (define-public r-subplex
16011 (uri (cran-uri "subplex" version))
16014 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
16015 (build-system r-build-system)
16017 `(("gfortran" ,gfortran)))
16018 (home-page "https://cran.r-project.org/web/packages/subplex")
16019 (synopsis "Unconstrained optimization using the subplex algorithm")
16021 "This package implements the Subplex optimization algorithm.
16022 It solves unconstrained optimization problems using a simplex method on
16023 subspaces. The method is well suited for optimizing objective functions that
16024 are noisy or are discontinuous at the solution.")
16025 (license license:gpl3+)))
16027 (define-public r-txtplot
16034 (uri (cran-uri "txtplot" version))
16037 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16038 (build-system r-build-system)
16039 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16040 (synopsis "Text-based plotting")
16041 (description "This package provides functions to produce rudimentary ASCII
16042 graphics directly in the terminal window. This package provides a basic
16043 plotting function (and equivalents of curve, density, acf and barplot) as well
16044 as a boxplot function.")
16045 (license license:lgpl3+)))
16047 (define-public r-bio3d
16054 (uri (cran-uri "bio3d" version))
16057 "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
16058 (properties `((upstream-name . "bio3d")))
16059 (build-system r-build-system)
16060 (inputs `(("zlib" ,zlib)))
16061 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16062 (home-page "http://thegrantlab.org/bio3d/")
16063 (synopsis "Biological structure analysis")
16065 "This package provides utilities to process, organize and explore protein
16066 structure, sequence and dynamics data. Features include the ability to read
16067 and write structure, sequence and dynamic trajectory data, perform sequence
16068 and structure database searches, data summaries, atom selection, alignment,
16069 superposition, rigid core identification, clustering, torsion analysis,
16070 distance matrix analysis, structure and sequence conservation analysis, normal
16071 mode analysis, principal component analysis of heterogeneous structure data,
16072 and correlation network analysis from normal mode and molecular dynamics data.
16073 In addition, various utility functions are provided to enable the statistical
16074 and graphical power of the R environment to work with biological sequence and
16076 (license license:gpl2+)))
16078 (define-public r-bios2cor
16080 (name "r-bios2cor")
16085 (uri (cran-uri "Bios2cor" version))
16088 "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
16089 (properties `((upstream-name . "Bios2cor")))
16090 (build-system r-build-system)
16092 `(("r-bigmemory" ,r-bigmemory)
16093 ("r-bio3d" ,r-bio3d)
16094 ("r-circular" ,r-circular)
16095 ("r-igraph" ,r-igraph)))
16096 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16097 (synopsis "From biological sequences and simulations to correlation analysis")
16099 "This package provides utilities for computation and analysis of
16100 correlation/covariation in multiple sequence alignments and in side chain
16101 motions during molecular dynamics simulations. Features include the
16102 computation of correlation/covariation scores using a variety of scoring
16103 functions between either sequence positions in alignments or side chain
16104 dihedral angles in molecular dynamics simulations and utilities to analyze the
16105 correlation/covariation matrix through a variety of tools including network
16106 representation and principal components analysis. In addition, several
16107 utility functions are based on the R graphical environment to provide friendly
16108 tools for help in data interpretation.")
16109 (license license:gpl2+)))
16111 ;; This package includes minified JavaScript files. When upgrading please
16112 ;; check that there are no new minified JavaScript files.
16113 (define-public r-networkd3
16115 (name "r-networkd3")
16120 (uri (cran-uri "networkD3" version))
16123 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16126 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16128 (properties `((upstream-name . "networkD3")))
16129 (build-system r-build-system)
16131 `(#:modules ((guix build utils)
16132 (guix build r-build-system)
16136 (modify-phases %standard-phases
16137 (add-after 'unpack 'process-javascript
16138 (lambda* (#:key inputs #:allow-other-keys)
16139 (with-directory-excursion "inst/htmlwidgets/lib/"
16143 `((,(assoc-ref inputs "d3.v4.js")
16144 "d3-4.5.0/d3.min.js"))))
16145 (lambda (sources targets)
16146 (for-each (lambda (source target)
16147 (format #t "Processing ~a --> ~a~%"
16149 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16150 (call-with-output-file target
16152 (dump-port minified port)))))
16153 sources targets))))
16156 `(("uglify-js" ,uglify-js)
16157 ;; NOTE: Make sure that this version of d3 is still valid when
16158 ;; upgrading the package.
16162 (uri "https://d3js.org/d3.v4.js")
16165 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16167 `(("r-htmlwidgets" ,r-htmlwidgets)
16168 ("r-igraph" ,r-igraph)
16169 ("r-magrittr" ,r-magrittr)))
16170 (home-page "https://cran.r-project.org/package=networkD3")
16171 (synopsis "D3 JavaScript network graphs from R")
16173 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16175 (license license:gpl3+)))
16177 (define-public r-aasea
16184 (uri (cran-uri "aaSEA" version))
16187 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16188 (properties `((upstream-name . "aaSEA")))
16189 (build-system r-build-system)
16191 `(("r-bios2cor" ,r-bios2cor)
16193 ("r-hmisc" ,r-hmisc)
16194 ("r-magrittr" ,r-magrittr)
16195 ("r-networkd3" ,r-networkd3)
16196 ("r-plotly" ,r-plotly)
16197 ("r-seqinr" ,r-seqinr)
16198 ("r-shiny" ,r-shiny)
16199 ("r-shinydashboard" ,r-shinydashboard)))
16200 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16201 (synopsis "Amino acid substitution effect analyzer")
16203 "Given a protein multiple sequence alignment, it is a daunting task to
16204 assess the effects of substitutions along sequence length. The aaSEA package
16205 is intended to help researchers to rapidly analyze property changes caused by
16206 single, multiple and correlated amino acid substitutions in proteins.")
16207 (license license:gpl3)))
16209 (define-public r-abacus
16216 (uri (cran-uri "ABACUS" version))
16219 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16220 (properties `((upstream-name . "ABACUS")))
16221 (build-system r-build-system)
16223 `(("r-ggplot2" ,r-ggplot2)
16224 ("r-shiny" ,r-shiny)))
16225 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16226 (synopsis "Apps-based activities for communicating and understanding statistics")
16228 "This package provides a set of Shiny apps for effective communication
16229 and understanding in statistics. The current version includes properties of
16230 normal distribution, properties of sampling distribution, one-sample z and t
16231 tests, two samples independent (unpaired) t test and analysis of variance.")
16232 (license license:gpl3)))
16234 (define-public r-abc-rap
16241 (uri (cran-uri "ABC.RAP" version))
16244 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16245 (properties `((upstream-name . "ABC.RAP")))
16246 (build-system r-build-system)
16247 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16248 (synopsis "Array-based CpG region analysis pipeline")
16250 "This package aims to identify candidate genes that are differentially
16251 methylated between cases and controls. It applies Student's t-test and delta
16252 beta analysis to identify candidate genes containing multiple CpG sites.")
16253 (license license:gpl3)))
16255 (define-public r-abcadm
16262 (uri (cran-uri "abcADM" version))
16265 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16266 (properties `((upstream-name . "abcADM")))
16267 (build-system r-build-system)
16270 ("r-rcpp" ,r-rcpp)))
16271 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16272 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16274 "This package provides tools to estimate parameters of accumulated
16275 damage (load duration) models based on failure time data under a Bayesian
16276 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16277 long-term reliability under stochastic load profiles.")
16278 (license license:gpl3)))
16280 (define-public r-rglpk
16287 (uri (cran-uri "Rglpk" version))
16290 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16291 (properties `((upstream-name . "Rglpk")))
16292 (build-system r-build-system)
16294 `(("r-slam" ,r-slam)))
16297 (home-page "http://R-Forge.R-project.org/projects/rglp/")
16298 (synopsis "R interface to the GNU Linear Programming Kit")
16300 "This package provides an R interface to the GNU Linear Programming Kit,
16301 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16302 integer linear programming} (MILP) and other related problems.")
16304 (license (list license:gpl2 license:gpl3))))
16306 (define-public r-abcdefba
16308 (name "r-abcdefba")
16313 (uri (cran-uri "abcdeFBA" version))
16316 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16317 (properties `((upstream-name . "abcdeFBA")))
16318 (build-system r-build-system)
16320 `(("r-corrplot" ,r-corrplot)
16321 ("r-lattice" ,r-lattice)
16323 ("r-rglpk" ,r-rglpk)))
16324 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16325 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16327 "This package provides functions for Constraint Based Simulation using
16328 Flux Balance Analysis and informative analysis of the data generated during
16330 (license license:gpl2)))
16332 (define-public r-abcrlda
16339 (uri (cran-uri "abcrlda" version))
16342 "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
16343 (properties `((upstream-name . "abcrlda")))
16344 (build-system r-build-system)
16345 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16346 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16348 "This package offers methods to perform @dfn{asymptotically
16349 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16350 cost-sensitive binary classification. The bias-correction is an estimate of
16351 the bias term added to regularized discriminant analysis that minimizes the
16353 (license license:gpl3)))
16355 (define-public r-abemus
16362 (uri (cran-uri "abemus" version))
16365 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16366 (properties `((upstream-name . "abemus")))
16367 (build-system r-build-system)
16369 `(("r-data-table" ,r-data-table)))
16370 (home-page "https://cran.r-project.org/web/packages/abemus/")
16371 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16373 "This package provides an implementation of @dfn{Adaptive Base Error
16374 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16375 platform-specific genetic knowledge and empirical signal to readily detect and
16376 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16377 cell free DNA} (cfDNA).")
16378 (license license:gpl3)))
16380 ;; This package includes minified JavaScript files. When upgrading please
16381 ;; check that there are no new minified JavaScript files.
16382 (define-public r-rintrojs
16384 (name "r-rintrojs")
16389 (uri (cran-uri "rintrojs" version))
16392 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16393 (properties `((upstream-name . "rintrojs")))
16394 (build-system r-build-system)
16396 `(#:modules ((guix build utils)
16397 (guix build r-build-system)
16401 (modify-phases %standard-phases
16402 (add-after 'unpack 'process-javascript
16403 (lambda* (#:key inputs #:allow-other-keys)
16404 (with-directory-excursion "inst/javascript/introjs/"
16408 `((,(assoc-ref inputs "intro.js")
16410 (lambda (sources targets)
16411 (for-each (lambda (source target)
16412 (format #t "Processing ~a --> ~a~%"
16414 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16415 (call-with-output-file target
16417 (dump-port minified port)))))
16418 sources targets))))
16421 `(("uglify-js" ,uglify-js)
16425 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16428 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16430 `(("r-jsonlite" ,r-jsonlite)
16431 ("r-shiny" ,r-shiny)))
16432 (home-page "https://github.com/carlganz/rintrojs")
16433 (synopsis "Wrapper for the Intro.js library")
16435 "This package provides a wrapper for the @url{http://www.introjs.com,
16436 Intro.js} library. This package makes it easy to include step-by-step
16437 introductions, and clickable hints in a Shiny application. It supports both
16438 static introductions in the UI, and programmatic introductions from the
16440 (license license:agpl3+)))
16442 (define-public r-sysfonts
16444 (name "r-sysfonts")
16449 (uri (cran-uri "sysfonts" version))
16452 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16453 (properties `((upstream-name . "sysfonts")))
16454 (build-system r-build-system)
16456 `(("freetype" ,freetype)
16460 `(("pkg-config" ,pkg-config)))
16461 (home-page "https://github.com/yixuan/sysfonts")
16462 (synopsis "Loading fonts into R")
16464 "This is a package to simplify loading of system fonts and Google Fonts
16465 into R, in order to support other packages.")
16466 (license license:gpl2)))
16468 (define-public r-showtextdb
16470 (name "r-showtextdb")
16475 (uri (cran-uri "showtextdb" version))
16478 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16479 (properties `((upstream-name . "showtextdb")))
16480 (build-system r-build-system)
16482 `(("r-sysfonts" ,r-sysfonts)))
16483 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16484 (synopsis "Font files for the 'showtext' package")
16486 "This package provides font files that can be used by the @code{showtext}
16488 (license license:asl2.0)))
16490 (define-public r-showtext
16492 (name "r-showtext")
16497 (uri (cran-uri "showtext" version))
16500 "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
16501 (properties `((upstream-name . "showtext")))
16502 (build-system r-build-system)
16504 `(("freetype" ,freetype)
16508 `(("r-showtextdb" ,r-showtextdb)
16509 ("r-sysfonts" ,r-sysfonts)))
16510 (native-inputs `(("pkg-config" ,pkg-config)))
16511 (home-page "https://github.com/yixuan/showtext")
16512 (synopsis "Using fonts more easily in R graphs")
16514 "This package aims to make it easy to use various types of
16515 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16516 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16517 will be converted into polygons or raster images, hence after the plot has
16518 been created, it no longer relies on the font files. No external software
16519 such as Ghostscript is needed to use this package.")
16520 (license license:asl2.0)))
16522 (define-public r-emojifont
16524 (name "r-emojifont")
16529 (uri (cran-uri "emojifont" version))
16532 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16533 (properties `((upstream-name . "emojifont")))
16534 (build-system r-build-system)
16536 `(("r-ggplot2" ,r-ggplot2)
16537 ("r-proto" ,r-proto)
16538 ("r-showtext" ,r-showtext)
16539 ("r-sysfonts" ,r-sysfonts)))
16540 (home-page "https://guangchuangyu.github.io/emojifont")
16541 (synopsis "Emoji and Font Awesome in R graphics")
16543 "This package enables the use of emoji and the Font Awesome glyphs in
16544 both base and ggplot2 graphics.")
16545 (license license:artistic2.0)))
16547 (define-public r-abstractr
16549 (name "r-abstractr")
16554 (uri (cran-uri "abstractr" version))
16557 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16558 (properties `((upstream-name . "abstractr")))
16559 (build-system r-build-system)
16561 `(("r-colourpicker" ,r-colourpicker)
16562 ("r-emojifont" ,r-emojifont)
16563 ("r-ggplot2" ,r-ggplot2)
16564 ("r-gridextra" ,r-gridextra)
16565 ("r-rintrojs" ,r-rintrojs)
16566 ("r-shiny" ,r-shiny)
16567 ("r-shinythemes" ,r-shinythemes)))
16568 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16569 (synopsis "R-Shiny application for creating visual abstracts")
16571 "This package provides an R Shiny application to create visual abstracts
16572 for original research. A variety of user defined options and formatting are
16574 (license license:gpl3)))
16576 (define-public r-abtest
16583 (uri (cran-uri "abtest" version))
16586 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16587 (properties `((upstream-name . "abtest")))
16588 (build-system r-build-system)
16590 `(("r-matrix" ,r-matrix)
16591 ("r-mvtnorm" ,r-mvtnorm)
16592 ("r-plotrix" ,r-plotrix)
16593 ("r-rcolorbrewer" ,r-rcolorbrewer)
16596 ("r-truncnorm" ,r-truncnorm)
16597 ("r-vgam" ,r-vgam)))
16598 (home-page "https://cran.r-project.org/web/packages/abtest/")
16599 (synopsis "Bayesian A/B testing")
16601 "This package provides functions for Bayesian A/B testing including prior
16602 elicitation options based on Kass and Vaidyanathan (1992)
16603 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16604 (license license:gpl2+)))
16606 (define-public r-accept
16613 (uri (cran-uri "accept" version))
16616 "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
16617 (properties `((upstream-name . "accept")))
16618 (build-system r-build-system)
16620 `(("r-dplyr" ,r-dplyr)
16621 ("r-extrafont" ,r-extrafont)
16623 ("r-plotly" ,r-plotly)
16624 ("r-stringr" ,r-stringr)
16625 ("r-viridis" ,r-viridis)))
16626 (home-page "https://cran.r-project.org/web/packages/accept/")
16627 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16629 "This package allows clinicians to predict the rate and severity of
16630 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16631 Disease} (COPD) patients, based on the clinical prediction model published in
16632 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16633 (license license:gpl3)))
16635 (define-public r-smpracticals
16637 (name "r-smpracticals")
16642 (uri (cran-uri "SMPracticals" version))
16645 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16646 (properties `((upstream-name . "SMPracticals")))
16647 (build-system r-build-system)
16649 `(("r-ellipse" ,r-ellipse)
16652 ("r-survival" ,r-survival)))
16653 (home-page "http://statwww.epfl.ch/davison/SM/")
16654 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16656 "This package contains the datasets and a few functions for use with the
16657 practicals outlined in Appendix A of the book Statistical Models (Davison,
16658 2003, Cambridge University Press). The practicals themselves can be found at
16659 @url{http://statwww.epfl.ch/davison/SM/}.")
16660 (license license:gpl2+)))
16662 (define-public r-fgui
16669 (uri (cran-uri "fgui" version))
16672 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16673 (properties `((upstream-name . "fgui")))
16674 (build-system r-build-system)
16676 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16677 (synopsis "Create GUI for R functions")
16679 "Rapidly create a GUI for a function you created by automatically
16680 creating widgets for arguments of the function. This package automatically
16681 parses help routines for context-sensitive help to these arguments. The
16682 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16683 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16684 incorporated into the interface for greater customization for the more
16686 ;; Any version of the GPL.
16687 (license (list license:gpl2+ license:gpl3+))))
16689 (define-public r-tcltk2
16696 (uri (cran-uri "tcltk2" version))
16699 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16700 (properties `((upstream-name . "tcltk2")))
16701 (build-system r-build-system)
16705 (home-page "http://www.sciviews.org/SciViews-R")
16706 (synopsis "Tcl/Tk additions")
16708 "This package provides a series of additional Tcl commands and Tk widgets
16709 with style and various functions to supplement the tcltk package")
16710 (license license:lgpl3)))
16712 (define-public r-accrual
16719 (uri (cran-uri "accrual" version))
16722 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16723 (properties `((upstream-name . "accrual")))
16724 (build-system r-build-system)
16726 `(("r-fgui" ,r-fgui)
16727 ("r-smpracticals" ,r-smpracticals)
16728 ("r-tcltk2" ,r-tcltk2)))
16729 (home-page "https://cran.r-project.org/web/packages/accrual/")
16730 (synopsis "Bayesian accrual prediction")
16732 "Subject recruitment for medical research is challenging. Slow patient
16733 accrual leads to delay in research. Accrual monitoring during the process of
16734 recruitment is critical. Researchers need reliable tools to manage the
16735 accrual rate. This package provides an implementation of a Bayesian method
16736 that integrates researcher's experience on previous trials and data from the
16737 current study, providing reliable prediction on accrual rate for clinical
16738 studies. It provides functions for Bayesian accrual prediction which can be
16739 easily used by statisticians and clinical researchers.")
16740 (license license:gpl2)))
16742 (define-public r-accrued
16749 (uri (cran-uri "accrued" version))
16752 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16753 (properties `((upstream-name . "accrued")))
16754 (build-system r-build-system)
16755 (home-page "https://cran.r-project.org/web/packages/accrued/")
16756 (synopsis "Data quality visualization tools for partially accruing data")
16758 "This is a package for visualizing data quality of partially accruing
16760 (license license:gpl3)))
16762 (define-public r-mda
16769 (uri (cran-uri "mda" version))
16772 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16773 (properties `((upstream-name . "mda")))
16774 (build-system r-build-system)
16775 (propagated-inputs `(("r-class" ,r-class)))
16776 (native-inputs `(("gfortran" ,gfortran)))
16777 (home-page "https://cran.r-project.org/web/packages/mda/")
16778 (synopsis "Mixture and flexible discriminant analysis")
16780 "This is a package for mixture and flexible discriminant analysis,
16781 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16782 (license license:gpl2)))
16784 (define-public r-elasticnet
16786 (name "r-elasticnet")
16791 (uri (cran-uri "elasticnet" version))
16794 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16795 (properties `((upstream-name . "elasticnet")))
16796 (build-system r-build-system)
16798 `(("r-lars" ,r-lars)))
16799 (home-page "http://www.stat.umn.edu/~hzou")
16800 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16802 "This package provides functions for fitting the entire solution path of
16803 the Elastic-Net and also provides functions for estimating sparse Principal
16804 Components. The Lasso solution paths can be computed by the same function.")
16805 (license license:gpl2+)))
16807 (define-public r-sparselda
16809 (name "r-sparselda")
16814 (uri (cran-uri "sparseLDA" version))
16817 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16818 (properties `((upstream-name . "sparseLDA")))
16819 (build-system r-build-system)
16821 `(("r-elasticnet" ,r-elasticnet)
16824 (home-page "http://www.imm.dtu.dk/~lhc")
16825 (synopsis "Sparse discriminant analysis")
16827 "This package performs sparse linear discriminant analysis for Gaussians
16828 and mixture of Gaussian models.")
16829 (license license:gpl2+)))
16831 (define-public r-accsda
16838 (uri (cran-uri "accSDA" version))
16841 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
16842 (properties `((upstream-name . "accSDA")))
16843 (build-system r-build-system)
16845 `(("r-ggplot2" ,r-ggplot2)
16846 ("r-ggthemes" ,r-ggthemes)
16847 ("r-gridextra" ,r-gridextra)
16849 ("r-rarpack" ,r-rarpack)
16850 ("r-sparselda" ,r-sparselda)))
16851 (home-page "https://github.com/gumeo/accSDA/wiki")
16852 (synopsis "Accelerated sparse discriminant analysis")
16854 "This package provides an implementation of sparse linear discriminant
16855 analysis, which is a supervised classification method for multiple classes.
16856 Various novel optimization approaches to this problem are implemented
16857 including @dfn{alternating direction method of multipliers} (ADMM),
16858 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
16859 Functions for performing cross validation are also supplied along with basic
16860 prediction and plotting functions. @dfn{Sparse zero variance
16861 discriminant} (SZVD) analysis is also included in the package.")
16862 (license license:gpl2+)))
16864 (define-public r-ace2fastq
16866 (name "r-ace2fastq")
16871 (uri (cran-uri "ace2fastq" version))
16874 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
16875 (properties `((upstream-name . "ace2fastq")))
16876 (build-system r-build-system)
16878 `(("r-stringr" ,r-stringr)))
16879 (home-page "https://github.com/c5sire/ace2fastq")
16880 (synopsis "ACE file to FASTQ converter")
16882 "The ACE file format is used in genomics to store contigs from sequencing
16883 machines. This tools converts it into FASTQ format. Both formats contain the
16884 sequence characters and their corresponding quality information. Unlike the
16885 FASTQ file, the ACE file stores the quality values numerically. The
16886 conversion algorithm uses the standard Sanger formula. The package
16887 facilitates insertion into pipelines, and content inspection.")
16888 (license license:gpl3)))
16890 (define-public r-rngwell
16897 (uri (cran-uri "rngWELL" version))
16900 "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
16901 (properties `((upstream-name . "rngWELL")))
16902 (build-system r-build-system)
16903 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
16904 (synopsis "Toolbox for WELL random number generators")
16906 "This is a dedicated package to WELL pseudo random generators, which were
16907 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
16908 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
16909 (license license:bsd-3)))
16911 (define-public r-randtoolbox
16913 (name "r-randtoolbox")
16918 (uri (cran-uri "randtoolbox" version))
16921 "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd"))))
16922 (properties `((upstream-name . "randtoolbox")))
16923 (build-system r-build-system)
16925 `(("r-rngwell" ,r-rngwell)))
16927 `(("gfortran" ,gfortran)))
16928 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
16929 (synopsis "Toolbox for pseudo and quasi random number generation")
16931 "This package provides
16934 @item pseudo random generators, such as general linear
16935 congruential generators, multiple recursive generators and generalized
16936 feedback shift register (SF-Mersenne Twister algorithm and WELL
16939 @item quasi random generators, such as the Torus algorithm, the Sobol
16940 sequence, the Halton sequence (including the Van der Corput sequence), and
16942 @item some generator tests: the gap test, the serial test, the poker test.
16945 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
16946 (license license:bsd-3)))
16948 (define-public r-lhs
16955 (uri (cran-uri "lhs" version))
16958 "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
16959 (properties `((upstream-name . "lhs")))
16960 (build-system r-build-system)
16961 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16962 (home-page "https://github.com/bertcarnell/lhs")
16963 (synopsis "Latin Hypercube Samples")
16965 "This package provides a number of methods for creating and augmenting
16966 Latin Hypercube Samples.")
16967 (license license:gpl3)))
16969 (define-public r-acebayes
16971 (name "r-acebayes")
16976 (uri (cran-uri "acebayes" version))
16979 "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln"))))
16980 (properties `((upstream-name . "acebayes")))
16981 (build-system r-build-system)
16983 `(("r-compare" ,r-compare)
16985 ("r-randtoolbox" ,r-randtoolbox)
16987 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16988 (home-page "https://cran.r-project.org/web/packages/acebayes/")
16989 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
16991 "Finding an optimal Bayesian experimental design involves maximizing an
16992 objective function given by the expectation of some appropriately chosen
16993 utility function with respect to the joint distribution of unknown
16994 quantities (including responses). This objective function is usually not
16995 available in closed form and the design space can be continuous and of high
16996 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
16997 to maximise an approximation to the expectation of the utility function.")
16998 (license license:gpl2)))
17000 (define-public r-acet
17007 (uri (cran-uri "ACEt" version))
17010 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17011 (properties `((upstream-name . "ACEt")))
17012 (build-system r-build-system)
17017 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17018 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17019 (synopsis "Estimating dynamic heritability and twin model comparison")
17021 "This package supports twin models that are able to estimate the dynamic
17022 behaviour of the variance components in the classical twin models with respect
17023 to age using B-splines and P-splines.")
17024 (license license:gpl2+)))
17026 (define-public r-acfmperiod
17028 (name "r-acfmperiod")
17033 (uri (cran-uri "acfMPeriod" version))
17036 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17037 (properties `((upstream-name . "acfMPeriod")))
17038 (build-system r-build-system)
17040 `(("r-mass" ,r-mass)))
17041 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17042 (synopsis "Estimation of the ACF from the M-periodogram")
17044 "This package support non-robust and robust computations of the sample
17045 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17046 univariate and multivariate processes. The methodology consists in reversing
17047 the diagonalization procedure involving the periodogram or the
17048 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17049 ACOVF or the ACF as discussed in Fuller (1995)
17050 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17051 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17052 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17053 (license license:gpl2+)))
17055 (define-public r-gamlss-data
17057 (name "r-gamlss-data")
17062 (uri (cran-uri "gamlss.data" version))
17065 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17066 (properties `((upstream-name . "gamlss.data")))
17067 (build-system r-build-system)
17068 (home-page "http://www.gamlss.org/")
17069 (synopsis "GAMLSS data")
17071 "This package provides data used as examples to demonstrate GAMLSS
17073 ;; Either version of the license
17074 (license (list license:gpl2 license:gpl3))))