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, 2019 Brett Gilio <brettg@posteo.net>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; This file is part of GNU Guix.
23 ;;; GNU Guix is free software; you can redistribute it and/or modify it
24 ;;; under the terms of the GNU General Public License as published by
25 ;;; the Free Software Foundation; either version 3 of the License, or (at
26 ;;; your option) any later version.
28 ;;; GNU Guix is distributed in the hope that it will be useful, but
29 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
30 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
31 ;;; GNU General Public License for more details.
33 ;;; You should have received a copy of the GNU General Public License
34 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
36 (define-module (gnu packages cran)
37 #:use-module ((guix licenses) #:prefix license:)
38 #:use-module (guix packages)
39 #:use-module (guix download)
40 #:use-module (guix git-download)
41 #:use-module (guix utils)
42 #:use-module (guix build-system r)
43 #:use-module (gnu packages algebra)
44 #:use-module (gnu packages base)
45 #:use-module (gnu packages bioinformatics)
46 #:use-module (gnu packages c)
47 #:use-module (gnu packages compression)
48 #:use-module (gnu packages curl)
49 #:use-module (gnu packages databases)
50 #:use-module (gnu packages fontutils)
51 #:use-module (gnu packages gcc)
52 #:use-module (gnu packages geo)
53 #:use-module (gnu packages ghostscript)
54 #:use-module (gnu packages gl)
55 #:use-module (gnu packages gnome)
56 #:use-module (gnu packages graph)
57 #:use-module (gnu packages gtk)
58 #:use-module (gnu packages haskell-xyz)
59 #:use-module (gnu packages icu4c)
60 #:use-module (gnu packages image)
61 #:use-module (gnu packages imagemagick)
62 #:use-module (gnu packages java)
63 #:use-module (gnu packages javascript)
64 #:use-module (gnu packages lisp)
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 tls)
77 #:use-module (gnu packages web)
78 #:use-module (gnu packages xorg))
80 (define-public r-clipr
87 (uri (cran-uri "clipr" version))
90 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
91 (build-system r-build-system)
92 (home-page "https://github.com/mdlincoln/clipr")
93 (synopsis "Read and write from the system clipboard")
95 "This package provides simple utility functions to read from and write to
96 the system clipboards.")
97 (license license:gpl3)))
99 (define-public r-scales
106 (uri (cran-uri "scales" version))
108 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
109 (build-system r-build-system)
111 `(("r-farver" ,r-farver)
112 ("r-labeling" ,r-labeling)
113 ("r-lifecycle" ,r-lifecycle)
114 ("r-munsell" ,r-munsell)
115 ("r-rcolorbrewer" ,r-rcolorbrewer)
117 ("r-viridislite" ,r-viridislite)))
118 (home-page "https://github.com/hadley/scales")
119 (synopsis "Scale functions for visualization")
121 "This package provides graphical scales that map data to aesthetics, and
122 provides methods for automatically determining breaks and labels for axes and
124 (license license:expat)))
126 (define-public r-pheatmap
133 (uri (cran-uri "pheatmap" version))
136 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
137 (build-system r-build-system)
139 `(("r-gtable" ,r-gtable)
140 ("r-rcolorbrewer" ,r-rcolorbrewer)
141 ("r-scales" ,r-scales)))
142 (home-page "https://cran.r-project.org/web/packages/pheatmap")
143 (synopsis "Pretty heatmaps")
145 "This package provides an implementation of heatmaps that offers more
146 control over dimensions and appearance.")
147 (license license:gpl2+)))
149 (define-public r-ellipsis
156 (uri (cran-uri "ellipsis" version))
159 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
160 (build-system r-build-system)
162 `(("r-rlang" ,r-rlang)))
163 (home-page "https://github.com/hadley/ellipsis")
164 (synopsis "Tools for working with additional arguments")
166 "In S3 generics, it's useful to take @code{...} so that methods can have
167 additional arguments. But this flexibility comes at a cost: misspelled
168 arguments will be silently ignored. The @code{ellipsis} package is an
169 experiment that allows a generic to warn if any arguments passed in @code{...}
171 (license license:gpl3)))
180 (uri (cran-uri "grr" version))
183 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
184 (build-system r-build-system)
185 (home-page "https://cran.r-project.org/web/packages/grr")
186 (synopsis "Alternative implementations of base R functions")
188 "This package provides alternative implementations of some base R
189 functions, including @code{sort}, @code{order}, and @code{match}. The
190 functions are simplified but can be faster or have other advantages.")
191 (license license:gpl3)))
193 (define-public r-matrix-utils
195 (name "r-matrix-utils")
200 (uri (cran-uri "Matrix.utils" version))
203 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
204 (properties `((upstream-name . "Matrix.utils")))
205 (build-system r-build-system)
208 ("r-matrix" ,r-matrix)))
209 (home-page "https://github.com/cvarrichio/Matrix.utils")
211 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
213 "This package implements data manipulation methods such as @code{cast},
214 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
216 (license license:gpl3)))
225 (uri (cran-uri "sys" version))
228 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
229 (build-system r-build-system)
230 (home-page "https://github.com/jeroen/sys")
231 (synopsis "Powerful and reliable tools for running system commands in R")
233 "This package provides drop-in replacements for the base @code{system2()}
234 function with fine control and consistent behavior across platforms. It
235 supports clean interruption, timeout, background tasks, and streaming STDIN /
236 STDOUT / STDERR over binary or text connections. The package also provides
237 functions for evaluating expressions inside a temporary fork. Such
238 evaluations have no side effects on the main R process, and support reliable
239 interrupts and timeouts. This provides the basis for a sandboxing
241 (license license:expat)))
243 (define-public r-askpass
250 (uri (cran-uri "askpass" version))
253 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
254 (build-system r-build-system)
255 (propagated-inputs `(("r-sys" ,r-sys)))
256 (home-page "https://github.com/jeroen/askpass")
257 (synopsis "Safe password entry for R")
259 "This package provides cross-platform utilities for prompting the user
260 for credentials or a passphrase, for example to authenticate with a server or
261 read a protected key.")
262 (license license:expat)))
264 (define-public r-vegan
271 (uri (cran-uri "vegan" version))
274 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
275 (build-system r-build-system)
277 `(("gfortran" ,gfortran)))
279 `(("r-cluster" ,r-cluster)
280 ("r-knitr" ,r-knitr) ; needed for vignettes
281 ("r-lattice" ,r-lattice)
284 ("r-permute" ,r-permute)))
285 (home-page "https://cran.r-project.org/web/packages/vegan")
286 (synopsis "Functions for community ecology")
288 "The vegan package provides tools for descriptive community ecology. It
289 has most basic functions of diversity analysis, community ordination and
290 dissimilarity analysis. Most of its multivariate tools can be used for other
291 data types as well.")
292 (license license:gpl2+)))
294 (define-public r-tidyverse
301 (uri (cran-uri "tidyverse" version))
304 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
305 (build-system r-build-system)
307 `(("r-broom" ,r-broom)
309 ("r-crayon" ,r-crayon)
310 ("r-dbplyr" ,r-dbplyr)
312 ("r-forcats" ,r-forcats)
313 ("r-ggplot2" ,r-ggplot2)
317 ("r-jsonlite" ,r-jsonlite)
318 ("r-lubridate" ,r-lubridate)
319 ("r-magrittr" ,r-magrittr)
320 ("r-modelr" ,r-modelr)
321 ("r-pillar" ,r-pillar)
324 ("r-readxl" ,r-readxl)
325 ("r-reprex" ,r-reprex)
327 ("r-rstudioapi" ,r-rstudioapi)
329 ("r-stringr" ,r-stringr)
330 ("r-tibble" ,r-tibble)
333 (home-page "https://tidyverse.tidyverse.org")
334 (synopsis "Install and load packages from the \"Tidyverse\"")
336 "The @code{tidyverse} is a set of packages that work in harmony because
337 they share common data representations and API design. This package is
338 designed to make it easy to install and load multiple tidyverse packages in a
340 (license license:gpl3)))
342 (define-public r-rvest
349 (uri (cran-uri "rvest" version))
351 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
352 (build-system r-build-system)
355 ("r-magrittr" ,r-magrittr)
356 ("r-selectr" ,r-selectr)
358 (home-page "https://github.com/hadley/rvest")
359 (synopsis "Simple web scraping for R")
361 "@code{r-rvest} helps you scrape information from web pages. It is
362 designed to work with @code{magrittr} to make it easy to express common web
363 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
364 (license license:gpl3)))
366 (define-public r-selectr
373 (uri (cran-uri "selectr" version))
375 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
376 (build-system r-build-system)
378 `(("r-stringr" ,r-stringr)
380 (home-page "https://sjp.co.nz/projects/selectr/")
381 (synopsis "Translate CSS selectors to XPath expressions")
383 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
384 expression. This allows you to use CSS selectors when working with the XML
385 package as it can only evaluate XPath expressions. Also provided are
386 convenience functions useful for using CSS selectors on XML nodes. This
387 package is a port of the Python package @code{cssselect}.")
388 (license license:bsd-3)))
390 (define-public r-reprex
397 (uri (cran-uri "reprex" version))
400 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
401 (build-system r-build-system)
403 `(("r-callr" ,r-callr)
407 ("r-rmarkdown" ,r-rmarkdown)
408 ("r-whisker" ,r-whisker)
409 ("r-withr" ,r-withr)))
410 (home-page "https://github.com/tidyverse/reprex")
411 (synopsis "Prepare reproducible R code examples for sharing")
413 "This package provides a convenience wrapper that uses the
414 @code{rmarkdown} package to render small snippets of code to target formats
415 that include both code and output. The goal is to encourage the sharing of
416 small, reproducible, and runnable examples on code-oriented websites or email.
417 @code{reprex} also extracts clean, runnable R code from various common formats,
418 such as copy/paste from an R session.")
419 (license license:expat)))
421 (define-public r-callr
428 (uri (cran-uri "callr" version))
431 "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh"))))
432 (build-system r-build-system)
435 ("r-processx" ,r-processx)))
436 (home-page "https://github.com/r-lib/callr#readme")
437 (synopsis "Call R from R")
439 "It is sometimes useful to perform a computation in a separate R process,
440 without affecting the current R process at all. This package does exactly
442 (license license:expat)))
444 (define-public r-readxl
451 (uri (cran-uri "readxl" version))
454 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
455 (build-system r-build-system)
457 `(("r-cellranger" ,r-cellranger)
458 ("r-progress" ,r-progress)
460 ("r-tibble" ,r-tibble)))
461 (home-page "https://readxl.tidyverse.org")
462 (synopsis "Read Excel files")
464 "This package lets you import Excel files into R. It supports
465 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
466 the embedded @code{RapidXML} C++ library.")
467 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
468 ;; 'rapidxml' which is Boost.
469 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
471 (define-public r-modelr
478 (uri (cran-uri "modelr" version))
481 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
482 (build-system r-build-system)
484 `(("r-broom" ,r-broom)
486 ("r-magrittr" ,r-magrittr)
489 ("r-tibble" ,r-tibble)
490 ("r-tidyr" ,r-tidyr)))
491 (home-page "https://github.com/tidyverse/modelr")
492 (synopsis "Helper functions for modelling in pipelines")
494 "Functions for modelling that help you seamlessly integrate modelling
495 into a pipeline of data manipulation and visualisation.")
496 (license license:gpl3)))
498 (define-public r-httpuv
504 (uri (cran-uri "httpuv" version))
507 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
508 (build-system r-build-system)
512 ("r-promises" ,r-promises)
515 (home-page "https://github.com/rstudio/httpuv")
516 (synopsis "HTTP and WebSocket server library for R")
518 "The httpuv package provides low-level socket and protocol support for
519 handling HTTP and WebSocket requests directly from within R. It is primarily
520 intended as a building block for other packages, rather than making it
521 particularly easy to create complete web applications using httpuv alone.")
522 ;; This package includes third-party code that was originally released
523 ;; under various non-copyleft licenses. Full licensing information can be
524 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
525 (license license:gpl3+)))
527 (define-public r-jsonlite
533 (uri (cran-uri "jsonlite" version))
536 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
537 (build-system r-build-system)
538 (home-page "http://arxiv.org/abs/1403.2805")
539 (synopsis "Robust, high performance JSON parser and generator for R")
541 "The jsonlite package provides a fast JSON parser and generator optimized
542 for statistical data and the web. It offers flexible, robust, high
543 performance tools for working with JSON in R and is particularly powerful for
544 building pipelines and interacting with a web API. In addition to converting
545 JSON data from/to R objects, jsonlite contains functions to stream, validate,
546 and prettify JSON data. The unit tests included with the package verify that
547 all edge cases are encoded and decoded consistently for use with dynamic data
548 in systems and applications.")
549 (license license:expat)))
551 (define-public r-servr
557 (uri (cran-uri "servr" version))
560 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
561 (build-system r-build-system)
563 `(("r-httpuv" ,r-httpuv)
564 ("r-jsonlite" ,r-jsonlite)
567 (home-page "https://github.com/yihui/servr")
568 (synopsis "Simple HTTP server to serve static files or dynamic documents")
570 "Servr provides an HTTP server in R to serve static files, or dynamic
571 documents that can be converted to HTML files (e.g., R Markdown) under a given
573 (license license:expat)))
575 (define-public r-htmltools
581 (uri (cran-uri "htmltools" version))
584 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
585 (build-system r-build-system)
587 `(("r-digest" ,r-digest)
589 ("r-rlang" ,r-rlang)))
590 (home-page "https://cran.r-project.org/web/packages/htmltools")
591 (synopsis "R tools for HTML")
593 "This package provides tools for HTML generation and output in R.")
594 (license license:expat)))
596 (define-public r-htmlwidgets
598 (name "r-htmlwidgets")
602 (uri (cran-uri "htmlwidgets" version))
605 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
606 (build-system r-build-system)
608 `(("r-htmltools" ,r-htmltools)
609 ("r-jsonlite" ,r-jsonlite)
611 (home-page "https://github.com/ramnathv/htmlwidgets")
612 (synopsis "HTML Widgets for R")
614 "HTML widgets is a framework for creating HTML widgets that render in
615 various contexts including the R console, R Markdown documents, and Shiny web
617 (license license:expat)))
619 (define-public r-htmltable
626 (uri (cran-uri "htmlTable" version))
629 "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh"))))
630 (properties `((upstream-name . "htmlTable")))
631 (build-system r-build-system)
633 `(("r-checkmate" ,r-checkmate)
634 ("r-htmltools" ,r-htmltools)
635 ("r-htmlwidgets" ,r-htmlwidgets)
637 ("r-magrittr" ,r-magrittr)
638 ("r-rstudioapi" ,r-rstudioapi)
639 ("r-stringr" ,r-stringr)))
640 (home-page "http://gforge.se/packages/")
641 (synopsis "Advanced tables for Markdown/HTML")
643 "This package provides functions to build tables with advanced layout
644 elements such as row spanners, column spanners, table spanners, zebra
645 striping, and more. While allowing advanced layout, the underlying
646 CSS-structure is simple in order to maximize compatibility with word
647 processors such as LibreOffice. The package also contains a few text
648 formatting functions that help outputting text compatible with HTML or
650 (license license:gpl3+)))
652 (define-public r-curl
658 (uri (cran-uri "curl" version))
661 "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp"))))
662 (build-system r-build-system)
665 (modify-phases %standard-phases
666 ;; The environment variable CURL_CA_BUNDLE is only respected when
667 ;; running Windows, so we disable the platform checks.
668 ;; This can be removed once the libcurl has been patched.
669 (add-after 'unpack 'allow-CURL_CA_BUNDLE
671 (substitute* "R/onload.R"
672 (("if \\(!grepl\\(\"mingw\".*")
674 (substitute* "src/handle.c"
675 (("#ifdef _WIN32") "#if 1"))
681 `(("pkg-config" ,pkg-config)))
682 (home-page "https://github.com/jeroenooms/curl")
683 (synopsis "HTTP client for R")
685 "The @code{curl()} and @code{curl_download()} functions provide highly
686 configurable drop-in replacements for base @code{url()} and
687 @code{download.file()} with better performance, support for encryption, gzip
688 compression, authentication, and other @code{libcurl} goodies. The core of
689 the package implements a framework for performing fully customized requests
690 where data can be processed either in memory, on disk, or streaming via the
691 callback or connection interfaces.")
692 (license license:expat)))
694 (define-public r-hwriter
701 (uri (cran-uri "hwriter" version))
704 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
705 (build-system r-build-system)
706 (home-page "https://cran.r-project.org/web/packages/hwriter")
707 (synopsis "Output R objects in HTML format")
709 "This package provides easy-to-use and versatile functions to output R
710 objects in HTML format.")
711 (license license:lgpl2.1+)))
713 (define-public r-rjson
720 (uri (cran-uri "rjson" version))
723 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
724 (build-system r-build-system)
725 (home-page "https://cran.r-project.org/web/packages/rjson")
726 (synopsis "JSON library for R")
728 "This package provides functions to convert R objects into JSON objects
730 (license license:gpl2+)))
732 (define-public r-shiny
740 (url "https://github.com/rstudio/shiny.git")
741 (commit (string-append "v" version))))
742 (file-name (git-file-name name version))
745 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
746 (build-system r-build-system)
748 `(#:modules ((guix build r-build-system)
749 (guix build minify-build-system)
752 #:imported-modules (,@%r-build-system-modules
753 (guix build minify-build-system))
755 (modify-phases (@ (guix build r-build-system) %standard-phases)
756 (add-after 'unpack 'replace-bundled-minified-JavaScript
757 (lambda* (#:key inputs #:allow-other-keys)
758 (let ((replace-file (lambda (old new)
759 (format #t "replacing ~a with ~a\n" old new)
762 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
763 ;; contain just data. They are not minified code, so we don't
765 (with-directory-excursion "inst/www/shared"
766 (replace-file "bootstrap/shim/respond.min.js"
767 (string-append (assoc-ref inputs "js-respond")
768 "/share/javascript/respond.min.js"))
769 (replace-file "bootstrap/shim/html5shiv.min.js"
770 (string-append (assoc-ref inputs "js-html5shiv")
771 "/share/javascript/html5shiv.min.js"))
772 (replace-file "json2-min.js"
773 (string-append (assoc-ref inputs "js-json2")
774 "/share/javascript/json2.min.js"))
775 (replace-file "strftime/strftime-min.js"
776 (string-append (assoc-ref inputs "js-strftime")
777 "/share/javascript/strftime.min.js"))
778 (replace-file "highlight/highlight.pack.js"
779 (string-append (assoc-ref inputs "js-highlight")
780 "/share/javascript/highlight.min.js"))
781 (replace-file "datatables/js/jquery.dataTables.min.js"
782 (string-append (assoc-ref inputs "js-datatables")
783 "/share/javascript/jquery.dataTables.min.js"))
784 (replace-file "selectize/js/selectize.min.js"
785 (string-append (assoc-ref inputs "js-selectize")
786 "/share/javascript/selectize.min.js"))
787 (replace-file "selectize/js/es5-shim.min.js"
788 (string-append (assoc-ref inputs "js-es5-shim")
789 "/share/javascript/es5-shim.min.js"))
790 (for-each (match-lambda
793 (minify source #:target target)))
794 '(("jqueryui/jquery-ui.js" .
795 "jqueryui/jquery-ui.min.js")
796 ("datepicker/js/bootstrap-datepicker.js" .
797 "datepicker/js/bootstrap-datepicker.min.js")
798 ("ionrangeslider/js/ion.rangeSlider.js" .
799 "ionrangeslider/js/ion.rangeSlider.min.js")
800 ("bootstrap/js/bootstrap.js" .
801 "bootstrap/js/bootstrap.min.js")
808 `(("r-crayon" ,r-crayon)
809 ("r-httpuv" ,r-httpuv)
811 ("r-jsonlite" ,r-jsonlite)
812 ("r-xtable" ,r-xtable)
813 ("r-digest" ,r-digest)
814 ("r-htmltools" ,r-htmltools)
816 ("r-sourcetools" ,r-sourcetools)))
818 `(("js-datatables" ,js-datatables)
819 ("js-html5shiv" ,js-html5shiv)
820 ("js-json2" ,js-json2)
821 ("js-respond" ,js-respond)
822 ("js-selectize" ,js-selectize)
823 ("js-strftime" ,js-strftime)
824 ("js-highlight" ,js-highlight)
825 ("js-es5-shim" ,js-es5-shim)))
827 `(("uglify-js" ,uglify-js)))
828 (home-page "http://shiny.rstudio.com")
829 (synopsis "Easy interactive web applications with R")
831 "Makes it incredibly easy to build interactive web applications
832 with R. Automatic \"reactive\" binding between inputs and outputs and
833 extensive prebuilt widgets make it possible to build beautiful,
834 responsive, and powerful applications with minimal effort.")
835 (license license:artistic2.0)))
837 ;; This package includes minified JavaScript files. When upgrading please
838 ;; check that there are no new minified JavaScript files.
839 (define-public r-shinytree
846 (uri (cran-uri "shinyTree" version))
849 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
850 (modules '((guix build utils)))
853 ;; Delete minified JavaScript
854 (for-each delete-file
855 '("inst/www/jsTree-3.3.7/libs/require.js"
856 "inst/www/jsTree-3.3.7/libs/jquery.js"
857 "inst/www/jsTree-3.3.7/jstree.min.js"))
859 (properties `((upstream-name . "shinyTree")))
860 (build-system r-build-system)
862 `(#:modules ((guix build utils)
863 (guix build r-build-system)
867 (modify-phases %standard-phases
868 (add-after 'unpack 'replace-minified-javascript
869 (lambda* (#:key inputs #:allow-other-keys)
870 (with-directory-excursion "inst/www/jsTree-3.3.7/"
871 (symlink (string-append (assoc-ref inputs "js-requirejs")
872 "/share/javascript/require.min.js")
877 `((,(assoc-ref inputs "js-jquery")
881 (lambda (sources targets)
882 (for-each (lambda (source target)
883 (format #t "Processing ~a --> ~a~%"
885 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
886 (call-with-output-file target
888 (dump-port minified port)))))
892 `(("r-htmlwidgets" ,r-htmlwidgets)
893 ("r-jsonlite" ,r-jsonlite)
894 ("r-promises" ,r-promises)
896 ("r-stringr" ,r-stringr)))
898 `(("js-requirejs" ,js-requirejs)))
900 `(("uglify-js" ,uglify-js)
904 (uri "https://code.jquery.com/jquery-3.3.1.js")
907 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
908 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
909 (synopsis "jsTree bindings for Shiny")
911 "This package exposes R bindings to jsTree, a JavaScript library that
912 supports interactive trees, to enable rich, editable trees in Shiny.")
913 (license license:expat)))
915 (define-public r-shinydashboard
917 (name "r-shinydashboard")
921 (uri (cran-uri "shinydashboard" version))
924 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
925 (build-system r-build-system)
926 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
927 ;; Regenerate it from the included sources.
929 `(#:modules ((guix build utils)
930 (guix build r-build-system)
933 (modify-phases %standard-phases
934 (add-after 'unpack 'generate-minified-javascript
936 (with-directory-excursion "inst/AdminLTE"
937 (delete-file "app.min.js")
938 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
939 (call-with-output-file "app.min.js"
941 (dump-port minified port))))))))))
943 `(("r-htmltools" ,r-htmltools)
944 ("r-promises" ,r-promises)
945 ("r-shiny" ,r-shiny)))
947 `(("uglify-js" ,uglify-js)))
948 (home-page "http://rstudio.github.io/shinydashboard/")
949 (synopsis "Create dashboards with shiny")
950 (description "This package provides an extension to the Shiny web
951 application framework for R, making it easy to create attractive dashboards.")
952 ;; This package includes software that was released under the Expat
953 ;; license, but the whole package is released under GPL version 2 or
955 (license license:gpl2+)))
957 (define-public r-shinyfiles
959 (name "r-shinyfiles")
964 (uri (cran-uri "shinyFiles" version))
966 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
967 (properties `((upstream-name . "shinyFiles")))
968 (build-system r-build-system)
971 ("r-htmltools" ,r-htmltools)
972 ("r-jsonlite" ,r-jsonlite)
974 ("r-tibble" ,r-tibble)))
975 (home-page "https://github.com/thomasp85/shinyFiles")
976 (synopsis "Server-side file system viewer for Shiny")
978 "This package provides functionality for client-side navigation of the
979 server side file system in shiny apps. In case the app is running locally
980 this gives the user direct access to the file system without the need to
981 \"download\" files to a temporary location. Both file and folder selection as
982 well as file saving is available.")
983 (license license:gpl2+)))
985 (define-public r-shinythemes
987 (name "r-shinythemes")
992 (uri (cran-uri "shinythemes" version))
995 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
996 (properties `((upstream-name . "shinythemes")))
997 (build-system r-build-system)
998 (propagated-inputs `(("r-shiny" ,r-shiny)))
999 (home-page "http://rstudio.github.io/shinythemes/")
1000 (synopsis "Themes for Shiny")
1002 "This package provides themes for use with Shiny. It includes several
1003 Bootstrap themes, which are packaged for use with Shiny applications.")
1004 ;; The package is released under version 3 of the GPL, but it includes
1005 ;; source files that are covered by the Expat license. It also includes
1006 ;; fonts under SIL or the ASL.
1007 (license (list license:gpl3 license:expat
1008 license:silofl1.1 license:asl2.0))))
1010 ;; The package sources include minified variants of d3.js and non-minified
1011 ;; source code of d3-jetpack.
1012 (define-public r-d3r
1019 (uri (cran-uri "d3r" version))
1022 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1023 (build-system r-build-system)
1025 `(#:modules ((guix build utils)
1026 (guix build r-build-system)
1030 (modify-phases %standard-phases
1031 (add-after 'unpack 'process-javascript
1032 (lambda* (#:key inputs #:allow-other-keys)
1033 (with-directory-excursion "inst/www/d3/"
1037 `((,(assoc-ref inputs "d3.v3.js")
1038 "v3/dist/d3.min.js")
1039 (,(assoc-ref inputs "d3.v4.js")
1040 "v4/dist/d3.min.js")
1041 (,(assoc-ref inputs "d3.v5.js")
1042 "v5/dist/d3.min.js"))))
1043 (lambda (sources targets)
1044 (for-each (lambda (source target)
1045 (format #t "Processing ~a --> ~a~%"
1047 (delete-file target)
1048 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1049 (call-with-output-file target
1051 (dump-port minified port)))))
1055 `(("r-dplyr" ,r-dplyr)
1056 ("r-htmltools" ,r-htmltools)
1057 ("r-tidyr" ,r-tidyr)))
1059 `(("uglify-js" ,uglify-js)
1063 (uri "https://d3js.org/d3.v3.js")
1066 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1070 (uri "https://d3js.org/d3.v4.js")
1073 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1077 (uri "https://d3js.org/d3.v5.js")
1080 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1081 (home-page "https://github.com/timelyportfolio/d3r")
1082 (synopsis "d3.js utilities for R")
1084 "This package provides a suite of functions to help ease the use of the
1085 d3.js visualization library in R. These helpers include
1086 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1087 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1088 R objects into the JSON format that the d3.js library expects.")
1089 (license license:bsd-3)))
1091 ;; We use the latest commit here because the last release was in 2016 while
1092 ;; the latest commit was in 2018.
1093 (define-public r-sankeyd3
1094 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1098 (version (git-version "0.3.2" revision commit))
1103 (url "https://github.com/fbreitwieser/sankeyD3.git")
1105 (file-name (git-file-name name version))
1108 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1109 (build-system r-build-system)
1112 ("r-htmlwidgets" ,r-htmlwidgets)
1113 ("r-shiny" ,r-shiny)
1114 ("r-magrittr" ,r-magrittr)))
1115 (home-page "https://github.com/fbreitwieser/sankeyD3")
1116 (synopsis "Sankey network graphs from R")
1118 "This package provides an R library to generate Sankey network graphs
1119 in R and Shiny via the D3 visualization library.")
1120 ;; The R code is licensed under GPLv3+. It includes the non-minified
1121 ;; JavaScript source code of d3-sankey, which is released under the
1122 ;; 3-clause BSD license.
1123 (license (list license:gpl3+ license:bsd-3)))))
1125 (define-public r-crosstalk
1127 (name "r-crosstalk")
1132 (uri (cran-uri "crosstalk" version))
1135 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1136 (build-system r-build-system)
1138 `(("r-ggplot2" ,r-ggplot2)
1139 ("r-htmltools" ,r-htmltools)
1140 ("r-jsonlite" ,r-jsonlite)
1141 ("r-lazyeval" ,r-lazyeval)
1143 ("r-shiny" ,r-shiny)))
1144 (home-page "https://rstudio.github.io/crosstalk/")
1145 (synopsis "Inter-widget interactivity for HTML widgets")
1147 "This package provides building blocks for allowing HTML widgets to
1148 communicate with each other, with Shiny or without (i.e. static @code{.html}
1149 files). It currently supports linked brushing and filtering.")
1150 (license license:expat)))
1152 (define-public r-rook
1159 (uri (cran-uri "Rook" version))
1162 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1163 (properties `((upstream-name . "Rook")))
1164 (build-system r-build-system)
1165 (propagated-inputs `(("r-brew" ,r-brew)))
1166 (home-page "https://cran.r-project.org/web/packages/Rook")
1167 (synopsis "Web server interface for R")
1169 "This package contains the Rook specification and convenience software
1170 for building and running Rook applications. A Rook application is an R
1171 reference class object that implements a @code{call} method or an R closure
1172 that takes exactly one argument, an environment, and returns a list with three
1173 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1174 (license license:gpl2)))
1176 (define-public r-miniui
1183 (uri (cran-uri "miniUI" version))
1186 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1187 (properties `((upstream-name . "miniUI")))
1188 (build-system r-build-system)
1190 `(("r-htmltools" ,r-htmltools)
1191 ("r-shiny" ,r-shiny)))
1192 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1193 (synopsis "Shiny UI widgets for small screens")
1195 "This package provides UI widget and layout functions for writing Shiny apps that
1196 work well on small screens.")
1197 (license license:gpl3)))
1199 (define-public r-feather
1206 (uri (cran-uri "feather" version))
1209 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1210 (build-system r-build-system)
1214 ("r-tibble" ,r-tibble)))
1215 (home-page "https://github.com/wesm/feather")
1216 (synopsis "R Bindings to the Feather API")
1217 (description "Read and write feather files, a lightweight binary columnar
1218 data store designed for maximum speed.")
1219 (license license:asl2.0)))
1221 (define-public r-maps
1228 (uri (cran-uri "maps" version))
1231 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1232 (build-system r-build-system)
1233 (home-page "https://cran.r-project.org/web/packages/maps")
1234 (synopsis "Draw geographical maps")
1235 (description "This package provides an R module for display of maps.
1236 Projection code and larger maps are in separate packages (@code{mapproj} and
1238 (license license:gpl2)))
1240 (define-public r-mapproj
1247 (uri (cran-uri "mapproj" version))
1250 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1251 (build-system r-build-system)
1252 (propagated-inputs `(("r-maps" ,r-maps)))
1253 (home-page "https://cran.r-project.org/web/packages/mapproj")
1254 (synopsis "Map projection in R")
1255 (description "This package converts latitude/longitude into projected
1257 (license (list license:gpl2 ; The R interface
1258 (license:non-copyleft ; The C code
1259 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1260 "Lucent Public License Version 1.02")))))
1262 (define-public r-rgooglemaps
1264 (name "r-rgooglemaps")
1269 (uri (cran-uri "RgoogleMaps" version))
1272 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
1273 (properties `((upstream-name . "RgoogleMaps")))
1274 (build-system r-build-system)
1275 (propagated-inputs `(("r-png" ,r-png)))
1276 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1277 (synopsis "Use Google Maps in R")
1278 (description "This package serves two purposes:
1280 @item Provide a comfortable R interface to query the Google server for static
1282 @item Use the map as a background image to overlay plots within R. This
1283 requires proper coordinate scaling.
1285 (license license:gpl2+)))
1287 (define-public r-geosphere
1289 (name "r-geosphere")
1294 (uri (cran-uri "geosphere" version))
1297 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1298 (build-system r-build-system)
1299 (propagated-inputs `(("r-sp" ,r-sp)))
1300 (home-page "https://cran.r-project.org/web/packages/geosphere")
1301 (synopsis "Spherical trigonometry")
1302 (description "This package computes spherical trigonometry for geographic
1303 applications. That is, compute distances and related measures for angular
1304 (longitude/latitude) locations.")
1305 (license license:gpl3+)))
1307 (define-public r-ggmap
1314 (uri (cran-uri "ggmap" version))
1317 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1318 (build-system r-build-system)
1320 `(("r-bitops" ,r-bitops)
1321 ("r-digest" ,r-digest)
1322 ("r-dplyr" ,r-dplyr)
1323 ("r-ggplot2" ,r-ggplot2)
1327 ("r-magrittr" ,r-magrittr)
1330 ("r-purrr" ,r-purrr)
1331 ("r-rgooglemaps" ,r-rgooglemaps)
1332 ("r-rjson" ,r-rjson)
1333 ("r-scales" ,r-scales)
1334 ("r-stringr" ,r-stringr)
1335 ("r-tibble" ,r-tibble)
1336 ("r-tidyr" ,r-tidyr)))
1337 (home-page "https://github.com/dkahle/ggmap")
1338 (synopsis "Spatial visualization with ggplot2")
1339 (description "This package provides a collection of functions to visualize
1340 spatial data and models on top of static maps from various online sources (e.g
1341 Google Maps and Stamen Maps). It includes tools common to those tasks,
1342 including functions for geolocation and routing.")
1343 (license license:gpl2)))
1345 (define-public r-haven
1352 (uri (cran-uri "haven" version))
1355 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1356 (build-system r-build-system)
1360 `(("r-forcats" ,r-forcats)
1363 ("r-rlang" ,r-rlang)
1364 ("r-readr" ,r-readr)
1365 ("r-tibble" ,r-tibble)
1366 ("r-tidyselect" ,r-tidyselect)))
1367 (home-page "https://haven.tidyverse.org")
1368 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1370 "This package lets you mport foreign statistical formats into R via the
1371 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1372 (license license:expat)))
1374 (define-public r-amap
1380 (uri (cran-uri "amap" version))
1383 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1384 (build-system r-build-system)
1386 `(("gfortran" ,gfortran)))
1387 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1388 (synopsis "Another multidimensional analysis package")
1389 (description "This package provides tools for clustering and principal
1390 component analysis (with robust methods, and parallelized functions).")
1391 (license license:gpl2+)))
1393 (define-public r-ape
1400 (uri (cran-uri "ape" version))
1403 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1404 (build-system r-build-system)
1406 `(("r-lattice" ,r-lattice)
1408 ("r-rcpp" ,r-rcpp)))
1409 (home-page "http://ape-package.ird.fr/")
1410 (synopsis "Analyses of phylogenetics and evolution")
1412 "This package provides functions for reading, writing, plotting, and
1413 manipulating phylogenetic trees, analyses of comparative data in a
1414 phylogenetic framework, ancestral character analyses, analyses of
1415 diversification and macroevolution, computing distances from DNA sequences,
1416 and several other tools.")
1417 (license license:gpl2+)))
1419 (define-public r-abbyyr
1426 (uri (cran-uri "abbyyR" version))
1429 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1430 (properties `((upstream-name . "abbyyR")))
1431 (build-system r-build-system)
1433 `(("r-curl" ,r-curl)
1436 ("r-progress" ,r-progress)
1437 ("r-readr" ,r-readr)
1439 (home-page "https://github.com/soodoku/abbyyR")
1440 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1442 "This package provides tools to get text from images of text using Abbyy
1443 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1444 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1445 passports and get the results in a variety of formats including plain text and
1446 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1447 (license license:expat)))
1449 (define-public r-colorspace
1451 (name "r-colorspace")
1456 (uri (cran-uri "colorspace" version))
1458 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1459 (build-system r-build-system)
1460 (home-page "https://cran.r-project.org/web/packages/colorspace")
1461 (synopsis "Color space manipulation")
1463 "This package carries out a mapping between assorted color spaces
1464 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1465 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1466 colors are provided.")
1467 (license license:bsd-3)))
1469 (define-public r-glue
1476 (uri (cran-uri "glue" version))
1479 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1480 (build-system r-build-system)
1481 (home-page "https://github.com/tidyverse/glue")
1482 (synopsis "Interpreted string literals")
1484 "This package provides an implementation of interpreted string literals,
1485 inspired by Python's Literal String Interpolation (PEP-0498) and
1486 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1487 (license license:expat)))
1489 (define-public r-pastecs
1495 (uri (cran-uri "pastecs" version))
1498 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1499 (build-system r-build-system)
1501 `(("r-boot" ,r-boot)))
1502 (home-page "http://www.sciviews.org/pastecs")
1503 (synopsis "Analysis of space-time ecological series")
1505 "This package provides functions for regulation, decomposition and analysis
1506 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1507 initiative to bring PASSTEC 2000 functionalities to R.")
1508 (license license:gpl2+)))
1510 (define-public r-plogr
1517 (uri (cran-uri "plogr" version))
1520 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1521 (build-system r-build-system)
1522 (home-page "https://github.com/krlmlr/plogr")
1523 (synopsis "R bindings for the plog C++ logging library")
1525 "This package provides the header files for a stripped-down version of
1526 the plog header-only C++ logging library, and a method to log to R's standard
1528 (license license:expat)))
1530 (define-public r-pls
1537 (uri (cran-uri "pls" version))
1539 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1540 (build-system r-build-system)
1541 (home-page "http://mevik.net/work/software/pls.html")
1542 (synopsis "Partial Least Squares and Principal Component Regression")
1544 "The pls package implements multivariate regression methods: Partial Least
1545 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1546 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1549 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1550 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1551 @item multi-response models (or @dfn{PLS2})
1552 @item flexible cross-validation
1553 @item Jackknife variance estimates of regression coefficients
1554 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1555 (R)MSEP, R², and correlation loadings
1556 @item formula interface, modelled after @code{lm()}, with methods for predict,
1557 print, summary, plot, update, etc.
1558 @item extraction functions for coefficients, scores, and loadings
1559 @item MSEP, RMSEP, and R² estimates
1560 @item multiplicative scatter correction (@dfn{MSC})
1562 (license license:gpl2)))
1571 (uri (cran-uri "ps" version))
1573 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1574 (build-system r-build-system)
1575 (home-page "http://ps.r-lib.org")
1576 (synopsis "List, query, and manipulate system processes")
1578 "The ps package implements an API to list, query, and manipulate system
1579 processes. Most of its code is based on the @code{psutil} Python package.")
1580 (license license:bsd-3)))
1582 (define-public r-pkgbuild
1589 (uri (cran-uri "pkgbuild" version))
1591 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1592 (build-system r-build-system)
1594 `(("r-callr" ,r-callr)
1596 ("r-crayon" ,r-crayon)
1598 ("r-prettyunits" ,r-prettyunits)
1600 ("r-rprojroot" ,r-rprojroot)
1601 ("r-withr" ,r-withr)))
1602 (home-page "https://github.com/r-pkgs/pkgbuild")
1603 (synopsis "Find tools needed to build R packages")
1605 "This package provides functions used to build R packages. It locates
1606 compilers needed to build R packages on various platforms and ensures the PATH
1607 is configured appropriately so R can use them.")
1608 (license license:gpl3)))
1610 (define-public r-pkgload
1617 (uri (cran-uri "pkgload" version))
1620 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1621 (build-system r-build-system)
1623 `(("r-desc" ,r-desc)
1624 ("r-pkgbuild" ,r-pkgbuild)
1625 ("r-rlang" ,r-rlang)
1626 ("r-rprojroot" ,r-rprojroot)
1627 ("r-rstudioapi" ,r-rstudioapi)
1628 ("r-withr" ,r-withr)))
1629 (home-page "https://github.com/r-lib/pkgload")
1630 (synopsis "Simulate package installation and attach")
1632 "This package simulates the process of installing a package and then
1633 attaching it. This is a key part of the @code{devtools} package as it allows
1634 you to rapidly iterate while developing a package.")
1635 (license license:gpl3)))
1637 (define-public r-rcpp
1644 (uri (cran-uri "Rcpp" version))
1646 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1647 (build-system r-build-system)
1649 `(("r-knitr" ,r-knitr))) ; for vignettes
1650 (home-page "http://www.rcpp.org")
1651 (synopsis "Seamless R and C++ integration")
1653 "The Rcpp package provides R functions as well as C++ classes which offer
1654 a seamless integration of R and C++. Many R data types and objects can be
1655 mapped back and forth to C++ equivalents which facilitates both writing of new
1656 code as well as easier integration of third-party libraries. Documentation
1657 about Rcpp is provided by several vignettes included in this package, via the
1658 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1659 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1660 @code{citation(\"Rcpp\")} for details on these last two.")
1661 (license license:gpl2+)))
1663 (define-public r-bindr
1670 (uri (cran-uri "bindr" version))
1673 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1674 (build-system r-build-system)
1675 (home-page "https://github.com/krlmlr/bindr")
1676 (synopsis "Parametrized active bindings")
1678 "This package provides a simple interface for creating active bindings
1679 where the bound function accepts additional arguments.")
1680 (license license:expat)))
1682 (define-public r-bindrcpp
1689 (uri (cran-uri "bindrcpp" version))
1692 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1693 (build-system r-build-system)
1695 `(("r-bindr" ,r-bindr)
1696 ("r-plogr" ,r-plogr)
1697 ("r-rcpp" ,r-rcpp)))
1698 (home-page "https://github.com/krlmlr/bindrcpp")
1699 (synopsis "Rcpp interface to active bindings")
1701 "This package provides an easy way to fill an environment with active
1702 bindings that call a C++ function.")
1703 (license license:expat)))
1705 (define-public r-auc
1712 (uri (cran-uri "AUC" version))
1715 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1716 (properties `((upstream-name . "AUC")))
1717 (build-system r-build-system)
1718 (home-page "https://cran.r-project.org/web/packages/AUC")
1719 (synopsis "Compute the area under the curve of selected measures")
1721 "This package includes functions to compute the area under the curve of
1722 selected measures: the area under the sensitivity curve (AUSEC), the area
1723 under the specificity curve (AUSPC), the area under the accuracy
1724 curve (AUACC), and the area under the receiver operating characteristic
1725 curve (AUROC). The curves can also be visualized. Support for partial areas
1727 (license license:gpl2+)))
1729 (define-public r-calibrate
1731 (name "r-calibrate")
1736 (uri (cran-uri "calibrate" version))
1738 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1739 (build-system r-build-system)
1741 `(("r-mass" ,r-mass)))
1742 (home-page "https://cran.r-project.org/web/packages/calibrate")
1743 (synopsis "Calibration of scatterplot and biplot axes")
1745 "This is a package for drawing calibrated scales with tick marks
1746 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1747 (license license:gpl2)))
1749 (define-public r-shape
1756 (uri (cran-uri "shape" version))
1759 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1760 (build-system r-build-system)
1761 (home-page "https://cran.r-project.org/web/packages/shape")
1762 (synopsis "Functions for plotting graphical shapes")
1764 "This package provides functions for plotting graphical shapes such as
1765 ellipses, circles, cylinders, arrows, ...")
1766 (license license:gpl3+)))
1768 (define-public r-globaloptions
1770 (name "r-globaloptions")
1775 (uri (cran-uri "GlobalOptions" version))
1777 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1778 (properties `((upstream-name . "GlobalOptions")))
1779 (build-system r-build-system)
1780 (home-page "https://github.com/jokergoo/GlobalOptions")
1781 (synopsis "Generate functions to get or set global options")
1783 "This package provides more controls on the option values such as
1784 validation and filtering on the values, making options invisible or private.")
1785 (license license:gpl2+)))
1787 (define-public r-circlize
1794 (uri (cran-uri "circlize" version))
1797 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1798 (build-system r-build-system)
1800 `(("r-colorspace" ,r-colorspace)
1801 ("r-globaloptions" ,r-globaloptions)
1802 ("r-shape" ,r-shape)))
1803 (home-page "https://github.com/jokergoo/circlize")
1804 (synopsis "Circular visualization")
1806 "Circular layout is an efficient way to visualise huge amounts of
1807 information. This package provides an implementation of circular layout
1808 generation in R as well as an enhancement of available software. Its
1809 flexibility is based on the usage of low-level graphics functions such that
1810 self-defined high-level graphics can be easily implemented by users for
1811 specific purposes. Together with the seamless connection between the powerful
1812 computational and visual environment in R, it gives users more convenience and
1813 freedom to design figures for better understanding complex patterns behind
1814 multi-dimensional data.")
1815 (license license:gpl2+)))
1817 (define-public r-powerlaw
1824 (uri (cran-uri "poweRlaw" version))
1827 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1828 (properties `((upstream-name . "poweRlaw")))
1829 (build-system r-build-system)
1831 `(("r-vgam" ,r-vgam)))
1832 (home-page "https://github.com/csgillespie/poweRlaw")
1833 (synopsis "Tools for the analysis of heavy tailed distributions")
1835 "This package provides an implementation of maximum likelihood estimators
1836 for a variety of heavy tailed distributions, including both the discrete and
1837 continuous power law distributions. Additionally, a goodness-of-fit based
1838 approach is used to estimate the lower cut-off for the scaling region.")
1839 ;; Any of these GPL versions.
1840 (license (list license:gpl2 license:gpl3))))
1842 (define-public r-compare
1849 (uri (cran-uri "compare" version))
1852 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1853 (build-system r-build-system)
1854 (home-page "https://cran.r-project.org/web/packages/compare")
1855 (synopsis "Comparing objects for differences")
1857 "This package provides functions to compare a model object to a
1858 comparison object. If the objects are not identical, the functions can be
1859 instructed to explore various modifications of the objects (e.g., sorting
1860 rows, dropping names) to see if the modified versions are identical.")
1861 (license license:gpl2+)))
1863 (define-public r-dendextend
1865 (name "r-dendextend")
1870 (uri (cran-uri "dendextend" version))
1873 "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
1874 (build-system r-build-system)
1876 `(("r-ggplot2" ,r-ggplot2)
1877 ("r-magrittr" ,r-magrittr)
1878 ("r-viridis" ,r-viridis)))
1879 (home-page "https://cran.r-project.org/web/packages/dendextend")
1880 (synopsis "Extending 'dendrogram' functionality in R")
1882 "This package offers a set of functions for extending @code{dendrogram}
1883 objects in R, letting you visualize and compare trees of hierarchical
1884 clusterings. You can adjust a tree's graphical parameters (the color, size,
1885 type, etc of its branches, nodes and labels) and visually and statistically
1886 compare different dendrograms to one another.")
1887 ;; Any of these versions
1888 (license (list license:gpl2 license:gpl3))))
1890 (define-public r-getoptlong
1892 (name "r-getoptlong")
1897 (uri (cran-uri "GetoptLong" version))
1900 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1901 (properties `((upstream-name . "GetoptLong")))
1902 (build-system r-build-system)
1906 `(("r-globaloptions" ,r-globaloptions)
1907 ("r-rjson" ,r-rjson)))
1908 (home-page "https://github.com/jokergoo/GetoptLong")
1909 (synopsis "Parsing command-line arguments and variable interpolation")
1911 "This is yet another command-line argument parser which wraps the
1912 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1913 use in R. It also provides a simple way for variable interpolation in R.")
1914 (license license:gpl2+)))
1916 (define-public r-fastmatch
1918 (name "r-fastmatch")
1923 (uri (cran-uri "fastmatch" version))
1926 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1927 (build-system r-build-system)
1928 (home-page "http://www.rforge.net/fastmatch")
1929 (synopsis "Fast match function")
1931 "This package provides a fast @code{match} replacement for cases that
1932 require repeated look-ups. It is slightly faster that R's built-in
1933 @code{match} function on first match against a table, but extremely fast on
1934 any subsequent lookup as it keeps the hash table in memory.")
1935 (license license:gpl2)))
1944 (uri (cran-uri "ff" version))
1947 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1948 (build-system r-build-system)
1949 (propagated-inputs `(("r-bit" ,r-bit)))
1950 (home-page "http://ff.r-forge.r-project.org/")
1951 (synopsis "Memory-efficient storage of large data on disk and access functions")
1953 "This package provides data structures that are stored on disk but
1954 behave (almost) as if they were in RAM by transparently mapping only a section
1956 ;; error Architecture not supported.
1957 (supported-systems (delete "aarch64-linux" %supported-systems))
1958 (license license:gpl2)))
1960 (define-public r-ffbase
1967 (uri (cran-uri "ffbase" version))
1970 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
1971 (build-system r-build-system)
1974 ("r-fastmatch" ,r-fastmatch)
1976 (home-page "http://github.com/edwindj/ffbase")
1977 (synopsis "Basic statistical functions for package 'ff'")
1979 "This package extends the out of memory vectors of @code{ff} with
1980 statistical functions and other utilities to ease their usage.")
1981 (license license:gpl3)))
1983 (define-public r-prettyunits
1985 (name "r-prettyunits")
1990 (uri (cran-uri "prettyunits" version))
1993 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
1994 (build-system r-build-system)
1996 `(("r-assertthat" ,r-assertthat)
1997 ("r-magrittr" ,r-magrittr)))
1998 (home-page "https://github.com/gaborcsardi/prettyunits")
1999 (synopsis "Pretty, human readable formatting of quantities")
2001 "This package provides tools for pretty, human readable formatting of
2003 (license license:expat)))
2005 (define-public r-reshape
2012 (uri (cran-uri "reshape" version))
2015 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2016 (build-system r-build-system)
2018 `(("r-plyr" ,r-plyr)
2019 ("r-rcpp" ,r-rcpp)))
2020 (home-page "http://had.co.nz/reshape")
2021 (synopsis "Flexibly reshape data")
2023 "Flexibly restructure and aggregate data using just two functions:
2024 @code{melt} and @code{cast}. This package provides them.")
2025 (license license:expat)))
2027 (define-public r-progress
2034 (uri (cran-uri "progress" version))
2037 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2038 (build-system r-build-system)
2040 `(("r-crayon" ,r-crayon)
2042 ("r-prettyunits" ,r-prettyunits)
2044 (home-page "https://github.com/gaborcsardi/progress")
2045 (synopsis "Terminal progress bars")
2047 "This package provides configurable progress bars. They may include
2048 percentage, elapsed time, and/or the estimated completion time. They work in
2049 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2050 package also provides a C++ API, that works with or without Rcpp.")
2051 (license license:expat)))
2053 (define-public r-ggally
2060 (uri (cran-uri "GGally" version))
2063 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2064 (properties `((upstream-name . "GGally")))
2065 (build-system r-build-system)
2067 `(("libressl" ,libressl)))
2069 `(("r-ggplot2" ,r-ggplot2)
2070 ("r-gtable" ,r-gtable)
2072 ("r-progress" ,r-progress)
2073 ("r-rcolorbrewer" ,r-rcolorbrewer)
2074 ("r-reshape" ,r-reshape)
2075 ("r-rlang" ,r-rlang)))
2076 (home-page "https://ggobi.github.io/ggally")
2077 (synopsis "Extension to ggplot2")
2079 "The R package ggplot2 is a plotting system based on the grammar of
2080 graphics. GGally extends ggplot2 by adding several functions to reduce the
2081 complexity of combining geometric objects with transformed data. Some of
2082 these functions include a pairwise plot matrix, a two group pairwise plot
2083 matrix, a parallel coordinates plot, a survival plot, and several functions to
2085 (license license:gpl2+)))
2087 (define-public r-proxy
2094 (uri (cran-uri "proxy" version))
2097 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2098 (build-system r-build-system)
2099 (home-page "https://cran.r-project.org/web/packages/proxy")
2100 (synopsis "Distance and similarity measures")
2102 "This package provides an extensible framework for the efficient
2103 calculation of auto- and cross-proximities, along with implementations of the
2104 most popular ones.")
2105 (license license:gpl2)))
2114 (uri (cran-uri "sp" version))
2116 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2117 (build-system r-build-system)
2119 `(("r-lattice" ,r-lattice)))
2120 (home-page "https://cran.r-project.org/web/packages/sp")
2121 (synopsis "Classes and methods for spatial data")
2123 "This package provides classes and methods for spatial data; the classes
2124 document where the spatial location information resides, for 2D or 3D data.
2125 Utility functions are provided, e.g. for plotting data as maps, spatial
2126 selection, as well as methods for retrieving coordinates, for subsetting,
2127 print, summary, etc.")
2128 (license license:gpl2+)))
2130 (define-public r-rmtstat
2137 (uri (cran-uri "RMTstat" version))
2140 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2141 (properties `((upstream-name . "RMTstat")))
2142 (build-system r-build-system)
2143 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2144 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2146 "This package provides functions for working with the Tracy-Widom laws
2147 and other distributions related to the eigenvalues of large Wishart
2149 (license license:bsd-3)))
2151 (define-public r-rmpi
2157 (uri (cran-uri "Rmpi" version))
2160 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2161 (properties `((upstream-name . "Rmpi")))
2162 (build-system r-build-system)
2164 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2165 #:phases (modify-phases %standard-phases
2166 (add-before 'install 'mpi-setup
2169 `(("openmpi" ,openmpi)))
2171 `(("pkg-config" ,pkg-config)))
2172 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2173 (synopsis "R interface to message-passing interface (MPI)")
2175 "This package provides an interface (wrapper) to MPI APIs. It also
2176 provides an interactive R manager and worker environment.")
2177 (license license:gpl2+)))
2179 (define-public r-lmoments
2186 (uri (cran-uri "Lmoments" version))
2189 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2190 (properties `((upstream-name . "Lmoments")))
2191 (build-system r-build-system)
2193 `(("r-rcpp" ,r-rcpp)
2194 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2195 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2196 (synopsis "L-moments and quantile mixtures")
2198 "This package contains functions to estimate L-moments and trimmed
2199 L-moments from the data. It also contains functions to estimate the
2200 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2201 quantile mixture from L-moments and trimmed L-moments.")
2202 (license license:gpl2)))
2204 (define-public r-distillery
2206 (name "r-distillery")
2211 (uri (cran-uri "distillery" version))
2214 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2215 (build-system r-build-system)
2216 (home-page "http://www.ral.ucar.edu/staff/ericg")
2217 (synopsis "Functions for confidence intervals and object information")
2219 "This package provides some very simple method functions for confidence
2220 interval calculation and to distill pertinent information from a potentially
2221 complex object; primarily used in common with the packages extRemes and
2223 (license license:gpl2+)))
2225 (define-public r-extremes
2232 (uri (cran-uri "extRemes" version))
2235 "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic"))))
2236 (properties `((upstream-name . "extRemes")))
2237 (build-system r-build-system)
2239 `(("r-distillery" ,r-distillery)
2240 ("r-lmoments" ,r-lmoments)))
2241 (home-page "http://www.assessment.ucar.edu/toolkit/")
2242 (synopsis "Extreme value analysis")
2244 "ExtRemes is a suite of functions for carrying out analyses on the
2245 extreme values of a process of interest; be they block maxima over long blocks
2246 or excesses over a high threshold.")
2247 (license license:gpl2+)))
2249 (define-public r-lmtest
2256 (uri (cran-uri "lmtest" version))
2259 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2260 (build-system r-build-system)
2262 `(("r-zoo" ,r-zoo)))
2264 `(("gfortran" ,gfortran)))
2265 (home-page "https://cran.r-project.org/web/packages/lmtest")
2266 (synopsis "Testing linear regression models")
2268 "This package provides a collection of tests, data sets, and examples for
2269 diagnostic checking in linear regression models. Furthermore, some generic
2270 tools for inference in parametric models are provided.")
2271 ;; Either version is okay
2272 (license (list license:gpl2 license:gpl3))))
2274 (define-public r-idr
2280 (uri (cran-uri "idr" version))
2283 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2284 (build-system r-build-system)
2285 (home-page "https://cran.r-project.org/web/packages/idr/")
2286 (synopsis "Irreproducible discovery rate")
2288 "This is a package for estimating the copula mixture model and plotting
2289 correspondence curves in \"Measuring reproducibility of high-throughput
2290 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2291 by Li, Brown, Huang, and Bickel")
2292 (license license:gpl2+)))
2294 (define-public r-inline
2300 (uri (cran-uri "inline" version))
2303 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2304 (build-system r-build-system)
2305 (home-page "https://cran.r-project.org/web/packages/inline")
2306 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2308 "This package provides functionality to dynamically define R functions
2309 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2310 @code{.Call} calling conventions.")
2311 ;; Any version of the LGPL.
2312 (license license:lgpl3+)))
2314 (define-public r-bbmle
2321 (uri (cran-uri "bbmle" version))
2324 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2325 (build-system r-build-system)
2327 `(("r-lattice" ,r-lattice)
2329 ("r-numderiv" ,r-numderiv)))
2330 (home-page "https://cran.r-project.org/web/packages/bbmle")
2331 (synopsis "Tools for General Maximum Likelihood Estimation")
2333 "This package provides methods and functions for fitting maximum
2334 likelihood models in R. This package modifies and extends the @code{mle}
2335 classes in the @code{stats4} package.")
2336 ;; Any version of the GPL
2337 (license license:gpl2+)))
2339 (define-public r-emdbook
2346 (uri (cran-uri "emdbook" version))
2349 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2350 (build-system r-build-system)
2352 `(("r-bbmle" ,r-bbmle)
2354 ("r-lattice" ,r-lattice)
2357 ("r-rcpp" ,r-rcpp)))
2358 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2359 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2361 "This package provides auxiliary functions and data sets for \"Ecological
2362 Models and Data\", a book presenting maximum likelihood estimation and related
2363 topics for ecologists (ISBN 978-0-691-12522-0).")
2365 (license (list license:gpl2 license:gpl3))))
2367 (define-public r-lpsolve
2370 (version "5.6.13.3")
2374 (uri (cran-uri "lpSolve" version))
2377 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2378 (properties `((upstream-name . "lpSolve")))
2379 (build-system r-build-system)
2380 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2381 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2383 "Lp_solve is software for solving linear, integer and mixed integer
2384 programs. This implementation supplies a \"wrapper\" function in C and some R
2385 functions that solve general linear/integer problems, assignment problems, and
2386 transportation problems.")
2387 (license license:lgpl2.0)))
2389 (define-public r-limsolve
2396 (uri (cran-uri "limSolve" version))
2399 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2400 (properties `((upstream-name . "limSolve")))
2401 (build-system r-build-system)
2403 `(("r-lpsolve" ,r-lpsolve)
2405 ("r-quadprog" ,r-quadprog)))
2406 (native-inputs `(("gfortran" ,gfortran)))
2407 (home-page "https://cran.r-project.org/web/packages/limSolve")
2408 (synopsis "Solving linear inverse models")
2410 "This package provides functions that:
2413 @item find the minimum/maximum of a linear or quadratic function,
2414 @item sample an underdetermined or overdetermined system,
2415 @item solve a linear system Ax=B for the unknown x.
2418 It includes banded and tridiagonal linear systems. The package calls Fortran
2419 functions from LINPACK.")
2421 (license (list license:gpl2+ license:gpl3+))))
2423 (define-public r-fitdistrplus
2425 (name "r-fitdistrplus")
2430 (uri (cran-uri "fitdistrplus" version))
2433 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2434 (build-system r-build-system)
2436 `(("r-mass" ,r-mass)
2437 ("r-npsurv" ,r-npsurv)
2438 ("r-survival" ,r-survival)))
2439 (home-page "http://riskassessment.r-forge.r-project.org")
2440 (synopsis "Fitting a parametric distribution from data")
2442 "This package extends the @code{fitdistr} function of the MASS package
2443 with several functions to help the fit of a parametric distribution to
2444 non-censored or censored data. Censored data may contain left-censored,
2445 right-censored and interval-censored values, with several lower and upper
2446 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2447 provides moment matching (MME), quantile matching (QME) and maximum
2448 goodness-of-fit estimation (MGE) methods (available only for non-censored
2449 data). Weighted versions of MLE, MME and QME are available.")
2450 (license license:gpl2+)))
2452 (define-public r-energy
2459 (uri (cran-uri "energy" version))
2462 "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
2463 (build-system r-build-system)
2465 `(("r-boot" ,r-boot)
2466 ("r-rcpp" ,r-rcpp)))
2467 (home-page "https://cran.r-project.org/web/packages/energy")
2468 (synopsis "Multivariate inference via the energy of data")
2470 "This package provides e-statistics (energy) tests and statistics for
2471 multivariate and univariate inference, including distance correlation,
2472 one-sample, two-sample, and multi-sample tests for comparing multivariate
2473 distributions, are implemented. Measuring and testing multivariate
2474 independence based on distance correlation, partial distance correlation,
2475 multivariate goodness-of-fit tests, clustering based on energy distance,
2476 testing for multivariate normality, distance components (disco) for
2477 non-parametric analysis of structured data, and other energy
2478 statistics/methods are implemented.")
2479 (license license:gpl2+)))
2481 (define-public r-suppdists
2483 (name "r-suppdists")
2488 (uri (cran-uri "SuppDists" version))
2491 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2492 (properties `((upstream-name . "SuppDists")))
2493 (build-system r-build-system)
2494 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2495 (synopsis "Supplementary distributions")
2497 "This package provides ten distributions supplementing those built into
2498 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2499 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2500 coefficient, Johnson distributions, normal scores and generalized
2501 hypergeometric distributions. In addition two random number generators of
2502 George Marsaglia are included.")
2503 (license license:gpl2+)))
2505 (define-public r-ksamples
2512 (uri (cran-uri "kSamples" version))
2515 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2516 (properties `((upstream-name . "kSamples")))
2517 (build-system r-build-system)
2519 `(("r-suppdists" ,r-suppdists)))
2520 (home-page "https://cran.r-project.org/web/packages/kSamples")
2521 (synopsis "K-Sample rank tests and their combinations")
2523 "This package provides tools to compares k samples using the
2524 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2525 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2526 test. It computes asymptotic, simulated or (limited) exact P-values, all
2527 valid under randomization, with or without ties, or conditionally under random
2528 sampling from populations, given the observed tie pattern. Except for Steel's
2529 test and the JT test it also combines these tests across several blocks of
2531 (license license:gpl2+)))
2533 (define-public r-cvst
2540 (uri (cran-uri "CVST" version))
2543 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2544 (properties `((upstream-name . "CVST")))
2545 (build-system r-build-system)
2547 `(("r-kernlab" ,r-kernlab)
2548 ("r-matrix" ,r-matrix)))
2549 (home-page "https://cran.r-project.org/web/packages/CVST")
2550 (synopsis "Fast cross-validation via sequential testing")
2552 "This package implements the fast cross-validation via sequential
2553 testing (CVST) procedure. CVST is an improved cross-validation procedure
2554 which uses non-parametric testing coupled with sequential analysis to
2555 determine the best parameter set on linearly increasing subsets of the data.
2556 Additionally to the CVST the package contains an implementation of the
2557 ordinary k-fold cross-validation with a flexible and powerful set of helper
2558 objects and methods to handle the overall model selection process. The
2559 implementations of the Cochran's Q test with permutations and the sequential
2560 testing framework of Wald are generic and can therefore also be used in other
2562 (license license:gpl2+)))
2564 (define-public r-squarem
2567 (version "2017.10-1")
2571 (uri (cran-uri "SQUAREM" version))
2574 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2575 (properties `((upstream-name . "SQUAREM")))
2576 (build-system r-build-system)
2577 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2578 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2580 "This package provides algorithms for accelerating the convergence of
2581 slow, monotone sequences from smooth, contraction mapping such as the EM
2582 algorithm. It can be used to accelerate any smooth, linearly convergent
2583 acceleration scheme. A tutorial style introduction to this package is
2584 available in a vignette.")
2585 (license license:gpl2+)))
2587 (define-public r-lava
2594 (uri (cran-uri "lava" version))
2597 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2598 (build-system r-build-system)
2600 `(("r-numderiv" ,r-numderiv)
2601 ("r-squarem" ,r-squarem)
2602 ("r-survival" ,r-survival)))
2603 (home-page "https://github.com/kkholst/lava")
2604 (synopsis "Latent variable models")
2606 "This package provides tools for the estimation and simulation of latent
2608 (license license:gpl3)))
2610 (define-public r-drr
2617 (uri (cran-uri "DRR" version))
2620 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2621 (properties `((upstream-name . "DRR")))
2622 (build-system r-build-system)
2624 `(("r-cvst" ,r-cvst)
2625 ("r-kernlab" ,r-kernlab)
2626 ("r-matrix" ,r-matrix)))
2627 (home-page "https://cran.r-project.org/web/packages/DRR")
2628 (synopsis "Dimensionality reduction via regression")
2630 "This package provides an implementation of dimensionality reduction via
2631 regression using Kernel Ridge Regression.")
2632 (license license:gpl3)))
2634 (define-public r-prodlim
2637 (version "2019.11.13")
2641 (uri (cran-uri "prodlim" version))
2644 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2645 (build-system r-build-system)
2647 `(("r-kernsmooth" ,r-kernsmooth)
2650 ("r-survival" ,r-survival)))
2651 (home-page "https://cran.r-project.org/web/packages/prodlim")
2652 (synopsis "Product-limit estimation for censored event history analysis")
2654 "This package provides a fast and user-friendly implementation of
2655 nonparametric estimators for censored event history (survival) analysis with
2656 the Kaplan-Meier and Aalen-Johansen methods.")
2657 (license license:gpl2+)))
2659 (define-public r-dimred
2666 (uri (cran-uri "dimRed" version))
2669 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2670 (properties `((upstream-name . "dimRed")))
2671 (build-system r-build-system)
2674 ("r-magrittr" ,r-magrittr)))
2675 (home-page "https://github.com/gdkrmr/dimRed")
2676 (synopsis "Framework for dimensionality reduction")
2678 "This package provides a collection of dimensionality reduction
2679 techniques from R packages and provides a common interface for calling the
2681 (license license:gpl3)))
2683 (define-public r-timedate
2686 (version "3043.102")
2690 (uri (cran-uri "timeDate" version))
2693 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2694 (properties `((upstream-name . "timeDate")))
2695 (build-system r-build-system)
2696 (home-page "https://www.rmetrics.org")
2697 (synopsis "Chronological and calendar objects")
2699 "This package provides an environment for teaching \"Financial
2700 Engineering and Computational Finance\" and for managing chronological and
2702 (license license:gpl2+)))
2704 (define-public r-magic
2711 (uri (cran-uri "magic" version))
2714 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2715 (build-system r-build-system)
2717 `(("r-abind" ,r-abind)))
2718 (home-page "https://github.com/RobinHankin/magic.git")
2719 (synopsis "Create and investigate magic squares")
2721 "This package provides a collection of efficient, vectorized algorithms
2722 for the creation and investigation of magic squares and hypercubes, including
2723 a variety of functions for the manipulation and analysis of arbitrarily
2724 dimensioned arrays.")
2725 (license license:gpl2)))
2727 (define-public r-rmysql
2734 (uri (cran-uri "RMySQL" version))
2737 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2738 (properties `((upstream-name . "RMySQL")))
2739 (build-system r-build-system)
2741 `(("mariadb" ,mariadb)
2744 `(("r-dbi" ,r-dbi)))
2745 (home-page "https://github.com/r-dbi/RMySQL")
2746 (synopsis "Database interface and MySQL driver for R")
2748 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2749 package contains an old implementation based on legacy code from S-PLUS which
2750 is being phased out. A modern MySQL client based on Rcpp is available from
2751 the RMariaDB package.")
2752 (license license:gpl2)))
2754 (define-public r-rpostgresql
2756 (name "r-rpostgresql")
2761 (uri (cran-uri "RPostgreSQL" version))
2764 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2765 (properties `((upstream-name . "RPostgreSQL")))
2766 (build-system r-build-system)
2768 `(("postgresql" ,postgresql)))
2770 `(("r-dbi" ,r-dbi)))
2771 (home-page "https://github.com/tomoakin/RPostgreSQL")
2772 (synopsis "R interface to the PostgreSQL database system")
2774 "This package provides a Database Interface (DBI) compliant driver for R
2775 to access PostgreSQL database systems.")
2776 ;; The whole package is released under GPL version 2. It includes code
2777 ;; under the PostgreSQL license.
2778 (license license:gpl2)))
2780 (define-public r-linprog
2787 (uri (cran-uri "linprog" version))
2790 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2791 (build-system r-build-system)
2792 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2793 (home-page "http://linprog.r-forge.r-project.org/")
2794 (synopsis "Linear programming and optimization")
2796 "This package can be used to solve Linear Programming / Linear
2797 Optimization problems by using the simplex algorithm.")
2798 (license license:gpl2+)))
2800 (define-public r-geometry
2807 (uri (cran-uri "geometry" version))
2810 "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8"))))
2811 (build-system r-build-system)
2813 `(("r-magic" ,r-magic)
2814 ("r-linprog" ,r-linprog)
2815 ("r-lpsolve" ,r-lpsolve)
2817 ("r-rcppprogress" ,r-rcppprogress)))
2818 (home-page "http://geometry.r-forge.r-project.org/")
2819 (synopsis "Mesh generation and surface tesselation")
2821 "This package makes the qhull library available in R, in a similar manner
2822 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2823 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2824 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2825 and higher dimensions. It implements the Quickhull algorithm for computing
2826 the convex hull. Qhull does not support constrained Delaunay triangulations,
2827 or mesh generation of non-convex objects, but the package does include some R
2828 functions that allow for this. Currently the package only gives access to
2829 Delaunay triangulation and convex hull computation.")
2830 ;; The Qhull sources are included and are distributed under a custom
2831 ;; non-copyleft license. The R sources are released under GPL version 2.
2832 (license (list license:gpl2
2833 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2835 (define-public r-ddalpha
2842 (uri (cran-uri "ddalpha" version))
2845 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2846 (build-system r-build-system)
2849 ("r-class" ,r-class)
2850 ("r-geometry" ,r-geometry)
2853 ("r-robustbase" ,r-robustbase)
2854 ("r-sfsmisc" ,r-sfsmisc)))
2856 `(("gfortran" ,gfortran)))
2857 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2858 (synopsis "Depth-Based classification and calculation of data depth")
2860 "This package contains procedures for depth-based supervised learning,
2861 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2862 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2863 statistical depth function to a compact low-dimensional space, where the final
2864 classification is done. It also offers an extension to functional data and
2865 routines for calculating certain notions of statistical depth functions. 50
2866 multivariate and 5 functional classification problems are included.")
2867 (license license:gpl2)))
2869 (define-public r-gower
2876 (uri (cran-uri "gower" version))
2879 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2880 (build-system r-build-system)
2881 (home-page "https://github.com/markvanderloo/gower")
2882 (synopsis "Gower's distance")
2884 "This package provides tools to compute Gower's distance (or similarity)
2885 coefficient between records, and to compute the top-n matches between records.
2886 Core algorithms are executed in parallel on systems supporting OpenMP.")
2887 (license license:gpl3)))
2889 (define-public r-rcpproll
2896 (uri (cran-uri "RcppRoll" version))
2899 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2900 (properties `((upstream-name . "RcppRoll")))
2901 (build-system r-build-system)
2903 `(("r-rcpp" ,r-rcpp)))
2904 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2905 (synopsis "Efficient rolling and windowed operations")
2907 "This package provides fast and efficient routines for common rolling /
2908 windowed operations. Routines for the efficient computation of windowed mean,
2909 median, sum, product, minimum, maximum, standard deviation and variance are
2911 (license license:gpl2+)))
2913 (define-public r-ipred
2920 (uri (cran-uri "ipred" version))
2923 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2924 (build-system r-build-system)
2926 `(("r-class" ,r-class)
2929 ("r-prodlim" ,r-prodlim)
2930 ("r-rpart" ,r-rpart)
2931 ("r-survival" ,r-survival)))
2932 (home-page "https://cran.r-project.org/web/packages/ipred")
2933 (synopsis "Improved predictors")
2935 "This package provides improved predictive models by indirect
2936 classification and bagging for classification, regression and survival
2937 problems as well as resampling based estimators of prediction error.")
2938 (license license:gpl2+)))
2940 (define-public r-psych
2947 (uri (cran-uri "psych" version))
2950 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
2951 (build-system r-build-system)
2953 `(("r-foreign" ,r-foreign)
2954 ("r-lattice" ,r-lattice)
2955 ("r-mnormt" ,r-mnormt)
2956 ("r-nlme" ,r-nlme)))
2957 (home-page "https://cran.r-project.org/web/packages/psych/")
2958 (synopsis "Procedures for psychological, psychometric, and personality research")
2960 "This package provides a general purpose toolbox for personality,
2961 psychometric theory and experimental psychology. Functions are primarily for
2962 multivariate analysis and scale construction using factor analysis, principal
2963 component analysis, cluster analysis and reliability analysis, although others
2964 provide basic descriptive statistics. Item Response Theory is done using
2965 factor analysis of tetrachoric and polychoric correlations. Functions for
2966 analyzing data at multiple levels include within and between group statistics,
2967 including correlations and factor analysis. Functions for simulating and
2968 testing particular item and test structures are included. Several functions
2969 serve as a useful front end for structural equation modeling. Graphical
2970 displays of path diagrams, factor analysis and structural equation models are
2971 created using basic graphics.")
2972 (license license:gpl2+)))
2974 (define-public r-generics
2981 (uri (cran-uri "generics" version))
2984 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
2985 (build-system r-build-system)
2986 (home-page "https://github.com/r-lib/generics")
2987 (synopsis "Common S3 generics not provided by base R methods")
2989 "In order to reduce potential package dependencies and conflicts,
2990 generics provides a number of commonly used S3 generics that are not provided
2991 by base R methods related to model fitting.")
2992 (license license:gpl2)))
2994 (define-public r-broom
3001 (uri (cran-uri "broom" version))
3004 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
3005 (build-system r-build-system)
3007 `(("r-backports" ,r-backports)
3008 ("r-dplyr" ,r-dplyr)
3009 ("r-generics" ,r-generics)
3011 ("r-purrr" ,r-purrr)
3012 ("r-reshape2" ,r-reshape2)
3013 ("r-stringr" ,r-stringr)
3014 ("r-tibble" ,r-tibble)
3015 ("r-tidyr" ,r-tidyr)))
3016 (home-page "https://github.com/tidyverse/broom")
3017 (synopsis "Convert statistical analysis objects into tidy data frames")
3019 "This package provides tools to convert statistical analysis objects from
3020 R into tidy data frames, so that they can more easily be combined, reshaped
3021 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3022 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3023 summarizes a model's statistical findings such as coefficients of a
3024 regression; @code{augment}, which adds columns to the original data such as
3025 predictions, residuals and cluster assignments; and @code{glance}, which
3026 provides a one-row summary of model-level statistics.")
3027 (license license:expat)))
3029 (define-public r-recipes
3036 (uri (cran-uri "recipes" version))
3039 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
3040 (build-system r-build-system)
3042 `(("r-dplyr" ,r-dplyr)
3043 ("r-generics" ,r-generics)
3045 ("r-gower" ,r-gower)
3046 ("r-ipred" ,r-ipred)
3047 ("r-lubridate" ,r-lubridate)
3048 ("r-magrittr" ,r-magrittr)
3049 ("r-matrix" ,r-matrix)
3050 ("r-purrr" ,r-purrr)
3051 ("r-rlang" ,r-rlang)
3052 ("r-tibble" ,r-tibble)
3053 ("r-tidyr" ,r-tidyr)
3054 ("r-tidyselect" ,r-tidyselect)
3055 ("r-timedate" ,r-timedate)
3056 ("r-withr" ,r-withr)))
3057 (home-page "https://github.com/topepo/recipes")
3058 (synopsis "Preprocessing tools to create design matrices")
3060 "Recipes is an extensible framework to create and preprocess design
3061 matrices. Recipes consist of one or more data manipulation and analysis
3062 \"steps\". Statistical parameters for the steps can be estimated from an
3063 initial data set and then applied to other data sets. The resulting design
3064 matrices can then be used as inputs into statistical or machine learning
3066 (license license:gpl2)))
3068 (define-public r-pdist
3075 (uri (cran-uri "pdist" version))
3078 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3079 (build-system r-build-system)
3080 (home-page "https://github.com/jeffwong/pdist")
3081 (synopsis "Partitioned distance function")
3083 "Pdist computes the euclidean distance between rows of a matrix X and
3084 rows of another matrix Y. Previously, this could be done by binding the two
3085 matrices together and calling @code{dist}, but this creates unnecessary
3086 computation by computing the distances between a row of X and another row of
3087 X, and likewise for Y. Pdist strictly computes distances across the two
3088 matrices, not within the same matrix, making computations significantly faster
3089 for certain use cases.")
3090 (license license:gpl3+)))
3092 (define-public r-ggrepel
3099 (uri (cran-uri "ggrepel" version))
3102 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3103 (build-system r-build-system)
3105 `(("r-ggplot2" ,r-ggplot2)
3107 ("r-scales" ,r-scales)))
3108 (home-page "http://github.com/slowkow/ggrepel")
3109 (synopsis "Repulsive text and label geometries for ggplot2")
3111 "This package provides text and label geometries for ggplot2 that help to
3112 avoid overlapping text labels. Labels repel away from each other and away
3113 from the data points.")
3114 (license license:gpl3)))
3116 (define-public r-corrplot
3123 (uri (cran-uri "corrplot" version))
3126 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3127 (build-system r-build-system)
3128 (home-page "https://github.com/taiyun/corrplot")
3129 (synopsis "Visualization of a correlation matrix")
3131 "This package provides a graphical display of a correlation matrix or
3132 general matrix. It also contains some algorithms to do matrix reordering. In
3133 addition, corrplot is good at details, including choosing color, text labels,
3134 color labels, layout, etc.")
3135 ;; Any version of the GPL
3136 (license license:gpl2+)))
3138 (define-public r-stringdist
3140 (name "r-stringdist")
3145 (uri (cran-uri "stringdist" version))
3147 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3148 (build-system r-build-system)
3149 (home-page "https://github.com/markvanderloo/stringdist")
3150 (synopsis "Approximate string matching and string distance functions")
3152 "This package implements an approximate string matching version of R's
3153 native @code{match} function. It can calculate various string distances based
3154 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3155 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3156 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3157 can be computed between character vectors while taking proper care of encoding
3158 or between integer vectors representing generic sequences.")
3159 (license license:gpl3+)))
3161 (define-public r-ucminf
3168 (uri (cran-uri "ucminf" version))
3171 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3172 (build-system r-build-system)
3173 (native-inputs `(("gfortran" ,gfortran)))
3174 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3175 (synopsis "General-purpose unconstrained non-linear optimization")
3177 "This package provides an implementation of an algorithm for
3178 general-purpose unconstrained non-linear optimization. The algorithm is of
3179 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3180 search with a trust region type monitoring of the input to the line search
3181 algorithm. The interface of @code{ucminf} is designed for easy interchange
3182 with the package @code{optim}.")
3183 (license license:gpl2+)))
3185 (define-public r-ordinal
3188 (version "2019.4-25")
3192 (uri (cran-uri "ordinal" version))
3195 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3196 (build-system r-build-system)
3198 `(("r-mass" ,r-mass)
3199 ("r-matrix" ,r-matrix)
3200 ("r-numderiv" ,r-numderiv)
3201 ("r-ucminf" ,r-ucminf)))
3202 (home-page "https://github.com/runehaubo/ordinal")
3203 (synopsis "Regression models for ordinal data")
3205 "This package provides an implementation of cumulative link (mixed)
3206 models also known as ordered regression models, proportional odds models,
3207 proportional hazards models for grouped survival times and ordered models.
3208 Estimation is via maximum likelihood and mixed models are fitted with the
3209 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3210 (license license:gpl2+)))
3212 (define-public r-jomo
3219 (uri (cran-uri "jomo" version))
3222 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3223 (build-system r-build-system)
3225 `(("r-lme4" ,r-lme4)
3227 ("r-ordinal" ,r-ordinal)
3228 ("r-survival" ,r-survival)))
3229 (home-page "https://cran.r-project.org/web/packages/jomo/")
3230 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3232 "Similarly to Schafer's package pan, jomo is a package for multilevel
3233 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3234 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3235 possibility of handling binary and categorical data through latent normal
3236 variables, the option to use cluster-specific covariance matrices and to
3237 impute compatibly with the substantive model.")
3238 (license license:gpl2)))
3240 (define-public r-pan
3247 (uri (cran-uri "pan" version))
3250 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3251 (build-system r-build-system)
3252 (native-inputs `(("gfortran" ,gfortran)))
3253 (home-page "https://cran.r-project.org/web/packages/pan/")
3254 (synopsis "Multiple imputation for multivariate panel or clustered data")
3256 "This package implements multiple imputation for multivariate panel or
3258 (license license:gpl3)))
3260 (define-public r-mitml
3267 (uri (cran-uri "mitml" version))
3270 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3271 (build-system r-build-system)
3273 `(("r-haven" ,r-haven)
3276 (home-page "https://cran.r-project.org/web/packages/mitml/")
3277 (synopsis "Tools for multiple imputation in multilevel modeling")
3279 "This package provides tools for multiple imputation of missing data in
3280 multilevel modeling. It includes a user-friendly interface to the packages
3281 pan and jomo, and several functions for visualization, data management and the
3282 analysis of multiply imputed data sets.")
3283 (license license:gpl2+)))
3285 (define-public r-mice
3292 (uri (cran-uri "mice" version))
3295 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3296 (build-system r-build-system)
3298 `(("r-broom" ,r-broom)
3299 ("r-dplyr" ,r-dplyr)
3300 ("r-lattice" ,r-lattice)
3302 ("r-mitml" ,r-mitml)
3305 ("r-rlang" ,r-rlang)
3306 ("r-rpart" ,r-rpart)
3307 ("r-survival" ,r-survival)))
3308 (home-page "https://cran.r-project.org/web/packages/mice/")
3309 (synopsis "Multivariate imputation by chained equations")
3311 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3312 implemented by the MICE algorithm as described in @url{Van Buuren and
3313 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3314 variable has its own imputation model. Built-in imputation models are
3315 provided for continuous data (predictive mean matching, normal), binary
3316 data (logistic regression), unordered categorical data (polytomous logistic
3317 regression) and ordered categorical data (proportional odds). MICE can also
3318 impute continuous two-level data (normal model, pan, second-level variables).
3319 Passive imputation can be used to maintain consistency between variables.
3320 Various diagnostic plots are available to inspect the quality of the
3322 ;; Any of these two versions.
3323 (license (list license:gpl2 license:gpl3))))
3325 (define-public r-truncnorm
3327 (name "r-truncnorm")
3332 (uri (cran-uri "truncnorm" version))
3335 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3336 (build-system r-build-system)
3337 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3338 (synopsis "Truncated normal distribution")
3339 (description "This package provides functions for the truncated normal
3340 distribution with mean equal to @code{mean} and standard deviation equal to
3341 @code{sd}. It includes density, distribution, quantile, and expected value
3342 functions, as well as a random generation function.")
3343 (license license:gpl2)))
3345 (define-public r-rsolnp
3352 (uri (cran-uri "Rsolnp" version))
3355 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3356 (properties `((upstream-name . "Rsolnp")))
3357 (build-system r-build-system)
3359 `(("r-truncnorm" ,r-truncnorm)))
3360 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3361 (synopsis "General non-linear optimization")
3362 (description "The Rsolnp package implements a general non-linear augmented
3363 Lagrange multiplier method solver, a @dfn{sequential quadratic
3364 programming} (SQP) based solver).")
3365 ;; Any version of the GPL.
3366 (license license:gpl2+)))
3368 (define-public r-hardyweinberg
3370 (name "r-hardyweinberg")
3375 (uri (cran-uri "HardyWeinberg" version))
3378 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3379 (properties `((upstream-name . "HardyWeinberg")))
3380 (build-system r-build-system)
3382 `(("r-mice" ,r-mice)
3384 ("r-rsolnp" ,r-rsolnp)))
3385 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3386 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3388 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3389 diallelic genetic marker data. All classical tests (chi-square, exact,
3390 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3391 included in the package, as well as functions for power computation and for
3392 the simulation of marker data under equilibrium and disequilibrium. Routines
3393 for dealing with markers on the X-chromosome are included. Functions for
3394 testing equilibrium in the presence of missing data by using multiple
3395 imputation are also provided. Implements several graphics for exploring the
3396 equilibrium status of a large set of diallelic markers: ternary plots with
3397 acceptance regions, log-ratio plots and Q-Q plots.")
3398 (license license:gpl2+)))
3407 (uri (cran-uri "sm" version))
3410 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3411 (build-system r-build-system)
3412 (native-inputs `(("gfortran" ,gfortran)))
3413 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3414 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3416 "This is software accompanying the book 'Applied Smoothing Techniques for
3417 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3418 University Press. It provides smoothing methods for nonparametric regression
3419 and density estimation")
3420 (license license:gpl2+)))
3422 (define-public r-venndiagram
3424 (name "r-venndiagram")
3428 (uri (cran-uri "VennDiagram" version))
3431 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3432 (properties `((upstream-name . "VennDiagram")))
3433 (build-system r-build-system)
3435 `(("r-futile-logger" ,r-futile-logger)))
3436 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3437 (synopsis "Generate High-Resolution Venn and Euler Plots")
3439 "This package provides a set of functions to generate high-resolution
3440 Venn and Euler plots. It includes handling for several special cases,
3441 including two-case scaling, and extensive customization of plot shape and
3443 (license license:gpl2+)))
3445 (define-public r-vioplot
3452 (uri (cran-uri "vioplot" version))
3455 "1jjrsds7p1jnnr4970h43526b9cdv3azizjbalbfzjjylc53lrca"))))
3456 (build-system r-build-system)
3460 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3461 (synopsis "Violin plot")
3463 "This package provides a violin plot, which is a combination of a box
3464 plot and a kernel density plot.")
3465 (license license:bsd-3)))
3467 (define-public r-rsofia
3473 ;; This package has been removed from CRAN, so we can
3474 ;; only fetch it from the archives.
3475 (uri (string-append "https://cran.r-project.org/src/"
3476 "contrib/Archive/RSofia/RSofia_"
3480 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3481 (properties `((upstream-name . "RSofia")))
3482 (build-system r-build-system)
3484 `(("r-rcpp" ,r-rcpp)))
3485 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3486 (synopsis "Port of sofia-ml to R")
3487 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3488 suite of fast incremental algorithms for machine learning that can be used for
3489 training models for classification or ranking.")
3490 (license license:asl2.0)))
3492 (define-public r-xts
3499 (uri (cran-uri "xts" version))
3502 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3503 (build-system r-build-system)
3504 (propagated-inputs `(("r-zoo" ,r-zoo)))
3505 (home-page "https://github.com/joshuaulrich/xts")
3506 (synopsis "Extensible time series")
3508 "This package provides for uniform handling of R's different time-based
3509 data classes by extending @code{zoo}, maximizing native format information
3510 preservation and allowing for user-level customization and extension, while
3511 simplifying cross-class interoperability.")
3512 (license license:gpl2+)))
3514 (define-public r-performanceanalytics
3516 (name "r-performanceanalytics")
3521 (uri (cran-uri "PerformanceAnalytics" version))
3524 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3526 `((upstream-name . "PerformanceAnalytics")))
3527 (build-system r-build-system)
3529 `(("r-quadprog" ,r-quadprog)
3532 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3533 (synopsis "Econometric tools for performance and risk analysis")
3534 (description "This is a collection of econometric functions for
3535 performance and risk analysis. This package aims to aid practitioners and
3536 researchers in utilizing the latest research in analysis of non-normal return
3537 streams. In general, it is most tested on return (rather than price) data on
3538 a regular scale, but most functions will work with irregular return data as
3539 well, and increasing numbers of functions will work with P&L or price data
3541 ;; Either version may be picked.
3542 (license (list license:gpl2 license:gpl3))))
3544 (define-public r-laeken
3551 (uri (cran-uri "laeken" version))
3554 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3555 (build-system r-build-system)
3557 `(("r-boot" ,r-boot)
3558 ("r-mass" ,r-mass)))
3559 (home-page "https://cran.r-project.org/web/packages/laeken/")
3560 (synopsis "Estimation of indicators on social exclusion and poverty")
3561 (description "This package provides tools for the estimation of indicators
3562 on social exclusion and poverty, as well as an implementation of Pareto tail
3563 modeling for empirical income distributions.")
3564 (license license:gpl2+)))
3566 (define-public r-vcd
3573 (uri (cran-uri "vcd" version))
3576 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3577 (build-system r-build-system)
3579 `(("r-colorspace" ,r-colorspace)
3580 ("r-lmtest" ,r-lmtest)
3581 ("r-mass" ,r-mass)))
3582 (home-page "https://cran.r-project.org/web/packages/vcd/")
3583 (synopsis "Visualizing categorical data")
3584 (description "This package provides visualization techniques, data sets,
3585 summary and inference procedures aimed particularly at categorical data.
3586 Special emphasis is given to highly extensible grid graphics. The package was
3587 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3588 Friendly and is now the main support package for a new book, \"Discrete Data
3589 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3590 (license license:gpl2)))
3592 (define-public r-ica
3599 (uri (cran-uri "ica" version))
3602 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3603 (build-system r-build-system)
3604 (home-page "https://cran.r-project.org/web/packages/ica/")
3605 (synopsis "Independent component analysis")
3606 (description "This package provides tools for @dfn{Independent Component
3607 Analysis} (ICA) using various algorithms: FastICA,
3608 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3609 of Eigenmatrices} (JADE).")
3610 (license license:gpl2+)))
3612 (define-public r-dtw
3619 (uri (cran-uri "dtw" version))
3622 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3623 (build-system r-build-system)
3624 (propagated-inputs `(("r-proxy" ,r-proxy)))
3625 (home-page "http://dtw.r-forge.r-project.org/")
3626 (synopsis "Dynamic Time Warping Algorithms")
3627 (description "This package provides a comprehensive implementation of
3628 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3629 optimal (least cumulative distance) alignment between points of two time
3630 series. Common DTW variants covered include local (slope) and global (window)
3631 constraints, subsequence matches, arbitrary distance definitions,
3632 normalizations, minimum variance matching, and so on.")
3633 (license license:gpl2+)))
3635 (define-public r-sdmtools
3638 (version "1.1-221.1")
3642 (uri (cran-uri "SDMTools" version))
3645 "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
3646 (properties `((upstream-name . "SDMTools")))
3647 (build-system r-build-system)
3648 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3649 (home-page "http://www.rforge.net/SDMTools/")
3650 (synopsis "Species distribution modelling tools")
3651 (description "This package provides a set of tools for post processing
3652 the outcomes of species distribution modeling exercises. It includes novel
3653 methods for comparing models and tracking changes in distributions through
3654 time. It further includes methods for visualizing outcomes, selecting
3655 thresholds, calculating measures of accuracy and landscape fragmentation
3657 (license license:gpl3+)))
3659 (define-public r-scatterplot3d
3661 (name "r-scatterplot3d")
3666 (uri (cran-uri "scatterplot3d" version))
3669 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3670 (build-system r-build-system)
3671 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3672 (synopsis "3D scatter plot")
3673 (description "This package provides an implementation of scatter plots for
3674 plotting. a three dimensional point cloud.")
3675 (license license:gpl2)))
3677 (define-public r-ggridges
3684 (uri (cran-uri "ggridges" version))
3687 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3688 (build-system r-build-system)
3690 `(("r-ggplot2" ,r-ggplot2)
3692 ("r-scales" ,r-scales)
3693 ("r-withr" ,r-withr)))
3694 (home-page "https://github.com/clauswilke/ggridges")
3695 (synopsis "Ridgeline plots in ggplot2")
3697 "Ridgeline plots provide a convenient way of visualizing changes in
3698 distributions over time or space. This package enables the creation of such
3699 plots in @code{ggplot2}.")
3700 (license license:gpl2)))
3702 (define-public r-ggjoy
3709 (uri (cran-uri "ggjoy" version))
3712 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3713 (build-system r-build-system)
3715 `(("r-ggplot2" ,r-ggplot2)
3716 ("r-ggridges" ,r-ggridges)))
3717 (home-page "https://github.com/clauswilke/ggjoy")
3718 (synopsis "Joyplots in ggplot2")
3719 (description "Joyplots provide a convenient way of visualizing changes in
3720 distributions over time or space. This package enables the creation of such
3721 plots in @code{ggplot2}.")
3722 (license license:gpl2)))
3724 (define-public r-cli
3731 (uri (cran-uri "cli" version))
3734 "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g"))))
3735 (build-system r-build-system)
3737 `(("r-assertthat" ,r-assertthat)
3738 ("r-crayon" ,r-crayon)))
3739 (home-page "https://github.com/r-lib/cli#readme")
3740 (synopsis "Helpers for developing command line interfaces")
3741 (description "This package provides a suite of tools designed to build
3742 attractive command line interfaces (CLIs). It includes tools for drawing
3743 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3744 (license license:expat)))
3746 (define-public r-argparser
3748 (name "r-argparser")
3753 (uri (cran-uri "argparser" version))
3756 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3757 (build-system r-build-system)
3758 (home-page "https://bitbucket.org/djhshih/argparser")
3759 (synopsis "Command-line argument parser")
3761 "This package provides a cross-platform command-line argument parser
3762 written purely in R with no external dependencies. It is useful with the
3763 Rscript front-end and facilitates turning an R script into an executable
3765 (license license:gpl3+)))
3767 (define-public r-debugme
3774 (uri (cran-uri "debugme" version))
3777 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3778 (build-system r-build-system)
3779 (propagated-inputs `(("r-crayon" ,r-crayon)))
3780 (home-page "https://github.com/r-lib/debugme#readme")
3781 (synopsis "Debug R packages")
3783 "This package allows the user to specify debug messages as special string
3784 constants, and control debugging of packages via environment variables.")
3785 (license license:expat)))
3787 (define-public r-processx
3794 (uri (cran-uri "processx" version))
3797 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3798 (build-system r-build-system)
3802 (home-page "https://github.com/r-lib/processx3")
3803 (synopsis "Execute and control system processes")
3805 "This package provides portable tools to run system processes in the
3806 background. It can check if a background process is running; wait on a
3807 background process to finish; get the exit status of finished processes; kill
3808 background processes and their children; restart processes. It can read the
3809 standard output and error of the processes, using non-blocking connections.
3810 @code{processx} can poll a process for standard output or error, with a
3811 timeout. It can also poll several processes at once.")
3812 (license license:expat)))
3814 (define-public r-tsp
3821 (uri (cran-uri "TSP" version))
3824 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3825 (properties `((upstream-name . "TSP")))
3826 (build-system r-build-system)
3827 (propagated-inputs `(("r-foreach" ,r-foreach)))
3828 (home-page "https://cran.r-project.org/web/packages/TSP/")
3829 (synopsis "Traveling salesperson problem (TSP)")
3830 (description "This package provides basic infrastructure and some
3831 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3832 traveling salesman problem).")
3833 (license license:gpl3)))
3835 (define-public r-qap
3842 (uri (cran-uri "qap" version))
3845 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3846 (build-system r-build-system)
3847 (native-inputs `(("gfortran" ,gfortran)))
3848 (home-page "https://cran.r-project.org/web/packages/qap/")
3849 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3850 (description "This package implements heuristics for the @dfn{quadratic
3851 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3853 (license license:gpl3)))
3855 (define-public r-gclus
3862 (uri (cran-uri "gclus" version))
3865 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3866 (build-system r-build-system)
3867 (propagated-inputs `(("r-cluster" ,r-cluster)))
3868 (home-page "https://cran.r-project.org/web/packages/gclus/")
3869 (synopsis "Clustering graphics")
3870 (description "This package orders panels in scatterplot matrices and
3871 parallel coordinate displays by some merit index. It contains various indices
3872 of merit, ordering functions, and enhanced versions of @code{pairs} and
3873 @code{parcoord} which color panels according to their merit level.")
3874 (license license:gpl2+)))
3876 (define-public r-webshot
3883 (uri (cran-uri "webshot" version))
3886 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3887 (build-system r-build-system)
3889 `(("r-callr" ,r-callr)
3890 ("r-jsonlite" ,r-jsonlite)
3891 ("r-magrittr" ,r-magrittr)))
3892 (home-page "https://github.com/wch/webshot/")
3893 (synopsis "Take screenshots of web pages")
3895 "Webshot makes it easy to take screenshots of web pages from within R.
3896 It can also run Shiny applications locally and take screenshots of the
3897 application; and it can render and screenshot static as well as interactive R
3898 Markdown documents.")
3899 (license license:gpl2)))
3901 (define-public r-seriation
3903 (name "r-seriation")
3908 (uri (cran-uri "seriation" version))
3911 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3912 (build-system r-build-system)
3914 `(("r-cluster" ,r-cluster)
3915 ("r-colorspace" ,r-colorspace)
3916 ("r-dendextend" ,r-dendextend)
3917 ("r-gclus" ,r-gclus)
3918 ("r-gplots" ,r-gplots)
3921 ("r-registry" ,r-registry)
3923 (native-inputs `(("gfortran" ,gfortran)))
3924 (home-page "http://s2.smu.edu/IDA/seriation/")
3925 (synopsis "Infrastructure for ordering objects using seriation")
3927 "This package provides infrastructure for seriation with an
3928 implementation of several seriation/sequencing techniques to reorder matrices,
3929 dissimilarity matrices, and dendrograms. It also provides (optimally)
3930 reordered heatmaps, color images and clustering visualizations like
3931 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3933 (license license:gpl3)))
3935 (define-public r-xfun
3942 (uri (cran-uri "xfun" version))
3944 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
3945 (build-system r-build-system)
3946 (home-page "https://github.com/yihui/xfun")
3947 (synopsis "Miscellaneous functions")
3949 "This package provides miscellaneous functions commonly used in other
3950 packages maintained by Yihui Xie.")
3951 (license license:expat)))
3953 (define-public r-utf8
3960 (uri (cran-uri "utf8" version))
3963 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
3964 (build-system r-build-system)
3965 (home-page "https://github.com/patperry/r-utf8")
3966 (synopsis "Unicode text processing")
3968 "This package provides tools to process and print UTF-8 encoded
3969 international text (Unicode). Input, validate, normalize, encode, format, and
3971 (license license:asl2.0)))
3973 (define-public r-zeallot
3980 (uri (cran-uri "zeallot" version))
3983 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
3984 (build-system r-build-system)
3985 (home-page "https://github.com/nteetor/zeallot")
3986 (synopsis "Multiple, unpacking, and destructuring assignment")
3988 "This package provides a @code{%<-%} operator to perform multiple,
3989 unpacking, and destructuring assignment in R. The operator unpacks the
3990 right-hand side of an assignment into multiple values and assigns these values
3991 to variables on the left-hand side of the assignment.")
3992 (license license:expat)))
3994 (define-public r-vctrs
4001 (uri (cran-uri "vctrs" version))
4004 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
4005 (build-system r-build-system)
4007 `(("r-backports" ,r-backports)
4008 ("r-digest" ,r-digest)
4009 ("r-ellipsis" ,r-ellipsis)
4011 ("r-rlang" ,r-rlang)
4012 ("r-zeallot" ,r-zeallot)))
4013 (home-page "https://github.com/r-lib/vctrs")
4014 (synopsis "Vector helpers")
4016 "There are three main goals to the @code{vctrs} package:
4019 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4020 @code{length()} and @code{class()}. These definitions are paired with a
4021 framework for type-coercion and size-recycling.
4022 @item To define type- and size-stability as desirable function properties, use
4023 them to analyse existing base function, and to propose better alternatives.
4024 This work has been particularly motivated by thinking about the ideal
4025 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4026 @item To provide a new @code{vctr} base class that makes it easy to create new
4027 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4028 a few new @code{vctrs} generics, making implementation considerably simpler
4031 (license license:gpl3)))
4033 (define-public r-pillar
4040 (uri (cran-uri "pillar" version))
4043 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
4044 (build-system r-build-system)
4047 ("r-crayon" ,r-crayon)
4048 ("r-fansi" ,r-fansi)
4049 ("r-rlang" ,r-rlang)
4051 ("r-vctrs" ,r-vctrs)))
4052 (home-page "https://github.com/r-lib/pillar")
4053 (synopsis "Coloured formatting for columns")
4055 "This package provides a @code{pillar} generic designed for formatting
4056 columns of data using the full range of colours provided by modern
4058 (license license:gpl3)))
4060 (define-public r-uuid
4067 (uri (cran-uri "uuid" version))
4070 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4071 (build-system r-build-system)
4072 (home-page "http://www.rforge.net/uuid")
4073 (synopsis "Tools for generating and handling of UUIDs")
4075 "This package provides tools for generating and handling of
4076 @dfn{Universally Unique Identifiers} (UUIDs).")
4077 (license license:expat)))
4079 (define-public r-tinytex
4086 (uri (cran-uri "tinytex" version))
4089 "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
4090 (build-system r-build-system)
4092 `(("r-xfun" ,r-xfun)))
4093 (home-page "https://github.com/yihui/tinytex")
4094 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4096 "This package provides helper functions to install and maintain the LaTeX
4097 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4098 easy-to-maintain version of TeX Live. This package also contains helper
4099 functions to compile LaTeX documents, and install missing LaTeX packages
4101 (license license:expat)))
4103 (define-public r-metap
4110 (uri (cran-uri "metap" version))
4113 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
4114 (build-system r-build-system)
4116 `(("r-lattice" ,r-lattice)
4117 ("r-rdpack" ,r-rdpack)))
4118 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4119 (synopsis "Meta-analysis of significance values")
4121 "The canonical way to perform meta-analysis involves using effect sizes.
4122 When they are not available this package provides a number of methods for
4123 meta-analysis of significance values including the methods of Edgington,
4124 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4125 published results; and a routine for graphical display.")
4126 (license license:gpl2)))
4128 (define-public r-network
4135 (uri (cran-uri "network" version))
4138 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
4139 (build-system r-build-system)
4141 `(("r-magrittr" ,r-magrittr)
4142 ("r-tibble" ,r-tibble)))
4143 (home-page "https://statnet.org/")
4144 (synopsis "Classes for relational data")
4146 "This package provides tools to create and modify network objects. The
4147 @code{network} class can represent a range of relational data types, and
4148 supports arbitrary vertex/edge/graph attributes.")
4149 (license license:gpl2+)))
4151 (define-public r-statnet-common
4153 (name "r-statnet-common")
4158 (uri (cran-uri "statnet.common" version))
4161 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4163 `((upstream-name . "statnet.common")))
4164 (build-system r-build-system)
4166 `(("r-coda" ,r-coda)))
4167 (home-page "https://statnet.org")
4168 (synopsis "R scripts and utilities used by the Statnet software")
4169 (description "This package provides non-statistical utilities used by the
4170 software developed by the Statnet Project.")
4171 (license license:gpl3)))
4173 (define-public r-sna
4180 (uri (cran-uri "sna" version))
4183 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4184 (build-system r-build-system)
4186 `(("r-network" ,r-network)
4187 ("r-statnet-common" ,r-statnet-common)))
4188 (home-page "https://statnet.org")
4189 (synopsis "Tools for social network analysis")
4191 "This package provides a range of tools for social network analysis,
4192 including node and graph-level indices, structural distance and covariance
4193 methods, structural equivalence detection, network regression, random graph
4194 generation, and 2D/3D network visualization.")
4195 (license license:gpl2+)))
4197 (define-public r-ttr
4204 (uri (cran-uri "TTR" version))
4207 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
4208 (properties `((upstream-name . "TTR")))
4209 (build-system r-build-system)
4211 `(("r-curl" ,r-curl)
4214 (home-page "https://github.com/joshuaulrich/TTR")
4215 (synopsis "Technical trading rules")
4217 "This package provides functions and data to construct technical trading
4219 (license license:gpl2)))
4221 (define-public r-leaps
4228 (uri (cran-uri "leaps" version))
4231 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4232 (build-system r-build-system)
4233 (native-inputs `(("gfortran" ,gfortran)))
4234 (home-page "https://cran.r-project.org/web/packages/leaps/")
4235 (synopsis "Regression subset selection")
4237 "This package provides tools for regression subset selection, including
4238 exhaustive search.")
4239 (license license:gpl2+)))
4241 (define-public r-splus2r
4248 (uri (cran-uri "splus2R" version))
4251 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4252 (properties `((upstream-name . "splus2R")))
4253 (build-system r-build-system)
4254 (native-inputs `(("gfortran" ,gfortran)))
4255 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4256 (synopsis "Supplemental S-PLUS functionality in R")
4258 "Currently there are many functions in S-PLUS that are missing in R. To
4259 facilitate the conversion of S-PLUS packages to R packages, this package
4260 provides some missing S-PLUS functionality in R.")
4261 (license license:gpl2)))
4263 (define-public r-ifultools
4265 (name "r-ifultools")
4270 (uri (cran-uri "ifultools" version))
4273 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4274 (build-system r-build-system)
4276 `(("r-mass" ,r-mass)
4277 ("r-splus2r" ,r-splus2r)))
4278 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4279 (synopsis "Insightful research tools")
4280 (description "This package provides C code used by the wmtsa, fractal, and
4282 (license license:gpl2)))
4284 (define-public r-sapa
4291 (uri (cran-uri "sapa" version))
4294 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4295 (build-system r-build-system)
4297 `(("r-ifultools" ,r-ifultools)
4298 ("r-splus2r" ,r-splus2r)))
4299 (home-page "https://cran.r-project.org/web/packages/sapa/")
4300 (synopsis "Spectral analysis for physical applications")
4301 (description "This package provides software for the book Spectral
4302 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4303 Cambridge University Press, 1993.")
4304 (license license:gpl2)))
4306 (define-public r-aggregation
4308 (name "r-aggregation")
4313 (uri (cran-uri "aggregation" version))
4316 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4317 (build-system r-build-system)
4318 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4319 (synopsis "Methods for p-value aggregation")
4321 "This package contains functionality for performing the following methods
4322 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4323 Fisher's method), and Sidak correction.")
4324 (license license:gpl3)))
4326 (define-public r-quantmod
4333 (uri (cran-uri "quantmod" version))
4336 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4337 (build-system r-build-system)
4339 `(("r-curl" ,r-curl)
4343 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4344 (synopsis "Quantitative financial modelling framework")
4345 (description "This package provides a quantitative financial modelling
4346 framework to allow users to specify, build, trade, and analyse quantitative
4347 financial trading strategies.")
4348 (license license:gpl3)))
4350 (define-public r-tseries
4357 (uri (cran-uri "tseries" version))
4360 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4361 (build-system r-build-system)
4363 `(("r-quadprog" ,r-quadprog)
4364 ("r-quantmod" ,r-quantmod)
4367 `(("gfortran" ,gfortran)))
4368 (home-page "https://cran.r-project.org/web/packages/tseries/")
4369 (synopsis "Time series analysis and computational finance")
4371 "This package provides functions relating to time series analysis and
4372 computational finance.")
4373 (license license:gpl2)))
4375 (define-public r-wmtsa
4382 (uri (cran-uri "wmtsa" version))
4385 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4386 (build-system r-build-system)
4388 `(("r-ifultools" ,r-ifultools)
4390 ("r-splus2r" ,r-splus2r)))
4391 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4392 (synopsis "Wavelet methods for time series analysis")
4394 "This package provides software to accompany the book \"Wavelet Methods
4395 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4396 University Press, 2000.")
4397 (license license:gpl2)))
4399 (define-public r-tsa
4406 (uri (cran-uri "TSA" version))
4409 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4410 (properties `((upstream-name . "TSA")))
4411 (build-system r-build-system)
4413 `(("r-leaps" ,r-leaps)
4414 ("r-locfit" ,r-locfit)
4415 ("r-mgcv" ,r-mgcv)))
4416 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4417 (synopsis "Time series analysis")
4419 "This package contains R functions and datasets detailed in the book
4420 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4421 Cryer and Kung-Sik Chan.")
4422 (license license:gpl2+)))
4424 (define-public r-extradistr
4426 (name "r-extradistr")
4431 (uri (cran-uri "extraDistr" version))
4434 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4435 (properties `((upstream-name . "extraDistr")))
4436 (build-system r-build-system)
4438 `(("r-rcpp" ,r-rcpp)))
4439 (home-page "https://github.com/twolodzko/extraDistr")
4440 (synopsis "Additional univariate and multivariate distributions")
4442 "This package implements density, distribution functions, quantile
4443 functions and random generation functions for a large number of univariate and
4444 multivariate distributions.")
4445 (license license:gpl2)))
4447 (define-public r-fractal
4454 (uri (cran-uri "fractal" version))
4457 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4458 (build-system r-build-system)
4460 `(("r-ifultools" ,r-ifultools)
4463 ("r-scatterplot3d" ,r-scatterplot3d)
4464 ("r-splus2r" ,r-splus2r)
4465 ("r-wmtsa" ,r-wmtsa)))
4466 (home-page "https://cran.r-project.org/web/packages/fractal/")
4467 (synopsis "Fractal time series modeling and analysis")
4469 "This package provides tools for stochastic fractal and deterministic
4470 chaotic time series analysis.")
4471 (license license:gpl2)))
4473 (define-public r-urca
4480 (uri (cran-uri "urca" version))
4483 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4484 (build-system r-build-system)
4485 (propagated-inputs `(("r-nlme" ,r-nlme)))
4486 (native-inputs `(("gfortran" ,gfortran)))
4487 (home-page "https://cran.r-project.org/web/packages/urca/")
4488 (synopsis "Unit root and cointegration tests for time series data")
4490 "This package provides unit root and cointegration tests encountered in
4491 applied econometric analysis.")
4492 (license license:gpl2+)))
4494 (define-public r-cubature
4501 (uri (cran-uri "cubature" version))
4504 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
4505 (build-system r-build-system)
4507 `(("r-rcpp" ,r-rcpp)))
4508 (home-page "https://github.com/bnaras/cubature")
4509 (synopsis "Adaptive multivariate integration over hypercubes")
4511 "This package is an R wrapper around the cubature C library for adaptive
4512 multivariate integration over hypercubes. This version provides both
4513 @code{hcubature} and @code{pcubature} routines in addition to a vector
4515 ;; The included cubature C library is released under GPLv2+, but the
4516 ;; wrapper declares the license to be GPLv3+.
4517 (license (list license:gpl2+ license:gpl3+))))
4519 (define-public r-trend
4526 (uri (cran-uri "trend" version))
4529 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4530 (build-system r-build-system)
4532 `(("r-extradistr" ,r-extradistr)))
4534 `(("gfortran" ,gfortran)))
4535 (home-page "https://cran.r-project.org/web/packages/trend/")
4536 (synopsis "Non-parametric trend tests and change-point detection")
4538 "The analysis of environmental data often requires the detection of
4539 trends and change-points. This package includes tests for trend
4540 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4541 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4542 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4543 correlation trend test), change-point detection (Lanzante's test procedures,
4544 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4545 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4546 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4547 sample Robust Rank-Order Distributional Test.")
4548 (license license:gpl3)))
4550 (define-public r-expm
4557 (uri (cran-uri "expm" version))
4560 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4561 (build-system r-build-system)
4562 (propagated-inputs `(("r-matrix" ,r-matrix)))
4563 (native-inputs `(("gfortran" ,gfortran)))
4564 (home-page "https://r-forge.r-project.org/projects/expm/")
4565 (synopsis "Tools for matrix exponentials and related quantities")
4567 "This package provides tools for the computation of the matrix
4568 exponential, logarithm, square root, and related quantities.")
4569 (license license:gpl2+)))
4571 (define-public r-complexplus
4573 (name "r-complexplus")
4578 (uri (cran-uri "complexplus" version))
4581 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4582 (build-system r-build-system)
4584 `(("r-expm" ,r-expm)
4585 ("r-matrix" ,r-matrix)))
4586 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4587 (synopsis "Functions of complex or real variables")
4589 "This package extends several functions to the complex domain, including
4590 the matrix exponential and logarithm, and the determinant.")
4591 (license license:gpl2)))
4593 (define-public r-phontools
4595 (name "r-phontools")
4600 (uri (cran-uri "phonTools" version))
4603 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4604 (properties `((upstream-name . "phonTools")))
4605 (build-system r-build-system)
4606 (home-page "http://www.santiagobarreda.com/rscripts.html")
4607 (synopsis "Tools for phonetic and acoustic analyses")
4609 "This package contains tools for the organization, display, and analysis
4610 of the sorts of data frequently encountered in phonetics research and
4611 experimentation, including the easy creation of IPA vowel plots, and the
4612 creation and manipulation of WAVE audio files.")
4613 (license license:bsd-2)))
4622 (uri (cran-uri "np" version))
4625 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4626 (build-system r-build-system)
4628 `(("r-boot" ,r-boot)
4629 ("r-cubature" ,r-cubature)
4630 ("r-quadprog" ,r-quadprog)
4631 ("r-quantreg" ,r-quantreg)))
4632 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4633 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4634 (description "This package provides non-parametric (and semi-parametric)
4635 kernel methods that seamlessly handle a mix of continuous, unordered, and
4636 ordered factor data types.")
4637 ;; Any version of the GPL.
4638 (license license:gpl3+)))
4640 (define-public r-powerplus
4642 (name "r-powerplus")
4647 (uri (cran-uri "powerplus" version))
4650 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4651 (build-system r-build-system)
4653 `(("r-complexplus" ,r-complexplus)
4656 ("r-matrix" ,r-matrix)
4657 ("r-phontools" ,r-phontools)))
4658 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4659 (synopsis "Exponentiation operations")
4661 "This package provides tools for the computation of matrix and scalar
4663 (license license:gpl2)))
4665 (define-public r-heatmaply
4667 (name "r-heatmaply")
4672 (uri (cran-uri "heatmaply" version))
4675 "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1"))))
4676 (build-system r-build-system)
4678 `(("r-assertthat" ,r-assertthat)
4679 ("r-colorspace" ,r-colorspace)
4680 ("r-dendextend" ,r-dendextend)
4681 ("r-ggplot2" ,r-ggplot2)
4682 ("r-htmlwidgets" ,r-htmlwidgets)
4683 ("r-magrittr" ,r-magrittr)
4684 ("r-plotly" ,r-plotly)
4685 ("r-rcolorbrewer" ,r-rcolorbrewer)
4686 ("r-reshape2" ,r-reshape2)
4687 ("r-scales" ,r-scales)
4688 ("r-seriation" ,r-seriation)
4689 ("r-viridis" ,r-viridis)
4690 ("r-webshot" ,r-webshot)))
4691 (home-page "https://cran.r-project.org/package=heatmaply")
4692 (synopsis "Interactive cluster heat maps using plotly")
4694 "This package enables you to create interactive cluster heatmaps that can
4695 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4696 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4697 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4698 a popular graphical method for visualizing high-dimensional data, in which a
4699 table of numbers is encoded as a grid of colored cells. The rows and columns
4700 of the matrix are ordered to highlight patterns and are often accompanied by
4702 ;; Either version of the license.
4703 (license (list license:gpl2 license:gpl3))))
4712 (uri (cran-uri "h5" version))
4715 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4716 (build-system r-build-system)
4721 `(("which" ,which)))
4723 `(("r-rcpp" ,r-rcpp)))
4724 (home-page "https://github.com/mannau/h5")
4725 (synopsis "Interface to the HDF5 Library")
4727 "This package provides an S4 interface to the HDF5 library supporting
4728 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4729 binary files in a language independent format. The HDF5 format can therefore
4730 be used as an alternative to R's save/load mechanism. Since h5 is able to
4731 access only subsets of stored data it can also handle data sets which do not
4733 (license license:bsd-2)))
4735 (define-public r-cgdsr
4742 (uri (cran-uri "cgdsr" version))
4745 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4746 (build-system r-build-system)
4748 `(("r-httr" ,r-httr)
4749 ("r-r-methodss3" ,r-r-methodss3)
4750 ("r-r-oo" ,r-r-oo)))
4751 (home-page "https://github.com/cBioPortal/cgdsr")
4752 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4754 "This package provides a basic set of R functions for querying the Cancer
4755 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4756 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4757 (license license:lgpl3)))
4759 (define-public r-import
4766 (uri (cran-uri "import" version))
4769 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4770 (build-system r-build-system)
4771 (home-page "https://github.com/smbache/import")
4772 (synopsis "Import mechanism for R")
4774 "This is an alternative mechanism for importing objects from packages.
4775 The syntax allows for importing multiple objects from a package with a single
4776 command in an expressive way. The import package bridges some of the gap
4777 between using @code{library} (or @code{require}) and direct (single-object)
4778 imports. Furthermore the imported objects are not placed in the current
4779 environment. It is also possible to import objects from stand-alone @code{.R}
4781 (license license:expat)))
4783 (define-public r-shinyace
4790 (uri (cran-uri "shinyAce" version))
4793 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4794 (properties `((upstream-name . "shinyAce")))
4795 (build-system r-build-system)
4797 `(("r-shiny" ,r-shiny)
4798 ("r-jsonlite" ,r-jsonlite)))
4799 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4800 (synopsis "Ace editor bindings for Shiny")
4802 "This package provides Ace editor bindings to enable a rich text editing
4803 environment within Shiny.")
4804 (license license:expat)))
4806 (define-public r-base64url
4808 (name "r-base64url")
4813 (uri (cran-uri "base64url" version))
4816 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4817 (build-system r-build-system)
4819 `(("r-backports" ,r-backports)))
4820 (home-page "https://github.com/mllg/base64url")
4821 (synopsis "Fast and URL-safe base64 encoder and decoder")
4823 "This package provides a URL-safe base64 encoder and decoder. In
4824 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4825 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4826 encoder does not fill the string with trailing @code{=}. The resulting
4827 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4828 and thus are safe to use in URLs or for file names. The package also comes
4829 with a simple base32 encoder/decoder suited for case insensitive file
4831 (license license:gpl3)))
4833 (define-public r-radiant-data
4835 (name "r-radiant-data")
4840 (uri (cran-uri "radiant.data" version))
4843 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4844 (modules '((guix build utils)))
4847 ;; Delete files that are under CC-NC-SA.
4848 (delete-file-recursively "inst/app/tools/help")
4850 (properties `((upstream-name . "radiant.data")))
4851 (build-system r-build-system)
4853 `(("r-base64enc" ,r-base64enc)
4854 ("r-broom" ,r-broom)
4857 ("r-dplyr" ,r-dplyr)
4860 ("r-ggplot2" ,r-ggplot2)
4861 ("r-gridextra" ,r-gridextra)
4862 ("r-import" ,r-import)
4863 ("r-jsonlite" ,r-jsonlite)
4864 ("r-knitr" ,r-knitr)
4865 ("r-lubridate" ,r-lubridate)
4866 ("r-magrittr" ,r-magrittr)
4867 ("r-markdown" ,r-markdown)
4868 ("r-plotly" ,r-plotly)
4869 ("r-psych" ,r-psych)
4870 ("r-readr" ,r-readr)
4871 ("r-readxl" ,r-readxl)
4872 ("r-rlang" ,r-rlang)
4873 ("r-rmarkdown" ,r-rmarkdown)
4874 ("r-rstudioapi" ,r-rstudioapi)
4875 ("r-scales" ,r-scales)
4876 ("r-shiny" ,r-shiny)
4877 ("r-shinyfiles" ,r-shinyfiles)
4878 ("r-shinyace" ,r-shinyace)
4879 ("r-stringi" ,r-stringi)
4880 ("r-tibble" ,r-tibble)
4881 ("r-tidyr" ,r-tidyr)
4882 ("r-writexl" ,r-writexl)))
4883 (home-page "https://github.com/radiant-rstats/radiant.data")
4884 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4886 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4887 visualizing, summarizing, transforming, and combining data. It also contains
4888 functionality to generate reproducible reports of the analyses conducted in
4890 (license license:agpl3)))
4892 (define-public r-algdesign
4894 (name "r-algdesign")
4895 (version "1.1-7.3.1")
4899 (uri (cran-uri "AlgDesign" version))
4901 (base32 "1s69yx0wxi9kqj9kyib0yvd363d7g4zrz0cvz1hn97ladr8656bz"))))
4902 (properties `((upstream-name . "AlgDesign")))
4903 (build-system r-build-system)
4904 (home-page "https://github.com/jvbraun/AlgDesign")
4905 (synopsis "Algorithmic experimental design")
4907 "This package provides tools to calculate exact and approximate theory
4908 experimental designs for D, A, and I criteria. Very large designs may be
4909 created. Experimental designs may be blocked or blocked designs created from
4910 a candidate list, using several criteria. The blocking can be done when whole
4911 and within plot factors interact.")
4912 (license license:gpl2+)))
4914 (define-public r-signal
4921 (uri (cran-uri "signal" version))
4924 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
4925 (build-system r-build-system)
4926 (propagated-inputs `(("r-mass" ,r-mass)))
4927 (native-inputs `(("gfortran" ,gfortran)))
4928 (home-page "https://cran.r-project.org/web/packages/signal/")
4929 (synopsis "Signal processing")
4931 "This package provides a set of signal processing functions originally
4932 written for Matlab and GNU Octave. It includes filter generation utilities,
4933 filtering functions, resampling routines, and visualization of filter models.
4934 It also includes interpolation functions.")
4935 (license license:gpl2)))
4937 (define-public r-gsubfn
4944 (uri (cran-uri "gsubfn" version))
4947 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
4948 (build-system r-build-system)
4949 (propagated-inputs `(("r-proto" ,r-proto)))
4950 (home-page "http://gsubfn.googlecode.com")
4951 (synopsis "Utilities for strings and function arguments.")
4953 "This package provides @code{gsubfn} which is like @code{gsub} but can
4954 take a replacement function or certain other objects instead of the
4955 replacement string. Matches and back references are input to the replacement
4956 function and replaced by the function output. @code{gsubfn} can be used to
4957 split strings based on content rather than delimiters and for quasi-perl-style
4958 string interpolation. The package also has facilities for translating
4959 formulas to functions and allowing such formulas in function calls instead of
4961 (license license:gpl2+)))
4963 (define-public r-sqldf
4970 (uri (cran-uri "sqldf" version))
4973 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
4974 (build-system r-build-system)
4976 `(("r-chron" ,r-chron)
4978 ("r-gsubfn" ,r-gsubfn)
4979 ("r-proto" ,r-proto)
4980 ("r-rsqlite" ,r-rsqlite)))
4981 (home-page "https://github.com/ggrothendieck/sqldf")
4982 (synopsis "Manipulate R data frames using SQL")
4984 "The @code{sqldf} function is typically passed a single argument which is
4985 an SQL select statement where the table names are ordinary R data frame names.
4986 @code{sqldf} transparently sets up a database, imports the data frames into
4987 that database, performs the SQL statement and returns the result using a
4988 heuristic to determine which class to assign to each column of the returned
4989 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
4990 used to read filtered files into R even if the original files are larger than
4991 R itself can handle.")
4992 (license license:gpl2)))
4994 (define-public r-abind
5001 (uri (cran-uri "abind" version))
5004 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5005 (build-system r-build-system)
5006 (home-page "https://cran.r-project.org/web/packages/abind/")
5007 (synopsis "Combine multidimensional arrays")
5009 "This package provides tools to combine multidimensional arrays into a
5010 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5011 works with vectors, matrices, and higher-dimensional arrays. It also provides
5012 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5013 extracting and replacing data in arrays.")
5014 (license license:lgpl2.0+)))
5016 (define-public r-prroc
5023 (uri (cran-uri "PRROC" version))
5026 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5027 (properties `((upstream-name . "PRROC")))
5028 (build-system r-build-system)
5029 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5030 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5032 "This package computes the areas under the @dfn{precision-recall} (PR)
5033 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5034 contrast to other implementations, the interpolation between points of the PR
5035 curve is done by a non-linear piecewise function. In addition to the areas
5036 under the curves, the curves themselves can also be computed and plotted by a
5037 specific S3-method.")
5038 (license license:gpl3)))
5040 (define-public r-vim
5047 (uri (cran-uri "VIM" version))
5050 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5051 (properties `((upstream-name . "VIM")))
5052 (build-system r-build-system)
5055 ("r-colorspace" ,r-colorspace)
5056 ("r-data-table" ,r-data-table)
5057 ("r-e1071" ,r-e1071)
5058 ("r-laeken" ,r-laeken)
5061 ("r-ranger" ,r-ranger)
5063 ("r-robustbase" ,r-robustbase)
5066 (home-page "https://github.com/alexkowa/VIM")
5067 (synopsis "Visualization and imputation of missing values")
5069 "This package provides tools for the visualization of missing and/or
5070 imputed values are introduced, which can be used for exploring the data and
5071 the structure of the missing and/or imputed values. Depending on this
5072 structure of the missing values, the corresponding methods may help to
5073 identify the mechanism generating the missing values and allows to explore the
5074 data including missing values. In addition, the quality of imputation can be
5075 visually explored using various univariate, bivariate, multiple and
5076 multivariate plot methods.")
5077 (license license:gpl2+)))
5079 (define-public r-fnn
5086 (uri (cran-uri "FNN" version))
5089 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5090 (properties `((upstream-name . "FNN")))
5091 (build-system r-build-system)
5092 (home-page "https://cran.r-project.org/web/packages/FNN")
5093 (synopsis "Fast nearest neighbor search algorithms and applications")
5095 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5096 search algorithms. Related applications including KNN classification,
5097 regression and information measures are implemented.")
5098 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5099 ;; later can be used.
5100 (license license:gpl2+)))
5102 (define-public r-smoother
5109 (uri (cran-uri "smoother" version))
5112 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5113 (build-system r-build-system)
5115 `(("r-ttr" ,r-ttr)))
5116 (home-page "http://cran.r-project.org/web/packages/smoother")
5117 (synopsis "Functions relating to the smoothing of numerical data")
5119 "This package provides a collection of methods for smoothing numerical
5120 data, commencing with a port of the Matlab gaussian window smoothing function.
5121 In addition, several functions typically used in smoothing of financial data
5123 (license license:gpl2)))
5125 (define-public r-riverplot
5127 (name "r-riverplot")
5132 (uri (cran-uri "riverplot" version))
5135 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5136 (build-system r-build-system)
5137 (home-page "https://logfc.wordpress.com")
5138 (synopsis "Sankey or ribbon plots")
5140 "Sankey plots are a type of diagram that is convenient to illustrate how
5141 flow of information, resources etc. separates and joins, much like observing
5142 how rivers split and merge. For example, they can be used to compare
5143 different clusterings. This package provides an implementation of Sankey
5145 (license license:gpl2+)))
5147 (define-public r-dyn
5154 (uri (cran-uri "dyn" version))
5157 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5158 (build-system r-build-system)
5160 `(("r-zoo" ,r-zoo)))
5161 (home-page "https://cran.r-project.org/web/packages/dyn")
5162 (synopsis "Time series regression")
5164 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5165 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5166 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5167 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5168 @code{randomForest::randomForest()} and other regression functions, allowing
5169 those functions to be used with time series including specifications that may
5170 contain lags, diffs and missing values.")
5172 (license license:gpl2+)))
5174 (define-public r-catdap
5181 (uri (cran-uri "catdap" version))
5184 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5185 (build-system r-build-system)
5187 `(("gfortran" ,gfortran)))
5188 (home-page "https://cran.r-project.org/web/packages/catdap/")
5189 (synopsis "Tools for categorical data analysis")
5191 "This package provides functions for analyzing multivariate data.
5192 Dependencies of the distribution of the specified variable (response
5193 variable) to other variables (explanatory variables) are derived and
5194 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5195 (license license:gpl2+)))
5197 (define-public r-arules
5204 (uri (cran-uri "arules" version))
5207 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5208 (build-system r-build-system)
5210 `(("r-matrix" ,r-matrix)))
5211 (home-page "https://github.com/mhahsler/arules")
5212 (synopsis "Mining association rules and frequent itemsets")
5214 "This package provides an infrastructure for representing, manipulating
5215 and analyzing transaction data and patterns (frequent itemsets and association rules).
5216 It also provides C implementations of the association mining algorithms Apriori
5218 (license license:gpl3)))
5220 (define-public r-parsedate
5222 (name "r-parsedate")
5227 (uri (cran-uri "parsedate" version))
5230 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5231 (build-system r-build-system)
5233 `(("r-rematch2" ,r-rematch2)))
5234 (home-page "https://github.com/gaborcsardi/parsedate")
5236 "Recognize and parse dates in various formats")
5238 "This package provides three functions for dealing with dates:
5239 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5240 time formats, @code{parse_date} parses dates in unspecified formats,
5241 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5242 (license license:gpl2)))
5244 (define-public r-abc-data
5251 (uri (cran-uri "abc.data" version))
5254 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5255 (properties `((upstream-name . "abc.data")))
5256 (build-system r-build-system)
5257 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5258 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5260 "This package contains data which are used by functions of the abc
5261 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5262 algorithms for performing parameter estimation, model selection, and
5264 (license license:gpl3+)))
5266 (define-public r-abc
5273 (uri (cran-uri "abc" version))
5276 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5277 (build-system r-build-system)
5279 `(("r-abc-data" ,r-abc-data)
5280 ("r-locfit" ,r-locfit)
5283 ("r-quantreg" ,r-quantreg)))
5284 (home-page "https://cran.r-project.org/web/packages/abc/")
5285 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5287 "This package implements several @dfn{Approximate Bayesian
5288 Computation} (ABC) algorithms for performing parameter estimation, model
5289 selection, and goodness-of-fit. Cross-validation tools are also available for
5290 measuring the accuracy of ABC estimates, and to calculate the
5291 misclassification probabilities of different models.")
5292 (license license:gpl3+)))
5294 (define-public r-zip
5301 (uri (cran-uri "zip" version))
5304 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5305 (build-system r-build-system)
5306 (home-page "https://github.com/gaborcsardi/zip")
5307 (synopsis "Cross-platform Zip compression")
5309 "This package provides a cross-platform Zip compression library for R.
5310 It is a replacement for the @code{zip} function, that does not require any
5311 additional external tools on any platform.")
5312 (license license:cc0)))
5314 (define-public r-openxlsx
5321 (uri (cran-uri "openxlsx" version))
5324 "087zivh9xdh1kk8zci67ys0m2xq0slzwgnf0jl05yy4gsgb6nmyx"))))
5325 (build-system r-build-system)
5327 `(("r-rcpp" ,r-rcpp)
5328 ("r-rlang" ,r-rlang)
5329 ("r-stringi" ,r-stringi)
5331 (home-page "https://github.com/awalker89/openxlsx")
5332 (synopsis "Read, write and edit XLSX files")
5334 "This package simplifies the creation of Excel @code{.xlsx} files by
5335 providing a high level interface to writing, styling and editing worksheets.
5336 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5337 and @code{XLConnect} packages with the added benefit of removing the
5338 dependency on Java.")
5339 (license license:gpl3)))
5341 (define-public r-rio
5348 (uri (cran-uri "rio" version))
5351 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5352 (build-system r-build-system)
5354 `(("r-curl" ,r-curl)
5355 ("r-data-table" ,r-data-table)
5356 ("r-foreign" ,r-foreign)
5357 ("r-haven" ,r-haven)
5358 ("r-openxlsx" ,r-openxlsx)
5359 ("r-readxl" ,r-readxl)
5360 ("r-tibble" ,r-tibble)))
5361 (home-page "https://github.com/leeper/rio")
5362 (synopsis "Swiss-army knife for data I/O")
5364 "This package provides streamlined data import and export infrastructure
5365 by making assumptions that the user is probably willing to make: @code{import}
5366 and @code{export} determine the data structure from the file extension,
5367 reasonable defaults are used for data import and export (e.g.,
5368 @code{stringsAsFactors=FALSE}), web-based import is natively
5369 supported (including from SSL/HTTPS), compressed files can be read directly
5370 without explicit decompression, and fast import packages are used where
5371 appropriate. An additional convenience function, @code{convert}, provides a
5372 simple method for converting between file types.")
5373 (license license:gpl2)))
5375 (define-public r-maptools
5382 (uri (cran-uri "maptools" version))
5385 "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
5386 (build-system r-build-system)
5388 `(("r-foreign" ,r-foreign)
5389 ("r-lattice" ,r-lattice)
5391 (home-page "http://r-forge.r-project.org/projects/maptools/")
5392 (synopsis "Tools for reading and handling spatial objects")
5394 "This package provides a set of tools for manipulating and reading
5395 geographic data, in particular ESRI Shapefiles. It includes binary access to
5396 GSHHG shoreline files. The package also provides interface wrappers for
5397 exchanging spatial objects with other R packages.")
5398 ;; The C source files from shapelib are released under the Expat license.
5399 ;; The R code is released under GPL version 2 or later.
5400 (license (list license:gpl2+
5403 (define-public r-later
5410 (uri (cran-uri "later" version))
5413 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5414 (build-system r-build-system)
5418 ("r-rlang" ,r-rlang)))
5419 (home-page "https://github.com/r-lib/later")
5420 (synopsis "Utilities for delaying function execution")
5422 "This package provides tools to execute arbitrary R or C functions some
5423 time after the current time, after the R execution stack has emptied.")
5424 (license license:gpl2+)))
5426 (define-public r-promises
5433 (uri (cran-uri "promises" version))
5436 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5437 (build-system r-build-system)
5439 `(("r-later" ,r-later)
5440 ("r-magrittr" ,r-magrittr)
5443 ("r-rlang" ,r-rlang)))
5444 (home-page "https://rstudio.github.io/promises")
5445 (synopsis "Abstractions for promise-based asynchronous programming")
5447 "This package provides fundamental abstractions for doing asynchronous
5448 programming in R using promises. Asynchronous programming is useful for
5449 allowing a single R process to orchestrate multiple tasks in the background
5450 while also attending to something else. Semantics are similar to JavaScript
5451 promises, but with a syntax that is idiomatic R.")
5452 (license license:expat)))
5454 (define-public r-dosnow
5461 (uri (cran-uri "doSNOW" version))
5464 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5465 (properties `((upstream-name . "doSNOW")))
5466 (build-system r-build-system)
5468 `(("r-foreach" ,r-foreach)
5469 ("r-iterators" ,r-iterators)
5470 ("r-snow" ,r-snow)))
5471 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5472 (synopsis "Foreach parallel adaptor for the snow package")
5474 "This package provides a parallel backend for the @code{%dopar%} function
5475 using the @code{snow} package.")
5476 (license license:gpl2)))
5478 (define-public r-snowfall
5481 (version "1.84-6.1")
5484 (uri (cran-uri "snowfall" version))
5486 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5487 (build-system r-build-system)
5489 `(("r-snow" ,r-snow)))
5490 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5491 (synopsis "Easier cluster computing")
5492 (description "This package is a usability wrapper around snow for easier
5493 development of parallel R programs. This package offers e.g. extended error
5494 checks, and additional functions. All functions work in sequential mode, too,
5495 if no cluster is present or wished. The package is also designed as connector
5496 to the cluster management tool @code{sfCluster}, but can also used without
5498 (license license:gpl2+)))
5500 (define-public r-rappdirs
5507 (uri (cran-uri "rappdirs" version))
5510 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5511 (build-system r-build-system)
5512 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5513 (synopsis "Determine where to save data, caches, and logs")
5515 "This package provides an easy way to determine which directories on the
5516 user's computer should be used to save data, caches and logs. It is a port of
5517 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5518 (license license:expat)))
5520 (define-public r-renv
5527 (uri (cran-uri "renv" version))
5530 "0034jlaq7z40q3hcpkjlaff37dpn46kvxvzw4scbwlw4x9q8sx9j"))))
5531 (properties `((upstream-name . "renv")))
5532 (build-system r-build-system)
5533 (home-page "https://rstudio.github.io/renv")
5534 (synopsis "Project environments")
5536 "This package provides a dependency management toolkit for R. Using
5537 renv, you can create and manage project-local R libraries, save the state of
5538 these libraries to a lockfile, and later restore your library as required.
5539 Together, these tools can help make your projects more isolated, portable, and
5541 (license license:expat)))
5543 (define-public r-learnr
5550 (uri (cran-uri "learnr" version))
5553 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5554 (build-system r-build-system)
5556 `(("r-checkmate" ,r-checkmate)
5557 ("r-ellipsis" ,r-ellipsis)
5558 ("r-evaluate" ,r-evaluate)
5559 ("r-htmltools" ,r-htmltools)
5560 ("r-htmlwidgets" ,r-htmlwidgets)
5561 ("r-jsonlite" ,r-jsonlite)
5562 ("r-knitr" ,r-knitr)
5563 ("r-markdown" ,r-markdown)
5564 ("r-rappdirs" ,r-rappdirs)
5566 ("r-rmarkdown" ,r-rmarkdown)
5567 ("r-rprojroot" ,r-rprojroot)
5568 ("r-shiny" ,r-shiny)
5569 ("r-withr" ,r-withr)))
5570 (home-page "https://rstudio.github.io/learnr/")
5571 (synopsis "Interactive tutorials for R")
5573 "This package provides tools to create interactive tutorials using R
5574 Markdown. Use a combination of narrative, figures, videos, exercises, and
5575 quizzes to create self-paced tutorials for learning about R and R packages.")
5576 (license license:asl2.0)))
5578 (define-public r-analytics
5580 (name "r-analytics")
5585 (uri (cran-uri "analytics" version))
5588 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5589 (build-system r-build-system)
5592 ("r-cluster" ,r-cluster)
5593 ("r-fractal" ,r-fractal)
5594 ("r-lmtest" ,r-lmtest)
5597 ("r-powerplus" ,r-powerplus)
5598 ("r-robust" ,r-robust)
5599 ("r-trend" ,r-trend)
5603 (home-page "https://cran.r-project.org/web/packages/analytics/")
5604 (synopsis "Collection of data analysis tools")
5606 "This package is a collection of data analysis tools. It includes tools
5607 for regression outlier detection in a fitted linear model, stationary
5608 bootstrap using a truncated geometric distribution, a comprehensive test for
5609 weak stationarity, column means by group, weighted biplots, and a heuristic to
5610 obtain a better initial configuration in non-metric MDS.")
5611 (license license:gpl2)))
5613 (define-public r-reticulate
5615 (name "r-reticulate")
5620 (uri (cran-uri "reticulate" version))
5623 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5624 (build-system r-build-system)
5625 (inputs `(("python" ,python)))
5627 `(("r-jsonlite" ,r-jsonlite)
5628 ("r-matrix" ,r-matrix)
5629 ("r-rcpp" ,r-rcpp)))
5630 (home-page "https://github.com/rstudio/reticulate")
5631 (synopsis "R interface to Python")
5633 "This package provides an interface from R to Python modules, classes,
5634 and functions. When calling into Python, R data types are automatically
5635 converted to their equivalent Python types. When values are returned from
5636 Python to R they are converted back to R types.")
5637 (license license:asl2.0)))
5639 (define-public r-bibtex
5646 (uri (cran-uri "bibtex" version))
5649 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5650 (build-system r-build-system)
5651 (propagated-inputs `(("r-stringr" ,r-stringr)))
5652 (home-page "https://github.com/romainfrancois/bibtex")
5653 (synopsis "Bibtex parser")
5654 (description "This package provides a utility for R to parse a bibtex
5656 (license license:gpl2+)))
5658 (define-public r-ggseqlogo
5660 (name "r-ggseqlogo")
5665 (uri (cran-uri "ggseqlogo" version))
5668 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5669 (build-system r-build-system)
5670 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5671 (home-page "https://github.com/omarwagih/ggseqlogo")
5672 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5674 "The range of functions provided by this package makes it possible to
5675 draw highly versatile genomic sequence logos. Features include, but are not
5676 limited to, modifying colour schemes and fonts used to draw the logo,
5677 generating multiple logo plots, and aiding the visualisation with annotations.
5678 Sequence logos can easily be combined with other ggplot2 plots.")
5679 ;; Unspecified version of the LGPL.
5680 (license license:lgpl3+)))
5682 (define-public r-ggsci
5689 (uri (cran-uri "ggsci" version))
5692 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5693 (build-system r-build-system)
5695 `(("r-ggplot2" ,r-ggplot2)
5696 ("r-scales" ,r-scales)))
5697 (home-page "https://nanx.me/ggsci/")
5698 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5700 "This package provides a collection of ggplot2 color palettes inspired by
5701 plots in scientific journals, data visualization libraries, science fiction
5702 movies, and TV shows.")
5703 (license license:gpl3)))
5705 (define-public r-ggsignif
5712 (uri (cran-uri "ggsignif" version))
5715 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5716 (build-system r-build-system)
5718 `(("r-ggplot2" ,r-ggplot2)))
5719 (home-page "https://github.com/const-ae/ggsignif")
5720 (synopsis "Significance brackets for ggplot2")
5722 "Enrich your ggplots with group-wise comparisons. This package provides
5723 an easy way to indicate if two groups are significantly different. Commonly
5724 this is shown by a bracket on top connecting the groups of interest which
5725 itself is annotated with the level of significance. The package provides a
5726 single layer that takes the groups for comparison and the test as arguments
5727 and adds the annotation to the plot.")
5728 (license license:gpl3)))
5730 (define-public r-ggpubr
5737 (uri (cran-uri "ggpubr" version))
5740 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5741 (build-system r-build-system)
5743 `(("r-cowplot" ,r-cowplot)
5744 ("r-dplyr" ,r-dplyr)
5745 ("r-ggplot2" ,r-ggplot2)
5746 ("r-ggrepel" ,r-ggrepel)
5747 ("r-ggsci" ,r-ggsci)
5748 ("r-ggsignif" ,r-ggsignif)
5750 ("r-gridextra" ,r-gridextra)
5751 ("r-magrittr" ,r-magrittr)
5752 ("r-polynom" ,r-polynom)
5753 ("r-purrr" ,r-purrr)
5754 ("r-rlang" ,r-rlang)
5755 ("r-scales" ,r-scales)
5756 ("r-tidyr" ,r-tidyr)))
5757 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5758 (synopsis "ggplot2-based publication-ready plots")
5760 "The ggplot2 package is an excellent and flexible package for elegant
5761 data visualization in R. However the default generated plots require some
5762 formatting before we can send them for publication. The ggpubr package
5763 provides some easy-to-use functions for creating and customizing ggplot2-based
5764 publication-ready plots.")
5765 (license license:gpl2)))
5767 (define-public r-ellipse
5774 (uri (cran-uri "ellipse" version))
5777 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5778 (build-system r-build-system)
5779 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5780 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5782 "This package contains various routines for drawing ellipses and
5783 ellipse-like confidence regions, implementing the plots described in Murdoch
5784 and Chow (1996), A graphical display of large correlation matrices, The
5785 American Statistician 50, 178-180. There are also routines implementing the
5786 profile plots described in Bates and Watts (1988), Nonlinear Regression
5787 Analysis and its Applications.")
5788 (license license:gpl2+)))
5790 (define-public r-flashclust
5792 (name "r-flashclust")
5797 (uri (cran-uri "flashClust" version))
5800 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5801 (properties `((upstream-name . "flashClust")))
5802 (build-system r-build-system)
5803 (native-inputs `(("gfortran" ,gfortran)))
5804 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5805 (synopsis "Implementation of optimal hierarchical clustering")
5807 "This package provides a fast implementation of hierarchical
5809 (license license:gpl2+)))
5811 (define-public r-factominer
5813 (name "r-factominer")
5818 (uri (cran-uri "FactoMineR" version))
5821 "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
5822 (properties `((upstream-name . "FactoMineR")))
5823 (build-system r-build-system)
5826 ("r-cluster" ,r-cluster)
5827 ("r-ellipse" ,r-ellipse)
5828 ("r-flashclust" ,r-flashclust)
5829 ("r-lattice" ,r-lattice)
5830 ("r-leaps" ,r-leaps)
5832 ("r-scatterplot3d" ,r-scatterplot3d)))
5833 (home-page "http://factominer.free.fr")
5834 (synopsis "Multivariate exploratory data analysis and data mining")
5836 "This package provides exploratory data analysis methods to summarize,
5837 visualize and describe datasets. The main principal component methods are
5838 available, those with the largest potential in terms of applications:
5839 principal component analysis (PCA) when variables are quantitative,
5840 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5841 variables are categorical, Multiple Factor Analysis when variables are
5842 structured in groups, etc. and hierarchical cluster analysis.")
5843 (license license:gpl2+)))
5845 (define-public r-factoextra
5847 (name "r-factoextra")
5852 (uri (cran-uri "factoextra" version))
5855 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
5856 (build-system r-build-system)
5858 `(("r-abind" ,r-abind)
5859 ("r-cluster" ,r-cluster)
5860 ("r-dendextend" ,r-dendextend)
5861 ("r-factominer" ,r-factominer)
5862 ("r-ggplot2" ,r-ggplot2)
5863 ("r-ggpubr" ,r-ggpubr)
5864 ("r-ggrepel" ,r-ggrepel)
5865 ("r-reshape2" ,r-reshape2)
5866 ("r-tidyr" ,r-tidyr)))
5867 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5868 (synopsis "Extract and visualize the results of multivariate data analyses")
5870 "This package provides some easy-to-use functions to extract and
5871 visualize the output of multivariate data analyses, including
5872 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5873 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5874 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5875 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5876 packages. It contains also functions for simplifying some clustering analysis
5877 steps and provides ggplot2-based elegant data visualization.")
5878 (license license:gpl2)))
5880 (define-public r-fansi
5887 (uri (cran-uri "fansi" version))
5890 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5891 (build-system r-build-system)
5893 `(("r-knitr" ,r-knitr))) ; for vignettes
5894 (home-page "https://github.com/brodieG/fansi")
5895 (synopsis "ANSI control sequence aware string functions")
5897 "This package provides counterparts to R string manipulation functions
5898 that account for the effects of ANSI text formatting control sequences.")
5899 (license license:gpl2+)))
5901 (define-public r-nbclust
5908 (uri (cran-uri "NbClust" version))
5911 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5912 (properties `((upstream-name . "NbClust")))
5913 (build-system r-build-system)
5914 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5915 (synopsis "Determine the best number of clusters in a data set")
5917 "NbClust provides 30 indexes for determining the optimal number of
5918 clusters in a data set and offers the best clustering scheme from different
5919 results to the user.")
5920 (license license:gpl2)))
5922 (define-public r-hdf5r
5929 (uri (cran-uri "hdf5r" version))
5932 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
5933 (build-system r-build-system)
5938 `(("r-bit64" ,r-bit64)
5940 (home-page "https://hhoeflin.github.io/hdf5r")
5941 (synopsis "Interface to the HDF5 binary data format")
5943 "HDF5 is a data model, library and file format for storing and managing
5944 large amounts of data. This package provides a nearly feature complete,
5945 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
5946 functionality is added so that HDF5 objects behave very similar to their
5947 corresponding R counterparts.")
5948 (license license:asl2.0)))
5950 (define-public r-itertools
5952 (name "r-itertools")
5957 (uri (cran-uri "itertools" version))
5960 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
5961 (build-system r-build-system)
5963 `(("r-iterators" ,r-iterators)))
5964 (home-page "https://cran.r-project.org/web/packages/itertools/")
5965 (synopsis "Iterator tools")
5967 "This package provides various tools for creating iterators, many
5968 patterned after functions in the Python @code{itertools} module, and others
5969 patterned after functions in the snow package.")
5970 (license license:gpl2)))
5972 (define-public r-polynom
5979 (uri (cran-uri "polynom" version))
5982 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
5983 (build-system r-build-system)
5984 (home-page "https://cran.r-project.org/web/packages/polynom/")
5985 (synopsis "Functions for univariate polynomial manipulations")
5987 "This package provides a collection of functions to implement a class for
5988 univariate polynomial manipulations.")
5989 (license license:gpl2)))
5991 (define-public r-gbrd
5998 (uri (cran-uri "gbRd" version))
6001 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6002 (properties `((upstream-name . "gbRd")))
6003 (build-system r-build-system)
6004 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6005 (synopsis "Utilities for processing Rd objects and files")
6007 "This package provides utilities for processing Rd objects and files.
6008 Extract argument descriptions and other parts of the help pages of
6010 (license license:gpl2+)))
6012 (define-public r-rjags
6019 (uri (cran-uri "rjags" version))
6022 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6023 (build-system r-build-system)
6025 `(("r-coda" ,r-coda)))
6029 `(("pkg-config" ,pkg-config)))
6030 (home-page "http://mcmc-jags.sourceforge.net")
6031 (synopsis "Bayesian graphical models using MCMC")
6033 "This package provides an R interface to the JAGS MCMC library. JAGS is
6034 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6035 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6036 (license license:gpl2)))
6038 (define-public r-rdpack
6045 (uri (cran-uri "Rdpack" version))
6048 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
6049 (properties `((upstream-name . "Rdpack")))
6050 (build-system r-build-system)
6052 `(("r-bibtex" ,r-bibtex)
6053 ("r-gbrd" ,r-gbrd)))
6054 (home-page "https://github.com/GeoBosh/Rdpack")
6055 (synopsis "Update and manipulate Rd documentation objects")
6057 "This package provides functions for manipulation of R documentation
6058 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6059 updating Rd documentation for functions, methods and classes; it also includes
6060 Rd macros for citations and import of references from bibtex files for use in
6061 Rd files and roxygen2 comments, as well as many functions for manipulation of
6062 references and Rd files.")
6063 (license license:gpl2+)))
6065 (define-public r-officer
6072 (uri (cran-uri "officer" version))
6075 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6076 (build-system r-build-system)
6078 `(("r-base64enc" ,r-base64enc)
6079 ("r-digest" ,r-digest)
6080 ("r-htmltools" ,r-htmltools)
6081 ("r-magrittr" ,r-magrittr)
6084 ("r-rlang" ,r-rlang)
6088 (home-page "https://davidgohel.github.io/officer")
6089 (synopsis "Manipulation of Word and PowerPoint documents")
6091 "This package provides tools to access and manipulate Word and PowerPoint
6092 documents from R. The package focuses on tabular and graphical reporting from
6093 R; it also provides two functions that let users get document content into
6094 data objects. A set of functions lets add and remove images, tables and
6095 paragraphs of text in new or existing documents. When working with PowerPoint
6096 presentations, slides can be added or removed; shapes inside slides can also
6097 be added or removed. When working with Word documents, a cursor can be used
6098 to help insert or delete content at a specific location in the document.")
6099 (license license:gpl3)))
6101 (define-public r-abn
6108 (uri (cran-uri "abn" version))
6111 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6112 (build-system r-build-system)
6116 `(("r-lme4" ,r-lme4)
6120 ("r-rcpparmadillo" ,r-rcpparmadillo)
6121 ("r-rjags" ,r-rjags)))
6122 (home-page "http://www.r-bayesian-networks.org")
6123 (synopsis "Modelling multivariate data with additive bayesian networks")
6125 "Bayesian network analysis is a form of probabilistic graphical models
6126 which derives from empirical data a directed acyclic graph, DAG, describing
6127 the dependency structure between random variables. An additive Bayesian
6128 network model consists of a form of a DAG where each node comprises a
6129 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6130 equivalent to Bayesian multivariate regression using graphical modelling, they
6131 generalises the usual multivariable regression, GLM, to multiple dependent
6132 variables. This package provides routines to help determine optimal Bayesian
6133 network models for a given data set, where these models are used to identify
6134 statistical dependencies in messy, complex data.")
6135 (license license:gpl2+)))
6137 (define-public r-acd
6144 (uri (cran-uri "ACD" version))
6147 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6148 (properties `((upstream-name . "ACD")))
6149 (build-system r-build-system)
6150 (home-page "https://cran.r-project.org/web/packages/ACD/")
6151 (synopsis "Categorical data analysis with complete or missing responses")
6153 "This package provides tools for categorical data analysis with complete
6154 or missing responses.")
6155 (license license:gpl2+)))
6157 (define-public r-acdm
6164 (uri (cran-uri "ACDm" version))
6167 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6168 (properties `((upstream-name . "ACDm")))
6169 (build-system r-build-system)
6171 `(("r-dplyr" ,r-dplyr)
6172 ("r-ggplot2" ,r-ggplot2)
6174 ("r-rsolnp" ,r-rsolnp)
6176 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6177 (synopsis "Tools for Autoregressive Conditional Duration Models")
6179 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6180 and Russell, 1998) models. It creates trade, price or volume durations from
6181 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6183 (license license:gpl2+)))
6185 (define-public r-overlap
6192 (uri (cran-uri "overlap" version))
6195 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6196 (build-system r-build-system)
6197 (home-page "https://cran.r-project.org/web/packages/overlap/")
6198 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6200 "This package provides functions to fit kernel density functions to data
6201 on temporal activity patterns of animals; estimate coefficients of overlapping
6202 of densities for two species; and calculate bootstrap estimates of confidence
6204 (license license:gpl3+)))
6206 (define-public r-snakecase
6208 (name "r-snakecase")
6213 (uri (cran-uri "snakecase" version))
6216 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6217 (build-system r-build-system)
6219 `(("r-stringi" ,r-stringi)
6220 ("r-stringr" ,r-stringr)))
6221 (home-page "https://github.com/Tazinho/snakecase")
6222 (synopsis "Convert strings into any case")
6224 "This package provides a consistent, flexible and easy to use tool to
6225 parse and convert strings into cases like snake or camel among others.")
6226 (license license:gpl3)))
6228 (define-public r-prediction
6230 (name "r-prediction")
6235 (uri (cran-uri "prediction" version))
6238 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6239 (build-system r-build-system)
6241 `(("r-data-table" ,r-data-table)))
6242 (home-page "https://github.com/leeper/prediction")
6243 (synopsis "Tidy, type-safe prediction methods")
6245 "This package provides the @code{prediction()} function, a type-safe
6246 alternative to @code{predict()} that always returns a data frame. The package
6247 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6248 from the @code{stats} package, as well as numerous other model classes from
6249 other add-on packages.")
6250 (license license:expat)))
6252 (define-public r-insight
6259 (uri (cran-uri "insight" version))
6262 "1alxc483r3d1ydp983m2872mxd4nj3j25qv47zzgj10nbi4y32sq"))))
6263 (build-system r-build-system)
6264 (home-page "https://easystats.github.io/insight/")
6265 (synopsis "Easy access to model information for various model objects")
6267 "This package provides a tool to provide an easy, intuitive and
6268 consistent access to information contained in various R models, like model
6269 formulas, model terms, information about random effects, data that was used to
6270 fit the model or data from response variables. The package mainly revolves
6271 around two types of functions: Functions that find (the names of) information,
6272 starting with @code{find_}, and functions that get the underlying data,
6273 starting with @code{get_}. The package has a consistent syntax and works with
6274 many different model objects, where otherwise functions to access these
6275 information are missing.")
6276 (license license:gpl3)))
6278 (define-public r-sjlabelled
6280 (name "r-sjlabelled")
6285 (uri (cran-uri "sjlabelled" version))
6288 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6289 (build-system r-build-system)
6291 `(("r-haven" ,r-haven)
6292 ("r-insight" ,r-insight)
6293 ("r-magrittr" ,r-magrittr)
6294 ("r-purrr" ,r-purrr)
6295 ("r-rlang" ,r-rlang)
6296 ("r-tidyselect" ,r-tidyselect)))
6297 (home-page "https://github.com/strengejacke/sjlabelled")
6298 (synopsis "Labelled data utility functions")
6300 "This package provides a collection of functions dealing with labelled
6301 data, like reading and writing data between R and other statistical software
6302 packages. This includes easy ways to get, set or change value and variable
6303 label attributes, to convert labelled vectors into factors or numeric (and
6304 vice versa), or to deal with multiple declared missing values.")
6305 (license license:gpl3)))
6307 (define-public r-sjmisc
6314 (uri (cran-uri "sjmisc" version))
6317 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6318 (build-system r-build-system)
6320 `(("r-dplyr" ,r-dplyr)
6321 ("r-insight" ,r-insight)
6322 ("r-magrittr" ,r-magrittr)
6323 ("r-purrr" ,r-purrr)
6324 ("r-rlang" ,r-rlang)
6325 ("r-sjlabelled" ,r-sjlabelled)
6326 ("r-tidyselect" ,r-tidyselect)))
6327 (home-page "https://github.com/strengejacke/sjmisc")
6328 (synopsis "Data and variable transformation functions")
6330 "This package is a collection of miscellaneous utility functions,
6331 supporting data transformation tasks like recoding, dichotomizing or grouping
6332 variables, setting and replacing missing values. The data transformation
6333 functions also support labelled data, and all integrate seamlessly into a
6334 tidyverse workflow.")
6335 (license license:gpl3)))
6337 (define-public r-nortest
6344 (uri (cran-uri "nortest" version))
6347 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6348 (build-system r-build-system)
6349 (home-page "https://cran.r-project.org/web/packages/nortest/")
6350 (synopsis "Tests for normality")
6352 "This package provides five omnibus tests for testing the composite
6353 hypothesis of normality.")
6354 (license license:gpl2+)))
6356 (define-public r-moonbook
6363 (uri (cran-uri "moonBook" version))
6366 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6367 (properties `((upstream-name . "moonBook")))
6368 (build-system r-build-system)
6370 `(("r-magrittr" ,r-magrittr)
6371 ("r-nortest" ,r-nortest)
6372 ("r-purrr" ,r-purrr)
6373 ("r-sjmisc" ,r-sjmisc)
6374 ("r-stringr" ,r-stringr)
6375 ("r-survival" ,r-survival)))
6376 (home-page "https://github.com/cardiomoon/moonBook")
6377 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6379 "This package provides several analysis-related functions for the book
6380 entitled \"R statistics and graph for medical articles\" (written in Korean),
6381 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6383 (license license:gpl2)))
6385 (define-public r-flextable
6387 (name "r-flextable")
6392 (uri (cran-uri "flextable" version))
6395 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6396 (build-system r-build-system)
6398 `(("r-base64enc" ,r-base64enc)
6399 ("r-data-table" ,r-data-table)
6400 ("r-gdtools" ,r-gdtools)
6401 ("r-htmltools" ,r-htmltools)
6402 ("r-knitr" ,r-knitr)
6403 ("r-officer" ,r-officer)
6404 ("r-rlang" ,r-rlang)
6405 ("r-rmarkdown" ,r-rmarkdown)
6406 ("r-xml2" ,r-xml2)))
6407 (home-page "https://davidgohel.github.io/flextable")
6408 (synopsis "Functions for tabular reporting")
6410 "This package provides tools to create pretty tables for HTML documents
6411 and other formats. Functions are provided to let users create tables, modify
6412 and format their content. It extends the @code{officer} package and can be
6413 used within R markdown documents when rendering to HTML and to Word
6415 (license license:gpl3)))
6417 (define-public r-writexl
6424 (uri (cran-uri "writexl" version))
6427 "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
6428 (build-system r-build-system)
6429 (inputs `(("zlib" ,zlib)))
6430 (home-page "https://github.com/ropensci/writexl")
6431 (synopsis "Export data frames to xlsx format")
6433 "This package provides a data frame to xlsx exporter based on
6435 (license license:bsd-2)))
6437 (define-public r-biasedurn
6439 (name "r-biasedurn")
6444 (uri (cran-uri "BiasedUrn" version))
6447 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6448 (properties `((upstream-name . "BiasedUrn")))
6449 (build-system r-build-system)
6450 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6451 (synopsis "Biased Urn model distributions")
6453 "This package provides statistical models of biased sampling in the form
6454 of univariate and multivariate noncentral hypergeometric distributions,
6455 including Wallenius' noncentral hypergeometric distribution and Fisher's
6456 noncentral hypergeometric distribution (also called extended hypergeometric
6458 (license license:gpl3)))
6460 (define-public r-goplot
6467 (uri (cran-uri "GOplot" version))
6470 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6471 (properties `((upstream-name . "GOplot")))
6472 (build-system r-build-system)
6474 `(("r-ggdendro" ,r-ggdendro)
6475 ("r-ggplot2" ,r-ggplot2)
6476 ("r-gridextra" ,r-gridextra)
6477 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6478 (home-page "https://github.com/wencke/wencke.github.io")
6479 (synopsis "Visualization of functional analysis data")
6481 "This package provides an implementation of multilayered visualizations
6482 for enhanced graphical representation of functional analysis data. It
6483 combines and integrates omics data derived from expression and functional
6484 annotation enrichment analyses. Its plotting functions have been developed
6485 with an hierarchical structure in mind: starting from a general overview to
6486 identify the most enriched categories (modified bar plot, bubble plot) to a
6487 more detailed one displaying different types of relevant information for the
6488 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6489 Venn diagram, heatmap).")
6490 (license license:gpl2)))
6492 (define-public r-getopt
6499 (uri (cran-uri "getopt" version))
6502 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6503 (build-system r-build-system)
6504 (home-page "https://github.com/trevorld/getopt")
6505 (synopsis "Command-line option processor for R")
6507 "This package is designed to be used with Rscript to write shebang
6508 scripts that accept short and long options. Many users will prefer to
6509 use the packages @code{optparse} or @code{argparse} which add extra
6510 features like automatically generated help options and usage texts,
6511 support for default values, positional argument support, etc.")
6512 (license license:gpl2+)))
6514 (define-public r-findpython
6516 (name "r-findpython")
6521 (uri (cran-uri "findpython" version))
6524 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6525 (build-system r-build-system)
6526 (home-page "https://github.com/trevorld/findpython")
6527 (synopsis "Functions to find an acceptable Python binary")
6529 "This package was designed to find an acceptable Python binary that
6530 matches version and feature constraints.")
6531 (license license:expat)))
6533 ;; This in not the same as "r-argparser"
6534 (define-public r-argparse
6541 (uri (cran-uri "argparse" version))
6544 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6545 (build-system r-build-system)
6546 (inputs `(("python" ,python)))
6548 `(("r-findpython" ,r-findpython)
6549 ("r-jsonlite" ,r-jsonlite)
6551 (home-page "https://github.com/trevorld/argparse")
6552 (synopsis "Command line optional and positional argument parser")
6554 "This package provides a command line parser to be used with Rscript to
6555 write shebang scripts that gracefully accept positional and optional arguments
6556 and automatically generate usage notices.")
6557 (license license:gpl2+)))
6559 (define-public r-hash
6566 (uri (cran-uri "hash" version))
6569 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6570 (build-system r-build-system)
6571 (home-page "https://cran.r-project.org/web/packages/hash/")
6572 (synopsis "Implementation of hash/associated arrays/dictionaries")
6574 "This package implements a data structure similar to hashes in Perl and
6575 dictionaries in Python but with a purposefully R flavor. For objects of
6576 appreciable size, access using hashes outperforms native named lists and
6578 (license license:gpl2+)))
6580 (define-public r-orddom
6587 (uri (cran-uri "orddom" version))
6590 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6591 (build-system r-build-system)
6592 (propagated-inputs `(("r-psych" ,r-psych)))
6593 (home-page "https://cran.r-project.org/web/packages/orddom/")
6594 (synopsis "Ordinal dominance statistics")
6596 "This package provides tools to compute ordinal, statistics and effect
6597 sizes as an alternative to mean comparison: Cliff's delta or success rate
6598 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6599 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6600 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6601 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6602 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6603 Group (Non-)Overlap considerations.")
6604 (license license:gpl2)))
6606 (define-public r-deriv
6613 (uri (cran-uri "Deriv" version))
6616 "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
6617 (properties `((upstream-name . "Deriv")))
6618 (build-system r-build-system)
6619 (home-page "https://cran.r-project.org/web/packages/Deriv")
6620 (synopsis "Symbolic differentiation")
6622 "This package provides an R-based solution for symbolic differentiation.
6623 It admits user-defined functions as well as function substitution in arguments
6624 of functions to be differentiated. Some symbolic simplification is part of
6626 (license license:gpl3+)))
6628 (define-public r-doby
6635 (uri (cran-uri "doBy" version))
6638 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6639 (properties `((upstream-name . "doBy")))
6640 (build-system r-build-system)
6642 `(("r-broom" ,r-broom)
6643 ("r-deriv" ,r-deriv)
6644 ("r-dplyr" ,r-dplyr)
6645 ("r-magrittr" ,r-magrittr)
6647 ("r-matrix" ,r-matrix)
6649 ("r-pbkrtest" ,r-pbkrtest)
6650 ("r-tibble" ,r-tibble)))
6651 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6652 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6654 "This package contains:
6657 @item facilities for working with grouped data: @code{do}
6658 something to data stratified @code{by} some variables.
6659 @item implementations of least-squares means, general linear contrasts, and
6660 @item miscellaneous other utilities.
6662 (license license:gpl2+)))
6664 (define-public r-refgenome
6666 (name "r-refgenome")
6671 (uri (cran-uri "refGenome" version))
6674 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6675 (properties `((upstream-name . "refGenome")))
6676 (build-system r-build-system)
6680 ("r-rsqlite" ,r-rsqlite)))
6681 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6683 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6685 "This package contains functionality for importing and managing of
6686 downloaded genome annotation data from the Ensembl genome browser (European
6687 Bioinformatics Institute) and from the UCSC genome browser (University of
6688 California, Santa Cruz) and annotation routines for genomic positions and
6689 splice site positions.")
6690 (license license:gpl2)))
6692 (define-public r-basix
6699 (uri (cran-uri "BASIX" version))
6702 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6703 (properties `((upstream-name . "BASIX")))
6704 (build-system r-build-system)
6705 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6706 (synopsis "Efficient C/C++ toolset for R")
6708 "BASIX provides some efficient C/C++ implementations of native R
6709 procedures to speed up calculations in R.")
6710 (license license:gpl2)))
6712 (define-public r-blockfest
6714 (name "r-blockfest")
6719 (uri (cran-uri "BlockFeST" version))
6722 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6723 (properties `((upstream-name . "BlockFeST")))
6724 (build-system r-build-system)
6725 (propagated-inputs `(("r-basix" ,r-basix)))
6726 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6727 (synopsis "Bayesian calculation of region-specific fixation index")
6729 "This package provides an R implementation of an extension of the
6730 BayeScan software for codominant markers, adding the option to group
6731 individual SNPs into pre-defined blocks. A typical application of this new
6732 approach is the identification of genomic regions, genes, or gene sets
6733 containing one or more SNPs that evolved under directional selection.")
6734 (license license:gpl2)))
6736 (define-public r-proc
6743 (uri (cran-uri "pROC" version))
6746 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6747 (properties `((upstream-name . "pROC")))
6748 (build-system r-build-system)
6750 `(("r-plyr" ,r-plyr)
6751 ("r-rcpp" ,r-rcpp)))
6752 (home-page "http://expasy.org/tools/pROC/")
6753 (synopsis "Display and analyze ROC curves")
6755 "This package provides tools for visualizing, smoothing and comparing
6756 receiver operating characteristic (ROC curves). The area under the
6757 curve (AUC) can be compared with statistical tests based on U-statistics or
6758 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6759 (license license:gpl3+)))
6761 (define-public r-rootsolve
6763 (name "r-rootsolve")
6768 (uri (cran-uri "rootSolve" version))
6771 "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx"))))
6772 (properties `((upstream-name . "rootSolve")))
6773 (build-system r-build-system)
6774 (native-inputs `(("gfortran" ,gfortran)))
6775 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6776 (synopsis "Tools for the analysis of ordinary differential equations")
6778 "This package provides routines to find the root of nonlinear functions,
6779 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6780 differential equations} (ODE). It includes routines that:
6783 @item generate gradient and jacobian matrices (full and banded),
6784 @item find roots of non-linear equations by the Newton-Raphson method,
6785 @item estimate steady-state conditions of a system of (differential) equations
6786 in full, banded or sparse form, using the Newton-Raphson method, or by
6787 dynamically running,
6788 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6789 and 3-D partial differential equations, that have been converted to ordinary
6790 differential equations by numerical differencing (using the method-of-lines
6793 (license license:gpl2+)))
6795 (define-public r-abcanalysis
6797 (name "r-abcanalysis")
6802 (uri (cran-uri "ABCanalysis" version))
6804 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6805 (properties `((upstream-name . "ABCanalysis")))
6806 (build-system r-build-system)
6807 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6808 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6809 (synopsis "Computed ABC Analysis")
6811 "Multivariate data sets often differ in several factors or derived statistical
6812 parameters, which have to be selected for a valid interpretation. Basing this
6813 selection on traditional statistical limits leads occasionally to the perception
6814 of losing information from a data set. This package provides tools to calculate
6815 these limits on the basis of the mathematical properties of the distribution of
6816 the analyzed items.")
6817 (license license:gpl3)))
6819 (define-public r-slam
6826 (uri (cran-uri "slam" version))
6828 (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
6829 (build-system r-build-system)
6830 (home-page "https://cran.r-project.org/web/packages/slam/")
6831 (synopsis "Sparse lightweight arrays and matrices")
6833 "This package contains data structures and algorithms for sparse arrays and matrices,
6834 based on index arrays and simple triplet representations, respectively.")
6835 (license license:gpl2)))
6837 (define-public r-manipulatewidget
6839 (name "r-manipulatewidget")
6844 (uri (cran-uri "manipulateWidget" version))
6846 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6848 `((upstream-name . "manipulateWidget")))
6849 (build-system r-build-system)
6851 `(("r-base64enc" ,r-base64enc)
6852 ("r-codetools" ,r-codetools)
6853 ("r-htmltools" ,r-htmltools)
6854 ("r-htmlwidgets" ,r-htmlwidgets)
6855 ("r-knitr" ,r-knitr)
6856 ("r-miniui" ,r-miniui)
6857 ("r-shiny" ,r-shiny)
6858 ("r-webshot" ,r-webshot)))
6859 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6860 (synopsis "Add even more interactivity to interactive charts")
6862 "This package lets you create in just a few lines of R code a nice user interface to
6863 modify the data or the graphical parameters of one or multiple interactive
6864 charts. It is useful to quickly explore visually some data or for package
6865 developers to generate user interfaces easy to maintain.")
6866 (license license:gpl2+)))
6875 (uri (cran-uri "A3" version))
6877 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6878 (properties `((upstream-name . "A3")))
6879 (build-system r-build-system)
6881 `(("r-pbapply" ,r-pbapply)
6882 ("r-xtable" ,r-xtable)))
6883 (home-page "https://cran.r-project.org/web/packages/A3/")
6884 (synopsis "Error metrics for predictive models")
6886 "This package supplies tools for tabulating and analyzing the results of predictive
6887 models. The methods employed are applicable to virtually any predictive model
6888 and make comparisons between different methodologies straightforward.")
6889 (license license:gpl2+)))
6891 (define-public r-infotheo
6898 (uri (cran-uri "infotheo" version))
6901 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6902 (build-system r-build-system)
6903 (home-page "http://homepage.meyerp.com/software")
6904 (synopsis "Information-theoretic measures")
6906 "This package implements various measures of information theory based on
6907 several entropy estimators.")
6908 (license license:gpl3+)))
6910 (define-public r-abcoptim
6917 (uri (cran-uri "ABCoptim" version))
6919 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
6920 (properties `((upstream-name . "ABCoptim")))
6921 (build-system r-build-system)
6922 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6923 (home-page "https://github.com/gvegayon/ABCoptim/")
6924 (synopsis "Optimization of Artificial Bee Colony algorithm")
6926 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
6927 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
6928 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
6929 algorithms, and uses only common control parameters such as colony size and
6930 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
6931 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
6932 This version is a work-in-progress and is written in R code.")
6933 (license license:expat)))
6935 (define-public r-abcp2
6942 (uri (cran-uri "ABCp2" version))
6944 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
6945 (properties `((upstream-name . "ABCp2")))
6946 (build-system r-build-system)
6947 (propagated-inputs `(("r-mass" ,r-mass)))
6948 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
6949 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
6951 "This package tests the goodness of fit of a distribution of offspring to the Normal,
6952 Poisson, and Gamma distribution and estimates the proportional paternity of the
6953 second male (P2) based on the best fit distribution.")
6954 (license license:gpl2)))
6956 (define-public r-abcrf
6963 (uri (cran-uri "abcrf" version))
6965 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
6966 (build-system r-build-system)
6968 `(("r-doparallel" ,r-doparallel)
6969 ("r-foreach" ,r-foreach)
6971 ("r-matrixstats" ,r-matrixstats)
6972 ("r-ranger" ,r-ranger)
6974 ("r-rcpparmadillo" ,r-rcpparmadillo)
6975 ("r-readr" ,r-readr)
6976 ("r-stringr" ,r-stringr)))
6977 (home-page "https://cran.r-project.org/web/packages/abcrf/")
6978 (synopsis "Approximate bayesian computation via random forests")
6980 "This package performs approximate bayesian computation (ABC) model choice and
6981 parameter inference via random forests. This machine learning tool named random
6982 forests (RF) can conduct selection among the highly complex models covered by
6984 (license license:gpl2+)))
6986 (define-public r-abctools
6993 (uri (cran-uri "abctools" version))
6995 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
6996 (build-system r-build-system)
6999 ("r-abind" ,r-abind)
7000 ("r-hmisc" ,r-hmisc)
7001 ("r-plyr" ,r-plyr)))
7002 (home-page "https://github.com/dennisprangle/abctools/")
7003 (synopsis "Tools for ABC analyses")
7005 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7006 including summary statistic selection and assessing coverage. This includes
7007 recent dimension reduction algorithms to tune the choice of summary statistics,
7008 and coverage methods to tune the choice of threshold.")
7009 (license license:gpl2+)))
7011 (define-public r-ggstance
7018 (uri (cran-uri "ggstance" version))
7020 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7021 (build-system r-build-system)
7023 `(("r-ggplot2" ,r-ggplot2)
7025 ("r-rlang" ,r-rlang)
7026 ("r-withr" ,r-withr)))
7027 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7028 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7030 "This package is a @code{r-ggplot2} extension that provides flipped components:
7032 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7033 @item vertical versions of @code{r-ggplot2} positions.
7035 (license license:gpl3)))
7037 (define-public r-mosaiccore
7039 (name "r-mosaiccore")
7044 (uri (cran-uri "mosaicCore" version))
7046 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7047 (properties `((upstream-name . "mosaicCore")))
7048 (build-system r-build-system)
7050 `(("r-dplyr" ,r-dplyr)
7051 ("r-lazyeval" ,r-lazyeval)
7053 ("r-rlang" ,r-rlang)
7054 ("r-tidyr" ,r-tidyr)))
7055 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7056 (synopsis "Common utilities for mosaic family packages")
7058 "Common utilities used in other Mosaic family packages are collected here.")
7059 (license license:gpl2+)))
7061 (define-public r-ggformula
7063 (name "r-ggformula")
7068 (uri (cran-uri "ggformula" version))
7070 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7071 (build-system r-build-system)
7073 `(("r-ggplot2" ,r-ggplot2)
7074 ("r-ggstance" ,r-ggstance)
7075 ("r-magrittr" ,r-magrittr)
7076 ("r-mosaiccore" ,r-mosaiccore)
7077 ("r-rlang" ,r-rlang)
7078 ("r-stringr" ,r-stringr)
7079 ("r-tibble" ,r-tibble)
7080 ("r-tidyr" ,r-tidyr)))
7081 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7082 (synopsis "Formula interface for the @code{r-ggplot2}")
7084 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7085 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7086 and extends the excellent simplicity of the lattice-graphics formula interface,
7087 while providing the intuitive capabilities of @code{r-ggplot2}.")
7088 (license license:expat)))
7090 (define-public r-mosaicdata
7092 (name "r-mosaicdata")
7097 (uri (cran-uri "mosaicData" version))
7099 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7100 (properties `((upstream-name . "mosaicData")))
7101 (build-system r-build-system)
7102 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7103 (synopsis "Data sets for project Mosaic")
7105 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7106 used to teach mathematics, statistics, computation and modeling.")
7107 (license license:gpl2+)))
7109 (define-public r-raster
7116 (uri (cran-uri "raster" version))
7119 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7120 (build-system r-build-system)
7122 `(("r-rcpp" ,r-rcpp)
7124 (home-page "https://www.rspatial.org/")
7125 (synopsis "Geographic data analysis and modeling")
7127 "The package implements basic and high-level functions for reading,
7128 writing, manipulating, analyzing and modeling of gridded spatial data.
7129 Processing of very large files is supported.")
7130 (license license:gpl3+)))
7132 (define-public r-mosaic
7139 (uri (cran-uri "mosaic" version))
7141 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7142 (build-system r-build-system)
7144 `(("r-broom" ,r-broom)
7145 ("r-dplyr" ,r-dplyr)
7146 ("r-ggdendro" ,r-ggdendro)
7147 ("r-ggformula" ,r-ggformula)
7148 ("r-ggplot2" ,r-ggplot2)
7149 ("r-ggrepel" ,r-ggrepel)
7151 ("r-gridextra" ,r-gridextra)
7152 ("r-lattice" ,r-lattice)
7153 ("r-latticeextra" ,r-latticeextra)
7154 ("r-lazyeval" ,r-lazyeval)
7156 ("r-matrix" ,r-matrix)
7157 ("r-mosaiccore" ,r-mosaiccore)
7158 ("r-mosaicdata" ,r-mosaicdata)
7159 ("r-readr" ,r-readr)
7160 ("r-tidyr" ,r-tidyr)))
7161 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7162 (synopsis "Mathematics, statistics, and computation teaching utilities")
7164 "This package contain data sets and utilities from
7165 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7166 statistics, computation and modeling. Project MOSAIC is a community of
7167 educators working to tie together aspects of quantitative work that students
7168 in science, technology, engineering and mathematics will need in their
7169 professional lives, but which are usually taught in isolation, if at all.")
7170 (license license:gpl2+)))
7172 (define-public r-abd
7179 (uri (cran-uri "abd" version))
7181 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7182 (build-system r-build-system)
7184 `(("r-lattice" ,r-lattice)
7185 ("r-mosaic" ,r-mosaic)
7186 ("r-nlme" ,r-nlme)))
7187 (home-page "https://cran.r-project.org/web/packages/abd/")
7188 (synopsis "Analysis of biological data")
7190 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7191 biological data by Michael Whitlock and Dolph Schluter.")
7192 (license license:gpl2)))
7194 (define-public r-svgui
7201 (uri (cran-uri "svGUI" version))
7203 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7204 (properties `((upstream-name . "svGUI")))
7205 (build-system r-build-system)
7206 (home-page "https://github.com/SciViews/svGUI/")
7207 (synopsis "Functions for managing GUI clients in R")
7209 "The SciViews @code{svGUI} package eases the management of Graphical User
7210 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7211 centralizes info about GUI elements currently used, and it dispatches GUI
7212 calls to the particular toolkits in use in function of the context.")
7213 (license license:gpl2)))
7215 (define-public r-svdialogs
7217 (name "r-svdialogs")
7222 (uri (cran-uri "svDialogs" version))
7224 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7225 (properties `((upstream-name . "svDialogs")))
7226 (build-system r-build-system)
7229 ("zenity" ,zenity)))
7231 `(("r-rstudioapi" ,r-rstudioapi)
7232 ("r-svgui" ,r-svgui)))
7233 (home-page "https://github.com/SciViews/svDialogs/")
7234 (synopsis "Portable dialog boxes")
7236 "This package helps to construct standard dialog boxes for your GUI, including
7237 message boxes, input boxes, list, file or directory selection, and others. In
7238 case R cannot display GUI dialog boxes, a simpler command line version of these
7239 interactive elements is also provided as a fallback solution.")
7240 (license license:gpl2)))
7242 (define-public r-abe
7249 (uri (cran-uri "abe" version))
7252 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7253 (build-system r-build-system)
7254 (home-page "https://cran.r-project.org/web/packages/abe/")
7255 (synopsis "Augmented backward elimination")
7257 "This package performs augmented backward elimination and checks the
7258 stability of the obtained model. Augmented backward elimination combines
7259 significance or information based criteria with the change in estimate to
7260 either select the optimal model for prediction purposes or to serve as a tool
7261 to obtain a practically sound, highly interpretable model.")
7262 (license license:gpl2+)))
7264 (define-public r-abf2
7271 (uri (cran-uri "abf2" version))
7273 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7274 (build-system r-build-system)
7275 (home-page "https://cran.r-project.org/web/packages/abf2/")
7276 (synopsis "Load gap-free axon @code{r-abf2} files")
7278 "This package loads electrophysiology data from ABF2 files, as created by
7279 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7280 mode are currently supported.")
7281 (license license:artistic2.0)))
7283 (define-public r-abhgenotyper
7285 (name "r-abhgenotyper")
7290 (uri (cran-uri "ABHgenotypeR" version))
7292 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7293 (properties `((upstream-name . "ABHgenotypeR")))
7294 (build-system r-build-system)
7296 `(("r-ggplot2" ,r-ggplot2)
7297 ("r-reshape2" ,r-reshape2)))
7298 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7299 (synopsis "Visualize and manipulate ABH genotypes")
7301 "The @code{r-abhgenotyper} package provides simple imputation,
7302 error-correction and plotting capacities for genotype data. The package is
7303 supposed to serve as an intermediate but independent analysis tool between the
7304 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7305 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7306 genotypes as \"graphical genotypes\".")
7307 (license license:gpl3)))
7309 (define-public r-furrr
7316 (uri (cran-uri "furrr" version))
7319 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7320 (build-system r-build-system)
7322 `(("r-future" ,r-future)
7323 ("r-globals" ,r-globals)
7324 ("r-purrr" ,r-purrr)
7325 ("r-rlang" ,r-rlang)))
7326 (home-page "https://github.com/DavisVaughan/furrr")
7327 (synopsis "Apply mapping functions in parallel using futures")
7329 "This package provides implementations of the family of @code{map()}
7330 functions from the @code{purrr} package that can be resolved using any
7331 @code{future}-supported backend, e.g. parallel on the local machine or
7332 distributed on a compute cluster.")
7333 (license license:lgpl2.1+)))
7335 (define-public r-abjutils
7342 (uri (cran-uri "abjutils" version))
7344 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7345 (build-system r-build-system)
7347 `(("r-devtools" ,r-devtools)
7348 ("r-dplyr" ,r-dplyr)
7349 ("r-furrr" ,r-furrr)
7350 ("r-future" ,r-future)
7353 ("r-magrittr" ,r-magrittr)
7354 ("r-progress" ,r-progress)
7355 ("r-purrr" ,r-purrr)
7356 ("r-readr" ,r-readr)
7357 ("r-rlang" ,r-rlang)
7358 ("r-rstudioapi" ,r-rstudioapi)
7359 ("r-scales" ,r-scales)
7360 ("r-stringi" ,r-stringi)
7361 ("r-stringr" ,r-stringr)
7362 ("r-tibble" ,r-tibble)
7363 ("r-tidyr" ,r-tidyr)))
7364 (home-page "https://github.com/abjur/abjutils/")
7365 (synopsis "Collection of tools for jurimetrical analysis")
7367 "This package implements general purpose tools, such as functions for
7368 sampling and basic manipulation of Brazilian lawsuits identification number.
7369 It also implements functions for text cleaning, such as accentuation
7371 (license license:expat)))
7373 (define-public r-abnormality
7375 (name "r-abnormality")
7380 (uri (cran-uri "abnormality" version))
7382 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7383 (build-system r-build-system)
7385 `(("r-mass" ,r-mass)
7386 ("r-matrix" ,r-matrix)))
7387 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7388 (synopsis "Measure a subject's abnormality with respect to a reference population")
7390 "This package contains functions to implement the methodology and
7391 considerations laid out by Marks et al. in the article \"Measuring abnormality
7392 in high dimensional spaces: applications in biomechanical gait analysis\".
7393 Using high-dimensional datasets to measure a subject's overall level of
7394 abnormality as compared to a reference population is often needed in outcomes
7396 (license license:expat)))
7398 (define-public r-abodoutlier
7400 (name "r-abodoutlier")
7405 (uri (cran-uri "abodOutlier" version))
7407 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7408 (properties `((upstream-name . "abodOutlier")))
7409 (build-system r-build-system)
7411 `(("r-cluster" ,r-cluster)))
7412 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7413 (synopsis "Angle-based outlier detection")
7415 "This package performs angle-based outlier detection on a given data
7416 frame. It offers three methods to process data:
7418 @item full but slow implementation using all the data that has cubic
7420 @item a fully randomized method;
7421 @item a method using k-nearest neighbours.
7423 These algorithms are well suited for high dimensional data outlier
7425 (license license:expat)))
7427 (define-public r-abps
7434 (uri (cran-uri "ABPS" version))
7436 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7437 (properties `((upstream-name . "ABPS")))
7438 (build-system r-build-system)
7439 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7440 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7441 (synopsis "Abnormal blood profile score to detect blood doping")
7443 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7444 The ABPS is a part of the Athlete biological passport program of the World
7445 anti-doping agency, which combines several blood parameters into a single
7446 score in order to detect blood doping. The package also contains functions to
7447 calculate other scores used in anti-doping programs, such as the ratio of
7448 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7449 (license license:gpl2+)))
7451 (define-public r-parmigene
7453 (name "r-parmigene")
7458 (uri (cran-uri "parmigene" version))
7461 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7462 (build-system r-build-system)
7463 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7464 (synopsis "Mutual information estimation for gene network reconstruction")
7466 "This package provides a parallel estimation of the mutual information
7467 based on entropy estimates from k-nearest neighbors distances and algorithms
7468 for the reconstruction of gene regulatory networks.")
7469 (license license:agpl3+)))
7471 (define-public r-pscl
7478 (uri (cran-uri "pscl" version))
7480 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7481 (build-system r-build-system)
7483 `(("r-mass" ,r-mass)))
7484 (home-page "https://github.com/atahk/pscl/")
7485 (synopsis "Political science computational laboratory")
7487 "The @code{pscl} is an R package providing classes and methods for:
7489 @item Bayesian analysis of roll call data (item-response models);
7490 @item elementary Bayesian statistics;
7491 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7493 @item utility functions.
7495 (license license:gpl2)))
7497 (define-public r-accelmissing
7499 (name "r-accelmissing")
7504 (uri (cran-uri "accelmissing" version))
7506 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7507 (build-system r-build-system)
7509 `(("r-mice" ,r-mice)
7510 ("r-pscl" ,r-pscl)))
7511 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7512 (synopsis "Missing value imputation for accelerometer data")
7514 "This package provides a statistical method to impute the missing values in
7515 accelerometer data. The methodology includes both parametric and
7516 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7517 model. It also provides multiple functions to preprocess the accelerometer data
7518 previous to the missing data imputation. These include detecting the wearing
7519 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7520 (license license:gpl2+)))
7522 (define-public r-mhsmm
7529 (uri (cran-uri "mhsmm" version))
7531 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7532 (build-system r-build-system)
7533 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7534 (home-page "https://github.com/jaredo/mhsmm/")
7535 (synopsis "Inference for hidden Markov and semi-Markov models")
7537 "The @code{r-mhsmm} package implements estimation and prediction methods for
7538 hidden Markov and semi-Markov models for multiple observation sequences. Such
7539 techniques are of interest when observed data is thought to be dependent on some
7540 unobserved (or hidden) state. Also, this package is suitable for equidistant
7541 time series data, with multivariate and/or missing data. Allows user defined
7542 emission distributions.")
7543 (license license:gpl2+)))
7545 (define-public r-nleqslv
7552 (uri (cran-uri "nleqslv" version))
7554 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7555 (build-system r-build-system)
7556 (native-inputs `(("gfortran" ,gfortran)))
7557 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7558 (synopsis "Solve systems of nonlinear equations")
7560 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7561 Broyden or a Newton method with a choice of global strategies such as line
7562 search and trust region. There are options for using a numerical or user
7563 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7564 singular or ill-conditioned Jacobian.")
7565 (license license:gpl2+)))
7567 (define-public r-physicalactivity
7569 (name "r-physicalactivity")
7574 (uri (cran-uri "PhysicalActivity" version))
7576 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7578 `((upstream-name . "PhysicalActivity")))
7579 (build-system r-build-system)
7580 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7581 (synopsis "Procesing accelerometer data for physical activity measurement")
7583 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7584 for classification of monitor wear and nonwear time intervals in accelerometer
7585 data collected to assess physical activity. The package also contains functions
7586 for making plots of accelerometer data and obtaining the summary of various
7587 information including daily monitor wear time and the mean monitor wear time
7588 during valid days. The revised package version 0.2-1 improved the functions
7589 regarding speed, robustness and add better support for time zones and daylight
7590 saving. In addition, several functions were added:
7592 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7593 @item the @code{markPAI} can categorize physical activity intensity level based
7594 on user-defined cut-points of accelerometer counts.
7596 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7597 @code{queryActigraph} functions.")
7598 (license license:gpl3+)))
7600 (define-public r-acc
7607 (uri (cran-uri "acc" version))
7609 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7610 (build-system r-build-system)
7612 `(("r-circlize" ,r-circlize)
7614 ("r-ggplot2" ,r-ggplot2)
7615 ("r-iterators" ,r-iterators)
7616 ("r-mhsmm" ,r-mhsmm)
7617 ("r-nleqslv" ,r-nleqslv)
7618 ("r-physicalactivity" ,r-physicalactivity)
7620 ("r-r-utils" ,r-r-utils)
7622 ("r-rcpparmadillo" ,r-rcpparmadillo)
7623 ("r-rsqlite" ,r-rsqlite)
7625 (home-page "https://cran.r-project.org/web/packages/acc/")
7626 (synopsis "Exploring accelerometer data")
7628 "This package processes accelerometer data from uni-axial and tri-axial devices
7629 and generates data summaries. Also, includes functions to plot, analyze, and
7630 simulate accelerometer data.")
7631 (license license:gpl2+)))
7633 (define-public r-rbenchmark
7635 (name "r-rbenchmark")
7640 (uri (cran-uri "rbenchmark" version))
7642 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7643 (build-system r-build-system)
7644 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7645 (synopsis "Benchmarking routine for R")
7647 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7648 and is intended to facilitate benchmarking of arbitrary R code. The library
7649 consists of just one function, benchmark, which is a simple wrapper around
7650 system.time. Given a specification of the benchmarking process (counts of
7651 replications, evaluation environment) and an arbitrary number of expressions,
7652 benchmark evaluates each of the expressions in the specified environment,
7653 replicating the evaluation as many times as specified, and returning the results
7654 conveniently wrapped into a data frame.")
7655 (license license:gpl2+)))
7657 (define-public r-mitools
7664 (uri (cran-uri "mitools" version))
7667 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7668 (build-system r-build-system)
7669 (propagated-inputs `(("r-dbi" ,r-dbi)))
7670 (home-page "https://cran.r-project.org/web/packages/mitools/")
7671 (synopsis "Tools for multiple imputation of missing data")
7673 "This package provides tools to perform analyses and combine results from
7674 multiple-imputation datasets.")
7675 (license license:gpl2)))
7677 (define-public r-magick
7684 (uri (cran-uri "magick" version))
7687 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7688 (build-system r-build-system)
7690 `(("imagemagick" ,imagemagick)
7693 `(("r-curl" ,r-curl)
7694 ("r-magrittr" ,r-magrittr)
7695 ("r-rcpp" ,r-rcpp)))
7697 `(("pkg-config" ,pkg-config)))
7698 (home-page "https://github.com/ropensci/magick")
7699 (synopsis "Advanced graphics and image-processing in R")
7701 "This package provides bindings to ImageMagick, a comprehensive image
7702 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7703 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7704 operations are vectorized via the Magick++ STL meaning they operate either on
7705 a single frame or a series of frames for working with layers, collages, or
7706 animation. In RStudio, images are automatically previewed when printed to the
7707 console, resulting in an interactive editing environment.")
7708 (license license:expat)))
7710 (define-public r-survey
7717 (uri (cran-uri "survey" version))
7720 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7721 (build-system r-build-system)
7723 `(("r-lattice" ,r-lattice)
7724 ("r-matrix" ,r-matrix)
7725 ("r-minqa" ,r-minqa)
7726 ("r-mitools" ,r-mitools)
7727 ("r-numderiv" ,r-numderiv)
7728 ("r-survival" ,r-survival)))
7729 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7730 (synopsis "Analysis of complex survey samples")
7732 "This package provides tools for the analysis of complex survey samples.
7733 The provided features include: summary statistics, two-sample tests, rank
7734 tests, generalised linear models, cumulative link models, Cox models,
7735 loglinear models, and general maximum pseudolikelihood estimation for
7736 multistage stratified, cluster-sampled, unequally weighted survey samples;
7737 variances by Taylor series linearisation or replicate weights;
7738 post-stratification, calibration, and raking; two-phase subsampling designs;
7739 graphics; PPS sampling without replacement; principal components, and factor
7741 ;; Either version of the GPL.
7742 (license (list license:gpl2 license:gpl3))))
7744 (define-public r-dvmisc
7751 (uri (cran-uri "dvmisc" version))
7753 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7754 (build-system r-build-system)
7756 `(("r-cubature" ,r-cubature)
7757 ("r-data-table" ,r-data-table)
7758 ("r-dplyr" ,r-dplyr)
7759 ("r-ggplot2" ,r-ggplot2)
7761 ("r-mvtnorm" ,r-mvtnorm)
7762 ("r-pracma" ,r-pracma)
7763 ("r-purrr" ,r-purrr)
7764 ("r-rbenchmark" ,r-rbenchmark)
7766 ("r-survey" ,r-survey)))
7767 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7768 (synopsis "Faster computation of common statistics and miscellaneous functions")
7770 "This package implements faster versions of base R functions (e.g. mean, standard
7771 deviation, covariance, weighted mean), mostly written in C++, along with
7772 miscellaneous functions for various purposes (e.g. create the histogram with
7773 fitted probability density function or probability mass function curve, create
7774 the body mass index groups, assess the linearity assumption in logistic
7776 (license license:gpl2)))
7778 (define-public r-accelerometry
7780 (name "r-accelerometry")
7785 (uri (cran-uri "accelerometry" version))
7787 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7788 (build-system r-build-system)
7790 `(("r-dvmisc" ,r-dvmisc)
7791 ("r-rcpp" ,r-rcpp)))
7792 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7793 (synopsis "Functions for processing accelerometer data")
7795 "This package provides a collection of functions that perform operations on
7796 time-series accelerometer data, such as identify the non-wear time, flag minutes
7797 that are part of an activity bout, and find the maximum 10-minute average count
7798 value. The functions are generally very flexible, allowing for a variety of
7799 algorithms to be implemented.")
7800 (license license:gpl3)))
7802 (define-public r-absim
7809 (uri (cran-uri "AbSim" version))
7811 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7812 (properties `((upstream-name . "AbSim")))
7813 (build-system r-build-system)
7816 ("r-powerlaw" ,r-powerlaw)))
7817 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7818 (synopsis "Time resolved simulations of antibody repertoires")
7820 "This package provides simulation methods for the evolution of antibody repertoires.
7821 The heavy and light chain variable region of both human and C57BL/6 mice can
7822 be simulated in a time-dependent fashion. Both single lineages using one set of
7823 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7824 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7825 Upon completion, the main loop of the algorithm begins, with each iteration
7826 representing one simulated time step. Various mutation events are possible at
7827 each time step, contributing to a diverse final repertoire.")
7828 (license license:gpl2)))
7830 (define-public r-quic
7837 (uri (cran-uri "QUIC" version))
7839 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7840 (properties `((upstream-name . "QUIC")))
7841 (build-system r-build-system)
7842 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7843 (synopsis "Regularized sparse inverse covariance matrix estimation")
7845 "This package implements the regularized Gaussian maximum likelihood
7846 estimation of the inverse of a covariance matrix. It uses Newton's method and
7847 coordinate descent to solve the regularized inverse covariance matrix
7848 estimation problem.")
7849 ;; The project home page states that the release is under GPLv3 or later.
7850 ;; The CRAN page only says GPL-3.
7851 (license license:gpl3+)))
7853 (define-public r-abundant
7860 (uri (cran-uri "abundant" version))
7862 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7863 (build-system r-build-system)
7865 `(("r-quic" ,r-quic)))
7866 (home-page "https://cran.r-project.org/web/packages/abundant/")
7867 (synopsis "Abundant regression and high-dimensional principal fitted components")
7869 "This package provides tools to fit and predict with the high-dimensional
7870 principal fitted components model. This model is described by Cook, Forzani,
7871 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7872 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7873 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7874 (license license:gpl2+)))
7876 (define-public r-ac3net
7883 (uri (cran-uri "Ac3net" version))
7885 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7886 (properties `((upstream-name . "Ac3net")))
7887 (build-system r-build-system)
7889 `(("r-data-table" ,r-data-table)))
7890 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7891 (synopsis "Inferring directional conservative causal core gene networks")
7892 (description "This package infers directional Conservative causal core
7893 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7894 directional network.")
7895 (license license:gpl3+)))
7897 (define-public r-aca
7904 (uri (cran-uri "ACA" version))
7906 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7907 (properties `((upstream-name . "ACA")))
7908 (build-system r-build-system)
7909 (home-page "https://cran.r-project.org/web/packages/ACA/")
7910 (synopsis "Abrupt change-point or aberration detection in point series")
7912 "This package offers an interactive function for the detection of breakpoints in
7914 ;; Any version of the GPL
7915 (license (list license:gpl2+ license:gpl3+))))
7917 (define-public r-acceptancesampling
7919 (name "r-acceptancesampling")
7924 (uri (cran-uri "AcceptanceSampling" version))
7926 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
7928 `((upstream-name . "AcceptanceSampling")))
7929 (build-system r-build-system)
7930 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
7931 (synopsis "Creation and evaluation of acceptance sampling plans")
7933 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
7934 acceptance sampling plans. Acceptance sampling is a methodology commonly used
7935 in quality control and improvement. International standards of acceptance
7936 sampling provide sampling plans for specific circumstances. The aim of this
7937 package is to provide an easy-to-use interface to visualize single, double or
7938 multiple sampling plans. In addition, methods have been provided to enable the
7939 user to assess sampling plans against pre-specified levels of performance, as
7940 measured by the probability of acceptance for a given level of quality in the
7942 (license license:gpl3+)))
7944 (define-public r-acclma
7951 (uri (cran-uri "ACCLMA" version))
7953 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
7954 (properties `((upstream-name . "ACCLMA")))
7955 (build-system r-build-system)
7956 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
7957 (synopsis "ACC & LMA graph plotting")
7959 "This package contains a function that imports data from a @acronym{CSV,
7960 Comma-Separated Values} file, or uses manually entered data from the format (x,
7961 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
7962 Curve} vs @acronym{LOI, Line of Independence} graph and
7963 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
7964 function is @code{plotLMA} (source file, header) that takes a data set and plots the
7965 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
7966 string) was passed, a manual data entry window is opened. The header parameter
7967 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
7968 a header row or not. The dataset should contain only one independent variable
7969 (x) and one dependent variable (y) and can contain a weight for each
7971 (license license:gpl2)))
7973 (define-public r-aspi
7980 (uri (cran-uri "aspi" version))
7982 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
7983 (build-system r-build-system)
7985 "https://cran.r-project.org/web/packages/aspi/")
7987 "Analysis of symmetry of parasitic infections")
7989 "This package provides tools for the analysis and visualization of bilateral
7990 asymmetry in parasitic infections.")
7991 (license license:gpl3+)))
7993 (define-public r-sandwich
8000 (uri (cran-uri "sandwich" version))
8003 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8004 (build-system r-build-system)
8006 `(("r-zoo" ,r-zoo)))
8007 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8008 (synopsis "Robust Covariance Matrix Estimators")
8010 "This package provides model-robust standard error estimators for
8011 cross-sectional, time series, clustered, panel, and longitudinal data.")
8012 ;; Either version of the license.
8013 (license (list license:gpl2 license:gpl3))))
8015 (define-public r-th-data
8022 (uri (cran-uri "TH.data" version))
8025 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8026 (properties `((upstream-name . "TH.data")))
8027 (build-system r-build-system)
8029 `(("r-mass" ,r-mass)
8030 ("r-survival" ,r-survival)))
8031 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8032 (synopsis "Shared data sets")
8034 "This package contains supporting data sets that are used in other
8035 packages maintained by Torsten Hothorn.")
8036 (license license:gpl3)))
8038 (define-public r-multcomp
8045 (uri (cran-uri "multcomp" version))
8048 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
8049 (build-system r-build-system)
8051 `(("r-codetools" ,r-codetools)
8052 ("r-mvtnorm" ,r-mvtnorm)
8053 ("r-sandwich" ,r-sandwich)
8054 ("r-survival" ,r-survival)
8055 ("r-th-data" ,r-th-data)))
8056 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8057 (synopsis "Simultaneous inference in general parametric models")
8059 "Simultaneous tests and confidence intervals for general linear
8060 hypotheses in parametric models, including linear, generalized linear, linear
8061 mixed effects, and survival models. The package includes demos reproducing
8062 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8063 Hothorn, Westfall, 2010, CRC Press).")
8064 (license license:gpl2)))
8066 (define-public r-emmeans
8073 (uri (cran-uri "emmeans" version))
8076 "1sxwbh6sym2shrj7gva8q96ca2csqz3081q4d84avpxz15dfz1z1"))))
8077 (build-system r-build-system)
8079 `(("r-estimability" ,r-estimability)
8080 ("r-mvtnorm" ,r-mvtnorm)
8081 ("r-numderiv" ,r-numderiv)
8083 ("r-xtable" ,r-xtable)))
8084 (home-page "https://github.com/rvlenth/emmeans")
8085 (synopsis "Estimated marginal means, aka least-squares means")
8087 "This package provides tools to obtain @dfn{estimated marginal
8088 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8089 be used to compute contrasts or linear functions of EMMs, trends, and
8090 comparisons of slopes.")
8091 ;; Either version of the license.
8092 (license (list license:gpl2 license:gpl3))))
8094 (define-public r-pwr
8101 (uri (cran-uri "pwr" version))
8104 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8105 (build-system r-build-system)
8107 `(("r-knitr" ,r-knitr)))
8108 (home-page "https://github.com/heliosdrm/pwr")
8109 (synopsis "Basic functions for power analysis")
8111 "This package provides power analysis functions along the lines of
8113 (license license:gpl3+)))
8115 (define-public r-libcoin
8122 (uri (cran-uri "libcoin" version))
8125 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8126 (build-system r-build-system)
8127 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8128 (home-page "https://cran.r-project.org/web/packages/libcoin")
8129 (synopsis "Linear test statistics for permutation inference")
8131 "This package provides basic infrastructure for linear test statistics
8132 and permutation inference in the framework of Strasser and Weber (1999).")
8133 (license license:gpl2)))
8135 (define-public r-coin
8142 (uri (cran-uri "coin" version))
8145 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8146 (build-system r-build-system)
8148 `(("r-libcoin" ,r-libcoin)
8149 ("r-matrixstats" ,r-matrixstats)
8150 ("r-modeltools" ,r-modeltools)
8151 ("r-multcomp" ,r-multcomp)
8152 ("r-mvtnorm" ,r-mvtnorm)
8153 ("r-survival" ,r-survival)))
8154 (home-page "http://coin.r-forge.r-project.org")
8155 (synopsis "Conditional inference procedures in a permutation test framework")
8157 "This package provides conditional inference procedures for the general
8158 independence problem including two-sample, K-sample (non-parametric ANOVA),
8159 correlation, censored, ordered and multivariate problems.")
8160 (license license:gpl2)))
8162 (define-public r-bayesplot
8164 (name "r-bayesplot")
8169 (uri (cran-uri "bayesplot" version))
8172 "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
8173 (build-system r-build-system)
8175 `(("pandoc" ,ghc-pandoc)
8176 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8178 `(("r-dplyr" ,r-dplyr)
8179 ("r-ggplot2" ,r-ggplot2)
8180 ("r-ggridges" ,r-ggridges)
8182 ("r-reshape2" ,r-reshape2)
8183 ("r-rlang" ,r-rlang)
8184 ("r-tibble" ,r-tibble)
8185 ("r-tidyselect" ,r-tidyselect)))
8186 (home-page "http://mc-stan.org/bayesplot")
8187 (synopsis "Plotting for Bayesian models")
8189 "This package provides plotting functions for posterior analysis, model
8190 checking, and MCMC diagnostics. The package is designed not only to provide
8191 convenient functionality for users, but also a common set of functions that
8192 can be easily used by developers working on a variety of R packages for
8193 Bayesian modeling.")
8194 (license license:gpl3+)))
8196 (define-public r-tmb
8203 (uri (cran-uri "TMB" version))
8206 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8207 (properties `((upstream-name . "TMB")))
8208 (build-system r-build-system)
8210 `(("r-matrix" ,r-matrix)
8211 ("r-rcppeigen" ,r-rcppeigen)))
8212 (home-page "http://tmb-project.org")
8213 (synopsis "Template model builder: a general random effect tool")
8215 "With this tool, a user should be able to quickly implement complex
8216 random effect models through simple C++ templates. The package combines
8217 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8218 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8219 from R) to obtain an efficient implementation of the applied Laplace
8220 approximation with exact derivatives. Key features are: Automatic sparseness
8221 detection, parallelism through BLAS and parallel user templates.")
8222 (license license:gpl2)))
8224 (define-public r-sjstats
8231 (uri (cran-uri "sjstats" version))
8233 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8234 (build-system r-build-system)
8236 `(("r-bayestestr" ,r-bayestestr)
8237 ("r-broom" ,r-broom)
8238 ("r-dplyr" ,r-dplyr)
8239 ("r-emmeans" ,r-emmeans)
8240 ("r-insight" ,r-insight)
8242 ("r-magrittr" ,r-magrittr)
8244 ("r-modelr" ,r-modelr)
8245 ("r-parameters" ,r-parameters)
8246 ("r-performance" ,r-performance)
8247 ("r-purrr" ,r-purrr)
8248 ("r-rlang" ,r-rlang)
8249 ("r-sjlabelled" ,r-sjlabelled)
8250 ("r-sjmisc" ,r-sjmisc)
8251 ("r-tidyr" ,r-tidyr)))
8252 (home-page "https://github.com/strengejacke/sjstats")
8253 (synopsis "Functions for common statistical computations")
8255 "This package provides a collection of convenient functions for common
8256 statistical computations, which are not directly provided by R's @code{base}
8257 or @code{stats} packages. This package aims at providing, first, shortcuts
8258 for statistical measures, which otherwise could only be calculated with
8259 additional effort. Second, these shortcut functions are generic, and can be
8260 applied not only to vectors, but also to other objects as well. The focus of
8261 most functions lies on summary statistics or fit measures for regression
8262 models, including generalized linear models, mixed effects models and Bayesian
8264 (license license:gpl3)))
8266 (define-public r-glmmtmb
8273 (uri (cran-uri "glmmTMB" version))
8276 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8277 (properties `((upstream-name . "glmmTMB")))
8278 (build-system r-build-system)
8280 `(("r-lme4" ,r-lme4)
8281 ("r-matrix" ,r-matrix)
8283 ("r-rcppeigen" ,r-rcppeigen)
8286 `(("r-knitr" ,r-knitr))) ; for vignettes
8287 (home-page "https://github.com/glmmTMB")
8288 (synopsis "Generalized linear mixed models")
8290 "Fit linear and generalized linear mixed models with various extensions,
8291 including zero-inflation. The models are fitted using maximum likelihood
8292 estimation via the Template Model Builder. Random effects are assumed to be
8293 Gaussian on the scale of the linear predictor and are integrated out using the
8294 Laplace approximation. Gradients are calculated using automatic
8296 (license license:agpl3+)))
8298 (define-public r-bayestestr
8300 (name "r-bayestestr")
8305 (uri (cran-uri "bayestestR" version))
8308 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8309 (properties `((upstream-name . "bayestestR")))
8310 (build-system r-build-system)
8312 `(("r-insight" ,r-insight)))
8313 (home-page "https://github.com/easystats/bayestestR")
8314 (synopsis "Describe Bayesian models and posterior distributions")
8316 "This package provides utilities to understand and describe posterior
8317 distributions and Bayesian models. It includes point-estimates such as
8318 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8319 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8320 ROPE percentage and pd).")
8321 (license license:gpl3)))
8323 (define-public r-performance
8325 (name "r-performance")
8330 (uri (cran-uri "performance" version))
8333 "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
8334 (build-system r-build-system)
8336 `(("r-bayestestr" ,r-bayestestr)
8337 ("r-insight" ,r-insight)))
8338 (home-page "https://easystats.github.io/performance/")
8339 (synopsis "Assessment of regression models performance")
8341 "This package provides utilities for computing measures to assess model
8342 quality, which are not directly provided by R's @code{base} or @code{stats}
8343 packages. These include e.g. measures like r-squared, intraclass correlation
8344 coefficient, root mean squared error or functions to check models for
8345 overdispersion, singularity or zero-inflation and more. Functions apply to a
8346 large variety of regression models, including generalized linear models, mixed
8347 effects models and Bayesian models.")
8348 (license license:gpl3)))
8350 (define-public r-ggeffects
8352 (name "r-ggeffects")
8357 (uri (cran-uri "ggeffects" version))
8360 "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
8361 (build-system r-build-system)
8363 `(("r-dplyr" ,r-dplyr)
8364 ("r-insight" ,r-insight)
8365 ("r-magrittr" ,r-magrittr)
8367 ("r-purrr" ,r-purrr)
8368 ("r-rlang" ,r-rlang)
8369 ("r-sjlabelled" ,r-sjlabelled)
8370 ("r-sjmisc" ,r-sjmisc)))
8371 (home-page "https://github.com/strengejacke/ggeffects")
8372 (synopsis "Create tidy data frames of marginal effects for ggplot")
8374 "This package provides tools to compute marginal effects from statistical
8375 models and return the result as tidy data frames. These data frames are ready
8376 to use with the @code{ggplot2} package. Marginal effects can be calculated
8377 for many different models. Interaction terms, splines and polynomial terms
8378 are also supported. The two main functions are @code{ggpredict()} and
8379 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8380 results using @code{ggplot2}.")
8381 (license license:gpl3)))
8383 (define-public r-effectsize
8385 (name "r-effectsize")
8390 (uri (cran-uri "effectsize" version))
8393 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8394 (properties `((upstream-name . "effectsize")))
8395 (build-system r-build-system)
8397 `(("r-bayestestr" ,r-bayestestr)
8398 ("r-insight" ,r-insight)
8399 ("r-parameters" ,r-parameters)))
8400 (home-page "https://github.com/easystats/effectsize")
8401 (synopsis "Indices of effect size and standardized parameters")
8403 "This package provides utilities to work with indices of effect size and
8404 standardized parameters for a wide variety of models, allowing computation and
8405 conversion of indices such as Cohen's d, r, odds, etc.")
8406 (license license:gpl3)))
8408 (define-public r-sjplot
8415 (uri (cran-uri "sjPlot" version))
8417 (base32 "0ahz6v6bhvq1537inwakmrafs44hs2m9w0ra8q17fz626nn9rb9b"))))
8418 (properties `((upstream-name . "sjPlot")))
8419 (build-system r-build-system)
8421 `(("r-bayestestr" ,r-bayestestr)
8422 ("r-dplyr" ,r-dplyr)
8423 ("r-effectsize" ,r-effectsize)
8424 ("r-forcats" ,r-forcats)
8425 ("r-ggeffects" ,r-ggeffects)
8426 ("r-ggplot2" ,r-ggplot2)
8427 ("r-ggrepel" ,r-ggrepel)
8428 ("r-glmmtmb" ,r-glmmtmb)
8429 ("r-insight" ,r-insight)
8430 ("r-knitr" ,r-knitr)
8432 ("r-magrittr" ,r-magrittr)
8434 ("r-modelr" ,r-modelr)
8435 ("r-parameters" ,r-parameters)
8436 ("r-performance" ,r-performance)
8437 ("r-psych" ,r-psych)
8438 ("r-purrr" ,r-purrr)
8439 ("r-rlang" ,r-rlang)
8440 ("r-scales" ,r-scales)
8441 ("r-sjlabelled" ,r-sjlabelled)
8442 ("r-sjmisc" ,r-sjmisc)
8443 ("r-sjstats" ,r-sjstats)
8444 ("r-tidyr" ,r-tidyr)))
8445 (home-page "https://strengejacke.github.io/sjPlot/")
8446 (synopsis "Data visualization for statistics in social science")
8448 "This package represents a collection of plotting and table output
8449 functions for data visualization. Results of various statistical
8450 analyses (that are commonly used in social sciences) can be visualized using
8451 this package, including simple and cross tabulated frequencies, histograms,
8452 box plots, (generalized) linear models, mixed effects models, principal
8453 component analysis and correlation matrices, cluster analyses, scatter plots,
8454 stacked scales, effects plots of regression models (including interaction
8455 terms) and much more. This package supports labelled data.")
8456 (license license:gpl3)))
8458 (define-public r-ini
8465 (uri (cran-uri "ini" version))
8468 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8469 (build-system r-build-system)
8470 (home-page "https://github.com/dvdscripter/ini")
8471 (synopsis "Read and write configuration files")
8473 "This package provides tools to parse simple @code{.ini} configuration
8474 files to an structured list. Users can manipulate this resulting list with
8475 @code{lapply()} functions. This same structured list can be used to write
8476 back to file after modifications.")
8477 (license license:gpl3)))
8486 (uri (cran-uri "gh" version))
8489 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8490 (build-system r-build-system)
8492 `(("r-httr" ,r-httr)
8494 ("r-jsonlite" ,r-jsonlite)))
8495 (home-page "https://github.com/r-lib/gh#readme")
8496 (synopsis "Access the GitHub API via R")
8498 "This package provides a minimal R client to access the GitHub API.")
8499 (license license:expat)))
8508 (uri (cran-uri "fs" version))
8511 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8512 (build-system r-build-system)
8514 `(("r-rcpp" ,r-rcpp)))
8516 `(("pkg-config" ,pkg-config)))
8517 (home-page "http://fs.r-lib.org")
8518 (synopsis "Cross-platform file system operations based on libuv")
8520 "This package provides a cross-platform interface to file system
8521 operations, built on top of the libuv C library.")
8522 (license license:gpl3)))
8524 (define-public r-clisymbols
8526 (name "r-clisymbols")
8531 (uri (cran-uri "clisymbols" version))
8534 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8535 (build-system r-build-system)
8536 (home-page "https://github.com/gaborcsardi/clisymbols")
8537 (synopsis "Unicode symbols at the R prompt")
8539 "This package provides a small subset of Unicode symbols, that are useful
8540 when building command line applications. They fall back to alternatives on
8541 terminals that do not support Unicode.")
8542 (license license:expat)))
8544 (define-public r-usethis
8551 (uri (cran-uri "usethis" version))
8554 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8555 (build-system r-build-system)
8557 `(("r-clipr" ,r-clipr)
8558 ("r-clisymbols" ,r-clisymbols)
8559 ("r-crayon" ,r-crayon)
8564 ("r-git2r" ,r-git2r)
8566 ("r-purrr" ,r-purrr)
8567 ("r-rlang" ,r-rlang)
8568 ("r-rprojroot" ,r-rprojroot)
8569 ("r-rstudioapi" ,r-rstudioapi)
8570 ("r-whisker" ,r-whisker)
8571 ("r-withr" ,r-withr)
8572 ("r-yaml" ,r-yaml)))
8573 (home-page "https://github.com/r-lib/usethis")
8574 (synopsis "Automate R package and project setup")
8576 "This package helps you to automate R package and project setup tasks
8577 that are otherwise performed manually. This includes setting up unit testing,
8578 test coverage, continuous integration, Git, GitHub integration, licenses,
8579 Rcpp, RStudio projects, and more.")
8580 (license license:gpl3)))
8582 (define-public r-sessioninfo
8584 (name "r-sessioninfo")
8589 (uri (cran-uri "sessioninfo" version))
8592 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8593 (build-system r-build-system)
8596 ("r-withr" ,r-withr)))
8597 (home-page "https://github.com/r-lib/sessioninfo#readme")
8598 (synopsis "R session information")
8600 "This package provides tools to query and print information about the
8601 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8602 more information about packages, and where they were installed from.")
8603 (license license:gpl2)))
8605 (define-public r-remotes
8612 (uri (cran-uri "remotes" version))
8615 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8616 (build-system r-build-system)
8617 (home-page "https://github.com/r-lib/remotes#readme")
8618 (synopsis "R package installation from remote repositories")
8620 "Download and install R packages stored in GitHub, BitBucket, or plain
8621 subversion or git repositories. This package is a lightweight replacement of
8622 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8623 the code was copied over from @code{devtools}.")
8624 (license license:gpl2+)))
8626 (define-public r-xopen
8633 (uri (cran-uri "xopen" version))
8636 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8637 (build-system r-build-system)
8639 `(("r-processx" ,r-processx)))
8640 (home-page "https://github.com/r-lib/xopen#readme")
8641 (synopsis "Open system files, URLs, anything")
8643 "This package provides a cross-platform solution to open files,
8644 directories or URLs with their associated programs.")
8645 (license license:expat)))
8647 (define-public r-rcmdcheck
8649 (name "r-rcmdcheck")
8654 (uri (cran-uri "rcmdcheck" version))
8657 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8658 (build-system r-build-system)
8660 `(("r-callr" ,r-callr)
8662 ("r-crayon" ,r-crayon)
8664 ("r-digest" ,r-digest)
8665 ("r-pkgbuild" ,r-pkgbuild)
8666 ("r-prettyunits" ,r-prettyunits)
8668 ("r-rprojroot" ,r-rprojroot)
8669 ("r-sessioninfo" ,r-sessioninfo)
8670 ("r-withr" ,r-withr)
8671 ("r-xopen" ,r-xopen)))
8672 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8673 (synopsis "Run R CMD check from R and capture results")
8675 "Run @code{R CMD check} from R programmatically, and capture the results
8676 of the individual checks.")
8677 (license license:expat)))
8679 (define-public r-rapportools
8681 (name "r-rapportools")
8686 (uri (cran-uri "rapportools" version))
8689 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8690 (build-system r-build-system)
8692 `(("r-pander" ,r-pander)
8694 ("r-reshape" ,r-reshape)))
8695 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8696 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8698 "This package provides helper functions that act as wrappers to more
8699 advanced statistical methods with the advantage of having sane defaults for
8701 (license license:agpl3+)))
8703 (define-public r-pander
8710 (uri (cran-uri "pander" version))
8713 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8714 (build-system r-build-system)
8716 `(("r-digest" ,r-digest)
8717 ("r-rcpp" ,r-rcpp)))
8718 (home-page "https://rapporter.github.io/pander")
8719 (synopsis "Render R objects into Pandoc's markdown")
8721 "The main aim of the pander R package is to provide a minimal and easy
8722 tool for rendering R objects into Pandoc's markdown. The package is also
8723 capable of exporting/converting complex Pandoc documents (reports) in various
8725 ;; This package is licensed under either the AGPLv3+ or the very rarely
8727 (license license:agpl3+)))
8729 (define-public r-summarytools
8731 (name "r-summarytools")
8736 (uri (cran-uri "summarytools" version))
8739 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8740 (build-system r-build-system)
8742 `(("r-checkmate" ,r-checkmate)
8743 ("r-dplyr" ,r-dplyr)
8744 ("r-htmltools" ,r-htmltools)
8745 ("r-lubridate" ,r-lubridate)
8746 ("r-magick" ,r-magick)
8747 ("r-matrixstats" ,r-matrixstats)
8748 ("r-pander" ,r-pander)
8750 ("r-rapportools" ,r-rapportools)
8751 ("r-rcurl" ,r-rcurl)
8752 ("r-tibble" ,r-tibble)
8753 ("r-tidyr" ,r-tidyr)))
8754 (home-page "https://github.com/dcomtois/summarytools")
8755 (synopsis "Tools to quickly and neatly summarize data")
8757 "This package provides tools for data frame summaries, cross-tabulations,
8758 weight-enabled frequency tables and common univariate statistics in concise
8759 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8760 good point-of-entry for exploring data, both for experienced and new R
8762 (license license:gpl2)))
8764 (define-public r-lsei
8771 (uri (cran-uri "lsei" version))
8774 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8775 (build-system r-build-system)
8777 `(("gfortran" ,gfortran)))
8778 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8779 (synopsis "Solve regression problems under equality/inequality constraints")
8781 "It contains functions that solve least squares linear regression
8782 problems under linear equality/inequality constraints. Functions for solving
8783 quadratic programming problems are also available, which transform such
8784 problems into least squares ones first.")
8785 (license license:gpl2+)))
8787 (define-public r-npsurv
8794 (uri (cran-uri "npsurv" version))
8797 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8798 (build-system r-build-system)
8800 `(("r-lsei" ,r-lsei)))
8801 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8802 (synopsis "Nonparametric survival analysis")
8804 "This package contains functions for non-parametric survival analysis of
8805 exact and interval-censored observations.")
8806 (license license:gpl2+)))
8808 (define-public r-clusteval
8810 (name "r-clusteval")
8815 (uri (cran-uri "clusteval" version))
8818 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8819 (build-system r-build-system)
8821 `(("r-mvtnorm" ,r-mvtnorm)
8822 ("r-rcpp" ,r-rcpp)))
8823 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8824 (synopsis "Evaluation of clustering algorithms")
8826 "This R package provides a suite of tools to evaluate clustering
8827 algorithms, clusterings, and individual clusters.")
8828 (license license:expat)))
8830 (define-public r-tweedie
8837 (uri (cran-uri "tweedie" version))
8840 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8841 (build-system r-build-system)
8842 (native-inputs `(("gfortran" ,gfortran)))
8843 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8844 (synopsis "Evaluation of Tweedie exponential family models")
8846 "Maximum likelihood computations for Tweedie families, including the
8847 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8848 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8849 and related methods.")
8850 (license license:gpl2+)))
8852 (define-public r-rcppgsl
8859 (uri (cran-uri "RcppGSL" version))
8861 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
8862 (properties `((upstream-name . "RcppGSL")))
8863 (build-system r-build-system)
8865 `(("r-rcpp" ,r-rcpp)
8868 `(("r-knitr" ,r-knitr))) ; for vignettes
8869 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8870 (synopsis "Rcpp integration for GSL vectors and matrices")
8872 "The GNU Scientific Library (or GSL) is a collection of numerical
8873 routines for scientific computing. It is particularly useful for C and C++
8874 programs as it provides a standard C interface to a wide range of mathematical
8875 routines. There are over 1000 functions in total with an extensive test
8876 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8877 structures and R using concepts from Rcpp which is itself a package that eases
8878 the interfaces between R and C++.")
8879 (license license:gpl2+)))
8881 (define-public r-mvabund
8888 (uri (cran-uri "mvabund" version))
8891 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8892 (build-system r-build-system)
8894 `(("r-mass" ,r-mass)
8896 ("r-rcppgsl" ,r-rcppgsl)
8897 ("r-statmod" ,r-statmod)
8898 ("r-tweedie" ,r-tweedie)))
8899 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8900 (synopsis "Statistical methods for analysing multivariate abundance data")
8902 "This package provides a set of tools for displaying, modeling and
8903 analysing multivariate abundance data in community ecology.")
8904 (license license:lgpl2.1+)))
8906 (define-public r-afex
8913 (uri (cran-uri "afex" version))
8916 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
8917 (build-system r-build-system)
8921 ("r-lmertest" ,r-lmertest)
8922 ("r-pbkrtest" ,r-pbkrtest)
8923 ("r-reshape2" ,r-reshape2)))
8924 (home-page "https://afex.singmann.science/")
8925 (synopsis "Analysis of factorial experiments")
8927 "This package provides convenience functions for analyzing factorial
8928 experiments using ANOVA or mixed models.")
8929 (license license:gpl2+)))
8931 (define-public r-lmertest
8938 (uri (cran-uri "lmerTest" version))
8941 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
8942 (properties `((upstream-name . "lmerTest")))
8943 (build-system r-build-system)
8945 `(("r-ggplot2" ,r-ggplot2)
8948 ("r-numderiv" ,r-numderiv)))
8949 (home-page "https://github.com/runehaubo/lmerTestR")
8950 (synopsis "Tests in linear mixed effects models")
8952 "This package provides p-values in type I, II or III anova and summary
8953 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
8954 method. A Kenward-Roger method is also available via the @code{pbkrtest}
8955 package. Model selection methods include step, drop1 and anova-like tables
8956 for random effects (ranova). Methods for Least-Square means (LS-means) and
8957 tests of linear contrasts of fixed effects are also available.")
8958 (license license:gpl2+)))
8960 (define-public r-r2glmm
8967 (uri (cran-uri "r2glmm" version))
8970 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
8971 (build-system r-build-system)
8973 `(("r-afex" ,r-afex)
8974 ("r-data-table" ,r-data-table)
8975 ("r-dplyr" ,r-dplyr)
8976 ("r-ggplot2" ,r-ggplot2)
8977 ("r-gridextra" ,r-gridextra)
8978 ("r-lmertest" ,r-lmertest)
8980 ("r-matrix" ,r-matrix)
8982 ("r-pbkrtest" ,r-pbkrtest)))
8983 (home-page "https://github.com/bcjaeger/r2glmm")
8984 (synopsis "Compute R squared for mixed (multilevel) models")
8986 "This package computes model and semi partial R squared with confidence
8987 limits for the linear and generalized linear mixed model (LMM and GLMM). The
8988 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
8989 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
8991 (license license:gpl2)))
8993 (define-public r-weights
9000 (uri (cran-uri "weights" version))
9003 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9004 (build-system r-build-system)
9006 `(("r-gdata" ,r-gdata)
9007 ("r-hmisc" ,r-hmisc)
9008 ("r-mice" ,r-mice)))
9010 "https://cran.r-project.org/web/packages/weights/")
9011 (synopsis "Weighting and weighted statistics")
9012 (description "This package Provides a variety of functions for producing
9013 simple weighted statistics, such as weighted Pearson's correlations, partial
9014 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9015 includes some software for quickly recoding survey data and plotting point
9016 estimates from interaction terms in regressions (and multiply imputed
9017 regressions). NOTE: Weighted partial correlation calculations pulled to
9019 (license license:gpl2+)))
9021 (define-public r-rcppannoy
9023 (name "r-rcppannoy")
9028 (uri (cran-uri "RcppAnnoy" version))
9031 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9032 (properties `((upstream-name . "RcppAnnoy")))
9033 (build-system r-build-system)
9035 `(("r-rcpp" ,r-rcpp)))
9037 `(("r-knitr" ,r-knitr))) ; for vignettes
9038 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9039 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9041 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9042 for efficient memory usage as well an ability to load from and save to disk.
9043 This package provides an R interface.")
9044 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9046 (license (list license:gpl2+ license:asl2.0))))
9048 (define-public r-rcpphnsw
9055 (uri (cran-uri "RcppHNSW" version))
9058 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9059 (properties `((upstream-name . "RcppHNSW")))
9060 (build-system r-build-system)
9061 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9062 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9063 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9065 "Hnswlib is a C++ library for approximate nearest neighbors. This
9066 package provides a minimal R interface by relying on the Rcpp package.")
9067 ;; hnswlib is released under Version 2.0 of the Apache License.
9068 (license (list license:gpl3 license:asl2.0))))
9070 (define-public r-rcppparallel
9072 (name "r-rcppparallel")
9077 (uri (cran-uri "RcppParallel" version))
9080 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9081 (properties `((upstream-name . "RcppParallel")))
9082 (build-system r-build-system)
9083 (home-page "http://rcppcore.github.io/RcppParallel")
9084 (synopsis "Parallel programming tools for Rcpp")
9086 "This package provides high level functions for parallel programming with
9087 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9088 the work of a standard serial @code{for} loop into a parallel one and the
9089 @code{parallelReduce()} function can be used for accumulating aggregates or
9091 (license license:gpl2)))
9093 (define-public r-ncdf4
9100 (uri (cran-uri "ncdf4" version))
9103 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9104 (build-system r-build-system)
9106 `(("netcdf" ,netcdf)
9108 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9109 (synopsis "R interface to Unidata netCDF format data files")
9111 "This package provides a high-level R interface to data files written
9112 using Unidata's netCDF library (version 4 or earlier), which are binary data
9113 files that are portable across platforms and include metadata information in
9114 addition to the data sets. Using this package, netCDF files can be opened and
9115 data sets read in easily. It is also easy to create new netCDF dimensions,
9116 variables, and files, in either version 3 or 4 format, and manipulate existing
9118 (license license:gpl3+)))
9120 (define-public r-biocmanager
9122 (name "r-biocmanager")
9127 (uri (cran-uri "BiocManager" version))
9129 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9130 (properties `((upstream-name . "BiocManager")))
9131 (build-system r-build-system)
9132 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9133 (synopsis "Access the Bioconductor project package repository")
9135 "This package provides a convenient tool to install and update
9136 Bioconductor packages.")
9137 (license license:artistic2.0)))
9139 (define-public r-rgl
9142 (version "0.100.30")
9146 (uri (cran-uri "rgl" version))
9149 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9150 (build-system r-build-system)
9152 `(("pkg-config" ,pkg-config)))
9154 `(("freetype" ,freetype)
9158 ("ghc-pandoc" ,ghc-pandoc)
9161 `(("r-crosstalk" ,r-crosstalk)
9162 ("r-htmltools" ,r-htmltools)
9163 ("r-htmlwidgets" ,r-htmlwidgets)
9164 ("r-jsonlite" ,r-jsonlite)
9165 ("r-knitr" ,r-knitr)
9166 ("r-magrittr" ,r-magrittr)
9167 ("r-manipulatewidget" ,r-manipulatewidget)
9168 ("r-shiny" ,r-shiny)))
9169 (home-page "https://r-forge.r-project.org/projects/rgl/")
9170 (synopsis "3D visualization using OpenGL")
9172 "This package provides medium to high level functions for 3D interactive graphics,
9173 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9174 as functions for constructing representations of geometric
9175 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9176 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9177 image formats, including PNG, Postscript, SVG, PGF.")
9178 ;; Any version of the GPL.
9179 (license (list license:gpl2+ license:gpl3+))))
9181 (define-public r-multicool
9183 (name "r-multicool")
9188 (uri (cran-uri "multicool" version))
9191 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
9192 (build-system r-build-system)
9193 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9194 (home-page "https://cran.r-project.org/web/packages/multicool/")
9195 (synopsis "Permutations of multisets in cool-lex order")
9197 "This package provides a set of tools to permute multisets without loops
9198 or hash tables and to generate integer partitions. Cool-lex order is similar
9199 to colexicographical order.")
9200 (license license:gpl2)))
9202 (define-public r-misc3d
9209 (uri (cran-uri "misc3d" version))
9212 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9213 (build-system r-build-system)
9214 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9215 (synopsis "Miscellaneous 3D Plots")
9217 "This package provides a collection of miscellaneous 3d plots, including
9219 ;; Any version of the GPL.
9220 (license (list license:gpl2+ license:gpl3+))))
9229 (uri (cran-uri "ks" version))
9231 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9232 (build-system r-build-system)
9235 ("r-kernlab" ,r-kernlab)
9236 ("r-kernsmooth" ,r-kernsmooth)
9237 ("r-matrix" ,r-matrix)
9238 ("r-mclust" ,r-mclust)
9240 ("r-multicool" ,r-multicool)
9241 ("r-mvtnorm" ,r-mvtnorm)))
9242 (home-page "http://www.mvstat.net/tduong/")
9243 (synopsis "Kernel smoothing")
9245 "This package provides kernel smoothers for univariate and multivariate
9246 data, including density functions, density derivatives, cumulative
9247 distributions, modal clustering, discriminant analysis, and two-sample
9248 hypothesis testing.")
9249 ;; Either version of the GPL.
9250 (license (list license:gpl2 license:gpl3))))
9252 (define-public r-feature
9259 (uri (cran-uri "feature" version))
9262 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9263 (build-system r-build-system)
9266 ("r-misc3d" ,r-misc3d)
9268 (home-page "http://www.mvstat.net/tduong/")
9269 (synopsis "Inferential feature significance for kernel density estimation")
9271 "The feature package contains functions to display and compute kernel
9272 density estimates, significant gradient and significant curvature regions.
9273 Significant gradient and/or curvature regions often correspond to significant
9274 features (e.g. local modes).")
9275 ;; Either version of the GPL.
9276 (license (list license:gpl2 license:gpl3))))
9278 (define-public r-arm
9285 (uri (cran-uri "arm" version))
9288 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9289 (build-system r-build-system)
9291 `(("r-abind" ,r-abind)
9295 ("r-matrix" ,r-matrix)
9296 ("r-nlme" ,r-nlme)))
9297 (home-page "https://cran.r-project.org/web/packages/arm/")
9298 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9300 "This package provides functions to accompany A. Gelman and J. Hill,
9301 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9302 University Press, 2007.")
9303 (license license:gpl3+)))
9305 (define-public r-circular
9312 (uri (cran-uri "circular" version))
9315 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9316 (build-system r-build-system)
9318 `(("r-boot" ,r-boot)
9319 ("r-mvtnorm" ,r-mvtnorm)))
9321 `(("gfortran" ,gfortran)))
9322 (home-page "https://cran.r-project.org/web/packages/circular/")
9323 (synopsis "Circular statistics")
9325 "This package provides tools for circular statistics, from \"Topics in
9326 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9328 (license license:gpl2+)))
9330 (define-public r-activity
9337 (uri (cran-uri "activity" version))
9340 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9341 (build-system r-build-system)
9343 `(("r-circular" ,r-circular)
9344 ("r-insol" ,r-insol)
9345 ("r-pbapply" ,r-pbapply)))
9346 (home-page "https://cran.r-project.org/web/packages/activity/")
9347 (synopsis "Animal activity statistics")
9349 "This package provides functions to fit kernel density functions to
9350 animal activity time data; plot activity distributions; quantify overall
9351 levels of activity; statistically compare activity metrics through
9352 bootstrapping; and evaluate variation in linear variables with time (or other
9353 circular variables).")
9354 (license license:gpl3)))
9356 (define-public r-ouch
9363 (uri (cran-uri "ouch" version))
9366 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9367 (build-system r-build-system)
9368 (propagated-inputs `(("r-subplex" ,r-subplex)))
9369 (home-page "http://kingaa.github.io/ouch/")
9370 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9372 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9373 for evolution along a phylogenetic tree.")
9374 (license license:gpl2+)))
9376 (define-public r-fmsb
9383 (uri (cran-uri "fmsb" version))
9386 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9387 (build-system r-build-system)
9388 (home-page "http://minato.sip21c.org/msb/")
9389 (synopsis "Functions for medical statistics book with demographic data")
9391 "This package provides several utility functions for the book entitled
9392 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9393 Japan, 2007) with Japanese demographic data and some demographic analysis
9394 related functions.")
9395 (license license:gpl2+)))
9397 (define-public r-stabledist
9399 (name "r-stabledist")
9404 (uri (cran-uri "stabledist" version))
9407 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9408 (build-system r-build-system)
9409 (home-page "http://www.rmetrics.org")
9410 (synopsis "Stable distribution functions")
9412 "This package provides density, probability and quantile functions, and
9413 random number generation for (skew) stable distributions, using the
9414 parametrizations of Nolan.")
9415 (license license:gpl2+)))
9417 (define-public r-gsl
9424 (uri (cran-uri "gsl" version))
9427 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9428 (build-system r-build-system)
9431 (home-page "https://cran.r-project.org/web/packages/gsl")
9432 (synopsis "Wrapper for the GNU Scientific Library")
9434 "This package provides an R wrapper for the special functions and quasi
9435 random number generators of the GNU Scientific Library.")
9436 (license license:gpl2+)))
9438 (define-public r-adgoftest
9440 (name "r-adgoftest")
9445 (uri (cran-uri "ADGofTest" version))
9448 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9449 (properties `((upstream-name . "ADGofTest")))
9450 (build-system r-build-system)
9451 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9452 (synopsis "Anderson-Darling GoF test")
9454 "This package provides an implementation of the Anderson-Darling GoF test
9455 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9456 Anderson-Darling Distribution\".")
9457 ;; Any version of the GPL.
9458 (license license:gpl3+)))
9460 (define-public r-softimpute
9462 (name "r-softimpute")
9467 (uri (cran-uri "softImpute" version))
9470 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9471 (properties `((upstream-name . "softImpute")))
9472 (build-system r-build-system)
9474 `(("r-matrix" ,r-matrix)))
9476 `(("gfortran" ,gfortran)))
9477 (home-page "https://cran.r-project.org/web/packages/softImpute")
9478 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9480 "This package provides iterative methods for matrix completion that use
9481 nuclear-norm regularization. The package includes procedures for centering
9482 and scaling rows, columns or both, and for computing low-rank @dfn{single
9483 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9485 (license license:gpl2)))
9487 (define-public r-fftwtools
9489 (name "r-fftwtools")
9494 (uri (cran-uri "fftwtools" version))
9497 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9498 (build-system r-build-system)
9499 (inputs `(("fftw" ,fftw)))
9500 (home-page "https://github.com/krahim/fftwtools")
9501 (synopsis "Wrapper for FFTW3")
9503 "This package provides a wrapper for several FFTW functions. It provides
9504 access to the two-dimensional FFT, the multivariate FFT, and the
9505 one-dimensional real to complex FFT using the FFTW3 library. The package
9506 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9507 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9508 The FFT functions have a parameter that allows them to not return the
9509 redundant complex conjugate when the input is real data.")
9510 (license license:gpl2+)))
9512 (define-public r-tiff
9519 (uri (cran-uri "tiff" version))
9522 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9523 (build-system r-build-system)
9525 `(("libtiff" ,libtiff)
9526 ("libjpeg" ,libjpeg)
9528 (home-page "http://www.rforge.net/tiff/")
9529 (synopsis "Read and write TIFF images")
9531 "This package provides an easy and simple way to read, write and display
9532 bitmap images stored in the TIFF format. It can read and write both files and
9533 in-memory raw vectors.")
9534 ;; Either of these two license versions.
9535 (license (list license:gpl2 license:gpl3))))
9537 (define-public r-nlp
9544 (uri (cran-uri "NLP" version))
9547 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9548 (properties `((upstream-name . "NLP")))
9549 (build-system r-build-system)
9550 (home-page "https://cran.r-project.org/web/packages/NLP/")
9551 (synopsis "Natural language processing infrastructure")
9553 "This package provides basic classes and methods for Natural Language
9555 (license license:gpl3)))
9564 (uri (cran-uri "tm" version))
9567 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
9568 (properties `((upstream-name . "tm")))
9569 (build-system r-build-system)
9575 ("r-xml2" ,r-xml2)))
9576 (home-page "http://tm.r-forge.r-project.org/")
9577 (synopsis "Text mining package")
9579 "This package provides a framework for text mining applications within R.")
9580 (license license:gpl3)))
9582 (define-public r-waveslim
9589 (uri (cran-uri "waveslim" version))
9592 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9593 (build-system r-build-system)
9595 `(("gfortran" ,gfortran)))
9596 (home-page "http://waveslim.blogspot.com")
9597 (synopsis "Basic wavelet routines for signal processing")
9599 "This package provides basic wavelet routines for time series (1D),
9600 image (2D) and array (3D) analysis. The code provided here is based on
9601 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9602 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9603 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9604 pairs (Selesnick 2001, 2002).")
9605 (license license:bsd-3)))
9607 (define-public r-wordcloud
9609 (name "r-wordcloud")
9614 (uri (cran-uri "wordcloud" version))
9617 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9618 (build-system r-build-system)
9620 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9622 ;; The "tm" package is only "suggested" according to CRAN, but the
9623 ;; wordcloud package cannot be loaded without it.
9625 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9626 (synopsis "Word clouds")
9628 "This package provides functionality to create pretty word clouds,
9629 visualize differences and similarity between documents, and avoid
9630 over-plotting in scatter plots with text.")
9631 (license license:lgpl2.1)))
9633 (define-public r-colorramps
9635 (name "r-colorramps")
9640 (uri (cran-uri "colorRamps" version))
9643 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9644 (properties `((upstream-name . "colorRamps")))
9645 (build-system r-build-system)
9646 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9647 (synopsis "Build color tables")
9648 (description "This package provides features to build gradient color
9650 ;; Any version of the GPL
9651 (license license:gpl3+)))
9653 (define-public r-tidytree
9660 (uri (cran-uri "tidytree" version))
9662 (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
9663 (build-system r-build-system)
9666 ("r-dplyr" ,r-dplyr)
9667 ("r-lazyeval" ,r-lazyeval)
9668 ("r-magrittr" ,r-magrittr)
9669 ("r-rlang" ,r-rlang)
9670 ("r-tibble" ,r-tibble)))
9671 (home-page "https://github.com/GuangchuangYu/tidytree")
9672 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9674 "Phylogenetic trees generally contain multiple components including nodes,
9675 edges, branches and associated data. This package provides an approach to
9676 convert tree objects to tidy data frames. It also provides tidy interfaces to
9677 manipulate tree data.")
9678 (license license:artistic2.0)))
9680 (define-public r-rvcheck
9687 (uri (cran-uri "rvcheck" version))
9689 (base32 "11n3qxapxcqsa0771s9q8n95kxmfyflya1d6wz4mm0lz0i6q55ia"))))
9690 (build-system r-build-system)
9692 `(("r-biocmanager" ,r-biocmanager)
9693 ("r-rlang" ,r-rlang)))
9694 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9695 (synopsis "R package version check")
9697 "This package provides tools to check the latest release version of R and
9698 R packages (on CRAN, Bioconductor or Github).")
9699 (license license:artistic2.0)))
9701 (define-public r-docopt
9708 (uri (cran-uri "docopt" version))
9711 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9712 (build-system r-build-system)
9713 (home-page "https://github.com/docopt/docopt.R")
9714 (synopsis "Command-line interface specification language")
9716 "This package enables you to define a command-line interface by just
9717 giving it a description in the specific format.")
9718 (license license:expat)))
9720 (define-public r-sparsesvd
9722 (name "r-sparsesvd")
9727 (uri (cran-uri "sparsesvd" version))
9730 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9731 (build-system r-build-system)
9732 (propagated-inputs `(("r-matrix" ,r-matrix)))
9733 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9734 (synopsis "Sparse truncated singular value decomposition")
9736 "This package provides a Wrapper around the SVDLIBC library
9737 for (truncated) singular value decomposition of a sparse matrix. Currently,
9738 only sparse real matrices in Matrix package format are supported.")
9739 ;; SVDLIBC is released under BSD-2. The R interface is released under
9741 (license (list license:bsd-3 license:bsd-2))))
9743 (define-public r-speedglm
9750 (uri (cran-uri "speedglm" version))
9753 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9754 (build-system r-build-system)
9756 `(("r-mass" ,r-mass)
9757 ("r-matrix" ,r-matrix)))
9758 (home-page "https://cran.r-project.org/web/packages/speedglm")
9759 (synopsis "Fit linear and generalized linear models to large data sets")
9761 "This package provides tools for fitting linear models and generalized
9762 linear models to large data sets by updating algorithms.")
9763 ;; Any version of the GPL
9764 (license license:gpl2+)))
9766 (define-public r-densityclust
9768 (name "r-densityclust")
9773 (uri (cran-uri "densityClust" version))
9776 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9777 (properties `((upstream-name . "densityClust")))
9778 (build-system r-build-system)
9781 ("r-ggplot2" ,r-ggplot2)
9782 ("r-ggrepel" ,r-ggrepel)
9783 ("r-gridextra" ,r-gridextra)
9784 ("r-rcolorbrewer" ,r-rcolorbrewer)
9786 ("r-rtsne" ,r-rtsne)))
9787 (home-page "https://cran.r-project.org/web/packages/densityClust")
9788 (synopsis "Clustering by fast search and find of density peaks")
9790 "This package provides an improved implementation (based on k-nearest
9791 neighbors) of the density peak clustering algorithm, originally described by
9792 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9793 large datasets (> 100,000 samples) very efficiently.")
9794 (license license:gpl2+)))
9796 (define-public r-combinat
9803 (uri (cran-uri "combinat" version))
9806 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9807 (build-system r-build-system)
9808 (home-page "https://cran.r-project.org/web/packages/combinat")
9809 (synopsis "Combinatorics utilities")
9810 (description "This package provides assorted routines for combinatorics.")
9811 (license license:gpl2)))
9813 (define-public r-qlcmatrix
9815 (name "r-qlcmatrix")
9820 (uri (cran-uri "qlcMatrix" version))
9823 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9824 (properties `((upstream-name . "qlcMatrix")))
9825 (build-system r-build-system)
9827 `(("r-docopt" ,r-docopt)
9828 ("r-matrix" ,r-matrix)
9830 ("r-sparsesvd" ,r-sparsesvd)))
9831 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9832 (synopsis "Sparse matrix functions for quantitative language comparison")
9834 "This package provides an extension of the functionality of the Matrix
9835 package for using sparse matrices. Some of the functions are very general,
9836 while other are highly specific for the special data format used for
9837 @dfn{quantitative language comparison} (QLC).")
9838 (license license:gpl3)))
9840 (define-public r-ddrtree
9847 (uri (cran-uri "DDRTree" version))
9850 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9851 (properties `((upstream-name . "DDRTree")))
9852 (build-system r-build-system)
9855 ("r-irlba" ,r-irlba)
9857 ("r-rcppeigen" ,r-rcppeigen)))
9858 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9859 (synopsis "Learning principal graphs with DDRTree")
9861 "This package provides an implementation of the framework of
9862 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9863 dimensional space while constructs a principal tree which passes through the
9864 middle of the data simultaneously. DDRTree shows superiority to
9865 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9866 intrinsic structure of single cell genomics data. In general, it could be
9867 used to reconstruct the temporal progression as well as the bifurcation
9868 structure of any data type.")
9869 (license license:asl2.0)))
9871 (define-public r-corpcor
9878 (uri (cran-uri "corpcor" version))
9881 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9882 (build-system r-build-system)
9883 (home-page "http://strimmerlab.org/software/corpcor/")
9884 (synopsis "Efficient estimation of covariance and (partial) correlation")
9886 "This package implements a James-Stein-type shrinkage estimator for the
9887 covariance matrix, with separate shrinkage for variances and correlations.
9888 Furthermore, functions are available for fast singular value decomposition,
9889 for computing the pseudoinverse, and for checking the rank and positive
9890 definiteness of a matrix.")
9891 (license license:gpl3+)))
9893 (define-public r-rspectra
9900 (uri (cran-uri "RSpectra" version))
9903 "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s"))))
9904 (properties `((upstream-name . "RSpectra")))
9905 (build-system r-build-system)
9907 `(("r-matrix" ,r-matrix)
9909 ("r-rcppeigen" ,r-rcppeigen)))
9910 (home-page "https://github.com/yixuan/RSpectra")
9911 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9913 "This package provides an R interface to the Spectra library for
9914 large-scale eigenvalue and SVD problems. It is typically used to compute a
9915 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9916 which is usually more efficient than @code{eigen()} if k << n.")
9918 (license license:mpl2.0)))
9920 (define-public r-vbsr
9927 (uri (cran-uri "vbsr" version))
9930 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
9931 (build-system r-build-system)
9932 (home-page "https://cran.r-project.org/web/packages/vbsr")
9933 (synopsis "Variational Bayes spike regression regularized linear models")
9935 "This package provides an efficient algorithm for solving ultra-sparse
9936 regularized regression models using a variational Bayes algorithm with a spike
9937 prior. The algorithm is solved on a path, with coordinate updates, and is
9938 capable of generating very sparse models. Very general model
9939 diagnostics for controlling type-1 errors are also provided.")
9940 (license license:gpl2)))
9942 (define-public r-flare
9949 (uri (cran-uri "flare" version))
9952 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
9953 (build-system r-build-system)
9955 `(("r-igraph" ,r-igraph)
9956 ("r-lattice" ,r-lattice)
9958 ("r-matrix" ,r-matrix)))
9959 (home-page "https://cran.r-project.org/web/packages/flare")
9960 (synopsis "Family of Lasso regression implementations")
9962 "This package provides implementations of a family of Lasso variants
9963 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
9964 high dimensional sparse linear models.")
9965 (license license:gpl2)))
9967 (define-public r-lassopv
9974 (uri (cran-uri "lassopv" version))
9977 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
9978 (build-system r-build-system)
9979 (propagated-inputs `(("r-lars" ,r-lars)))
9980 (home-page "https://github.com/lingfeiwang/lassopv")
9981 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
9983 "This package enables you to estimate the p-values for predictors x
9984 against target variable y in Lasso regression, using the regularization
9985 strength when each predictor enters the active set of regularization path for
9986 the first time as the statistic.")
9987 (license license:gpl3)))
9989 (define-public r-splitstackshape
9991 (name "r-splitstackshape")
9996 (uri (cran-uri "splitstackshape" version))
9999 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10000 (build-system r-build-system)
10002 `(("r-data-table" ,r-data-table)))
10003 (home-page "https://github.com/mrdwab/splitstackshape")
10004 (synopsis "Stack and reshape datasets after splitting concatenated values")
10006 "Online data collection tools like Google Forms often export
10007 multiple-response questions with data concatenated in cells. The
10008 @code{concat.split} (cSplit) family of functions provided by this package
10009 splits such data into separate cells. This package also includes functions to
10010 stack groups of columns and to reshape wide data, even when the data are
10011 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10012 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10014 (license license:gpl3)))
10016 (define-public r-tfmpvalue
10018 (name "r-tfmpvalue")
10023 (uri (cran-uri "TFMPvalue" version))
10026 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10027 (properties `((upstream-name . "TFMPvalue")))
10028 (build-system r-build-system)
10029 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10030 (home-page "https://github.com/ge11232002/TFMPvalue")
10031 (synopsis "P-value computation for position weight matrices")
10033 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10034 identification from sequence/alignments, we are interested in the significance
10035 of certain match scores. TFMPvalue provides the accurate calculation of a
10036 p-value with a score threshold for position weight matrices, or the score with
10037 a given p-value. It is an interface to code originally made available by
10038 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10039 Touzet and Varre (2007).")
10040 (license license:gpl2)))
10042 (define-public r-rnifti
10049 (uri (cran-uri "RNifti" version))
10052 "0l61hjnzv043ibpkgrhc0yngaqmc58lkvii8j1dzh022z5wbqrj8"))))
10053 (properties `((upstream-name . "RNifti")))
10054 (build-system r-build-system)
10055 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10056 (home-page "https://github.com/jonclayden/RNifti")
10057 (synopsis "Fast R and C++ access to NIfTI images")
10059 "This package provides very fast read and write access to images stored
10060 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10061 compiled C and interpreted R code. It also provides a C/C++ API that can be
10062 used by other packages.")
10063 (license license:gpl2)))
10065 (define-public r-shades
10072 (uri (cran-uri "shades" version))
10075 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10076 (build-system r-build-system)
10077 (home-page "https://github.com/jonclayden/shades")
10078 (synopsis "Simple color manipulation")
10080 "This package provides functions for easily manipulating colors,
10081 creating color scales and calculating color distances.")
10082 (license license:bsd-3)))
10084 (define-public r-ore
10091 (uri (cran-uri "ore" version))
10093 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10094 (build-system r-build-system)
10095 (home-page "https://github.com/jonclayden/ore")
10096 (synopsis "R interface to the Onigmo regular expression library")
10098 "This package provides an alternative to R's built-in functionality for
10099 handling regular expressions, based on the Onigmo library. It offers
10100 first-class compiled regex objects, partial matching and function-based
10101 substitutions, amongst other features.")
10102 (license license:bsd-3)))
10104 (define-public r-reportr
10111 (uri (cran-uri "reportr" version))
10114 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10115 (build-system r-build-system)
10116 (propagated-inputs `(("r-ore" ,r-ore)))
10117 (home-page "https://github.com/jonclayden/reportr")
10118 (synopsis "General message and error reporting system")
10120 "This package provides a system for reporting messages, which offers
10121 certain useful features over the standard R system, such as the incorporation
10122 of output consolidation, message filtering, assertions, expression
10123 substitution, automatic generation of stack traces for debugging, and
10124 conditional reporting based on the current \"output level\".")
10125 (license license:gpl2)))
10127 (define-public r-tractor-base
10129 (name "r-tractor-base")
10134 (uri (cran-uri "tractor.base" version))
10137 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10138 (properties `((upstream-name . "tractor.base")))
10139 (build-system r-build-system)
10142 ("r-reportr" ,r-reportr)
10143 ("r-rnifti" ,r-rnifti)
10144 ("r-shades" ,r-shades)))
10145 (home-page "http://www.tractor-mri.org.uk")
10146 (synopsis "Read, manipulate and visualize magnetic resonance images")
10148 "This package provides functions for working with magnetic resonance
10149 images. It supports reading and writing of popular file formats (DICOM,
10150 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10151 visualization; flexible image manipulation; metadata and sparse image
10153 (license license:gpl2)))
10155 (define-public r-grimport
10157 (name "r-grimport")
10162 (uri (cran-uri "grImport" version))
10165 "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16"))))
10166 (properties `((upstream-name . "grImport")))
10167 (build-system r-build-system)
10169 `(("ghostscript" ,ghostscript)))
10171 `(("r-xml" ,r-xml)))
10172 (home-page "https://cran.r-project.org/web/packages/grImport")
10173 (synopsis "Convert, import, and draw PostScript pictures")
10175 "This package provides functions for converting, importing, and drawing
10176 PostScript pictures in R plots.")
10177 (license license:gpl2+)))
10179 (define-public r-grimport2
10181 (name "r-grimport2")
10186 (uri (cran-uri "grImport2" version))
10189 "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls"))))
10190 (properties `((upstream-name . "grImport2")))
10191 (build-system r-build-system)
10193 `(("r-base64enc" ,r-base64enc)
10197 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10198 (synopsis "Import SVG graphics")
10200 "This package provides functions for importing external vector images and
10201 drawing them as part of R plots. This package is different from the
10202 @code{grImport} package because, where that package imports PostScript format
10203 images, this package imports SVG format images. Furthermore, this package
10204 imports a specific subset of SVG, so external images must be preprocessed
10205 using a package like @code{rsvg} to produce SVG that this package can import.
10206 SVG features that are not supported by R graphics, such as gradient fills, can
10207 be imported and then exported via the @code{gridSVG} package.")
10208 (license license:gpl2+)))
10210 (define-public r-kohonen
10217 (uri (cran-uri "kohonen" version))
10220 "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
10221 (build-system r-build-system)
10223 `(("r-mass" ,r-mass)
10224 ("r-rcpp" ,r-rcpp)))
10225 (home-page "https://cran.r-project.org/web/packages/kohonen")
10226 (synopsis "Supervised and unsupervised self-organising maps")
10228 "This package provides functions to train @dfn{self-organising
10229 maps} (SOMs). Also interrogation of the maps and prediction using trained
10230 maps are supported. The name of the package refers to Teuvo Kohonen, the
10231 inventor of the SOM.")
10232 (license license:gpl2+)))
10234 (define-public r-nnls
10241 (uri (cran-uri "nnls" version))
10244 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10245 (build-system r-build-system)
10246 (native-inputs `(("gfortran" ,gfortran)))
10247 (home-page "https://cran.r-project.org/web/packages/nnls")
10248 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10250 "This package provides an R interface to the Lawson-Hanson implementation
10251 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10252 the combination of non-negative and non-positive constraints.")
10253 (license license:gpl2+)))
10255 (define-public r-iso
10262 (uri (cran-uri "Iso" version))
10265 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10266 (properties `((upstream-name . "Iso")))
10267 (build-system r-build-system)
10268 (native-inputs `(("gfortran" ,gfortran)))
10269 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10270 (synopsis "Functions to perform isotonic regression")
10272 "This package provides support for linear order and unimodal
10273 order (univariate) isotonic regression and bivariate isotonic regression with
10274 linear order on both variables.")
10275 (license license:gpl2+)))
10277 (define-public r-chemometricswithr
10279 (name "r-chemometricswithr")
10284 (uri (cran-uri "ChemometricsWithR" version))
10287 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10289 `((upstream-name . "ChemometricsWithR")))
10290 (build-system r-build-system)
10292 `(("r-devtools" ,r-devtools)
10293 ("r-kohonen" ,r-kohonen)
10296 (home-page "https://github.com/rwehrens/CWR")
10297 (synopsis "Chemometrics with R")
10299 "This package provides functions and scripts used in the book
10300 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10301 Life Sciences\" by Ron Wehrens, Springer (2011).")
10302 (license license:gpl2+)))
10304 (define-public r-als
10311 (uri (cran-uri "ALS" version))
10314 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10315 (properties `((upstream-name . "ALS")))
10316 (build-system r-build-system)
10319 ("r-nnls" ,r-nnls)))
10320 (home-page "https://cran.r-project.org/web/packages/ALS")
10321 (synopsis "Multivariate curve resolution alternating least squares")
10323 "Alternating least squares is often used to resolve components
10324 contributing to data with a bilinear structure; the basic technique may be
10325 extended to alternating constrained least squares. This package provides an
10326 implementation of @dfn{multivariate curve resolution alternating least
10327 squares} (MCR-ALS).
10329 Commonly applied constraints include unimodality, non-negativity, and
10330 normalization of components. Several data matrices may be decomposed
10331 simultaneously by assuming that one of the two matrices in the bilinear
10332 decomposition is shared between datasets.")
10333 (license license:gpl2+)))
10335 (define-public r-strucchange
10337 (name "r-strucchange")
10342 (uri (cran-uri "strucchange" version))
10345 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10346 (build-system r-build-system)
10348 `(("r-sandwich" ,r-sandwich)
10350 (home-page "https://cran.r-project.org/web/packages/strucchange")
10351 (synopsis "Testing, monitoring, and dating structural changes")
10353 "This package provides tools for testing, monitoring and dating
10354 structural changes in (linear) regression models. It features tests/methods
10355 from the generalized fluctuation test framework as well as from the F
10356 test (Chow test) framework. This includes methods to fit, plot and test
10357 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10358 statistics, respectively. It is possible to monitor incoming data online
10359 using fluctuation processes. Finally, the breakpoints in regression models
10360 with structural changes can be estimated together with confidence intervals.
10361 Emphasis is always given to methods for visualizing the data.")
10362 ;; Either of these two GPL versions
10363 (license (list license:gpl2 license:gpl3))))
10365 (define-public r-pixmap
10372 (uri (cran-uri "pixmap" version))
10375 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10376 (build-system r-build-system)
10377 (home-page "https://cran.r-project.org/web/packages/pixmap")
10378 (synopsis "Tools for bitmap images")
10380 "This package provides functions for importing, exporting, plotting and
10381 other manipulations of bitmapped images.")
10382 (license license:gpl2)))
10384 (define-public r-rapidjsonr
10386 (name "r-rapidjsonr")
10391 (uri (cran-uri "rapidjsonr" version))
10394 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10395 (build-system r-build-system)
10396 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10397 (synopsis "JSON parser")
10399 "This package provides JSON parsing capability through the Rapidjson
10401 (license license:expat)))
10403 (define-public r-ontologyindex
10405 (name "r-ontologyindex")
10410 (uri (cran-uri "ontologyIndex" version))
10413 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10414 (properties `((upstream-name . "ontologyIndex")))
10415 (build-system r-build-system)
10416 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10417 (synopsis "Functions for processing ontologies in R")
10419 "This package provides functions for reading ontologies into R as lists
10420 and manipulating sets of ontological terms.")
10421 (license license:gpl2+)))
10423 (define-public r-gargle
10430 (uri (cran-uri "gargle" version))
10433 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10434 (build-system r-build-system)
10439 ("r-jsonlite" ,r-jsonlite)
10440 ("r-rlang" ,r-rlang)
10441 ("r-withr" ,r-withr)))
10442 (home-page "https://gargle.r-lib.org")
10443 (synopsis "Utilities for working with Google APIs")
10445 "This package provides utilities for working with Google APIs. This
10446 includes functions and classes for handling common credential types and for
10447 preparing, executing, and processing HTTP requests.")
10448 (license license:expat)))
10450 (define-public r-bigrquery
10452 (name "r-bigrquery")
10457 (uri (cran-uri "bigrquery" version))
10460 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10461 (build-system r-build-system)
10463 `(("r-assertthat" ,r-assertthat)
10464 ("r-bit64" ,r-bit64)
10467 ("r-gargle" ,r-gargle)
10470 ("r-jsonlite" ,r-jsonlite)
10471 ("r-prettyunits" ,r-prettyunits)
10472 ("r-progress" ,r-progress)
10473 ("r-rapidjsonr" ,r-rapidjsonr)
10475 ("r-rlang" ,r-rlang)
10476 ("r-tibble" ,r-tibble)))
10477 (home-page "https://github.com/rstats-db/bigrquery")
10478 (synopsis "R interface to Google's BigQuery API")
10480 "This package provides an R interface to Google's BigQuery database.")
10481 (license license:gpl3)))
10483 (define-public r-gmp
10486 (version "0.5-13.5")
10490 (uri (cran-uri "gmp" version))
10493 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10494 (build-system r-build-system)
10497 (modify-phases %standard-phases
10498 (add-after 'unpack 'set-CC
10499 (lambda _ (setenv "CC" "gcc") #t)))))
10500 (inputs `(("gmp" ,gmp)))
10501 (home-page "https://cran.r-project.org/web/packages/gmp")
10502 (synopsis "Multiple precision arithmetic")
10504 "This package supports multiple precision arithmetic (big integers and
10505 rationals, prime number tests, matrix computation), \"arithmetic without
10506 limitations\" using the GNU Multiple Precision library.")
10507 ;; Any version of the GPL.
10508 (license license:gpl3+)))
10510 (define-public r-rmpfr
10517 (uri (cran-uri "Rmpfr" version))
10520 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10521 (properties `((upstream-name . "Rmpfr")))
10522 (build-system r-build-system)
10526 `(("r-gmp" ,r-gmp)))
10527 (home-page "http://rmpfr.r-forge.r-project.org/")
10528 (synopsis "R bindings to the MPFR library")
10530 "This package supports arithmetic (via S4 classes and methods) for
10531 arbitrary precision floating point numbers, including transcendental
10532 functions. To this end, the package interfaces with the @dfn{Multiple
10533 Precision Floating-Point Reliable} (MPFR) library.")
10534 (license license:gpl2+)))
10536 (define-public r-assertive-base
10538 (name "r-assertive-base")
10543 (uri (cran-uri "assertive.base" version))
10546 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10548 `((upstream-name . "assertive.base")))
10549 (build-system r-build-system)
10550 (home-page "https://bitbucket.org/richierocks/assertive.base")
10551 (synopsis "Core of the assertive package")
10553 "This package provides a minimal set of predicates and assertions used by
10554 the assertive package. This is mainly for use by other package developers who
10555 want to include run-time testing features in their own packages.")
10556 (license license:gpl3+)))
10558 (define-public r-assertive-properties
10560 (name "r-assertive-properties")
10565 (uri (cran-uri "assertive.properties" version))
10568 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10570 `((upstream-name . "assertive.properties")))
10571 (build-system r-build-system)
10573 `(("r-assertive-base" ,r-assertive-base)))
10574 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10575 (synopsis "Assertions to check properties of variables")
10577 "This package provides a set of predicates and assertions for checking
10578 the properties of variables, such as length, names and attributes. This is
10579 mainly for use by other package developers who want to include run-time
10580 testing features in their own packages.")
10581 (license license:gpl3+)))
10583 (define-public r-assertive-numbers
10585 (name "r-assertive-numbers")
10590 (uri (cran-uri "assertive.numbers" version))
10593 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10595 `((upstream-name . "assertive.numbers")))
10596 (build-system r-build-system)
10598 `(("r-assertive-base" ,r-assertive-base)))
10599 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10600 (synopsis "Assertions to check properties of numbers")
10602 "This package provides a set of predicates and assertions for checking
10603 the properties of numbers. This is mainly for use by other package developers
10604 who want to include run-time testing features in their own packages.")
10605 (license license:gpl3+)))
10607 (define-public r-assertive-sets
10609 (name "r-assertive-sets")
10614 (uri (cran-uri "assertive.sets" version))
10617 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10619 `((upstream-name . "assertive.sets")))
10620 (build-system r-build-system)
10622 `(("r-assertive-base" ,r-assertive-base)))
10623 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10624 (synopsis "Assertions to check properties of sets")
10626 "This package provides a set of predicates and assertions for checking
10627 the properties of sets. This is mainly for use by other package developers
10628 who want to include run-time testing features in their own packages.")
10629 (license license:gpl3+)))
10631 (define-public r-assertive-matrices
10633 (name "r-assertive-matrices")
10638 (uri (cran-uri "assertive.matrices" version))
10641 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10643 `((upstream-name . "assertive.matrices")))
10644 (build-system r-build-system)
10646 `(("r-assertive-base" ,r-assertive-base)))
10647 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10648 (synopsis "Assertions to check properties of matrices")
10650 "This package provides a set of predicates and assertions for checking
10651 the properties of matrices. This is mainly for use by other package
10652 developers who want to include run-time testing features in their own
10654 (license license:gpl3+)))
10656 (define-public r-assertive-models
10658 (name "r-assertive-models")
10663 (uri (cran-uri "assertive.models" version))
10666 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10668 `((upstream-name . "assertive.models")))
10669 (build-system r-build-system)
10671 `(("r-assertive-base" ,r-assertive-base)))
10672 (home-page "https://bitbucket.org/richierocks/assertive.models")
10673 (synopsis "Assertions to check properties of models")
10675 "This package provides a set of predicates and assertions for checking
10676 the properties of models. This is mainly for use by other package developers
10677 who want to include run-time testing features in their own packages.")
10678 (license license:gpl3+)))
10680 (define-public r-assertive-reflection
10682 (name "r-assertive-reflection")
10687 (uri (cran-uri "assertive.reflection" version))
10690 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10692 `((upstream-name . "assertive.reflection")))
10693 (build-system r-build-system)
10695 `(("r-assertive-base" ,r-assertive-base)))
10696 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10697 (synopsis "Assertions for checking the state of R")
10699 "This package provides a set of predicates and assertions for checking
10700 the state and capabilities of R, the operating system it is running on, and
10701 the IDE being used. This is mainly for use by other package developers who
10702 want to include run-time testing features in their own packages.")
10703 (license license:gpl3+)))
10705 (define-public r-assertive-types
10707 (name "r-assertive-types")
10712 (uri (cran-uri "assertive.types" version))
10715 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10717 `((upstream-name . "assertive.types")))
10718 (build-system r-build-system)
10720 `(("r-assertive-base" ,r-assertive-base)
10721 ("r-assertive-properties" ,r-assertive-properties)
10722 ("r-codetools" ,r-codetools)))
10723 (home-page "https://bitbucket.org/richierocks/assertive.types")
10724 (synopsis "Assertions to check types of variables")
10726 "This package provides a set of predicates and assertions for checking
10727 the types of variables. This is mainly for use by other package developers
10728 who want to include run-time testing features in their own packages.")
10729 (license license:gpl3+)))
10731 (define-public r-assertive-files
10733 (name "r-assertive-files")
10738 (uri (cran-uri "assertive.files" version))
10741 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10743 `((upstream-name . "assertive.files")))
10744 (build-system r-build-system)
10746 `(("r-assertive-base" ,r-assertive-base)
10747 ("r-assertive-numbers" ,r-assertive-numbers)))
10748 (home-page "https://bitbucket.org/richierocks/assertive.files")
10749 (synopsis "Assertions to check properties of files")
10751 "This package provides a set of predicates and assertions for checking
10752 the properties of files and connections. This is mainly for use by other
10753 package developers who want to include run-time testing features in their own
10755 (license license:gpl3+)))
10757 (define-public r-assertive-code
10759 (name "r-assertive-code")
10764 (uri (cran-uri "assertive.code" version))
10767 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10769 `((upstream-name . "assertive.code")))
10770 (build-system r-build-system)
10772 `(("r-assertive-base" ,r-assertive-base)
10773 ("r-assertive-properties" ,r-assertive-properties)
10774 ("r-assertive-types" ,r-assertive-types)))
10775 (home-page "https://bitbucket.org/richierocks/assertive.code")
10776 (synopsis "Assertions to check properties of code")
10778 "This package provides a set of predicates and assertions for checking
10779 the properties of code. This is mainly for use by other package developers
10780 who want to include run-time testing features in their own packages.")
10781 (license license:gpl3+)))
10783 (define-public r-assertive-datetimes
10785 (name "r-assertive-datetimes")
10790 (uri (cran-uri "assertive.datetimes" version))
10793 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10795 `((upstream-name . "assertive.datetimes")))
10796 (build-system r-build-system)
10798 `(("r-assertive-base" ,r-assertive-base)
10799 ("r-assertive-types" ,r-assertive-types)))
10800 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10801 (synopsis "Assertions to check properties of dates and times")
10803 "This package provides a set of predicates and assertions for checking
10804 the properties of dates and times. This is mainly for use by other package
10805 developers who want to include run-time testing features in their own
10807 (license license:gpl3+)))
10809 (define-public r-assertive-strings
10811 (name "r-assertive-strings")
10816 (uri (cran-uri "assertive.strings" version))
10819 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10821 `((upstream-name . "assertive.strings")))
10822 (build-system r-build-system)
10824 `(("r-assertive-base" ,r-assertive-base)
10825 ("r-assertive-types" ,r-assertive-types)
10826 ("r-stringi" ,r-stringi)))
10827 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10828 (synopsis "Assertions to check properties of strings")
10830 "This package provides a set of predicates and assertions for checking
10831 the properties of strings. This is mainly for use by other package developers
10832 who want to include run-time testing features in their own packages.")
10833 (license license:gpl3+)))
10835 (define-public r-assertive-data-us
10837 (name "r-assertive-data-us")
10842 (uri (cran-uri "assertive.data.us" version))
10845 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10847 `((upstream-name . "assertive.data.us")))
10848 (build-system r-build-system)
10850 `(("r-assertive-base" ,r-assertive-base)
10851 ("r-assertive-strings" ,r-assertive-strings)))
10852 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10853 (synopsis "Assertions to check properties of strings")
10855 "This package provides a set of predicates and assertions for checking
10856 the properties of US-specific complex data types. This is mainly for use by
10857 other package developers who want to include run-time testing features in
10858 their own packages.")
10859 (license license:gpl3+)))
10861 (define-public r-assertive-data-uk
10863 (name "r-assertive-data-uk")
10868 (uri (cran-uri "assertive.data.uk" version))
10871 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10873 `((upstream-name . "assertive.data.uk")))
10874 (build-system r-build-system)
10876 `(("r-assertive-base" ,r-assertive-base)
10877 ("r-assertive-strings" ,r-assertive-strings)))
10878 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10879 (synopsis "Assertions to check properties of strings")
10881 "This package provides a set of predicates and assertions for checking
10882 the properties of UK-specific complex data types. This is mainly for use by
10883 other package developers who want to include run-time testing features in
10884 their own packages.")
10885 (license license:gpl3+)))
10887 (define-public r-assertive-data
10889 (name "r-assertive-data")
10894 (uri (cran-uri "assertive.data" version))
10897 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10899 `((upstream-name . "assertive.data")))
10900 (build-system r-build-system)
10902 `(("r-assertive-base" ,r-assertive-base)
10903 ("r-assertive-strings" ,r-assertive-strings)))
10904 (home-page "https://bitbucket.org/richierocks/assertive.data")
10905 (synopsis "Assertions to check properties of data")
10907 "This package provides a set of predicates and assertions for checking
10908 the properties of (country independent) complex data types. This is mainly
10909 for use by other package developers who want to include run-time testing
10910 features in their own packages.")
10911 (license license:gpl3+)))
10913 (define-public r-assertive
10915 (name "r-assertive")
10920 (uri (cran-uri "assertive" version))
10923 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
10924 (build-system r-build-system)
10926 `(("r-assertive-base" ,r-assertive-base)
10927 ("r-assertive-code" ,r-assertive-code)
10928 ("r-assertive-data" ,r-assertive-data)
10929 ("r-assertive-data-uk" ,r-assertive-data-uk)
10930 ("r-assertive-data-us" ,r-assertive-data-us)
10931 ("r-assertive-datetimes" ,r-assertive-datetimes)
10932 ("r-assertive-files" ,r-assertive-files)
10933 ("r-assertive-matrices" ,r-assertive-matrices)
10934 ("r-assertive-models" ,r-assertive-models)
10935 ("r-assertive-numbers" ,r-assertive-numbers)
10936 ("r-assertive-properties" ,r-assertive-properties)
10937 ("r-assertive-reflection" ,r-assertive-reflection)
10938 ("r-assertive-sets" ,r-assertive-sets)
10939 ("r-assertive-strings" ,r-assertive-strings)
10940 ("r-assertive-types" ,r-assertive-types)
10941 ("r-knitr" ,r-knitr)))
10942 (home-page "https://bitbucket.org/richierocks/assertive")
10943 (synopsis "Readable check functions to ensure code integrity")
10945 "This package provides lots of predicates (@code{is_*} functions) to
10946 check the state of your variables, and assertions (@code{assert_*} functions)
10947 to throw errors if they aren't in the right form.")
10948 (license license:gpl3+)))
10950 (define-public r-dotcall64
10952 (name "r-dotcall64")
10957 (uri (cran-uri "dotCall64" version))
10960 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
10961 (properties `((upstream-name . "dotCall64")))
10962 (build-system r-build-system)
10963 (native-inputs `(("gfortran" ,gfortran)))
10964 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
10965 (synopsis "Enhanced foreign function interface supporting long vectors")
10967 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
10968 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
10969 supports long vectors, arguments of type 64-bit integer, and provides a
10970 mechanism to avoid unnecessary copies of read-only and write-only arguments.
10971 This makes it a convenient and fast interface to C/C++ and Fortran code.")
10972 (license license:gpl2+)))
10974 (define-public r-spam
10981 (uri (cran-uri "spam" version))
10983 (base32 "0xb7a0x1i93kzijr518m9plzmg8s3mxh5anwfx9xrkg5ipldvz10"))))
10984 (build-system r-build-system)
10986 `(("r-dotcall64" ,r-dotcall64)))
10987 (native-inputs `(("gfortran" ,gfortran)))
10988 (home-page "https://www.math.uzh.ch/pages/spam/")
10989 (synopsis "Sparse matrix algebra")
10991 "This package provides a set of functions for sparse matrix algebra.
10992 Differences with other sparse matrix packages are:
10995 @item it only supports (essentially) one sparse matrix format;
10996 @item it is based on transparent and simple structure(s);
10997 @item it is tailored for MCMC calculations within G(M)RF;
10998 @item and it is fast and scalable (with the extension package @code{spam64}).
11000 ;; Either of these licenses
11001 (license (list license:bsd-3 license:lgpl2.0))))
11003 (define-public r-fields
11010 (uri (cran-uri "fields" version))
11012 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11013 (build-system r-build-system)
11015 `(("r-maps" ,r-maps)
11016 ("r-spam" ,r-spam)))
11018 `(("gfortran" ,gfortran)))
11019 (home-page "https://www.image.ucar.edu/fields")
11020 (synopsis "Tools for spatial data")
11022 "This is a package for curve, surface and function fitting with an
11023 emphasis on splines, spatial data and spatial statistics. The major methods
11024 include cubic, and thin plate splines, Kriging, and compactly supported
11025 covariance functions for large data sets.")
11026 (license license:gpl2+)))
11028 (define-public r-spatialextremes
11030 (name "r-spatialextremes")
11031 (version "2.0-7.2")
11035 (uri (cran-uri "SpatialExtremes" version))
11038 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11040 `((upstream-name . "SpatialExtremes")))
11041 (build-system r-build-system)
11043 `(("r-fields" ,r-fields)
11044 ("r-maps" ,r-maps)))
11045 (home-page "http://spatialextremes.r-forge.r-project.org/")
11046 (synopsis "Modelling spatial extremes")
11048 "This package provides tools for the statistical modelling of spatial
11049 extremes using max-stable processes, copula or Bayesian hierarchical models.
11050 More precisely, this package allows (conditional) simulations from various
11051 parametric max-stable models, analysis of the extremal spatial dependence, the
11052 fitting of such processes using composite likelihoods or least square (simple
11053 max-stable processes only), model checking and selection and prediction.")
11054 (license license:gpl2+)))
11056 (define-public r-drc
11063 (uri (cran-uri "drc" version))
11066 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11067 (build-system r-build-system)
11070 ("r-gtools" ,r-gtools)
11072 ("r-multcomp" ,r-multcomp)
11073 ("r-plotrix" ,r-plotrix)
11074 ("r-scales" ,r-scales)))
11075 (home-page "https://cran.r-project.org/web/packages/drc")
11076 (synopsis "Analysis of dose-response curves")
11078 "This package provides a suite of flexible and versatile model fitting
11079 and after-fitting functions for the analysis of dose-response data.")
11080 (license license:gpl2+)))
11082 (define-public r-rmeta
11089 (uri (cran-uri "rmeta" version))
11092 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11093 (build-system r-build-system)
11094 (home-page "https://cran.r-project.org/web/packages/rmeta")
11095 (synopsis "Tools for meta-analysis")
11097 "This package provides functions for simple fixed and random effects
11098 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11099 draws standard summary plots, funnel plots, and computes summaries and tests
11100 for association and heterogeneity.")
11101 (license license:gpl2)))
11103 (define-public r-bootstrap
11105 (name "r-bootstrap")
11110 (uri (cran-uri "bootstrap" version))
11113 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11114 (build-system r-build-system)
11115 (native-inputs `(("gfortran" ,gfortran)))
11116 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11117 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11119 "This package provides software and data for the book \"An Introduction
11120 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11121 This package is primarily provided for projects already based on it, and for
11122 support of the book. New projects should preferentially use the recommended
11123 package \"boot\".")
11124 (license license:bsd-3)))
11126 (define-public r-survivalroc
11128 (name "r-survivalroc")
11133 (uri (cran-uri "survivalROC" version))
11136 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11137 (properties `((upstream-name . "survivalROC")))
11138 (build-system r-build-system)
11139 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11140 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11142 "Compute time-dependent ROC curve from censored survival data using
11143 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11144 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11145 (license license:gpl2+)))
11147 (define-public r-longitudinal
11149 (name "r-longitudinal")
11154 (uri (cran-uri "longitudinal" version))
11157 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11158 (build-system r-build-system)
11159 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11160 (home-page "http://strimmerlab.org/software/longitudinal/")
11161 (synopsis "Analysis of multiple time course data")
11163 "This package contains general data structures and functions for
11164 longitudinal data with multiple variables, repeated measurements, and
11165 irregularly spaced time points. It also implements a shrinkage estimator of
11166 dynamical correlation and dynamical covariance.")
11167 (license license:gpl3+)))
11169 (define-public r-genenet
11176 (uri (cran-uri "GeneNet" version))
11179 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11180 (properties `((upstream-name . "GeneNet")))
11181 (build-system r-build-system)
11183 `(("r-corpcor" ,r-corpcor)
11184 ("r-fdrtool" ,r-fdrtool)
11185 ("r-longitudinal" ,r-longitudinal)))
11186 (home-page "http://strimmerlab.org/software/genenet/")
11187 (synopsis "Modeling and inferring gene networks")
11189 "This package analyzes gene expression (time series) data with focus on
11190 the inference of gene networks. In particular, GeneNet implements the methods
11191 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11192 for learning large-scale gene association networks (including assignment of
11193 putative directions).")
11194 (license license:gpl3+)))
11196 (define-public r-rbamtools
11198 (name "r-rbamtools")
11199 (version "2.16.17")
11203 (uri (cran-uri "rbamtools" version))
11206 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11207 (build-system r-build-system)
11208 (inputs `(("zlib" ,zlib)))
11210 `(("r-refgenome" ,r-refgenome)))
11211 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11212 (synopsis "Read and write BAM (binary alignment) files")
11214 "This package provides an R interface to functions of the SAMtools
11216 (license license:artistic2.0)))
11218 (define-public r-protviz
11225 (uri (cran-uri "protViz" version))
11228 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11229 (properties `((upstream-name . "protViz")))
11230 (build-system r-build-system)
11231 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11232 (home-page "https://github.com/protViz/protViz/")
11233 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11235 "This package helps with quality checks, visualizations and analysis of
11236 mass spectrometry data, coming from proteomics experiments. The package is
11237 developed, tested and used at the Functional Genomics Center Zurich, where it
11238 is used mainly for prototyping, teaching, and having fun with proteomics data.
11239 But it can also be used to do data analysis for small scale data sets.")
11240 (license license:gpl3)))
11242 (define-public r-cmprsk
11249 (uri (cran-uri "cmprsk" version))
11251 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11252 (build-system r-build-system)
11254 `(("r-survival" ,r-survival)))
11256 `(("gfortran" ,gfortran)))
11257 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11258 (synopsis "Subdistribution analysis of competing risks")
11260 "This package provides tool for estimation, testing and regression
11261 modeling of subdistribution functions in competing risks, as described in
11262 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11263 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11264 A proportional hazards model for the subdistribution of a competing risk,
11265 JASA, 94:496-509.")
11266 (license license:gpl2+)))
11268 (define-public r-etm
11275 (uri (cran-uri "etm" version))
11278 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11279 (build-system r-build-system)
11281 `(("r-data-table" ,r-data-table)
11282 ("r-lattice" ,r-lattice)
11284 ("r-rcpparmadillo" ,r-rcpparmadillo)
11285 ("r-survival" ,r-survival)))
11286 (home-page "https://cran.r-project.org/web/packages/etm")
11287 (synopsis "Empirical transition matrix")
11289 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11290 the matrix of transition probabilities for any time-inhomogeneous multistate
11291 model with finite state space using the Aalen-Johansen estimator.")
11292 (license license:expat)))
11294 (define-public r-epi
11301 (uri (cran-uri "Epi" version))
11304 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11305 (properties `((upstream-name . "Epi")))
11306 (build-system r-build-system)
11308 `(("r-cmprsk" ,r-cmprsk)
11309 ("r-data-table" ,r-data-table)
11312 ("r-matrix" ,r-matrix)
11314 ("r-numderiv" ,r-numderiv)
11316 ("r-survival" ,r-survival)
11318 (home-page "http://BendixCarstensen.com/Epi/")
11319 (synopsis "Statistical analysis in epidemiology")
11321 "This package provides functions for demographic and epidemiological
11322 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11323 particular representation, manipulation and simulation of multistate data -
11324 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11325 @code{etm} and @code{cmprsk} packages. It also contains functions for
11326 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11327 data and some useful functions for tabulation and plotting, as well as a
11328 number of epidemiological data sets.")
11329 (license license:gpl2)))
11331 (define-public r-ppls
11334 (version "1.6-1.1")
11338 (uri (cran-uri "ppls" version))
11341 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11342 (build-system r-build-system)
11343 (propagated-inputs `(("r-mass" ,r-mass)))
11344 (home-page "https://cran.r-project.org/web/packages/ppls")
11345 (synopsis "Penalized partial least squares")
11347 "This package contains linear and nonlinear regression methods based on
11348 partial least squares and penalization techniques. Model parameters are
11349 selected via cross-validation, and confidence intervals ans tests for the
11350 regression coefficients can be conducted via jackknifing.")
11351 (license license:gpl2+)))
11353 (define-public r-huge
11360 (uri (cran-uri "huge" version))
11362 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11363 (build-system r-build-system)
11365 `(("r-igraph" ,r-igraph)
11367 ("r-matrix" ,r-matrix)
11369 ("r-rcppeigen" ,r-rcppeigen)))
11370 (home-page "https://cran.r-project.org/web/packages/huge")
11371 (synopsis "High-dimensional undirected graph estimation")
11373 "This package provides a general framework for high-dimensional
11374 undirected graph estimation. It integrates data preprocessing, neighborhood
11375 screening, graph estimation, and model selection techniques into a pipeline.")
11376 (license license:gpl2)))
11378 (define-public r-parcor
11385 (uri (cran-uri "parcor" version))
11388 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11389 (build-system r-build-system)
11392 ("r-genenet" ,r-genenet)
11393 ("r-glmnet" ,r-glmnet)
11395 ("r-ppls" ,r-ppls)))
11396 (home-page "https://cran.r-project.org/web/packages/parcor")
11397 (synopsis "Regularized estimation of partial correlation matrices")
11399 "This package estimates the matrix of partial correlations based on
11400 different regularized regression methods: lasso, adaptive lasso, PLS, and
11401 Ridge Regression. In addition, the package provides model selection for
11402 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11403 (license license:gpl2+)))
11405 (define-public r-mcmc
11412 (uri (cran-uri "mcmc" version))
11415 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11416 (build-system r-build-system)
11417 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11418 (synopsis "Markov chain Monte Carlo")
11420 "This package simulates continuous distributions of random vectors using
11421 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11422 function that evaluates the log unnormalized density. Algorithms are random
11423 walk Metropolis algorithm (function @code{metrop}), simulated
11424 tempering (function @code{temper}), and morphometric random walk
11425 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11426 by change of variable.")
11427 (license license:expat)))
11429 (define-public r-listenv
11436 (uri (cran-uri "listenv" version))
11439 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
11440 (build-system r-build-system)
11442 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11443 (home-page "https://github.com/HenrikBengtsson/listenv")
11444 (synopsis "Environments behaving (almost) as lists")
11446 "This package implements list environments. List environments are
11447 environments that have list-like properties. For instance, the elements of a
11448 list environment are ordered and can be accessed and iterated over using index
11450 (license license:lgpl2.1+)))
11452 (define-public r-globals
11459 (uri (cran-uri "globals" version))
11462 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
11463 (build-system r-build-system)
11465 `(("r-codetools" ,r-codetools)))
11466 (home-page "https://github.com/HenrikBengtsson/globals")
11467 (synopsis "Identify global objects in R expressions")
11469 "This package provides tools to identify global (\"unknown\" or \"free\")
11470 objects in R expressions by code inspection using various strategies, e.g.
11471 conservative or liberal. The objective of this package is to make it as
11472 simple as possible to identify global objects for the purpose of exporting
11473 them in distributed compute environments.")
11474 (license license:lgpl2.1+)))
11476 (define-public r-future
11483 (uri (cran-uri "future" version))
11486 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11487 (build-system r-build-system)
11489 `(("r-digest" ,r-digest)
11490 ("r-globals" ,r-globals)
11491 ("r-listenv" ,r-listenv)))
11493 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11494 (home-page "https://github.com/HenrikBengtsson/future")
11495 (synopsis "Unified parallel and distributed processing in R")
11497 "The purpose of this package is to provide a lightweight and unified
11498 Future API for sequential and parallel processing of R expression via futures.
11499 This package implements sequential, multicore, multisession, and cluster
11500 futures. With these, R expressions can be evaluated on the local machine, in
11501 parallel a set of local machines, or distributed on a mix of local and remote
11502 machines. Extensions to this package implement additional backends for
11503 processing futures via compute cluster schedulers etc. Because of its unified
11504 API, there is no need to modify any code in order to switch from sequential on
11505 the local machine to, say, distributed processing on a remote compute cluster.")
11506 (license license:lgpl2.1+)))
11508 (define-public r-future-apply
11510 (name "r-future-apply")
11515 (uri (cran-uri "future.apply" version))
11518 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11519 (properties `((upstream-name . "future.apply")))
11520 (build-system r-build-system)
11522 `(("r-future" ,r-future)
11523 ("r-globals" ,r-globals)))
11525 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11526 (home-page "https://github.com/HenrikBengtsson/future.apply")
11527 (synopsis "Apply function to elements in parallel using futures")
11529 "This package provides implementations of @code{apply()},
11530 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11531 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11532 can be resolved using any future-supported backend, e.g. parallel on the local
11533 machine or distributed on a compute cluster.")
11534 (license license:gpl2+)))
11536 (define-public r-rsvd
11543 (uri (cran-uri "rsvd" version))
11546 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11547 (build-system r-build-system)
11549 `(("r-matrix" ,r-matrix)))
11550 (home-page "https://github.com/erichson/rSVD")
11551 (synopsis "Randomized singular value decomposition")
11553 "Low-rank matrix decompositions are fundamental tools and widely used for
11554 data analysis, dimension reduction, and data compression. Classically, highly
11555 accurate deterministic matrix algorithms are used for this task. However, the
11556 emergence of large-scale data has severely challenged our computational
11557 ability to analyze big data. The concept of randomness has been demonstrated
11558 as an effective strategy to quickly produce approximate answers to familiar
11559 problems such as the @dfn{singular value decomposition} (SVD). This package
11560 provides several randomized matrix algorithms such as the randomized singular
11561 value decomposition (@code{rsvd}), randomized principal component
11562 analysis (@code{rpca}), randomized robust principal component
11563 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11564 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11565 functions are provided.")
11566 (license license:gpl3+)))
11568 (define-public r-sloop
11575 (uri (cran-uri "sloop" version))
11578 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11579 (build-system r-build-system)
11581 `(("r-codetools" ,r-codetools)
11582 ("r-crayon" ,r-crayon)
11583 ("r-purrr" ,r-purrr)
11584 ("r-rlang" ,r-rlang)
11585 ("r-tibble" ,r-tibble)))
11586 (home-page "https://github.com/r-lib/sloop")
11587 (synopsis "Helpers for object-oriented programming in R")
11589 "This package provides a collection of helper functions designed to
11590 help you to better understand object oriented programming in R, particularly
11592 (license license:gpl3)))
11594 (define-public r-capushe
11601 (uri (cran-uri "capushe" version))
11604 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11605 (build-system r-build-system)
11606 (propagated-inputs `(("r-mass" ,r-mass)))
11607 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11608 (synopsis "Calibrating penalties using slope heuristics")
11610 "This package provides tools for the calibration of penalized criteria
11611 for model selection. The calibration methods available are based on the slope
11613 (license license:gpl2+)))
11615 (define-public r-dorng
11622 (uri (cran-uri "doRNG" version))
11625 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11626 (properties `((upstream-name . "doRNG")))
11627 (build-system r-build-system)
11629 `(("r-foreach" ,r-foreach)
11630 ("r-iterators" ,r-iterators)
11631 ("r-pkgmaker" ,r-pkgmaker)
11632 ("r-rngtools" ,r-rngtools)))
11633 (home-page "https://renozao.github.io/doRNG/")
11634 (synopsis "Generic reproducible parallel backend for foreach loops")
11636 "This package provides functions to perform reproducible parallel
11637 @code{foreach} loops, using independent random streams as generated by
11638 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11639 convert standard @code{%dopar%} loops into fully reproducible loops,
11640 independently of the number of workers, the task scheduling strategy, or the
11641 chosen parallel environment and associated foreach backend.")
11642 (license license:gpl2+)))
11644 (define-public r-blockmodeling
11646 (name "r-blockmodeling")
11651 (uri (cran-uri "blockmodeling" version))
11654 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11655 (build-system r-build-system)
11657 `(("r-doparallel" ,r-doparallel)
11658 ("r-dorng" ,r-dorng)
11659 ("r-foreach" ,r-foreach)
11660 ("r-matrix" ,r-matrix)))
11661 (native-inputs `(("gfortran" ,gfortran)))
11662 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11663 (synopsis "Generalized and classical blockmodeling of valued networks")
11665 "This package is primarily meant as an implementation of generalized
11666 blockmodeling for valued networks. In addition, measures of similarity or
11667 dissimilarity based on structural equivalence and regular equivalence (REGE
11668 algorithms) can be computed and partitioned matrices can be plotted.")
11669 (license license:gpl2+)))
11671 (define-public r-upsetr
11678 (uri (cran-uri "UpSetR" version))
11681 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11682 (properties `((upstream-name . "UpSetR")))
11683 (build-system r-build-system)
11685 `(("r-ggplot2" ,r-ggplot2)
11686 ("r-gridextra" ,r-gridextra)
11688 ("r-scales" ,r-scales)))
11689 (home-page "https://github.com/hms-dbmi/UpSetR")
11690 (synopsis "Visualize intersecting sets")
11692 "This package provides a more scalable alternative to Venn and Euler
11693 diagrams for visualizing intersecting sets. Create visualizations of
11694 intersecting sets using a novel matrix design, along with visualizations of
11695 several common set, element and attribute related tasks.")
11696 (license license:expat)))
11698 ;; This package includes a JavaScript file, which is not minified. When
11699 ;; upgrading please check that there are no new minified JavaScript files.
11700 (define-public r-shinybs
11707 (uri (cran-uri "shinyBS" version))
11710 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11711 (properties `((upstream-name . "shinyBS")))
11712 (build-system r-build-system)
11713 ;; The tests spawn Shiny browser apps. They cannot be run
11714 ;; non-interactively.
11715 (arguments '(#:tests? #f))
11717 `(("r-htmltools" ,r-htmltools)
11718 ("r-shiny" ,r-shiny)))
11719 (home-page "https://ebailey78.github.io/shinyBS/")
11720 (synopsis "Twitter Bootstrap components for Shiny")
11722 "This package adds additional Twitter Bootstrap components to Shiny.")
11723 (license license:gpl3)))
11725 (define-public r-outliers
11727 (name "r-outliers")
11732 (uri (cran-uri "outliers" version))
11735 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11736 (build-system r-build-system)
11737 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11738 (synopsis "Tests for outliers")
11740 "This package provides a collection of some tests commonly used for
11741 identifying outliers.")
11742 (license license:gpl2+)))
11744 (define-public r-bayesm
11751 (uri (cran-uri "bayesm" version))
11753 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11754 (build-system r-build-system)
11756 `(("r-rcpp" ,r-rcpp)
11757 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11758 (home-page "http://www.perossi.org/home/bsm-1")
11759 (synopsis "Bayesian inference for marketing/micro-econometrics")
11761 "This package covers many important models used in marketing and
11762 micro-econometrics applications, including Bayes Regression (univariate or
11763 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11764 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11765 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11766 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11767 Estimation with normal base, Hierarchical Linear Models with normal prior and
11768 covariates, Hierarchical Linear Models with a mixture of normals prior and
11769 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11770 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11771 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11772 analysis of choice-based conjoint data, Bayesian treatment of linear
11773 instrumental variables models, Analysis of Multivariate Ordinal survey data
11774 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11775 Coefficient Logit Models.")
11776 (license license:gpl2+)))
11778 (define-public r-tensora
11785 (uri (cran-uri "tensorA" version))
11788 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11789 (properties `((upstream-name . "tensorA")))
11790 (build-system r-build-system)
11791 (home-page "http://www.stat.boogaart.de/tensorA")
11792 (synopsis "Advanced tensor arithmetic with named indices")
11794 "This package provides convenience functions for advanced linear algebra
11795 with tensors and computation with datasets of tensors on a higher level
11796 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11797 co- and contravariate indices, and parallel computations on sequences of
11799 (license license:gpl2+)))
11801 (define-public r-rarpack
11808 (uri (cran-uri "rARPACK" version))
11811 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11812 (properties `((upstream-name . "rARPACK")))
11813 (build-system r-build-system)
11814 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11815 (home-page "https://github.com/yixuan/rARPACK")
11816 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11818 "This package was previously an R wrapper of the ARPACK library, and now
11819 a shell of the R package RSpectra, an R interface to the Spectra library for
11820 solving large scale eigenvalue/vector problems. The current version of
11821 rARPACK simply imports and exports the functions provided by RSpectra. New
11822 users of rARPACK are advised to switch to the RSpectra package.")
11823 (license license:bsd-3)))
11825 (define-public r-compositions
11827 (name "r-compositions")
11832 (uri (cran-uri "compositions" version))
11835 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
11836 (build-system r-build-system)
11838 `(("r-bayesm" ,r-bayesm)
11839 ("r-robustbase" ,r-robustbase)
11840 ("r-tensora" ,r-tensora)))
11841 (home-page "http://www.stat.boogaart.de/compositions")
11842 (synopsis "Compositional data analysis")
11844 "This package provides functions for the consistent analysis of
11845 compositional data (e.g. portions of substances) and positive
11846 numbers (e.g. concentrations).")
11847 (license license:gpl2+)))
11849 (define-public r-cobs
11856 (uri (cran-uri "cobs" version))
11859 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11860 (build-system r-build-system)
11862 `(("r-quantreg" ,r-quantreg)
11863 ("r-sparsem" ,r-sparsem)))
11864 (home-page "https://cran.r-project.org/web/packages/cobs")
11865 (synopsis "Constrained B-Splines (sparse matrix based)")
11867 "This package provides qualitatively constrained (regression) smoothing
11868 splines via linear programming and sparse matrices.")
11869 (license license:gpl2+)))
11871 (define-public r-drimpute
11873 (name "r-drimpute")
11878 (uri (cran-uri "DrImpute" version))
11881 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11882 (properties `((upstream-name . "DrImpute")))
11883 (build-system r-build-system)
11885 `(("r-rcpp" ,r-rcpp)
11886 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11887 (home-page "https://github.com/ikwak2/DrImpute")
11888 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11890 "This is an R package for imputing dropout events. Many statistical
11891 methods in cell type identification, visualization and lineage reconstruction
11892 do not account for dropout events. DrImpute can improve the performance of
11893 such software by imputing dropout events.")
11894 (license license:gpl3)))
11896 (define-public r-gamlss-dist
11898 (name "r-gamlss-dist")
11903 (uri (cran-uri "gamlss.dist" version))
11905 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
11906 (properties `((upstream-name . "gamlss.dist")))
11907 (build-system r-build-system)
11908 (propagated-inputs `(("r-mass" ,r-mass)))
11909 (home-page "http://www.gamlss.org/")
11910 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11912 "This package provides a set of distributions which can be used for
11913 modelling the response variables in Generalized Additive Models for Location
11914 Scale and Shape. The distributions can be continuous, discrete or mixed
11915 distributions. Extra distributions can be created, by transforming, any
11916 continuous distribution defined on the real line, to a distribution defined on
11917 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11918 transformation, respectively.")
11919 ;; Either version of the GPL.
11920 (license (list license:gpl2 license:gpl3))))
11922 ;; This package includes JavaScript files, which are not minified. When
11923 ;; upgrading please check that there are no new minified JavaScript files.
11924 (define-public r-shinyjs
11931 (uri (cran-uri "shinyjs" version))
11934 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
11935 (build-system r-build-system)
11937 `(("r-digest" ,r-digest)
11938 ("r-htmltools" ,r-htmltools)
11939 ("r-jsonlite" ,r-jsonlite)
11940 ("r-shiny" ,r-shiny)))
11941 (home-page "https://deanattali.com/shinyjs")
11942 (synopsis "Improve the user experience of your Shiny apps")
11944 "Perform common useful JavaScript operations in Shiny apps that will
11945 greatly improve your apps without having to know any JavaScript. Examples
11946 include: hiding an element, disabling an input, resetting an input back to its
11947 original value, delaying code execution by a few seconds, and many more useful
11948 functions for both the end user and the developer. Shinyjs can also be used
11949 to easily call your own custom JavaScript functions from R.")
11950 (license license:agpl3+)))
11952 ;; This package includes minified JavaScript files. When upgrading please
11953 ;; check that there are no new minified JavaScript files.
11954 (define-public r-colourpicker
11956 (name "r-colourpicker")
11961 (uri (cran-uri "colourpicker" version))
11964 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
11965 (build-system r-build-system)
11967 `(#:modules ((guix build utils)
11968 (guix build r-build-system)
11972 (modify-phases %standard-phases
11973 (add-after 'unpack 'process-javascript
11974 (lambda* (#:key inputs #:allow-other-keys)
11975 (with-directory-excursion "inst"
11979 `((,(assoc-ref inputs "js-salvattore")
11980 "examples/colourInput/www/salvattore.min.js")
11981 (,(assoc-ref inputs "js-jquery")
11982 "htmlwidgets/lib/jquery/jquery.min.js")
11983 ("www/shared/colourpicker/js/colourpicker.js"
11984 "www/shared/colourpicker/js/colourpicker.min.js"))))
11985 (lambda (sources targets)
11986 (for-each (lambda (source target)
11987 (format #t "Processing ~a --> ~a~%"
11989 (delete-file target)
11990 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
11991 (call-with-output-file target
11993 (dump-port minified port)))))
11994 sources targets))))
11997 `(("r-ggplot2" ,r-ggplot2)
11998 ("r-htmltools" ,r-htmltools)
11999 ("r-htmlwidgets" ,r-htmlwidgets)
12000 ("r-jsonlite" ,r-jsonlite)
12001 ("r-miniui" ,r-miniui)
12002 ("r-shiny" ,r-shiny)
12003 ("r-shinyjs" ,r-shinyjs)))
12005 `(("uglify-js" ,uglify-js)
12009 (uri "https://code.jquery.com/jquery-3.3.1.js")
12012 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12016 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12019 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12020 (home-page "https://github.com/daattali/colourpicker")
12021 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12023 "This package provides a color picker that can be used as an input in
12024 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12025 custom color palettes, and many more options. A plot color helper tool is
12026 available as an RStudio Addin, which helps you pick colors to use in your
12027 plots. A more generic color picker RStudio Addin is also provided to let you
12028 select colors to use in your R code.")
12029 (license license:expat)))
12031 (define-public r-ggextra
12038 (uri (cran-uri "ggExtra" version))
12041 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12042 (properties `((upstream-name . "ggExtra")))
12043 (build-system r-build-system)
12045 `(("r-colourpicker" ,r-colourpicker)
12046 ("r-ggplot2" ,r-ggplot2)
12047 ("r-gtable" ,r-gtable)
12048 ("r-miniui" ,r-miniui)
12050 ("r-scales" ,r-scales)
12051 ("r-shiny" ,r-shiny)
12052 ("r-shinyjs" ,r-shinyjs)))
12053 (home-page "https://github.com/daattali/ggExtra")
12054 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12056 "This package is a collection of functions and layers to enhance ggplot2.
12057 The flagship function is @code{ggMarginal()}, which can be used to add
12058 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12059 (license license:expat)))
12061 (define-public r-minpack-lm
12063 (name "r-minpack-lm")
12068 (uri (cran-uri "minpack.lm" version))
12071 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12072 (properties `((upstream-name . "minpack.lm")))
12073 (build-system r-build-system)
12074 (native-inputs `(("gfortran" ,gfortran)))
12075 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12076 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12078 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12079 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12080 problems by a modification of the Levenberg-Marquardt algorithm, with support
12081 for lower and upper parameter bounds. The implementation can be used via
12082 @code{nls}-like calls using the @code{nlsLM} function.")
12083 (license license:gpl3)))
12085 (define-public r-moments
12092 (uri (cran-uri "moments" version))
12095 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12096 (build-system r-build-system)
12097 (home-page "https://cran.r-project.org/web/packages/moments")
12098 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12100 "This package provides functions to calculate: moments, Pearson's
12101 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12102 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12103 (license license:gpl2+)))
12105 (define-public r-msir
12112 (uri (cran-uri "msir" version))
12115 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12116 (build-system r-build-system)
12118 `(("r-mclust" ,r-mclust)))
12119 (home-page "https://cran.r-project.org/web/packages/msir")
12120 (synopsis "Model-based sliced inverse regression")
12122 "This is an R package for dimension reduction based on finite Gaussian
12123 mixture modeling of inverse regression.")
12124 (license license:gpl2+)))
12126 (define-public r-pbivnorm
12128 (name "r-pbivnorm")
12133 (uri (cran-uri "pbivnorm" version))
12136 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12137 (build-system r-build-system)
12138 (native-inputs `(("gfortran" ,gfortran)))
12139 (home-page "https://github.com/brentonk/pbivnorm")
12140 (synopsis "Vectorized bivariate normal CDF")
12142 "This package provides a vectorized R function for calculating
12143 probabilities from a standard bivariate normal CDF.")
12144 (license license:gpl2+)))
12146 (define-public r-lavaan
12153 (uri (cran-uri "lavaan" version))
12156 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12157 (build-system r-build-system)
12159 `(("r-mass" ,r-mass)
12160 ("r-mnormt" ,r-mnormt)
12161 ("r-numderiv" ,r-numderiv)
12162 ("r-pbivnorm" ,r-pbivnorm)))
12163 (home-page "http://lavaan.ugent.be")
12164 (synopsis "Latent variable analysis")
12166 "This package provides tools to fit a variety of latent variable models,
12167 including confirmatory factor analysis, structural equation modeling and
12168 latent growth curve models.")
12169 (license license:gpl2+)))
12171 (define-public r-nonnest2
12173 (name "r-nonnest2")
12178 (uri (cran-uri "nonnest2" version))
12181 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12182 (build-system r-build-system)
12184 `(("r-compquadform" ,r-compquadform)
12185 ("r-lavaan" ,r-lavaan)
12186 ("r-mvtnorm" ,r-mvtnorm)
12187 ("r-sandwich" ,r-sandwich)))
12188 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12189 (synopsis "Tests of non-nested models")
12191 "This package allows for testing of non-nested models. It includes tests
12192 of model distinguishability and of model fit that can be applied to both
12193 nested and non-nested models. The package also includes functionality to
12194 obtain confidence intervals associated with AIC and BIC.")
12195 ;; Either version of the GPL.
12196 (license (list license:gpl2 license:gpl3))))
12198 (define-public r-penalized
12200 (name "r-penalized")
12205 (uri (cran-uri "penalized" version))
12208 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12209 (build-system r-build-system)
12211 `(("r-rcpp" ,r-rcpp)
12212 ("r-rcpparmadillo" ,r-rcpparmadillo)
12213 ("r-survival" ,r-survival)))
12214 (home-page "https://cran.r-project.org/web/packages/penalized/")
12215 (synopsis "Penalized estimation in GLMs and in the Cox model")
12217 "This package provides tools for fitting possibly high dimensional
12218 penalized regression models. The penalty structure can be any combination of
12219 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12220 constraint on the regression coefficients. The supported regression models
12221 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12222 model. Cross-validation routines allow optimization of the tuning
12224 (license license:gpl2+)))
12226 (define-public r-zim
12233 (uri (cran-uri "ZIM" version))
12236 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12237 (properties `((upstream-name . "ZIM")))
12238 (build-system r-build-system)
12239 (propagated-inputs `(("r-mass" ,r-mass)))
12240 (home-page "https://github.com/biostatstudio/ZIM")
12241 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12243 "Analyze count time series with excess zeros. Two types of statistical
12244 models are supported: Markov regression and state-space models. They are also
12245 known as observation-driven and parameter-driven models respectively in the
12246 time series literature. The functions used for Markov regression or
12247 observation-driven models can also be used to fit ordinary regression models
12248 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12249 negative binomial (ZINB) assumption. The package also contains miscellaneous
12250 functions to compute density, distribution, quantile, and generate random
12251 numbers from ZIP and ZINB distributions.")
12252 (license license:gpl3)))
12254 (define-public r-nor1mix
12261 (uri (cran-uri "nor1mix" version))
12264 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12265 (build-system r-build-system)
12266 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12267 (synopsis "Normal (1-d) mixture models")
12269 "This package provides S3 classes and methods for one-dimensional normal
12270 mixture models, for, e.g., density estimation or clustering algorithms
12271 research and teaching; it provides the widely used Marron-Wand densities. It
12272 also provides tools for efficient random number generation and graphics.")
12273 (license license:gpl2+)))
12275 (define-public r-beanplot
12277 (name "r-beanplot")
12282 (uri (cran-uri "beanplot" version))
12285 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12286 (build-system r-build-system)
12287 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12288 (synopsis "Visualization via beanplots")
12290 "This package provides beanplots, an alternative to
12291 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12293 (license license:gpl2)))
12295 (define-public r-pbdzmq
12302 (uri (cran-uri "pbdZMQ" version))
12305 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12306 (properties `((upstream-name . "pbdZMQ")))
12307 (build-system r-build-system)
12309 `(("zeromq" ,zeromq)
12312 `(("pkg-config" ,pkg-config)))
12313 (home-page "https://pbdr.org/")
12314 (synopsis "R interface to ZeroMQ")
12316 "ZeroMQ is a well-known library for high-performance asynchronous
12317 messaging in scalable, distributed applications. This package provides high
12318 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12319 interactive client/server programming frameworks. A few wrapper functions
12320 compatible with @code{rzmq} are also provided.")
12321 (license license:gpl3)))
12323 (define-public r-repr
12330 (uri (cran-uri "repr" version))
12333 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12334 (build-system r-build-system)
12336 `(("r-base64enc" ,r-base64enc)
12337 ("r-htmltools" ,r-htmltools)
12338 ("r-jsonlite" ,r-jsonlite)
12339 ("r-pillar" ,r-pillar)))
12340 (home-page "https://cran.r-project.org/web/packages/repr/")
12341 (synopsis "Serializable representations")
12343 "This package provides string and binary representations of objects for
12344 several formats and MIME types.")
12345 (license license:gpl3)))
12347 (define-public r-irdisplay
12349 (name "r-irdisplay")
12354 (uri (cran-uri "IRdisplay" version))
12357 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12358 (properties `((upstream-name . "IRdisplay")))
12359 (build-system r-build-system)
12361 `(("r-repr" ,r-repr)))
12362 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12363 (synopsis "Jupyter display machinery")
12365 "This package provides an interface to the rich display capabilities of
12366 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12367 running IRkernel session.")
12368 (license license:expat)))
12370 (define-public r-irkernel
12372 (name "r-irkernel")
12377 (uri (cran-uri "IRkernel" version))
12380 "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
12381 (properties `((upstream-name . "IRkernel")))
12382 (build-system r-build-system)
12385 (modify-phases %standard-phases
12386 (add-after 'install 'install-kernelspec
12387 (lambda* (#:key outputs #:allow-other-keys)
12388 (let ((out (assoc-ref outputs "out")))
12389 (setenv "HOME" "/tmp")
12390 (invoke "jupyter" "kernelspec" "install"
12393 (string-append out "/site-library/IRkernel/kernelspec"))
12396 `(("jupyter" ,jupyter)))
12398 `(("r-crayon" ,r-crayon)
12399 ("r-digest" ,r-digest)
12400 ("r-evaluate" ,r-evaluate)
12401 ("r-irdisplay" ,r-irdisplay)
12402 ("r-jsonlite" ,r-jsonlite)
12403 ("r-pbdzmq" ,r-pbdzmq)
12405 ("r-uuid" ,r-uuid)))
12406 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12407 (synopsis "Native R kernel for Jupyter")
12409 "The R kernel for the Jupyter environment executes R code which the
12410 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12412 (license license:expat)))
12414 (define-public r-gmodels
12421 (uri (cran-uri "gmodels" version))
12424 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12425 (build-system r-build-system)
12427 `(("r-gdata" ,r-gdata)
12428 ("r-mass" ,r-mass)))
12429 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12430 (synopsis "Various R programming tools for model fitting")
12432 "This package provides various R programming tools for model fitting.")
12433 (license license:gpl2)))
12435 (define-public r-apcluster
12437 (name "r-apcluster")
12442 (uri (cran-uri "apcluster" version))
12445 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12446 (build-system r-build-system)
12448 `(("r-matrix" ,r-matrix)
12449 ("r-rcpp" ,r-rcpp)))
12450 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12451 (synopsis "Affinity propagation clustering")
12453 "This package implements affinity propagation clustering introduced by
12454 Frey and Dueck (2007). The package further provides leveraged affinity
12455 propagation and an algorithm for exemplar-based agglomerative clustering that
12456 can also be used to join clusters obtained from affinity propagation. Various
12457 plotting functions are available for analyzing clustering results.")
12458 (license license:gpl2+)))
12460 (define-public r-valr
12467 (uri (cran-uri "valr" version))
12470 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12471 (build-system r-build-system)
12473 `(("r-broom" ,r-broom)
12474 ("r-dplyr" ,r-dplyr)
12475 ("r-ggplot2" ,r-ggplot2)
12477 ("r-readr" ,r-readr)
12478 ("r-rlang" ,r-rlang)
12479 ("r-stringr" ,r-stringr)
12480 ("r-tibble" ,r-tibble)))
12481 (home-page "http://github.com/rnabioco/valr")
12482 (synopsis "Genome interval arithmetic in R")
12484 "This package enables you to read and manipulate genome intervals and
12485 signals. It provides functionality similar to command-line tool suites within
12486 R, enabling interactive analysis and visualization of genome-scale data.")
12487 (license license:expat)))
12489 (define-public r-rematch2
12491 (name "r-rematch2")
12496 (uri (cran-uri "rematch2" version))
12499 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12500 (build-system r-build-system)
12502 `(("r-tibble" ,r-tibble)))
12503 (home-page "https://github.com/r-lib/rematch2")
12504 (synopsis "Tidy output from regular expression matching")
12506 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12507 return the match results in tidy data frames.")
12508 (license license:expat)))
12510 (define-public r-picante
12517 (uri (cran-uri "picante" version))
12520 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12521 (build-system r-build-system)
12525 ("r-vegan" ,r-vegan)))
12526 (home-page "https://cran.r-project.org/web/packages/picante/")
12527 (synopsis "Integrating phylogenies and ecology")
12529 "This package provides functions for phylocom integration, community
12530 analyses, null-models, traits and evolution. It implements numerous
12531 ecophylogenetic approaches including measures of community phylogenetic and
12532 trait diversity, phylogenetic signal, estimation of trait values for
12533 unobserved taxa, null models for community and phylogeny randomizations, and
12534 utility functions for data input/output and phylogeny plotting. A full
12535 description of package functionality and methods are provided by Kembel et
12537 (license license:gpl2)))
12539 (define-public r-reinforcelearn
12541 (name "r-reinforcelearn")
12546 (uri (cran-uri "reinforcelearn" version))
12549 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12550 (build-system r-build-system)
12552 `(("r-checkmate" ,r-checkmate)
12554 ("r-purrr" ,r-purrr)
12556 (home-page "https://markusdumke.github.io/reinforcelearn")
12557 (synopsis "Reinforcement learning")
12559 "This package implements reinforcement learning environments and
12560 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12561 can be used with function approximation, eligibility traces (Singh & Sutton,
12562 1996) and experience replay (Mnih et al., 2013).")
12563 (license license:expat)))
12565 (define-public r-lemon
12572 (uri (cran-uri "lemon" version))
12575 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12576 (build-system r-build-system)
12578 `(("r-ggplot2" ,r-ggplot2)
12579 ("r-gridextra" ,r-gridextra)
12580 ("r-gtable" ,r-gtable)
12581 ("r-knitr" ,r-knitr)
12582 ("r-lattice" ,r-lattice)
12584 ("r-scales" ,r-scales)))
12585 (home-page "https://github.com/stefanedwards/lemon")
12586 (synopsis "Freshen up your ggplot2 plots")
12588 "This package provides functions for working with legends and axis lines
12589 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12591 (license license:gpl3)))
12593 (define-public r-wgaim
12600 (uri (cran-uri "wgaim" version))
12602 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12603 (build-system r-build-system)
12605 `(("r-ggplot2" ,r-ggplot2)
12607 (home-page "https://cran.r-project.org/web/packages/wgaim")
12608 (synopsis "Whole genome average interval mapping for QTL detection")
12610 "This package integrates sophisticated mixed modelling methods with a
12611 whole genome approach to detecting significant QTL in linkage maps.")
12612 (license license:gpl2+)))
12614 (define-public r-bedr
12621 (uri (cran-uri "bedr" version))
12624 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12625 (build-system r-build-system)
12627 `(("r-data-table" ,r-data-table)
12628 ("r-r-utils" ,r-r-utils)
12629 ("r-testthat" ,r-testthat)
12630 ("r-venndiagram" ,r-venndiagram)
12633 ("bedtools" ,bedtools)
12634 ("htslib" ,htslib))) ; for tabix
12636 `(("r-knitr" ,r-knitr))) ; for vignettes
12637 (home-page "https://cran.r-project.org/web/packages/bedr")
12638 (synopsis "Genomic region processing")
12640 "This package is for genomic regions processing using command line tools
12641 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12642 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12643 The bedr package's API enhances access to these tools as well as offers
12644 additional utilities for genomic regions processing.")
12645 (license license:gpl2)))
12647 (define-public r-sets
12654 (uri (cran-uri "sets" version))
12657 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12658 (properties `((upstream-name . "sets")))
12659 (build-system r-build-system)
12660 (home-page "https://cran.r-project.org/web/packages/sets")
12661 (synopsis "Sets, generalized sets, customizable sets and intervals")
12663 "This package provides data structures and basic operations for ordinary
12664 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12665 customizable sets, and intervals.")
12666 (license license:gpl2)))
12668 (define-public r-partitions
12670 (name "r-partitions")
12675 (uri (cran-uri "partitions" version))
12678 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12679 (build-system r-build-system)
12682 ("r-polynom" ,r-polynom)
12683 ("r-sets" ,r-sets)))
12684 (home-page "https://cran.r-project.org/web/packages/partitions")
12685 (synopsis "Additive partitions of integers")
12687 "This package provides tools to enumerates the partitions, unequal
12688 partitions, and restricted partitions of an integer; the three corresponding
12689 partition functions are also given.")
12690 ;; Any version of the GPL
12691 (license license:gpl2+)))
12693 (define-public r-brobdingnag
12695 (name "r-brobdingnag")
12700 (uri (cran-uri "Brobdingnag" version))
12703 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12704 (properties `((upstream-name . "Brobdingnag")))
12705 (build-system r-build-system)
12706 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12707 (synopsis "Very large numbers in R")
12709 "This package handles very large numbers in R. Real numbers are held
12710 using their natural logarithms, plus a logical flag indicating sign. The
12711 package includes a vignette that gives a step-by-step introduction to using S4
12713 ;; Any version of the GPL
12714 (license license:gpl2+)))
12716 (define-public r-untb
12723 (uri (cran-uri "untb" version))
12726 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12727 (build-system r-build-system)
12729 `(("r-brobdingnag" ,r-brobdingnag)
12730 ("r-partitions" ,r-partitions)
12731 ("r-polynom" ,r-polynom)))
12732 (home-page "https://github.com/RobinHankin/untb.git")
12733 (synopsis "Ecological drift under the UNTB")
12735 "This package provides numerical simulations, and visualizations, of
12736 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12737 (license license:gpl2+)))
12739 (define-public r-stepwise
12741 (name "r-stepwise")
12746 (uri (cran-uri "stepwise" version))
12749 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12750 (build-system r-build-system)
12751 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12752 (synopsis "Stepwise detection of recombination breakpoints")
12754 "This package provides a stepwise approach to identifying recombination
12755 breakpoints in a genomic sequence alignment.")
12756 (license license:gpl2+)))
12758 (define-public r-snpmaxsel
12760 (name "r-snpmaxsel")
12765 (uri (cran-uri "SNPmaxsel" version))
12768 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12769 (properties `((upstream-name . "SNPmaxsel")))
12770 (build-system r-build-system)
12772 `(("r-combinat" ,r-combinat)
12773 ("r-mvtnorm" ,r-mvtnorm)))
12774 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12775 (synopsis "Maximally selected statistics for SNP data")
12777 "This package implements asymptotic methods related to maximally selected
12778 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12780 (license license:gpl2+)))
12782 (define-public r-acsnminer
12784 (name "r-acsnminer")
12785 (version "0.16.8.25")
12788 (uri (cran-uri "ACSNMineR" version))
12791 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12792 (properties `((upstream-name . "ACSNMineR")))
12793 (build-system r-build-system)
12795 `(("r-ggplot2" ,r-ggplot2)
12796 ("r-gridextra" ,r-gridextra)))
12797 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12798 (synopsis "Gene enrichment analysis")
12800 "This package provides tools to compute and represent gene set enrichment
12801 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12802 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12803 enrichment can be run with hypergeometric test or Fisher exact test, and can
12804 use multiple corrections. Visualization of data can be done either by
12805 barplots or heatmaps.")
12806 (license license:gpl2+)))
12808 (define-public r-seqinr
12815 (uri (cran-uri "seqinr" version))
12818 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12819 (build-system r-build-system)
12821 `(("r-ade4" ,r-ade4)
12822 ("r-segmented" ,r-segmented)))
12825 (home-page "http://seqinr.r-forge.r-project.org/")
12826 (synopsis "Biological sequences retrieval and analysis")
12828 "This package provides tools for exploratory data analysis and data
12829 visualization of biological sequence (DNA and protein) data. It also includes
12830 utilities for sequence data management under the ACNUC system.")
12831 (license license:gpl2+)))
12833 (define-public r-units
12840 (uri (cran-uri "units" version))
12843 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
12844 (build-system r-build-system)
12846 `(("udunits" ,udunits)))
12848 `(("r-rcpp" ,r-rcpp)))
12849 (home-page "https://github.com/r-quantities/units/")
12850 (synopsis "Measurement Units for R Vectors")
12852 "This package provides support for measurement units in R vectors,
12853 matrices and arrays: automatic propagation, conversion, derivation and
12854 simplification of units; raising errors in case of unit incompatibility. It
12855 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12857 (license license:gpl2)))
12859 (define-public r-classint
12861 (name "r-classint")
12866 (uri (cran-uri "classInt" version))
12869 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
12870 (properties `((upstream-name . "classInt")))
12871 (build-system r-build-system)
12873 `(("r-class" ,r-class)
12874 ("r-e1071" ,r-e1071)
12875 ("r-kernsmooth" ,r-kernsmooth)))
12876 (native-inputs `(("gfortran" ,gfortran)))
12877 (home-page "https://github.com/r-spatial/classInt/")
12878 (synopsis "Choose univariate class intervals")
12880 "This package provides selected commonly used methods for choosing
12881 univariate class intervals for mapping or other graphics purposes.")
12882 (license license:gpl2+)))
12884 (define-public r-spdata
12891 (uri (cran-uri "spData" version))
12894 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
12895 (properties `((upstream-name . "spData")))
12896 (build-system r-build-system)
12897 (home-page "https://github.com/Nowosad/spData")
12898 (synopsis "Datasets for spatial analysis")
12900 "This a package containing diverse spatial datasets for demonstrating,
12901 benchmarking and teaching spatial data analysis. It includes R data of class
12902 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12903 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12904 of the datasets are designed to illustrate specific analysis techniques.
12905 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12906 illustrate point pattern analysis techniques.")
12907 (license license:cc0)))
12909 (define-public r-learnbayes
12911 (name "r-learnbayes")
12916 (uri (cran-uri "LearnBayes" version))
12919 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12920 (properties `((upstream-name . "LearnBayes")))
12921 (build-system r-build-system)
12922 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
12923 (synopsis "Functions for learning Bayesian inference")
12925 "This package provides a collection of functions helpful in learning the
12926 basic tenets of Bayesian statistical inference. It contains functions for
12927 summarizing basic one and two parameter posterior distributions and predictive
12928 distributions. It contains MCMC algorithms for summarizing posterior
12929 distributions defined by the user. It also contains functions for regression
12930 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
12932 (license license:gpl2+)))
12934 (define-public r-deldir
12941 (uri (cran-uri "deldir" version))
12944 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
12945 (build-system r-build-system)
12946 (native-inputs `(("gfortran" ,gfortran)))
12947 (home-page "https://cran.r-project.org/web/packages/deldir")
12948 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
12950 "This package provides tools for calculating the Delaunay triangulation
12951 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
12952 of a planar point set. It plots triangulations and tessellations in various
12953 ways, clips tessellations to sub-windows, calculates perimeters of
12954 tessellations, and summarizes information about the tiles of the
12956 (license license:gpl2+)))
12958 (define-public r-sf
12965 (uri (cran-uri "sf" version))
12968 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
12969 (build-system r-build-system)
12976 `(("r-classint" ,r-classint)
12978 ("r-magrittr" ,r-magrittr)
12980 ("r-units" ,r-units)))
12981 (native-inputs `(("pkg-config" ,pkg-config)))
12982 (home-page "https://github.com/r-spatial/sf/")
12983 (synopsis "Simple features for R")
12985 "This package provides support for simple features, a standardized way to
12986 encode spatial vector data. It binds to GDAL for reading and writing data, to
12987 GEOS for geometrical operations, and to PROJ for projection conversions and
12988 datum transformations.")
12989 ;; Either of these licenses
12990 (license (list license:gpl2 license:expat))))
12992 (define-public r-spdep
12999 (uri (cran-uri "spdep" version))
13002 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13003 (build-system r-build-system)
13005 `(("r-boot" ,r-boot)
13007 ("r-deldir" ,r-deldir)
13009 ("r-gmodels" ,r-gmodels)
13010 ("r-learnbayes" ,r-learnbayes)
13012 ("r-matrix" ,r-matrix)
13016 ("r-spdata" ,r-spdata)))
13017 (home-page "https://github.com/r-spatial/spdep/")
13018 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13020 "This package provides a collection of functions to create spatial
13021 weights matrix objects from polygon contiguities, from point patterns by
13022 distance and tessellations, for summarizing these objects, and for permitting
13023 their use in spatial data analysis, including regional aggregation by minimum
13025 (license license:gpl2+)))
13027 (define-public r-adegenet
13029 (name "r-adegenet")
13034 (uri (cran-uri "adegenet" version))
13037 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13038 (build-system r-build-system)
13040 `(("r-ade4" ,r-ade4)
13043 ("r-dplyr" ,r-dplyr)
13044 ("r-ggplot2" ,r-ggplot2)
13045 ("r-igraph" ,r-igraph)
13047 ("r-reshape2" ,r-reshape2)
13048 ("r-seqinr" ,r-seqinr)
13049 ("r-shiny" ,r-shiny)
13050 ("r-spdep" ,r-spdep)
13051 ("r-vegan" ,r-vegan)))
13052 (home-page "https://github.com/thibautjombart/adegenet")
13053 (synopsis "Exploratory analysis of genetic and genomic data")
13055 "This package provides a toolset for the exploration of genetic and
13056 genomic data. Adegenet provides formal (S4) classes for storing and handling
13057 various genetic data, including genetic markers with varying ploidy and
13058 hierarchical population structure (@code{genind} class), alleles counts by
13059 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13060 also implements original multivariate methods (DAPC, sPCA), graphics,
13061 statistical tests, simulation tools, distance and similarity measures, and
13062 several spatial methods. A range of both empirical and simulated datasets is
13063 also provided to illustrate various methods.")
13064 (license license:gpl2+)))
13066 (define-public r-pegas
13073 (uri (cran-uri "pegas" version))
13075 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13076 (build-system r-build-system)
13078 `(("r-adegenet" ,r-adegenet)
13080 (home-page "http://ape-package.ird.fr/pegas.html")
13081 (synopsis "Population and evolutionary genetics analysis system")
13083 "This package provides functions for reading, writing, plotting,
13084 analysing, and manipulating allelic and haplotypic data, including from VCF
13085 files, and for the analysis of population nucleotide sequences and
13086 micro-satellites including coalescent analyses, linkage disequilibrium,
13087 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13088 minimum spanning tree and network, and median-joining networks.")
13089 (license license:gpl2+)))
13091 (define-public r-rmetasim
13093 (name "r-rmetasim")
13098 (uri (cran-uri "rmetasim" version))
13101 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13102 (build-system r-build-system)
13104 `(("r-ade4" ,r-ade4)
13105 ("r-adegenet" ,r-adegenet)
13106 ("r-gtools" ,r-gtools)
13107 ("r-pegas" ,r-pegas)))
13108 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13109 (synopsis "Individual-based population genetic simulation environment")
13111 "This package provides an interface between R and the metasim simulation
13112 engine. The simulation environment is documented in: Strand, A.(2002),
13113 Metasim 1.0: an individual-based environment for simulating population
13114 genetics of complex population dynamics.")
13116 (license license:gpl2+)))
13118 (define-public r-genetics
13120 (name "r-genetics")
13121 (version "1.3.8.1.2")
13125 (uri (cran-uri "genetics" version))
13128 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13129 (build-system r-build-system)
13131 `(("r-combinat" ,r-combinat)
13132 ("r-gdata" ,r-gdata)
13133 ("r-gtools" ,r-gtools)
13135 ("r-mvtnorm" ,r-mvtnorm)))
13136 (home-page "https://cran.r-project.org/web/packages/genetics/")
13137 (synopsis "Population genetics")
13139 "This package provides classes and methods for handling genetic data.
13140 It includes classes to represent genotypes and haplotypes at single markers up
13141 to multiple markers on multiple chromosomes. Function include allele
13142 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13143 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13144 and testing for linkage disequilibrium, ...")
13145 ;; Any GPL version.
13146 (license license:gpl2+)))
13148 (define-public r-snp-plotter
13150 (name "r-snp-plotter")
13155 (uri (cran-uri "snp.plotter" version))
13158 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13159 (properties `((upstream-name . "snp.plotter")))
13160 (build-system r-build-system)
13161 (propagated-inputs `(("r-genetics" ,r-genetics)))
13162 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13163 (synopsis "Plot p-values using single SNP and/or haplotype data")
13165 "This package helps you create plots of p-values using single SNP and/or
13166 haplotype data. Main features of the package include options to display a
13167 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13168 datasets simultaneously. Plots can be created using global and/or individual
13169 haplotype p-values along with single SNP p-values. Images are created as
13170 either PDF/EPS files.")
13171 (license license:gpl2+)))
13173 (define-public r-polspline
13175 (name "r-polspline")
13180 (uri (cran-uri "polspline" version))
13182 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13183 (build-system r-build-system)
13184 (native-inputs `(("gfortran" ,gfortran)))
13185 (home-page "https://cran.r-project.org/web/packages/polspline/")
13186 (synopsis "Polynomial spline routines")
13188 "This package provides routines for the polynomial spline fitting
13189 routines hazard regression, hazard estimation with flexible tails, logspline,
13190 lspec, polyclass, and polymars.")
13191 (license license:gpl2+)))
13193 (define-public r-rms
13200 (uri (cran-uri "rms" version))
13202 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13203 (build-system r-build-system)
13205 `(("r-ggplot2" ,r-ggplot2)
13206 ("r-hmisc" ,r-hmisc)
13207 ("r-htmltable" ,r-htmltable)
13208 ("r-htmltools" ,r-htmltools)
13209 ("r-lattice" ,r-lattice)
13210 ("r-multcomp" ,r-multcomp)
13212 ("r-polspline" ,r-polspline)
13213 ("r-quantreg" ,r-quantreg)
13214 ("r-rpart" ,r-rpart)
13215 ("r-sparsem" ,r-sparsem)
13216 ("r-survival" ,r-survival)))
13217 (native-inputs `(("gfortran" ,gfortran)))
13218 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13219 (synopsis "Regression modeling strategies")
13221 "This is a package for regression modeling, testing, estimation,
13222 validation, graphics, prediction, and typesetting by storing enhanced model
13223 design attributes in the fit. The rms package is a collection of functions
13224 that assist with and streamline modeling. It also contains functions for
13225 binary and ordinal logistic regression models, ordinal models for continuous Y
13226 with a variety of distribution families, and the Buckley-James multiple
13227 regression model for right-censored responses, and implements penalized
13228 maximum likelihood estimation for logistic and ordinary linear models. The
13229 package works with almost any regression model, but it was especially written
13230 to work with binary or ordinal regression models, Cox regression, accelerated
13231 failure time models, ordinary linear models, the Buckley-James model,
13232 generalized least squares for serially or spatially correlated observations,
13233 generalized linear models, and quantile regression.")
13234 (license license:gpl2+)))
13236 (define-public r-haplo-stats
13238 (name "r-haplo-stats")
13243 (uri (cran-uri "haplo.stats" version))
13246 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13247 (properties `((upstream-name . "haplo.stats")))
13248 (build-system r-build-system)
13250 `(("r-rms" ,r-rms)))
13252 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13253 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13254 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13256 "This package provides routines for the analysis of indirectly measured
13257 haplotypes. The statistical methods assume that all subjects are unrelated
13258 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13259 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13260 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13261 examples in the vignette.")
13262 (license license:gpl2+)))
13264 (define-public r-bqtl
13271 (uri (cran-uri "bqtl" version))
13274 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13275 (build-system r-build-system)
13276 (native-inputs `(("gfortran" ,gfortran)))
13277 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13278 (synopsis "Bayesian QTL mapping toolkit")
13280 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13281 lines. It includes maximum likelihood and Bayesian tools.")
13282 (license license:gpl2+)))
13284 (define-public r-ibdreg
13291 (uri (cran-uri "ibdreg" version))
13294 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13295 (build-system r-build-system)
13296 (home-page "https://www.mayo.edu/research/labs/\
13297 statistical-genetics-genetic-epidemiology/software")
13298 (synopsis "Regression methods for IBD linkage with covariates")
13300 "This package provides a method to test genetic linkage with covariates
13301 by regression methods with response IBD sharing for relative pairs. Account
13302 for correlations of IBD statistics and covariates for relative pairs within
13303 the same pedigree.")
13304 (license license:gpl2+)))
13306 (define-public r-dlmap
13313 (uri (cran-uri "dlmap" version))
13316 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13317 (build-system r-build-system)
13319 `(("r-ibdreg" ,r-ibdreg)
13323 ("r-wgaim" ,r-wgaim)))
13324 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13325 (synopsis "Detection localization mapping for QTL")
13327 "This is package for QTL mapping in a mixed model framework with separate
13328 detection and localization stages. The first stage detects the number of QTL
13329 on each chromosome based on the genetic variation due to grouped markers on
13330 the chromosome; the second stage uses this information to determine the most
13331 likely QTL positions. The mixed model can accommodate general fixed and
13332 random effects, including spatial effects in field trials and pedigree
13333 effects. It is applicable to backcrosses, doubled haploids, recombinant
13334 inbred lines, F2 intercrosses, and association mapping populations.")
13335 (license license:gpl2)))
13337 (define-public r-ldheatmap
13339 (name "r-ldheatmap")
13344 (uri (cran-uri "LDheatmap" version))
13347 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13348 (properties `((upstream-name . "LDheatmap")))
13349 (build-system r-build-system)
13351 `(("r-genetics" ,r-genetics)
13353 ("r-snpstats" ,r-snpstats)))
13354 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13355 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13357 "This package provides tools to produce a graphical display, as a heat
13358 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13359 optionally include the physical locations or genetic map distances of each SNP
13361 (license license:gpl3)))
13363 (define-public r-hwde
13370 (uri (cran-uri "hwde" version))
13373 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13374 (build-system r-build-system)
13375 (home-page "https://cran.r-project.org/web/packages/hwde/")
13376 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13378 "This package fits models for genotypic disequilibria, as described in
13379 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13380 terms are available that account for first order interactions between loci.
13381 It also implements, for a single locus in a single population, a conditional
13382 exact test for Hardy-Weinberg equilibrium.")
13383 (license license:gpl2+)))
13385 (define-public r-tdthap
13392 (uri (cran-uri "tdthap" version))
13395 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13396 (build-system r-build-system)
13397 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13398 (synopsis "TDT tests for extended haplotypes")
13400 "Functions and examples are provided for transmission/disequilibrium
13401 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13402 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13403 (license license:artistic2.0)))
13405 (define-public r-sparql
13411 (uri (cran-uri "SPARQL" version))
13414 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13415 (properties `((upstream-name . "SPARQL")))
13416 (build-system r-build-system)
13418 `(("r-rcurl" ,r-rcurl)
13420 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13421 (synopsis "SPARQL client for R")
13422 (description "This package provides an interface to use SPARQL to pose
13423 SELECT or UPDATE queries to an end-point.")
13424 ;; The only license indication is found in the DESCRIPTION file,
13425 ;; which states GPL-3. So we cannot assume GPLv3+.
13426 (license license:gpl3)))
13428 (define-public r-bookdown
13430 (name "r-bookdown")
13434 (uri (cran-uri "bookdown" version))
13437 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13438 (build-system r-build-system)
13440 `(("r-htmltools" ,r-htmltools)
13441 ("r-knitr" ,r-knitr)
13442 ("r-rmarkdown" ,r-rmarkdown)
13443 ("r-tinytex" ,r-tinytex)
13445 ("pandoc" ,ghc-pandoc)))
13446 (home-page "https://github.com/rstudio/bookdown")
13447 (synopsis "Authoring books and technical documents with R markdown")
13448 (description "This package provides output formats and utilities for
13449 authoring books and technical documents with R Markdown.")
13450 (license license:gpl3)))
13452 (define-public r-optparse
13454 (name "r-optparse")
13459 (uri (cran-uri "optparse" version))
13462 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13463 (build-system r-build-system)
13465 `(("r-getopt" ,r-getopt)))
13466 (home-page "https://github.com/trevorld/optparse")
13467 (synopsis "Command line option parser")
13469 "This package provides a command line parser inspired by Python's
13470 @code{optparse} library to be used with Rscript to write shebang scripts
13471 that accept short and long options.")
13472 (license license:gpl2+)))
13474 (define-public r-wgcna
13481 (uri (cran-uri "WGCNA" version))
13484 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13485 (properties `((upstream-name . "WGCNA")))
13486 (build-system r-build-system)
13488 `(("r-annotationdbi" ,r-annotationdbi)
13489 ("r-doparallel" ,r-doparallel)
13490 ("r-dynamictreecut" ,r-dynamictreecut)
13491 ("r-fastcluster" ,r-fastcluster)
13492 ("r-foreach" ,r-foreach)
13493 ("r-go-db" ,r-go-db)
13494 ("r-hmisc" ,r-hmisc)
13495 ("r-impute" ,r-impute)
13497 ("r-robust" ,r-robust)
13498 ("r-survival" ,r-survival)
13499 ("r-matrixstats" ,r-matrixstats)
13500 ("r-preprocesscore" ,r-preprocesscore)))
13502 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13503 (synopsis "Weighted correlation network analysis")
13505 "This package provides functions necessary to perform Weighted
13506 Correlation Network Analysis on high-dimensional data. It includes functions
13507 for rudimentary data cleaning, construction and summarization of correlation
13508 networks, module identification and functions for relating both variables and
13509 modules to sample traits. It also includes a number of utility functions for
13510 data manipulation and visualization.")
13511 (license license:gpl2+)))
13513 (define-public r-kernlab
13520 (uri (cran-uri "kernlab" version))
13522 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13523 (build-system r-build-system)
13524 (home-page "https://cran.r-project.org/web/packages/kernlab")
13525 (synopsis "Kernel-based machine learning tools")
13527 "This package provides kernel-based machine learning methods for
13528 classification, regression, clustering, novelty detection, quantile regression
13529 and dimensionality reduction. Among other methods @code{kernlab} includes
13530 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13532 (license license:gpl2)))
13534 (define-public r-hierfstat
13536 (name "r-hierfstat")
13537 (version "0.04-22")
13541 (uri (cran-uri "hierfstat" version))
13544 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13545 (build-system r-build-system)
13547 `(("r-ade4" ,r-ade4)
13548 ("r-adegenet" ,r-adegenet)
13549 ("r-gtools" ,r-gtools)))
13550 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13551 (synopsis "Estimation and tests of hierarchical F-statistics")
13553 "This package allows the estimation of hierarchical F-statistics from
13554 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13555 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13556 are also given to test via randomisations the significance of each F and
13557 variance components, using the likelihood-ratio statistics G.")
13558 (license license:gpl2+)))
13560 (define-public r-hapassoc
13562 (name "r-hapassoc")
13567 (uri (cran-uri "hapassoc" version))
13570 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13571 (build-system r-build-system)
13572 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13573 (synopsis "Inference of trait associations with SNP haplotypes")
13575 "Hapassoc performs likelihood inference of trait associations with
13576 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13577 functions are developed primarily for data collected in cohort or
13578 cross-sectional studies. They can accommodate uncertain haplotype phase and
13579 handle missing genotypes at some SNPs.")
13580 (license license:gpl2)))
13582 (define-public r-sampling
13584 (name "r-sampling")
13589 (uri (cran-uri "sampling" version))
13592 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13593 (build-system r-build-system)
13595 `(("r-lpsolve" ,r-lpsolve)
13596 ("r-mass" ,r-mass)))
13597 (home-page "https://cran.r-project.org/web/packages/sampling/")
13598 (synopsis "Survey sampling")
13600 "This package provides functions for drawing and calibrating samples.")
13601 (license license:gpl2+)))
13603 (define-public r-r2html
13610 (uri (cran-uri "R2HTML" version))
13613 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13614 (properties `((upstream-name . "R2HTML")))
13615 (build-system r-build-system)
13616 (home-page "https://github.com/nalimilan/R2HTML")
13617 (synopsis "HTML export for R objects")
13619 "This package includes HTML functions and methods to write in an HTML
13620 file. Thus, making HTML reports is easy. It includes a function that allows
13621 redirection on the fly, which appears to be very useful for teaching purposes,
13622 as the student can keep a copy of the produced output to keep all that they
13623 did during the course. The package comes with a vignette describing how to
13624 write HTML reports for statistical analysis. Finally, a driver for Sweave
13625 allows to parse HTML flat files containing R code and to automatically write
13626 the corresponding outputs (tables and graphs).")
13627 (license license:gpl2+)))
13629 (define-public r-rjava
13636 (uri (cran-uri "rJava" version))
13639 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13640 (properties `((upstream-name . "rJava")))
13641 (build-system r-build-system)
13643 `(#:modules ((guix build utils)
13644 (guix build r-build-system)
13647 (modify-phases %standard-phases
13648 (add-after 'unpack 'set-JAVA_HOME
13649 (lambda* (#:key inputs #:allow-other-keys)
13650 (let ((jdk (assoc-ref inputs "jdk")))
13651 (setenv "JAVA_HOME" jdk)
13652 (setenv "JAVA" (which "java"))
13653 (setenv "JAR" (which "jar"))
13654 (setenv "JAVAC" (which "javac"))
13655 (setenv "JAVAH" (which "javah"))
13656 (setenv "JAVA_CPPFLAGS"
13657 (string-append "-I" jdk "/include "
13658 "-I" jdk "/include/linux"))
13659 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13660 ((lib) (setenv "JAVA_LIBS" lib))
13661 (_ (error "Could not find libjvm.so"))))
13665 ("jdk" ,icedtea-8 "jdk")
13668 (home-page "http://www.rforge.net/rJava/")
13669 (synopsis "Low-Level R to Java interface")
13671 "This package provides a low-level interface to the Java VM very much
13672 like .C/.Call and friends. It allows the creation of objects, calling methods
13673 and accessing fields.")
13674 (license license:gpl2)))
13676 (define-public r-svmisc
13683 (uri (cran-uri "svMisc" version))
13686 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13687 (properties `((upstream-name . "svMisc")))
13688 (build-system r-build-system)
13689 (home-page "https://github.com/SciViews/svMisc")
13690 (synopsis "Miscellaneous functions for SciViews")
13692 "This package provides miscellaneous functions for SciViews or general
13693 use, including tools to manage a temporary environment attached to the search
13694 path for temporary variables you do not want to @code{save()} or
13695 @code{load()}; test the current platform; showing progress bars, etc.")
13696 (license license:gpl2)))
13698 (define-public r-xyz
13705 (uri (cran-uri "xyz" version))
13708 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13709 (build-system r-build-system)
13711 `(("r-rcpp" ,r-rcpp)))
13712 (home-page "https://cran.r-project.org/web/packages/xyz/")
13713 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13715 "High dimensional interaction search by brute force requires a quadratic
13716 computational cost in the number of variables. The xyz algorithm provably
13717 finds strong interactions in almost linear time. For details of the algorithm
13718 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13719 interaction search in high-dimensional data.")
13720 ;; Any version of the GPL.
13721 (license license:gpl2+)))
13723 (define-public r-rttf2pt1
13725 (name "r-rttf2pt1")
13730 (uri (cran-uri "Rttf2pt1" version))
13733 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13734 (properties `((upstream-name . "Rttf2pt1")))
13735 (build-system r-build-system)
13736 (home-page "https://github.com/wch/Rttf2pt1")
13737 (synopsis "Font conversion utility")
13739 "This package contains the program @code{ttf2pt1}, for use with the
13740 @code{extrafont} package.")
13741 ;; Most of the files are covered under the Expat license. Some files are
13742 ;; covered under BSD-3. Deviations for individual files are recorded in
13743 ;; the LICENSE file.
13744 (license (list license:bsd-3 license:expat
13745 (license:non-copyleft "file://LICENSE")))))
13747 (define-public r-extrafontdb
13749 (name "r-extrafontdb")
13754 (uri (cran-uri "extrafontdb" version))
13757 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13758 (build-system r-build-system)
13759 (home-page "https://github.com/wch/extrafontdb")
13760 (synopsis "Database for the extrafont package")
13762 "This package holds the database for the @code{extrafont} package.")
13763 (license license:gpl2)))
13765 (define-public r-extrafont
13767 (name "r-extrafont")
13772 (uri (cran-uri "extrafont" version))
13775 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13776 (build-system r-build-system)
13778 `(("r-extrafontdb" ,r-extrafontdb)
13779 ("r-rttf2pt1" ,r-rttf2pt1)))
13780 (home-page "https://github.com/wch/extrafont")
13781 (synopsis "Tools for using fonts in R")
13783 "The extrafont package makes it easier to use fonts other than the basic
13784 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13785 used with PDF or PostScript output files. There are two hurdles for using
13786 fonts in PDF (or Postscript) output files:
13789 @item Making R aware of the font and the dimensions of the characters.
13790 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13791 properly on a device that doesn't have the font. This is usually needed if
13792 you want to print the PDF file or share it with others.
13795 The extrafont package makes both of these things easier.")
13796 (license license:gpl2)))
13798 (define-public r-xkcd
13805 (uri (cran-uri "xkcd" version))
13808 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13809 (build-system r-build-system)
13811 `(("r-extrafont" ,r-extrafont)
13812 ("r-ggplot2" ,r-ggplot2)
13813 ("r-hmisc" ,r-hmisc)))
13814 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13815 (synopsis "Plot ggplot2 graphics in the XKCD style")
13817 "This package provides the means to plot ggplot2 graphs in the style of
13818 the XKCD web comic.")
13819 (license license:gpl3)))
13821 (define-public r-msigdbr
13828 (uri (cran-uri "msigdbr" version))
13831 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
13832 (build-system r-build-system)
13834 `(("r-dplyr" ,r-dplyr)
13835 ("r-magrittr" ,r-magrittr)
13836 ("r-rlang" ,r-rlang)
13837 ("r-tibble" ,r-tibble)))
13838 (home-page "https://github.com/igordot/msigdbr")
13839 (synopsis "MSigDB gene sets for multiple organisms")
13841 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13842 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13843 software in a standard R data frame with key-value pairs. Included are the
13844 original human gene symbols and Entrez IDs as well as the equivalents for
13845 various frequently studied model organisms such as mouse, rat, pig, fly, and
13847 ;; The package is covered under the Expat license, but the upstream MSigDB
13848 ;; files are made available under the Creative Commons Attribution 4.0
13849 ;; International license.
13850 (license (list license:expat license:cc-by4.0))))
13852 (define-public r-gridgraphics
13854 (name "r-gridgraphics")
13859 (uri (cran-uri "gridGraphics" version))
13862 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13863 (properties `((upstream-name . "gridGraphics")))
13864 (build-system r-build-system)
13865 (home-page "https://github.com/pmur002/gridgraphics")
13866 (synopsis "Redraw base graphics using @code{grid} graphics")
13868 "This package provides functions to convert a page of plots drawn with
13869 the @code{graphics} package into identical output drawn with the @code{grid}
13870 package. The result looks like the original @code{graphics}-based plot, but
13871 consists of @code{grid} grobs and viewports that can then be manipulated with
13872 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13873 (license license:gpl2+)))
13875 (define-public r-farver
13882 (uri (cran-uri "farver" version))
13885 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
13886 (build-system r-build-system)
13887 (home-page "https://github.com/thomasp85/farver")
13888 (synopsis "Vectorized color conversion and comparison")
13890 "The encoding of color can be handled in many different ways, using
13891 different color spaces. As different color spaces have different uses,
13892 efficient conversion between these representations are important. This
13893 package provides a set of functions that gives access to very fast color space
13894 conversion and comparisons implemented in C++, and offers 100-fold speed
13895 improvements over the @code{convertColor} function in the @code{grDevices}
13897 (license license:expat)))
13899 (define-public r-ggplotify
13901 (name "r-ggplotify")
13906 (uri (cran-uri "ggplotify" version))
13909 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
13910 (build-system r-build-system)
13912 `(("r-ggplot2" ,r-ggplot2)
13913 ("r-gridgraphics" ,r-gridgraphics)
13914 ("r-rvcheck" ,r-rvcheck)))
13915 (home-page "https://github.com/GuangchuangYu/ggplotify")
13916 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13918 "This package provides tools to convert plot function calls (using
13919 expression or formula) to @code{grob} or @code{ggplot} objects that are
13920 compatible with the @code{grid} and @code{ggplot2} environment. With this
13921 package, we are able to e.g. use @code{cowplot} to align plots produced by
13922 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
13923 converting them to @code{ggplot} objects.")
13924 (license license:artistic2.0)))
13926 (define-public r-triebeard
13928 (name "r-triebeard")
13933 (uri (cran-uri "triebeard" version))
13936 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
13937 (build-system r-build-system)
13938 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13939 (home-page "https://github.com/Ironholds/triebeard/")
13940 (synopsis "Radix trees in Rcpp")
13942 "Radix trees, or tries, are key-value data structures optimized for
13943 efficient lookups, similar in purpose to hash tables. This package provides
13944 an implementation of radix trees for use in R programming and in developing
13945 packages with Rcpp.")
13946 (license license:expat)))
13948 (define-public r-tweenr
13955 (uri (cran-uri "tweenr" version))
13958 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
13959 (build-system r-build-system)
13961 `(("r-farver" ,r-farver)
13962 ("r-magrittr" ,r-magrittr)
13964 ("r-rlang" ,r-rlang)))
13965 (home-page "https://github.com/thomasp85/tweenr")
13966 (synopsis "Interpolate data for smooth animations")
13968 "In order to create smooth animation between states of data, tweening is
13969 necessary. This package provides a range of functions for creating tweened
13970 data that can be used as basis for animation. Furthermore it adds a number of
13971 vectorized interpolaters for common R data types such as numeric, date and
13973 (license license:expat)))
13975 (define-public r-polyclip
13977 (name "r-polyclip")
13982 (uri (cran-uri "polyclip" version))
13985 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
13986 (build-system r-build-system)
13987 (native-inputs `(("pkg-config" ,pkg-config)))
13988 (home-page "http://www.angusj.com/delphi/clipper.php")
13989 (synopsis "Polygon clipping")
13991 "This package provides an R port of the library Clipper. It performs
13992 polygon clipping operations (intersection, union, set minus, set difference)
13993 for polygonal regions of arbitrary complexity, including holes. It computes
13994 offset polygons (spatial buffer zones, morphological dilations, Minkowski
13995 dilations) for polygonal regions and polygonal lines. It computes the
13996 Minkowski Sum of general polygons. There is a function for removing
13997 self-intersections from polygon data.")
13998 (license license:boost1.0)))
14000 (define-public r-urltools
14002 (name "r-urltools")
14007 (uri (cran-uri "urltools" version))
14010 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14011 (build-system r-build-system)
14013 `(("r-rcpp" ,r-rcpp)
14014 ("r-triebeard" ,r-triebeard)))
14015 (home-page "https://github.com/Ironholds/urltools/")
14016 (synopsis "Vectorized tools for URL handling and parsing")
14018 "This package provides a toolkit for all URL-handling needs, including
14019 encoding and decoding, parsing, parameter extraction and modification. All
14020 functions are designed to be both fast and entirely vectorized. It is
14021 intended to be useful for people dealing with web-related datasets, such as
14022 server-side logs, although may be useful for other situations involving large
14024 (license license:expat)))
14026 (define-public r-ggforce
14033 (uri (cran-uri "ggforce" version))
14036 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14037 (build-system r-build-system)
14039 `(("r-ggplot2" ,r-ggplot2)
14040 ("r-gtable" ,r-gtable)
14042 ("r-polyclip" ,r-polyclip)
14044 ("r-rcppeigen" ,r-rcppeigen)
14045 ("r-rlang" ,r-rlang)
14046 ("r-scales" ,r-scales)
14047 ("r-tidyselect" ,r-tidyselect)
14048 ("r-tweenr" ,r-tweenr)
14049 ("r-withr" ,r-withr)))
14050 (home-page "https://ggforce.data-imaginist.com")
14051 (synopsis "Accelerating ggplot2")
14053 "The aim of the ggplot2 package is to aid in visual data investigations.
14054 This focus has led to a lack of facilities for composing specialized plots.
14055 Thi package aims to be a collection of mainly new statistics and geometries
14056 that fills this gap.")
14057 (license license:expat)))
14059 (define-public r-europepmc
14061 (name "r-europepmc")
14066 (uri (cran-uri "europepmc" version))
14069 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14070 (build-system r-build-system)
14072 `(("r-dplyr" ,r-dplyr)
14074 ("r-jsonlite" ,r-jsonlite)
14076 ("r-progress" ,r-progress)
14077 ("r-purrr" ,r-purrr)
14078 ("r-urltools" ,r-urltools)
14079 ("r-xml2" ,r-xml2)))
14080 (home-page "https://github.com/ropensci/europepmc/")
14081 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14083 "This package provides an R Client for the
14084 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14085 Service}. It gives access to both metadata on life science literature and
14086 open access full texts. Europe PMC indexes all PubMed content and other
14087 literature sources including Agricola, a bibliographic database of citations
14088 to the agricultural literature, or Biological Patents. In addition to
14089 bibliographic metadata, the client allows users to fetch citations and
14090 reference lists. Links between life-science literature and other EBI
14091 databases, including ENA, PDB or ChEMBL are also accessible.")
14092 (license license:gpl3)))
14094 (define-public r-ggraph
14101 (uri (cran-uri "ggraph" version))
14104 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14105 (build-system r-build-system)
14107 `(("r-digest" ,r-digest)
14108 ("r-dplyr" ,r-dplyr)
14109 ("r-ggforce" ,r-ggforce)
14110 ("r-ggplot2" ,r-ggplot2)
14111 ("r-ggrepel" ,r-ggrepel)
14112 ("r-graphlayouts" ,r-graphlayouts)
14113 ("r-gtable" ,r-gtable)
14114 ("r-igraph" ,r-igraph)
14117 ("r-rlang" ,r-rlang)
14118 ("r-scales" ,r-scales)
14119 ("r-tidygraph" ,r-tidygraph)
14120 ("r-viridis" ,r-viridis)))
14121 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14122 (synopsis "Implementation of grammar of graphics for graphs and networks")
14124 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14125 graph and network visualizations due to its reliance on tabular data input.
14126 The ggraph package is an extension of the ggplot2 API tailored to graph
14127 visualizations and provides the same flexible approach to building up plots
14129 (license license:gpl3)))
14131 (define-public r-varselrf
14133 (name "r-varselrf")
14138 (uri (cran-uri "varSelRF" version))
14141 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14142 (properties `((upstream-name . "varSelRF")))
14143 (build-system r-build-system)
14145 `(("r-randomforest" ,r-randomforest)))
14146 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14147 (synopsis "Variable selection using random forests")
14149 "This package provides tools for the variable selection from random
14150 forests using both backwards variable elimination (for the selection of small
14151 sets of non-redundant variables) and selection based on the importance
14152 spectrum (somewhat similar to scree plots; for the selection of large,
14153 potentially highly-correlated variables). The main applications are in
14154 high-dimensional data (e.g., microarray data, and other genomics and
14155 proteomics applications).")
14156 (license license:gpl2+)))
14158 (define-public r-pamr
14165 (uri (cran-uri "pamr" version))
14168 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14169 (build-system r-build-system)
14171 `(("r-cluster" ,r-cluster)
14172 ("r-survival" ,r-survival)))
14173 (native-inputs `(("gfortran" ,gfortran)))
14174 (home-page "https://cran.r-project.org/web/packages/pamr/")
14175 (synopsis "Prediction Analysis for Microarrays")
14177 "This package provides some functions for sample classification in
14179 (license license:gpl2)))
14181 (define-public r-rda
14184 (version "1.0.2-2.1")
14188 (uri (cran-uri "rda" version))
14191 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14192 (build-system r-build-system)
14193 (home-page "https://cran.r-project.org/web/packages/rda/")
14194 (synopsis "Shrunken centroids regularized discriminant analysis")
14196 "This package provides tools for shrunken centroids regularized
14197 discriminant analysis for the purpose of classifying high dimensional data.")
14198 (license license:gpl2+)))
14200 (define-public r-ggvis
14207 (uri (cran-uri "ggvis" version))
14210 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14211 (build-system r-build-system)
14213 `(("r-assertthat" ,r-assertthat)
14214 ("r-dplyr" ,r-dplyr)
14215 ("r-htmltools" ,r-htmltools)
14216 ("r-jsonlite" ,r-jsonlite)
14217 ("r-lazyeval" ,r-lazyeval)
14218 ("r-magrittr" ,r-magrittr)
14219 ("r-shiny" ,r-shiny)))
14220 (home-page "https://ggvis.rstudio.com/")
14221 (synopsis "Interactive grammar of graphics")
14223 "This package is a data visualization package for R providing an
14224 implementation of an interactive grammar of graphics, taking the best parts of
14225 ggplot2, combining them with the reactive framework of Shiny and drawing web
14226 graphics using Vega.")
14227 (license license:gpl2)))
14229 (define-public r-gbm
14236 (uri (cran-uri "gbm" version))
14239 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14240 (build-system r-build-system)
14242 `(("r-gridextra" ,r-gridextra)
14243 ("r-lattice" ,r-lattice)
14244 ("r-survival" ,r-survival)))
14245 (home-page "https://github.com/gbm-developers/gbm")
14246 (synopsis "Generalized boosted regression models")
14248 "This package is an implementation of extensions to Freund and Schapire's
14249 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14250 regression methods for least squares, absolute loss, t-distribution loss,
14251 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14252 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14253 and Learning to Rank measures (LambdaMart).")
14254 (license license:gpl2+)))
14256 (define-public r-threejs
14263 (uri (cran-uri "threejs" version))
14266 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14267 (build-system r-build-system)
14269 `(#:modules ((guix build utils)
14270 (guix build r-build-system)
14274 (modify-phases %standard-phases
14275 (add-after 'unpack 'process-javascript
14276 (lambda* (#:key inputs #:allow-other-keys)
14277 (with-directory-excursion "inst"
14281 `((,(assoc-ref inputs "js-jquery")
14282 "htmlwidgets/lib/jquery/jquery.min.js")
14283 (,(assoc-ref inputs "js-threejs-85")
14284 "htmlwidgets/lib/threejs-85/three.min.js"))))
14285 (lambda (sources targets)
14286 (for-each (lambda (source target)
14287 (format #t "Processing ~a --> ~a~%"
14289 (delete-file target)
14290 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14291 (call-with-output-file target
14293 (dump-port minified port)))))
14294 sources targets))))
14297 `(("r-base64enc" ,r-base64enc)
14298 ("r-crosstalk" ,r-crosstalk)
14299 ("r-htmlwidgets" ,r-htmlwidgets)
14300 ("r-igraph" ,r-igraph)))
14302 `(("uglify-js" ,uglify-js)
14306 (uri "https://code.jquery.com/jquery-3.3.1.js")
14309 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14313 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14316 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14317 (home-page "https://bwlewis.github.io/rthreejs")
14318 (synopsis "Interactive 3D scatter plots, networks and globes")
14320 "Create interactive 3D scatter plots, network plots, and globes in R
14321 using the three.js visualization library.")
14322 (license license:expat)))
14324 (define-public r-mlbench
14331 (uri (cran-uri "mlbench" version))
14334 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14335 (build-system r-build-system)
14336 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14337 (synopsis "Machine learning benchmark problems")
14339 "This package provides a collection of artificial and real-world machine
14340 learning benchmark problems, including, e.g., several data sets from the UCI
14342 (license license:gpl2)))
14344 (define-public r-mpm
14351 (uri (cran-uri "mpm" version))
14354 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14355 (build-system r-build-system)
14357 `(("r-kernsmooth" ,r-kernsmooth)
14358 ("r-mass" ,r-mass)))
14359 (home-page "http://mpm.r-forge.r-project.org")
14360 (synopsis "Multivariate projection methods")
14362 "This is a package for exploratory graphical analysis of multivariate
14363 data, specifically gene expression data with different projection methods:
14364 principal component analysis, correspondence analysis, spectral map
14366 (license license:gpl2+)))
14368 (define-public r-png
14374 (uri (cran-uri "png" version))
14377 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14378 (build-system r-build-system)
14380 `(("libpng" ,libpng)
14382 (home-page "http://www.rforge.net/png/")
14383 (synopsis "Read and write PNG images")
14385 "This package provides an easy and simple way to read, write and display
14386 bitmap images stored in the PNG format. It can read and write both files and
14387 in-memory raw vectors.")
14388 ;; Any of these GPL versions.
14389 (license (list license:gpl2 license:gpl3))))
14391 (define-public r-ggcorrplot
14393 (name "r-ggcorrplot")
14398 (uri (cran-uri "ggcorrplot" version))
14401 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14402 (build-system r-build-system)
14404 `(("r-ggplot2" ,r-ggplot2)
14405 ("r-reshape2" ,r-reshape2)))
14406 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14407 (synopsis "Visualization of a correlation matrix using ggplot2")
14409 "The ggcorrplot package can be used to visualize easily a correlation
14410 matrix using ggplot2. It provides a solution for reordering the correlation
14411 matrix and displays the significance level on the plot. It also includes a
14412 function for computing a matrix of correlation p-values.")
14413 (license license:gpl2)))
14415 (define-public r-flexdashboard
14417 (name "r-flexdashboard")
14418 (version "0.5.1.1")
14422 (uri (cran-uri "flexdashboard" version))
14425 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14426 (build-system r-build-system)
14428 `(#:modules ((guix build utils)
14429 (guix build r-build-system)
14433 (ice-9 textual-ports))
14435 (modify-phases %standard-phases
14436 (add-after 'unpack 'process-javascript
14437 (lambda* (#:key inputs #:allow-other-keys)
14438 (with-directory-excursion "inst"
14439 ;; Concatenate all components of prism.js
14440 (let ((contents (string-join
14441 (map (lambda (name)
14442 (call-with-input-file
14443 (assoc-ref inputs name)
14447 "js-prism-line-numbers"))
14449 (call-with-output-file "prism-src.js"
14450 (cut display contents <>)))
14454 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14455 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14457 "www/sly/sly.min.js")
14459 "www/prism/prism.js")
14460 (,(assoc-ref inputs "js-raphael")
14461 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14462 (,(assoc-ref inputs "js-featherlight")
14463 "www/featherlight/featherlight.min.js"))))
14464 (lambda (sources targets)
14465 (for-each (lambda (source target)
14466 (format #t "Processing ~a --> ~a~%"
14468 (delete-file target)
14469 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14470 (call-with-output-file target
14472 (dump-port minified port)))))
14473 sources targets))))
14476 `(("r-htmltools" ,r-htmltools)
14477 ("r-htmlwidgets" ,r-htmlwidgets)
14478 ("r-jsonlite" ,r-jsonlite)
14479 ("r-knitr" ,r-knitr)
14480 ("r-rmarkdown" ,r-rmarkdown)
14481 ("r-shiny" ,r-shiny)))
14483 `(("uglify-js" ,uglify-js)
14487 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14490 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14494 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14497 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14501 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14504 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14505 ("js-prism-line-numbers"
14508 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14511 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14515 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14518 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14519 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14520 (synopsis "R Markdown format for flexible dashboards")
14522 "This package provides an R Markdown format for converting an R Markdown
14523 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14524 of its components to the containing web page.")
14525 (license license:expat)))
14527 (define-public r-preseqr
14534 (uri (cran-uri "preseqR" version))
14537 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14538 (properties `((upstream-name . "preseqR")))
14539 (build-system r-build-system)
14541 `(("r-polynom" ,r-polynom)))
14542 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14543 (synopsis "Predicting species accumulation curves")
14545 "This package can be used to predict the r-species accumulation
14546 curve (r-SAC), which is the number of species represented at least r times as
14547 a function of the sampling effort. When r = 1, the curve is known as the
14548 species accumulation curve, or the library complexity curve in high-throughput
14549 genomic sequencing. The package includes both parametric and nonparametric
14550 methods, as described by Deng C, et al. (2018).")
14551 (license license:gpl3)))
14553 (define-public r-mapplots
14555 (name "r-mapplots")
14560 (uri (cran-uri "mapplots" version))
14563 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14564 (build-system r-build-system)
14565 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14566 (synopsis "Data visualization on maps")
14568 "This package helps you create simple maps; add sub-plots like pie plots
14569 to a map or any other plot; format, plot and export gridded data. The package
14570 was developed for displaying fisheries data but most functions can be used for
14571 more generic data visualisation.")
14572 (license license:gpl2+)))
14574 (define-public r-pmcmr
14581 (uri (cran-uri "PMCMR" version))
14584 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14585 (properties `((upstream-name . "PMCMR")))
14586 (build-system r-build-system)
14587 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14588 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14590 "This is a deprecated package for calculating pairwise multiple
14591 comparisons of mean rank sums. This package is superseded by the novel
14592 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14593 compatibility of dependent packages for some time.")
14594 (license license:gpl3+)))
14596 (define-public r-downloader
14598 (name "r-downloader")
14603 (uri (cran-uri "downloader" version))
14606 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14607 (build-system r-build-system)
14609 `(("r-digest" ,r-digest)))
14610 (home-page "https://github.com/wch/downloader")
14611 (synopsis "Download files over HTTP and HTTPS")
14613 "This package provides a wrapper for the @code{download.file} function,
14614 making it possible to download files over HTTPS across platforms. The
14615 @code{RCurl} package provides this functionality (and much more) but has
14616 external dependencies. This package has is implemented purely in R.")
14617 (license license:gpl2)))
14619 (define-public r-rex
14626 (uri (cran-uri "rex" version))
14629 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14630 (build-system r-build-system)
14632 `(("r-lazyeval" ,r-lazyeval)
14633 ("r-magrittr" ,r-magrittr)))
14634 (home-page "https://github.com/kevinushey/rex")
14635 (synopsis "Friendly regular expressions")
14637 "This package provides a friendly interface for the construction of
14638 regular expressions. Regular expressions are a very powerful feature, however
14639 they are often difficult to interpret. Rex allows you to build complex
14640 regular expressions from human readable expressions")
14641 (license license:expat)))
14643 (define-public r-sctransform
14645 (name "r-sctransform")
14650 (uri (cran-uri "sctransform" version))
14653 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14654 (build-system r-build-system)
14656 `(("r-future" ,r-future)
14657 ("r-future-apply" ,r-future-apply)
14658 ("r-ggplot2" ,r-ggplot2)
14659 ("r-gridextra" ,r-gridextra)
14661 ("r-matrix" ,r-matrix)
14663 ("r-rcppeigen" ,r-rcppeigen)
14664 ("r-reshape2" ,r-reshape2)))
14665 (home-page "https://github.com/ChristophH/sctransform")
14666 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14668 "This package provides a normalization method for single-cell UMI count
14669 data using a variance stabilizing transformation. The transformation is based
14670 on a negative binomial regression model with regularized parameters. As part
14671 of the same regression framework, this package also provides functions for
14672 batch correction, and data correction.")
14673 (license license:gpl3)))
14675 (define-public r-styler
14682 (uri (cran-uri "styler" version))
14685 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14686 (build-system r-build-system)
14688 `(("r-backports" ,r-backports)
14690 ("r-magrittr" ,r-magrittr)
14691 ("r-purrr" ,r-purrr)
14692 ("r-rematch2" ,r-rematch2)
14693 ("r-rlang" ,r-rlang)
14694 ("r-rprojroot" ,r-rprojroot)
14695 ("r-tibble" ,r-tibble)
14696 ("r-withr" ,r-withr)
14697 ("r-xfun" ,r-xfun)))
14698 (home-page "https://github.com/r-lib/styler")
14699 (synopsis "Non-invasive pretty printing of R code")
14701 "This is a package for pretty-printing R code without changing the user's
14702 formatting intent.")
14703 (license license:gpl3)))
14705 (define-public r-scrime
14712 (uri (cran-uri "scrime" version))
14715 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14716 (build-system r-build-system)
14717 (home-page "https://cran.r-project.org/web/packages/scrime/")
14718 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14720 "This package provides tools for the analysis of high-dimensional data
14721 developed/implemented at the group \"Statistical Complexity Reduction In
14722 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14723 the functions can also be applied to other types of categorical data.")
14724 (license license:gpl2)))
14726 (define-public r-pbmcapply
14728 (name "r-pbmcapply")
14733 (uri (cran-uri "pbmcapply" version))
14736 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14737 (build-system r-build-system)
14738 (home-page "https://github.com/kvnkuang/pbmcapply")
14739 (synopsis "Track the progress of apply procedures with a progress bar")
14741 "This light-weight package helps you track and visualize the progress of
14742 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14743 (license license:expat)))
14745 (define-public r-blme
14752 (uri (cran-uri "blme" version))
14755 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14756 (build-system r-build-system)
14757 (propagated-inputs `(("r-lme4" ,r-lme4)))
14758 (home-page "https://github.com/vdorie/blme")
14759 (synopsis "Bayesian linear mixed-effects models")
14761 "This package provides tools for maximum a posteriori estimation for
14762 linear and generalized linear mixed-effects models in a Bayesian setting. It
14763 extends the lme4 package.")
14764 (license license:gpl2+)))
14766 (define-public r-batchtools
14768 (name "r-batchtools")
14773 (uri (cran-uri "batchtools" version))
14776 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14777 (build-system r-build-system)
14779 `(("r-backports" ,r-backports)
14780 ("r-base64url" ,r-base64url)
14782 ("r-checkmate" ,r-checkmate)
14783 ("r-data-table" ,r-data-table)
14784 ("r-digest" ,r-digest)
14786 ("r-progress" ,r-progress)
14788 ("r-rappdirs" ,r-rappdirs)
14789 ("r-stringi" ,r-stringi)
14790 ("r-withr" ,r-withr)))
14791 (home-page "https://github.com/mllg/batchtools")
14792 (synopsis "Tools for computation on batch systems")
14794 "As a successor of the packages BatchJobs and BatchExperiments, this
14795 package provides a parallel implementation of the Map function for high
14796 performance computing systems managed by various schedulers. A multicore and
14797 socket mode allow the parallelization on a local machines, and multiple
14798 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14799 the package provides an abstraction mechanism to define large-scale computer
14800 experiments in a well-organized and reproducible way.")
14801 (license license:lgpl3)))
14803 (define-public r-clue
14810 (uri (cran-uri "clue" version))
14813 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14814 (build-system r-build-system)
14815 (propagated-inputs `(("r-cluster" ,r-cluster)))
14816 (home-page "https://cran.r-project.org/web/packages/clue/")
14817 (synopsis "Tools for analyzing cluster ensembles")
14818 (description "Cluster ensembles are collections of individual solutions to
14819 a given clustering problem which are useful or necessary to consider in a wide
14820 range of applications. This R package provides an extensible computational
14821 environment for creating and analyzing cluster ensembles, with basic data
14822 structures for representing partitions and hierarchies, and facilities for
14823 computing on them, including methods for measuring proximity and obtaining
14824 consensus and secondary clusterings.")
14825 (license license:gpl2)))
14827 (define-public r-sitmo
14834 (uri (cran-uri "sitmo" version))
14837 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
14838 (build-system r-build-system)
14839 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14840 (home-page "https://github.com/coatless/sitmo/")
14841 (synopsis "Parallel pseudo random number generator header files")
14843 "This package provides two high quality and fast PPRNGs that may be used
14844 in an OpenMP parallel environment. In addition, there is a generator for one
14845 dimensional low-discrepancy sequence.")
14846 (license license:expat)))
14848 (define-public r-dqrng
14855 (uri (cran-uri "dqrng" version))
14858 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
14859 (build-system r-build-system)
14863 ("r-sitmo" ,r-sitmo)))
14864 (home-page "https://www.daqana.org/dqrng")
14865 (synopsis "Fast pseudo random number generators")
14867 "Several fast random number generators are provided as C++ header-only
14868 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
14869 Additionally, fast functions for generating random numbers according to a
14870 uniform, normal and exponential distribution are included. The latter two use
14871 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
14872 functions are exported to R and as a C++ interface and are enabled for use
14873 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
14874 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
14875 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
14876 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
14877 ;; whole is distributed under the terms of the AGPL 3.
14878 (license license:agpl3)))
14880 (define-public r-dalex
14887 (uri (cran-uri "DALEX" version))
14890 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
14891 (properties `((upstream-name . "DALEX")))
14892 (build-system r-build-system)
14893 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
14894 (home-page "https://pbiecek.github.io/DALEX/")
14895 (synopsis "Descriptive machine learning explanations")
14897 "Machine Learning models are widely used and have various applications in
14898 classification or regression. Models created with boosting, bagging, stacking
14899 or similar techniques are often used due to their high performance, but such
14900 black-box models usually lack interpretability. The DALEX package contains
14901 various explainers that help to understand the link between input variables
14902 and model output.")
14903 ;; Any version of the GPL
14904 (license license:gpl3+)))
14906 (define-public r-enrichr
14913 (uri (cran-uri "enrichR" version))
14916 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
14917 (properties `((upstream-name . "enrichR")))
14918 (build-system r-build-system)
14920 `(("r-httr" ,r-httr)
14921 ("r-rjson" ,r-rjson)))
14922 (home-page "https://cran.r-project.org/web/packages/enrichR/")
14923 (synopsis "R Interface to Enrichr database for analyzing gene sets")
14925 "This package provides an R interface to all Enrichr databases, a
14926 web-based tool for analyzing gene sets and returns any enrichment of common
14927 annotated biological functions.")
14928 (license license:gpl2+)))
14930 (define-public r-plot3d
14937 (uri (cran-uri "plot3D" version))
14940 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
14941 (properties `((upstream-name . "plot3D")))
14942 (build-system r-build-system)
14943 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
14944 (home-page "https://cran.r-project.org/web/packages/plot3D")
14945 (synopsis "Plot multi-dimensional data")
14947 "This package provides functions for viewing 2D and 3D data, including
14948 perspective plots, slice plots, surface plots, scatter plots, etc. It
14949 includes data sets from oceanography.")
14950 (license license:gpl3+)))
14952 (define-public r-ggfortify
14954 (name "r-ggfortify")
14959 (uri (cran-uri "ggfortify" version))
14962 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
14963 (build-system r-build-system)
14965 `(("r-dplyr" ,r-dplyr)
14966 ("r-ggplot2" ,r-ggplot2)
14967 ("r-gridextra" ,r-gridextra)
14968 ("r-scales" ,r-scales)
14969 ("r-stringr" ,r-stringr)
14970 ("r-tibble" ,r-tibble)
14971 ("r-tidyr" ,r-tidyr)))
14972 (home-page "https://github.com/sinhrks/ggfortify")
14973 (synopsis "Data visualization tools for statistical analysis results")
14975 "This package provides unified plotting tools for statistics commonly
14976 used, such as GLM, time series, PCA families, clustering and survival
14977 analysis. The package offers a single plotting interface for these analysis
14978 results and plots in a unified style using the @code{ggplot2} package.")
14979 (license license:gpl2)))
14981 (define-public r-refmanager
14983 (name "r-refmanager")
14988 (uri (cran-uri "RefManageR" version))
14991 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
14992 (properties `((upstream-name . "RefManageR")))
14993 (build-system r-build-system)
14995 `(("r-bibtex" ,r-bibtex)
14997 ("r-jsonlite" ,r-jsonlite)
14998 ("r-lubridate" ,r-lubridate)
15000 ("r-stringr" ,r-stringr)
15001 ("r-xml2" ,r-xml2)))
15002 (home-page "https://github.com/ropensci/RefManageR/")
15003 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15005 "This package provides tools for importing and working with bibliographic
15006 references. It greatly enhances the @code{bibentry} class by providing a
15007 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15008 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15009 by various formats for name lists (author by last names, translator by full
15010 names, etc.). Entries can be updated, combined, sorted, printed in a number
15011 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15012 into R and converted to @code{BibEntry} objects.")
15013 ;; Any of these licenses may be picked.
15014 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15016 (define-public r-citr
15023 (uri (cran-uri "citr" version))
15026 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15027 (build-system r-build-system)
15029 `(("r-assertthat" ,r-assertthat)
15032 ("r-miniui" ,r-miniui)
15033 ("r-refmanager" ,r-refmanager)
15034 ("r-rstudioapi" ,r-rstudioapi)
15035 ("r-shiny" ,r-shiny)
15036 ("r-shinyjs" ,r-shinyjs)
15037 ("r-yaml" ,r-yaml)))
15038 (home-page "https://github.com/crsh/citr")
15039 (synopsis "RStudio add-in to insert Markdown citations")
15041 "This package provides functions and an RStudio add-in that search a
15042 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15043 the current document.")
15044 (license license:expat)))
15046 (define-public r-xgboost
15049 (version "0.90.0.2")
15053 (uri (cran-uri "xgboost" version))
15056 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15057 (build-system r-build-system)
15059 `(("r-data-table" ,r-data-table)
15060 ("r-magrittr" ,r-magrittr)
15061 ("r-matrix" ,r-matrix)
15062 ("r-stringi" ,r-stringi)))
15063 (home-page "https://github.com/dmlc/xgboost")
15064 (synopsis "Extreme gradient boosting")
15066 "This package provides an R interface to Extreme Gradient Boosting, which
15067 is an efficient implementation of the gradient boosting framework from Chen
15068 and Guestrin (2016). The package includes efficient linear model solver and
15069 tree learning algorithms. The package can automatically do parallel
15070 computation on a single machine. It supports various objective functions,
15071 including regression, classification and ranking. The package is made to be
15072 extensible, so that users are also allowed to define their own objectives
15074 (license license:asl2.0)))
15076 (define-public r-umap
15079 (version "0.2.3.1")
15083 (uri (cran-uri "umap" version))
15086 "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d"))))
15087 (build-system r-build-system)
15089 `(("r-openssl" ,r-openssl)
15091 ("r-reticulate" ,r-reticulate)
15092 ("r-rspectra" ,r-rspectra)))
15093 (home-page "https://github.com/tkonopka/umap")
15094 (synopsis "Uniform manifold approximation and projection")
15096 "Uniform manifold approximation and projection is a technique for
15097 dimension reduction. This package provides an interface to the UMAP algorithm
15098 in R, including a translation of the original algorithm into R.")
15099 (license license:expat)))
15101 (define-public r-uwot
15108 (uri (cran-uri "uwot" version))
15111 "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n"))))
15112 (build-system r-build-system)
15114 `(("r-dqrng" ,r-dqrng)
15116 ("r-irlba" ,r-irlba)
15117 ("r-matrix" ,r-matrix)
15119 ("r-rcppannoy" ,r-rcppannoy)
15120 ("r-rcppparallel" ,r-rcppparallel)
15121 ("r-rcppprogress" ,r-rcppprogress)
15122 ("r-rspectra" ,r-rspectra)))
15123 (home-page "https://github.com/jlmelville/uwot")
15124 (synopsis "Uniform manifold approximation and projection")
15126 "This package provides an implementation of the Uniform Manifold
15127 Approximation and Projection dimensionality reduction by McInnes et
15128 al. (2018). It also provides means to transform new data and to carry out
15129 supervised dimensionality reduction. An implementation of the related
15130 LargeVis method of Tang et al. (2016) is also provided.")
15131 (license license:gpl3)))
15133 (define-public r-kableextra
15135 (name "r-kableextra")
15140 (uri (cran-uri "kableExtra" version))
15143 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15144 (properties `((upstream-name . "kableExtra")))
15145 (build-system r-build-system)
15147 `(("r-digest" ,r-digest)
15149 ("r-htmltools" ,r-htmltools)
15150 ("r-knitr" ,r-knitr)
15151 ("r-magrittr" ,r-magrittr)
15152 ("r-readr" ,r-readr)
15153 ("r-rmarkdown" ,r-rmarkdown)
15154 ("r-rstudioapi" ,r-rstudioapi)
15155 ("r-rvest" ,r-rvest)
15156 ("r-scales" ,r-scales)
15157 ("r-stringr" ,r-stringr)
15158 ("r-viridislite" ,r-viridislite)
15159 ("r-webshot" ,r-webshot)
15160 ("r-xml2" ,r-xml2)))
15161 (home-page "https://haozhu233.github.io/kableExtra/")
15162 (synopsis "Construct complex tables with pipe syntax")
15164 "Build complex HTML or LaTeX tables using @code{kable()} from
15165 @code{knitr} and the piping syntax from @code{magrittr}. The function
15166 @code{kable()} is a light weight table generator coming from @code{knitr}.
15167 This package simplifies the way to manipulate the HTML or LaTeX codes
15168 generated by @code{kable()} and allows users to construct complex tables and
15169 customize styles using a readable syntax.")
15170 (license license:expat)))
15172 (define-public r-glasso
15179 (uri (cran-uri "glasso" version))
15181 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15182 (build-system r-build-system)
15183 (native-inputs `(("gfortran" ,gfortran)))
15184 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15185 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15187 "This is a package for estimation of a sparse inverse covariance matrix
15188 using a lasso (L1) penalty. Facilities are provided for estimates along a
15189 path of values for the regularization parameter.")
15190 (license license:gpl2)))
15192 (define-public r-rhpcblasctl
15194 (name "r-rhpcblasctl")
15195 (version "0.18-205")
15199 (uri (cran-uri "RhpcBLASctl" version))
15202 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15203 (properties `((upstream-name . "RhpcBLASctl")))
15204 (build-system r-build-system)
15205 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15206 (synopsis "Control the number of threads on BLAS")
15208 "This package allows you to control the number of threads the BLAS
15209 library uses. It is also possible to control the number of threads in
15211 (license license:agpl3+)))
15213 (define-public r-lda
15220 (uri (cran-uri "lda" version))
15223 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15224 (build-system r-build-system)
15225 (home-page "https://cran.r-project.org/web/packages/lda/")
15226 (synopsis "Collapsed Gibbs sampling methods for topic models")
15228 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15229 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15230 mixed-membership stochastic blockmodel. Inference for all of these models is
15231 implemented via a fast collapsed Gibbs sampler written in C. Utility
15232 functions for reading/writing data typically used in topic models, as well as
15233 tools for examining posterior distributions are also included.")
15234 ;; Any version of the LGPL
15235 (license license:lgpl3+)))
15237 (define-public r-rann-l1
15244 (uri (cran-uri "RANN.L1" version))
15247 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15248 (properties `((upstream-name . "RANN.L1")))
15249 (build-system r-build-system)
15250 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15251 (synopsis "Fast nearest neighbour search using L1 metric")
15253 "This package provides tools to find the k nearest neighbours for every
15254 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15255 library. There is support for approximate as well as exact searches, fixed
15256 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15257 computed using the L1 (Manhattan, taxicab) metric.")
15258 (license license:gpl3+)))
15260 (define-public r-leiden
15267 (uri (cran-uri "leiden" version))
15270 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15271 (properties `((upstream-name . "leiden")))
15272 (build-system r-build-system)
15274 `(("r-igraph" ,r-igraph)
15275 ("r-matrix" ,r-matrix)
15276 ("r-reticulate" ,r-reticulate)))
15277 (home-page "https://github.com/TomKellyGenetics/leiden")
15278 (synopsis "R implementation of Leiden clustering algorithm")
15280 "This package implements the Python @code{leidenalg} module to be called
15281 in R. It enables clustering using the Leiden algorithm for partitioning a
15282 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15283 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15284 (license license:gpl3)))
15286 (define-public r-patchwork
15287 ;; There has been no public release yet.
15288 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15291 (name "r-patchwork")
15292 (version (git-version "0.0.1" revision commit))
15296 (uri (git-reference
15297 (url "https://github.com/thomasp85/patchwork.git")
15299 (file-name (git-file-name name version))
15302 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15303 (build-system r-build-system)
15305 `(("r-ggplot2" ,r-ggplot2)
15306 ("r-gtable" ,r-gtable)))
15307 (home-page "https://github.com/thomasp85/patchwork")
15308 (synopsis "Compose ggplot2 plots")
15310 "The @code{ggplot2} package provides a strong API for sequentially
15311 building up a plot, but does not concern itself with composition of multiple
15312 plots. Patchwork is a package that expands the API to allow for arbitrarily
15313 complex composition of plots by providing mathmatical operators for combining
15315 (license license:expat))))
15317 (define-public r-liger
15324 (uri (git-reference
15325 (url "https://github.com/MacoskoLab/liger.git")
15326 (commit (string-append "v" version))))
15327 (file-name (git-file-name name version))
15330 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15331 (modules '((guix build utils)))
15334 (delete-file "inst/java/ModularityOptimizer.jar")
15336 (build-system r-build-system)
15339 (modify-phases %standard-phases
15340 (add-after 'unpack 'build-java-part
15341 (lambda* (#:key inputs #:allow-other-keys)
15342 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15343 (for-each (lambda (file) (invoke "javac" file))
15344 (find-files "." "\\.java$"))
15345 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15346 (find-files "." "\\.class$"))
15349 `(("r-cowplot" ,r-cowplot)
15350 ("r-dosnow" ,r-dosnow)
15351 ("r-dplyr" ,r-dplyr)
15353 ("r-foreach" ,r-foreach)
15354 ("r-ggplot2" ,r-ggplot2)
15355 ("r-ggrepel" ,r-ggrepel)
15356 ("r-hmisc" ,r-hmisc)
15358 ("r-irlba" ,r-irlba)
15359 ("r-matrix" ,r-matrix)
15360 ("r-mclust" ,r-mclust)
15361 ("r-patchwork" ,r-patchwork)
15363 ("r-rann-l1" ,r-rann-l1)
15365 ("r-rcpparmadillo" ,r-rcpparmadillo)
15366 ("r-riverplot" ,r-riverplot)
15367 ("r-rtsne" ,r-rtsne)
15368 ("r-snow" ,r-snow)))
15370 `(("jdk" ,icedtea "jdk")
15371 ;; See https://github.com/MacoskoLab/liger/issues/96
15372 ;; The optimizer is released under the Expat license.
15376 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15379 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15381 ("r-knitr" ,r-knitr))) ; for vignettes
15382 (home-page "https://github.com/MacoskoLab/liger")
15383 (synopsis "Integrate and analyze multiple single-cell datasets")
15385 "LIGER is a package for integrating and analyzing multiple single-cell
15386 datasets, developed and maintained by the Macosko lab. It relies on
15387 integrative non-negative matrix factorization to identify shared and
15388 dataset-specific factors.")
15389 (license license:gpl3)))
15391 (define-public r-harmony
15392 ;; There are no tagged commits
15393 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15397 (version (git-version "1.0" revision commit))
15401 (uri (git-reference
15402 (url "https://github.com/immunogenomics/harmony")
15404 (file-name (git-file-name name version))
15407 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15408 (build-system r-build-system)
15410 `(("r-cowplot" ,r-cowplot)
15411 ("r-dplyr" ,r-dplyr)
15412 ("r-ggplot2" ,r-ggplot2)
15413 ("r-irlba" ,r-irlba)
15414 ("r-matrix" ,r-matrix)
15416 ("r-rcpparmadillo" ,r-rcpparmadillo)
15417 ("r-rcppprogress" ,r-rcppprogress)
15418 ("r-rlang" ,r-rlang)
15419 ("r-tibble" ,r-tibble)
15420 ("r-tidyr" ,r-tidyr)))
15421 (home-page "https://github.com/immunogenomics/harmony")
15422 (synopsis "Integration of single cell sequencing data")
15424 "This package provides an implementation of the Harmony algorithm for
15425 single cell integration, described in Korsunsky et al
15426 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15427 function and interfaces to external frameworks.")
15428 (license license:gpl3))))
15430 (define-public r-covr
15437 (uri (cran-uri "covr" version))
15439 (base32 "160w0m2d06kdd8dar57lpph39rxx55xwncbpl3b21l7j9drh1s5f"))))
15440 (properties `((upstream-name . "covr")))
15441 (build-system r-build-system)
15443 `(("r-crayon" ,r-crayon)
15444 ("r-digest" ,r-digest)
15446 ("r-jsonlite" ,r-jsonlite)
15448 ("r-withr" ,r-withr)
15449 ("r-yaml" ,r-yaml)))
15450 (home-page "https://github.com/r-lib/covr")
15451 (synopsis "Test coverage for R packages")
15453 "Thisp package enables you to track and report code coverage for your
15454 package and (optionally) upload the results to a coverage service. Code
15455 coverage is a measure of the amount of code being exercised by a set of tests.
15456 It is an indirect measure of test quality and completeness. This package is
15457 compatible with any testing methodology or framework and tracks coverage of
15458 both R code and compiled C/C++/FORTRAN code.")
15459 (license license:gpl3)))
15461 (define-public r-systemfonts
15463 (name "r-systemfonts")
15468 (uri (cran-uri "systemfonts" version))
15471 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15472 (properties `((upstream-name . "systemfonts")))
15473 (build-system r-build-system)
15475 `(("fontconfig" ,fontconfig)
15476 ("freetype" ,freetype)
15479 `(("pkg-config" ,pkg-config)))
15480 (home-page "https://github.com/r-lib/systemfonts")
15481 (synopsis "System native font finding")
15483 "This package provides system native access to the font catalogue. As
15484 font handling varies between systems it is difficult to correctly locate
15485 installed fonts across different operating systems. The 'systemfonts' package
15486 provides bindings to the native libraries for finding font files that can then
15487 be used further by e.g. graphic devices.")
15488 (license license:expat)))
15490 (define-public r-graphlayouts
15492 (name "r-graphlayouts")
15497 (uri (cran-uri "graphlayouts" version))
15500 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15501 (properties `((upstream-name . "graphlayouts")))
15502 (build-system r-build-system)
15504 `(("r-igraph" ,r-igraph)
15506 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15507 (home-page "https://github.com/schochastics/graphlayouts")
15508 (synopsis "Additional layout algorithms for network visualizations")
15510 "This package provides several layout algorithms to visualize networks
15511 which are not part of the igraph library. Most are based on the concept of
15512 stress majorization by Gansner et al. (2004)
15513 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15514 emphasize hidden group structures in networks or focus on specific nodes.")
15515 (license license:expat)))
15517 (define-public r-tidygraph
15519 (name "r-tidygraph")
15524 (uri (cran-uri "tidygraph" version))
15527 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15528 (properties `((upstream-name . "tidygraph")))
15529 (build-system r-build-system)
15531 `(("r-dplyr" ,r-dplyr)
15532 ("r-igraph" ,r-igraph)
15533 ("r-magrittr" ,r-magrittr)
15534 ("r-pillar" ,r-pillar)
15537 ("r-rlang" ,r-rlang)
15538 ("r-tibble" ,r-tibble)
15539 ("r-tidyr" ,r-tidyr)))
15540 (home-page "https://github.com/thomasp85/tidygraph")
15541 (synopsis "Tidy API for graph manipulation")
15543 "This package provides a graph implementation that can be thought of as
15544 two tidy data frames describing node and edge data respectively. It provides
15545 an approach to manipulate these two virtual data frames using the API defined
15546 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15547 common graph algorithms.")
15548 (license license:expat)))
15550 (define-public r-soupx
15551 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15555 (version (git-version "0.3.1" revision commit))
15559 (uri (git-reference
15560 (url "https://github.com/constantAmateur/SoupX")
15562 (file-name (git-file-name name version))
15565 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15566 (properties `((upstream-name . "SoupX")))
15567 (build-system r-build-system)
15569 `(("r-ggplot2" ,r-ggplot2)
15570 ("r-matrix" ,r-matrix)
15571 ("r-seurat" ,r-seurat)))
15572 (home-page "https://github.com/constantAmateur/SoupX")
15573 (synopsis "Single cell mRNA Soup eXterminator")
15575 "This package provides a package for quantifying, profiling and
15576 removing cell free mRNA contamination (the \"soup\") from droplet based single
15577 cell RNA-seq experiments.")
15578 (license license:gpl2))))
15580 (define-public r-assertr
15587 (uri (cran-uri "assertr" version))
15590 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15591 (build-system r-build-system)
15593 `(("r-dplyr" ,r-dplyr)
15595 ("r-rlang" ,r-rlang)))
15597 `(("r-knitr" ,r-knitr))) ; needed for vignette
15598 (home-page "https://github.com/ropensci/assertr")
15599 (synopsis "Assertive programming for R analysis pipelines")
15601 "This package provides functionality to assert conditions that have to be
15602 met so that errors in data used in analysis pipelines can fail quickly. It is
15603 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15605 (license license:expat)))
15607 (define-public r-parameters
15609 (name "r-parameters")
15614 (uri (cran-uri "parameters" version))
15617 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15618 (properties `((upstream-name . "parameters")))
15619 (build-system r-build-system)
15621 `(("r-bayestestr" ,r-bayestestr)
15622 ("r-insight" ,r-insight)))
15623 (home-page "https://cran.r-project.org/web/packages/parameters")
15624 (synopsis "Processing of model parameters")
15626 "This package provides utilities for processing the parameters of various
15627 statistical models. Beyond computing p values, CIs, and other indices for a
15628 wide variety of models, this package implements features like standardization
15629 or bootstrapping of parameters and models, feature reduction (feature
15630 extraction and variable selection) as well as conversion between indices of
15632 (license license:gpl3)))
15634 (define-public r-rgdal
15641 (uri (cran-uri "rgdal" version))
15643 (base32 "05rvqy8lr2c3phaylmc4g5761208b0xrmgwn9c4a60x7p251dzjs"))))
15644 (properties `((upstream-name . "rgdal")))
15645 (build-system r-build-system)
15653 `(("pkg-config" ,pkg-config)))
15654 (home-page "http://rgdal.r-forge.r-project.org")
15655 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15657 "This package provides bindings to the Geospatial Data Abstraction
15658 Library (GDAL) and access to projection/transformation operations from the
15660 (license license:gpl2+)))
15662 (define-public r-insol
15669 (uri (cran-uri "insol" version))
15672 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
15673 (properties `((upstream-name . "insol")))
15674 (build-system r-build-system)
15676 `(("r-raster" ,r-raster)
15677 ("r-rgdal" ,r-rgdal)))
15679 `(("gfortran" ,gfortran)))
15680 (home-page "https://meteoexploration.com/R/insol/index.html")
15681 (synopsis "Tools for calculating solar radiation")
15683 "This package provides functions to compute insolation on tilted
15684 surfaces, computes atmospheric transmittance and related parameters such as:
15685 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15686 time, vector in the direction of the sun, vector normal to surface, and some
15687 atmospheric physics.")
15688 (license license:gpl2+)))
15690 (define-public r-lifecycle
15692 (name "r-lifecycle")
15697 (uri (cran-uri "lifecycle" version))
15700 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15701 (properties `((upstream-name . "lifecycle")))
15702 (build-system r-build-system)
15704 `(("r-glue" ,r-glue)
15705 ("r-rlang" ,r-rlang)))
15706 (home-page "https://github.com/r-lib/lifecycle")
15707 (synopsis "Manage the life cycle of your package functions")
15709 "Manage the life cycle of your exported functions with shared
15710 conventions, documentation badges, and non-invasive deprecation warnings. The
15711 lifecycle package defines four development stages (experimental, maturing,
15712 stable, and questioning) and three deprecation stages (soft-deprecated,
15713 deprecated, and defunct). It makes it easy to insert badges corresponding to
15714 these stages in your documentation. Usage of deprecated functions are
15715 signalled with increasing levels of non-invasive verbosity.")
15716 (license license:gpl3)))
15718 (define-public r-assertable
15720 (name "r-assertable")
15725 (uri (cran-uri "assertable" version))
15728 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15729 (build-system r-build-system)
15731 `(("r-data-table" ,r-data-table)))
15732 (home-page "https://cran.r-project.org/web/packages/assertable/")
15733 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15734 (description "This package provides simple, flexible assertions on
15735 data.frame or data.table objects with verbose output for vetting. While other
15736 assertion packages apply towards more general use-cases, @code{assertable} is
15737 tailored towards tabular data. It includes functions to check variable names
15738 and values, whether the dataset contains all combinations of a given set of
15739 unique identifiers, and whether it is a certain length. In addition,
15740 @code{assertable} includes utility functions to check the existence of target
15741 files and to efficiently import multiple tabular data files into one
15743 (license license:gpl3)))
15745 (define-public r-quadprog
15747 (name "r-quadprog")
15752 (uri (cran-uri "quadprog" version))
15754 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
15755 (build-system r-build-system)
15757 `(("gfortran" ,gfortran)))
15758 (home-page "https://cran.r-project.org/web/packages/quadprog")
15759 (synopsis "Functions to solve quadratic programming problems")
15761 "This package contains routines and documentation for solving quadratic
15762 programming problems.")
15763 (license license:gpl3+)))
15765 (define-public r-desolve
15772 (uri (cran-uri "deSolve" version))
15774 (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
15775 (properties `((upstream-name . "deSolve")))
15776 (build-system r-build-system)
15778 `(("gfortran" ,gfortran)))
15779 (home-page "https://desolve.r-forge.r-project.org/")
15780 (synopsis "Solvers for initial value problems of differential equations")
15781 (description "This package provides functions that solve initial
15782 value problems of a system of first-order ordinary differential equations (ODE),
15783 of partial differential equations (PDE), of differential algebraic equations
15784 (DAE), and of delay differential equations. The functions provide an interface
15785 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
15786 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
15787 the Runge-Kutta family with fixed or variable time steps. The package contains
15788 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
15789 differential equations (PDE) that have been converted to ODEs by numerical
15791 (license license:gpl2+)))
15793 (define-public r-pracma
15799 (uri (cran-uri "pracma" version))
15801 (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
15802 (build-system r-build-system)
15803 (home-page "https://cran.r-project.org/web/packages/pracma/")
15804 (synopsis "Practical numerical math functions")
15805 (description "This package provides functions for numerical analysis and
15806 linear algebra, numerical optimization, differential equations, plus some
15807 special functions. It uses Matlab function names where appropriate to simplify
15809 (license license:gpl3+)))